CoRIS Coral Glossary - NOAA's Coral Reef Conservation Program

NOAA's Coral Reef Data Discovery GlossaryHOME / Glossary /GlossaryThis SiteAll of NOAA●●Main PageReferencesGlossaryThis glossary contains nearly 3,000 technical terms, with their definitions,explanations, and illustrative materials where apropos. The aim of the CoRISglossary is to help the student or layperson, as well as the professionalscientist and manager, to understand the complex language and terminologyof coral reef ecosystem science when accessing any part of the NOAA CoralReef Information System (CoRIS), including the scientific and technicalliterature and data. Habitats and communities adjacent to the coral reefs,such as sea grass meadows, mangrove forests and associated hard and softsubstrate habitats are included within the scope of the coral reef ecosystem.The glossary contains terms concerned with ecology, biogeography, evolution,taxonomy, morphology, physiology, cell and molecular biology, genetics,mapping, development, fisheries, oceanography, geosciences, conservationprograms, remote-sensing, physics, chemistry, and data and informationmanagement.The glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (12.7 MB). Thedocument includes all terms, photographs, images, and literature sources.Glossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZMaking a ContributionWe encourage the professional and academic community to contribute termsto the glossary. Suggestions will be reviewed by glossary staff.Most terms related to corals, coral reefs, coral reef data and information, andcoral reef threats and hazards already are listed in the glossary.Contributors should provide:http://coris.noaa.gov/glossary/ (1 of 2) [2/26/2008 9:11:21 AM]

NOAA's Coral Reef Data Discovery Glossary1. the term, its definition, and a reference source;2. its relationship to coral reefs, if it is not evident;3. (optional) a related photograph and caption; and4. the contributor's name, affiliation, and phone and/or email.Please send your contributions to coris@noaa.gov. Write Glossary Addition inthe subject of the email.(top)Revised September 06, 2006 by CoRIS Webmaster | User Survey | Report Error On This PageSite hosted by National Oceanic and Atmospheric Administration, U.S. Department of Commercehttp://coris.noaa.gov/glossary/welcome.htmlBest viewed in Internet Explorer 5+ or Netscape 6+.http://coris.noaa.gov/glossary/ (2 of 2) [2/26/2008 9:11:21 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: AThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zabalone - a univalve mollusk (classGastropoda) of the genus Haliotis. Abalonesare harvested commercially for foodconsumption. The shell is lined with motherof-pearland used for commercial(ornamental) purposesSea otters are in directcompetition with humansfor abalone. (Photo: RonMcPeak)abatement - reducing the degree or intensity of, or eliminatingabaxial - away from, or distant from the axisabbreviate - shortenedabcauline - pertaining to hydrozoan polyps that extend outwards fromthe common stemhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (1 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataabdomen - in higher animals, the portionof the body that contains the intestines andother viscera other than the lungs andheart; in arthropods, the rearmost segmentof the body, which contains part of thedigestive tract and all the reproductiveorgansThe ventral surface of theabdomen of an Americanlobster. Prominent are theswimmerettes, uropods,and telson.abdominal fin - a term used to describe the location of the pelvic(ventral) fins when they are inserted far behind pectorals. This is the moreprimitive condition. More recently evolved conditions have the pelvic finsin the thoracic or jugular positions. A salmon, for example, has its pelvicfins in the abdominal position. An angelfish has the pelvic fins in thethoracic position, and blennies have the pelvic fins in the jugular position,anterior to the pelvic girdleabductor - a type of muscle whose function is to move an appendage orbody part away from the body of an animal. Abductors workantagonistically with adductorsaberrant - a term used to describe an atypical appearance or behavior inan animal or plantabient - avoiding or turning away from a source of stimulationabiogenic - refers to things not involved with or produced by livingorganismsabiotic - refers to nonliving objects, substances or processesablation - the experimental removal or killing of some part of an organismabnormal - not normal; contrary to the usual structure, position,behavior or rulehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (2 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaboral - situated opposite to, or away fromthe mouth; normally used to describeradially symmetrical animals, such asstarfishes, sea urchins, and jellyfishesSpines protect the aboralsurface of a sea urchin.(Photo: NOAA)abraded - worn or frayedabranchiate - lacking gillsabrasion - the mechanical process of gradually breaking down a hardlayerabsolute tautonymy - in taxonomy, the identical spelling of a genericgroupname and one of its included specific-group names, such as thefish, Badis badis, or the western lowland gorilla, Gorilla gorilla gorillaabsolute zero - the temperature at which all motion will cease (0degrees Kelvin or -273.15 degrees C)absorption - the biological process that follows digestion, by which theproducts of digestion are transferred into the organism's internalenvironment, enabling them to reach the cellsabsorptive feeder - an animal, such as aparasitic tapeworm, that absorbs digestedfood products through the body wallA parasitic tapeworm is anabsorptive feeder. Thenarrowest point is the"head" or scolex whichattaches the parasite tothe intestinal lining bymeans of suckers and/orlittle hooks. Predigestednutrients are absorbedthrough the wall of each ofthe progressively largersegments. These animalshave no digestive canal.(Photo: HHS/Centers forhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (3 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataDisease Control andPrevention)abundance - the number or amount of something, e.g., the number oforganisms per unit of habitat space or number of individuals in a stock ora populationabyssal plain - the ocean bottom offshore from the continental margin ,usually very flat with a slight slopeabyssal zone - the deep sea region below 2,000 meters (some considerit to be the region below 4000+ meters). This region is characterized bycontinuous cold, extremely high water pressure, low nutrients, and nearor total absence of light, except for bioluminescenceabyssalpelagic zone - the pelagic environment from a depth of 4000 mto 7000 m.The water temperature in this zone is constantly near freezing;also called the "abyssopelagic zone"acanthaceous - being armed with spines or other pointed projectionsAcanthaster - the Crown-of-Thornsstarfish genus. Acanthaster planci is avoracious Indo-Pacific predator of coralsCrown-of-Thorns starfish(Acanthaster sp.), avoracious predator ofcorals.acantho- - a prefix meaning "with spines"The phylumAcanthocephala containsabout 1,000 species ofspiny-headed worms. Allare endoparasites in theintestinal tract ofvertebrates, especiallyfishes. (Image: Dr. RickGillis, Biol. Dept., Univ. ofWisconsin)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (4 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacanthocaulus - a juvenile coral of some species that is attached to thesubstrate either directly or on a stalkacanthotrich (acanthotrichium) - in fishes, a spiny dorsal or anal finrayacaudal - lacking a tailacaudal - lacking a tailaccepted name - in taxonomy, a name adopted by an author as thecorrect name for a taxonaccessory pigment - a photosynthetic pigment which absorbs light andtransfers energy to chlorophylls during photosynthesisaccessory respiratory organ - in fishes, a superficial or internal organwhich complements the gills in respiration when the fish is in poorlyoxygenated water or in airaccidental host - a host in which a parasite is not commonly foundaccidental parasite - a parasite in or on an organism other than itsnormal host; an incidental parasiteacclimation (acclimatization) - a change that occurs in an organism toallow it to tolerate a new environmentaccretion - growth by virtue of an increase in intercellular materialaccuracy - the closeness by which a set of measurements approaches thetrue valueacellular - describes the construction of an organism or tissue that is amass of protoplasm which is not divided into cells, e.g., some structuralparts of slime molds and fungiacentric - not centeredacerate - needle-shapedacerose - having a sharp, rigid pointhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (5 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacetal - any organic compound formed by adding alcohol molecules toaldehyde moleculesachelate - lacking a claw or pincer-like structureachromic - unpigmented; without coloraciculate - needle-like or having needle-like partsaciculum - a chitinous basal seta or rod supporting the parapodial lobesin polychaete wormsacid - a substance that increases the hydrogen ion concentration in asolutionacid rain - the precipitation of sulfuric acid and other acids as rain. Theacids form when sulfur dioxide and nitrogen oxides released during thecombustion of fossil fuels combine with water and oxygen in theatmosphereacidic - having a pH of less than 7acidification - the lowering of pH in water or soils, commonly associatedwith changes caused by external processes such as greenhouse gases,acid precipitation and acidic runoff. Ocean acidification is the name givento the ongoing decrease in the pH of the Earth's oceans, caused by theiruptake of anthropogenic carbon dioxide from the atmosphere. It isbelieved that the resulting decrease in pH will have negativeconsequences, primarily for oceanic calcifying organisms such as corals,foraminiferans, coccolithophores, mollusks, crustaceans, and echinodermsacidophilia - an abnormal increase in the number of eosinophils in theblood which is characteristic of allergic states and various parasiticinfections; also called "eosinophilia"acidophilous - having an affinity for or thriving in acidic conditions, e.g.,in a bog or marshaciniform - resembling a cluster of berrieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (6 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacoelomate - an animal that does nothave a true coelom or body cavity, i.e., abody cavity between the outer wall and thegut and lined with mesoderm. Acoelomatephyla include the flatworms(Platyhelminthes), ribbonworms(Nemertea), and jaw worms(Gnathostomulida)Acoelomate flatwormssuch as this Pseudocerossp. lack a coelom (bodycavity). (Photo: AdamPetrusek)acolonial coral - a solitary coral that does not form a colonyacontioid - one of many adhesive threads of tube anemones situated onthe lower portion of the mesenteriesacontium - a thread-like part of a coral polyp's or anemone's digestivesystem and employed as defensive or aggressive structures when extrudedacoustic scattering - the irregular reflection, refraction, or diffraction ofa sound in many directionsacoustic signature - a set of characteristics used to describe a soundsignal. This may include sound echos from targets, radiated and ambientnoise, with salient echo characteristics including target strength, spectralreflectivity versus frequency, doppler shift, doppler spread and targetrange extentacoustic tag - a sound transmittorattached to an aquatic animal to track itsmovementsRadio tag (anterior) andacoustic tag (posterior)attached to a loggerheadturtle. (Photo: ALan Rees/ARCHELON)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (7 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacquired - developed in response to the environment, not inherited, suchas a character trait resulting from environmental effects (acquiredcharacteristic)acquired character - a non-inherited character, of function or structure,developed in an organism as a result of environmental influences duringthe individual's lifeacre - an area equal to 43,560 square feet or 4,046.87 square meters.One square mile equals 640 acresacrocyst - in hydrozoans, a sac containing a completely developedplanula larvaAcropora - a genus of hard (stony) coralsthat contain the elkhorn and staghorncorals. In May 2006, NOAA's nationalMarine Fisheries Service decided to listelkhorn corals (Acropora palmata) andstaghorn corals (Acropora cervicornis) asthreatened species under the EndangeredSpecies Act (ESA). A species is consideredthreatened if it is likely to become anendangered species within the foreseeablefutureStaghorn coral (Acroporasp.).acrorhagus - a sac, covered withnematocysts, that protrudes from belowthe sweeper tentacles or on the column ofcertain anthozoansLongitudinal section of A.alicemartinae (azocarminetriple staining). Ac:acrorhagus; Bm: basilarmuscle; Co: column; Me:mesenteries; Od: oraldisc; Pd: pedal disc; T:tentacles (Photo:V.Häussermann & G.Försterra/U.Frankfort)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (8 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacrosome - a protrusion on the anterior end of a sperm cell that containsdigestive enzymes that enables the sperm cell to penetrate the layersaround the oocyte (ovum)acrosphere - the knobbed tentacle tip of an anthozoan, usually bearingnumerous nematocystsacrotroch - a band of cilia anterior to the prototroch (preoral band) inlarvae of polychaete wormsactic - pertains to littoral rocky shores as a habitatactin - one of two proteins involved in muscle contraction. Actinassembles into long polymer rods called microfilaments which interactwith the other muscle protein, myosin, to cause shortening (contraction)in muscle cells. Actin also serves as an important structural molecule forthe cytoskeletons of many eukaryotic cellsactiniform - ray-like; star-shapedactinobiology - the study of effects of radiation upon living organismsactinometer - an instrument for measuring incident radiationactinopharynx - a short, flagellated tube between the mouth andgastrovascular cavity of an anthozoan polyp. It arises as an invaginationof the oral epidermis; the pharynx of an actinarian; also called the"stomodaeum"actinophore - a pterygiophore and its associated fin rayActinopterygii - a class of bony fishescomprising the ray-finned fishes, whichmake up about half of all vertebrate speciesknown. They are found in most aquatichabitats from the abyssal depths of theocean, greater than 10,000 m, to highaltitude freshwater streams and ponds; afew species can even move about on landfor short periods of time. Ray-finned fishesconstitute a major human food sourceThis squirrel fish is amember of the classActinopterygii, the rayfinnedfishes. Note thehard and soft rays in itsfins.actinostome - the mouth of a radially symmetrical animalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (9 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataactinotroch - a larval form found in the Phoronida (horseshoe worms)actinula - a hydrozoan larval stage thatlooks like either a polyp or medusa,depending upon whether the mouth isturned upward or downwardActinula larval stage of thehydrozoan, Tubularia.(photo: BIODIDAC)action potential - the electrical signal which rapidly propagates along themembrane of the axon of nerve cells, as well as over the surface of somemuscle and glandular cells. It is caused by change in membrane electricalpotential, the underlying cause of which is a change in flow of ions acrossthe membrane due to voltage-activated ion channels. It leads to an all-ornothingaction current, the nervous impulseactivated charcoal - a porous form of carbon that acts as a powerfuladsorbent. Activated charcoal is used to remove toxins from water andair, decolorize liquids, and recover solventsactivator - a substance or physical agent that stimulates transcription ofa specific gene or operonactive efflux - in microbiology, a mechanism responsible for theextrusion of toxic substances and antibiotics outside the cell. Itsimportance lies in its contribution to bacterial antimicrobial resistanceactive search - search behavior in which a herbivore or predator movesaround its environment looking for foodactive site - a specific region of an enzyme where a substrate binds andcatalysis takes placeactive transport - the pumping of molecules or ions through amembrane against their concentration gradient.This action requires theexpenditure of energy through ATP hydrolysisaculeate - bearing a sharp pointaculeiform - having a sharp point; needle-shapedacumen - the pointed tip of the rostrum in decapod crustaceanshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (10 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataacuminate - a shape which graduallytapers to a pointThe fierasfer, Carapusbermudensis, possess anacuminate shape. Thetapered end allows the fishto retreat tail first, forprotection, into thedigestive canal of a seacucumber whenthreatened. (Photo: D.Flescher, NOAA/NationalMarine Fisheries Service)acute - sudden or briefadambulacral - pertains to structures situated along the ambulacralgrooves of echinodermsadanal - located near the anusadapertural - in gastropods, a location near the shell apertureadaptation - changes in gene frequencies resulting from selectivepressures being placed upon a population by environmental factors. Thisresults in a greater fitness of the population to its ecological nicheadaptive behavior - any behavior that enables an organism to adjust toa particular situation or environmentadaptive management - the process of changing a managementstrategy in response to measuring its successadaptive radiation - the evolution of a single evolutionary stock into anumber of different speciesadaptive value - the degree to which a characteristic helps an organismto survive and reproduce, or affords greater fitness in its environmentadaptive zone - a particular type of environment requiring uniqueadaptations then allowing adaptive radiation to occuradaxial - situated on the side of, or facing toward an axisadcauline - pertaining to hydrozoan polyps that bend towards, or arenear to the common stemhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (11 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaddorsal - close to, but not on the middle of the dorsal surfaceadductor - a type of muscle whose function is to pull an appendage orbody part inwards, towards the body of an animaladeniform - gland-shaped; resembling a glandadenine - one of the four nitrogenousbases in DNA that make up the lettersATGC. Adenine is the "A". The others areguanine, cytosine, and thymine. Adeninealways pairs with thymineDiagram of the chemicalstructure of adenine, oneof the four nitrogenousbases in DNA.adenose - glandularadenosine triphosphate (ATP) - a nucleoside triphosphate, ATP is thepredominant supplier of metabolic energy in living cells. ATP supplies thechemical energy to drive endergonic reactions (requiring work or theexpenditure of energy), perform mechanical work, provide heat and evenproduce bioluminescenceadenovirus - a group of DNA-containing viruses which cause diseases inanimals. In humans, they produce acute respiratory tract infections withsymptoms resembling the common cold. They are used in gene cloning, asvectors for expressing large amounts of recombinant proteins in animalcells. They are also used to make live-virus vaccines against moredangerous pathogensadhesion - the molecular force of attraction between two unlike materialsthat acts to hold them togetherhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (12 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataadhesive disc - in fishes, a sucker-likeorgan for clinging to various surfaces, e.g.the modified pelvic fins in clingfishes andsnailfishes, and the dorsal fin in remoras(shark suckers)The dorsal fin of theremora (also called sharksucker or pilotfish) ismodified to function as anadhesive disc (Photo:NOAA)adhesive egg - an egg which adheres on contact to a substrate or toother eggsadhesive pad - an adhesive sucker located near the tip of a tentacle, insome hydrozoan medusae, utilized for clinging to plants or algaeadiabatic process - a process which occurs with no exchange of heatbetween a system and its environmentadient - tending toward or approaching a source of stimulationadipocyte - a fat cellAdipose tissue. The largeempty looking structuresare adipocytes (fat cells).(Photo: University ofSaskatuwan Biology Dept.)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (13 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataadipose fin - in fishes, a small fleshy finwhich lacks fin rays. It is found in fishessuch as salmon, and most catfishesThe adipose fin of thischum salmon lies betweenthe dorsal and caudal fins.(Image: U.S. Fish andWildlife Service)adjacently sympatric - pertains to those aspects of a parapatricspeciation event whereby the daughter species are minimally isolatedgeographicallyadmedial - near the medial planeadnate - joined togetherAdobe acrobat - Acrobat Reader is a software product from Adobe,designed to view .pdf (portable document format) documents downloadedfrom the World Wide Webadoral - near or toward the mouthadpressed - pressed close to or lying flat against something; apressedadradial canal - one of eight non-branched ciliated canals whichoriginates from the gastric pouches of scyphozoan medusae. The flow ofdigested food materials is toward the ring canaladsorbent - the solid substrate material onto which a substance isadsorbedadsorbtion - adhesion of an extremely thin layer of molecules to thesurface of a solid with which they are in contact, as when charcoal adsorbsgaseshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (14 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataadult - a fully developed and sexuallymature animal, physically capable ofreproducing under appropriatephysiological, ecological and sociobiologicalconditionsAn adult Nassau grouper.It is sexually mature andcapable of reproducing.advanced - new, unlike the evolutionary ancestral or primitive conditionadvection - the transport of substances in a fluid by the flow of that fluidadventitious - accidental or acquired; not natural or hereditary; foundsomewhere other than in the normal or usual place; additionaladventitious root - a root that originates from any part of the plantother than the root systemadventive plant - a species of plant that has been introduced into anarea but has not become permanently establishedaeolian - pertaining to the erosion, transport, and deposition of materialsby windaeolid nudibranch - a type of nudibranch(order Nudibranchia) in which the mantle isextended into long finger-like projections,the cerata (sing: ceras), rather than afeather-like external gill on the dorsalsurface. The cerata contain branches of thedigestive gland. The tips of the ceratacontain cnidosacs which usually storenematocysts that are obtained fromingested cnidarian prey, such as hydroids,sea anemones and soft corals. Ifthreatened, the nudibranch is capable ofdischarging these stinging cells through aterminal pore in the ceras. This action is aneffective deterrent to predatorsAeolid nudibranchs lackgills and utilize their dorsalcerata for respiration anddefense. (Photo: Dr BillRudman)aeration - the addition of air to a liquidhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (15 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaerenchyma - a specialized parenchymous tissue in seagrass leaves thathas regularly arranged air spaces or lacunae. These internal air spacesserve for flotation and exchange of gassesaerial photography - photographs taken from an aircraft or satelliteutilized to interpret environmental conditions and geographic featuresaerial root - a root which grows out from the stem above ground levelaerobic - deriving energy from a process requiring free oxygenaerobic respiration - a form of respiration in which molecular oxygen isconsumed and carbon dioxide and water are producedaesthetasc - an array of small hairs whichcontain chemosensory neurons (e.g.,olfactory neurons) on a branch of theantennules of malacostracan crustaceans,such as lobsters, crabs, and mantis shrimpThree antennularsegments with pairs ofaesthetasc sensilla ontheir ventral surfaces.(Photo: Deforest Mellon,Ph.D./University ofVirginia)aesthete - unique to chitons (Polyplacophora -Mollusca), aesthetes arephotosensitive mantle cells, present in very high densities. Although theyare involved in light responses, their exact function is unknownafferent - refers to a structure that leads to or toward a given position.For example, The portion of the peripheral nervous system that carriesinformation from the organs and tissues of the body to the centralnervous system (brain or nerve cord) or a small artery that carries bloodto the filtration system of the kidneyaffinity index - a measure of the relative similarity of the composition oftwo samples. Reciprocal affinity is a measure of distancehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (16 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaft - in, near, or toward the stern (rear) ofa vesselSunrise as viewed fromthe aft deck of the NOAAShip Albatross IV. (Photo:NOAA)agamogenesis - reproduction without fertilization by a male gamete;parthenogenesisagamospecies - species which replicate asexuallyagar - a gelatinous material extracted from the walls of some red algae,mainly species of Gelidium and Gracilaria. Agar is used as a supportmedium, when supplemented by appropriate buffers and/or nutrients andother ingredients, for cultures of microrganisms and tissues,electrophoresis, etcage class - a group of individuals of a species all of the same ageage distribution - the frequency of different ages or age groups in agiven populationage structure - the relative proportion of individuals in each age group ina populationagglomerate - to group or gather together in a dense clusteragglutinate - clumped together, as if by glueaggregate - a group of species, other than a subgenus, within a genus,or a group of subspecies within a species. An aggregate may be denotedby a group nameaggregate - a collection of units or particles forming a body or mass(noun); to form such a body or mass (verb)aggressive mimicry - a type of mimicry which results in a deceivedspecies being preyed upon or parasitized by a predator species. Themimic's cues may be visual, auditory, olfactory or behavioralhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (17 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAgnatha - agnathans are the mostprimitive and ancient of the vertebrates. Asthe name "Agnatha" implies, they lackjaws. Paired fins are also generally absent,and the the adult retains the notochord.The skeleton is cartilaginous. Theagnathans include the lampreys andhagfishesThe mouth of a jawlessagnathan, the sealamprey. Adults feed byattaching themselves totheir prey, rasping a holein the skin, and consumingblood and body fluids.(Photo: Minnesota SeaGrant)agonist - in pharmacology, a molecule that triggers a cellular response byinteracting with a receptoragonistic behavior - aggressive, negative behaviors, such as fighting,threatening, and fleeingagricultural pollution - the liquid and solid wastes from all types offarming, including runoff from pesticides, fertilizers and feedlots; erosionand dust from plowing, animal manure, carcasses, crop residues anddebrisagricultural run-off - the drainage of water from agricultural landaground - touching, resting or lodged on the bottom of shallow water.The opposite is "afloat"AGRRA (Atlantic and Gulf Rapid Reef Assessment) - an internationalcollaboration of scientists and managers aimed at determining theregional condition of reefs in the Western Atlantic and Gulf of MexicoAgulhas ring - large pulses of warm and salty water of Indian Oceanorigin which enter the Atlantic Ocean directly south of the Cape of GoodHope in the form of anticyclonic eddies. The process of ring detachment isassociated with perturbations of the Agulhas Current that retroflects southof Africaahead - in front of, or forward of the vesselahermatypic coral - a coral that lacks zooxanthellae and does not buildreefshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (18 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAIMS (Australian Institue of MarineScience) - the Australian Institute ofMarine Science (AIMS) was established bythe Commonwealth government in 1972 togenerate and transfer the knowledgeneeded for the sustainable use andprotection of the marine environmentthrough innovative, world-class scientificand technological research. It is a federallyfundedand independent statutory authoritygoverned by a Council appointed by theAustralian government. AIMS has itsheadquarters at Cape Ferguson, 25km eastof Townsville in North QueenslandAIMS field operations jettyat Cape Ferguson. (Photo:AIMS)air bladder - an air sac located in the coelomic cavity of many fishes. Insome fishes it may retain a tubular connection with the pharynx oresophagus; also known as a gas bladder or swim bladder, it functionsvariously as a hydrostatic organ, a sound conductor, a sound productionorgan, and in respiration. It is absent in sharks and rays, and some bonyfishesair compressor - an apparatus that compresses or pressurizes air forscuba tanks. Air is compressed from the atmospheric level (14.7 psi at sealevel) to the capacity of the tank, which is generally between 2500-3000psiaktological - pertaining to shallow inshore environments and communitiesaktology - the study of shallow inshore ecosystemsalate - wingedalbatross - any of large web-footed birds belonging to the familyDiomedeidae, chiefly distributed throughout the oceans of the southernhemisphere. Albatrosses have a hooked beak and long, narrow wingsalbedo - the ratio of the amount of light reflected by an object and theamount light falling on it (incident light); a measure of the reflectivity orintrinsic brightness of an object (a white, perfectly reflecting surfacewould have an albedo of 1.0; a black perfectly absorbing surface wouldhave an albedo of 0.0)albicant - whitish colorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (19 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataalbinism - hereditary absence of pigmentin an organism. Albino animals have nocolor in their skin, scales, hairs and eyes.The term is also used for absence ofchlorophyll in plants. Some organismsexhibit partial albinism. White tigers, forexample, possess black stripes on a whitebackgroundAn albino catfish. Thefish's skin cells contain nodark melanin granules.albino - a pigmentless white phenotype, determined by a mutation in agene which codes for a pigment-synthesizing enzymealbugineous - white coloredalcohol - any of a class of organic compounds in which one or morehydroxyl groups are attached to a carbon compoundalcyonarian - a soft coral of the orderAlcyonacea, class Anthozoa, phylumCnidaria. They consist of a firm body,throughout which calcareous spicules aredispersed. The surface is studded withpolyps. They are closely related to thescleractinian (hard or stony) corals but lackthe rigid, stony exoskeletonAlcyonarians are colonialsoft corals that lack theCaCO 3 exoskeleton of thehard or stony corals. Anendoskeleton of calcareousspicules provide supportfor the body, which isstudded with polyps.aldehyde - an organic molecule containing a -COH group. It is a colorlessvolatile liquid, obtained from alcohol by oxidation. An example of thesearomatic compounds is formaldehydealecithal - a type of egg that does not contain yolkhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (20 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAlee effect - the social dysfunction and failure to mate successfully whenpopulation density falls below a certain thresholdalgae - unicellular, multicellular, solitary, or colonial organisms thatcontain chlorophyll. They lack roots, stems, leaves, flowers, and seeds.Algae are in the Kingdom Protistaalgaecide - a chemical agent specifically designed and used to kill orinhibit the growth of algae; also called 'algicide'algaestat - a chemical agent which retards and prevents the reproductionand growth of algaealgal bloom - a sudden spurt of algal growth that can indicate potentiallyhazardous changes in local water chemistryalgal galls - a response of gorgonia (Pseudoplexaura spp.) to tissueinvasion by the algae, Entocladia endozoica, in Florida and Caribbeanwaters. The host gorgonia react to the algal filaments by producingcapsules (galls) composed of skeletal elements that isolate the algae fromthe host tissue, at the expense of the skeletons' tensile strength andelasticity. The gorgonium readily breaks apart at the sites of theweakened skeleton. For more information and illustrations, see: http://www.coral.noaa.gov/coral_disease/algal_galls.shtmlalgal mat - a dense layer of algae, usuallyfilamentous, which blankets the bottom in ashallow water environment. An algal matcan also be a ‘mat’ of microscopic species,usually diatoms, covering soft bottoms, ora mat of floating algaeA helmet conch feeding onan algal mat in sand(Photo: James Stuby)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (21 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataalgal reef - a reef, usually exposed towave action, composed of coralline algaeand vermatid gastropods. The corallinealgae occur in forms of cups or funnelsCoralline algae makes uppart of an algal reef.algal ridge - a low ridge at the seaward margin of a reef flat, largelycomposed of skeletons of calcareous algae. A synonym of Lithothamnionridgealgal turf - densely packed algae, usually filamentous, which rise lessthan one centimeter above the substratum upon which they are growing.A synonym of turf algaealgicolous - pertaining to an organism that lives on or around seaweedalgin - a polysaccharide derived from brown algae. Algins are used formany industrial processesalgophagous - refers to an organism that feeds upon algaealgorithm - A computer program (or set of programs) which is designedto systematically solve a certain kind of problemalien species - a species which does not naturally occur within an areaand which has usually arrived as a result of deliberate or accidentalhuman intervention. Alien species often have adverse effects on nativespecies as a result of competitionalima - a larval stage of a mantis shrimpalimentary canal - the canal, including the stomach and intestines,leading from the mouth to the anusaliquot - a portion of a sample; a subsamplehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (22 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataalizarin - a red dye made from the roots ofthe madder plant, Rubia tinctorum, orproduced synthetically from coal tar. Abone specific stain, alizarin red S iscommonly used to stain the skeletalelements of a fish specimen. In thisprocedure, the muscles are renderedtransparent by emersing the specimen in acaustic agent, such as potassium hydroxideA Dover sole, cleared andstained with alizarin red S,to highlight the bonystructures (Photo: NaturalHistory Museum, london)alkaline - having a pH of more than 7. Alkaline solutions are also said tobe basicAll Islands Coral Reef Initiative - a cooperative effort among Hawaii,American Samoa, Guam, the Commonwealth of the Northern MarianaIslands, Puerto Rico, and the U.S. Virgin Islands to improve themanagement of coral reefs in island areasALL Species Foundation - a non-profit organization dedicated to thecomplete inventory of all species of life on Earth within the next 25 years -a human generation (http://www.all-species.org/)all-or-none law - an action that occurs either completely or not at all,such as the generation of an action potential by a neuron, or thecontraction of a muscle cellallantois - a vascularized extra-embryonic membrane of amnioteembryos that forms as a narrow outgrowth of the hind portion of the gut.In birds and reptiles, it stores waste products of embryonic metabolism.The allantois fuses with the chorion to form the chorio-allantoic membranein birds and reptiles, and a part of the placenta in mammalsAllee's Principle - there is a positive relationship between individualfitness and either the numbers or density of conspecifics. In other words,as the number of individuals in a population increases, or as populationdensity increases, survival and reproduction also increaseallele - one of the variant forms of a gene at a particular locus, orlocation, on a chromosome. Different alleles produce variation in inheritedcharacteristics. In an individual, one form of the allele (the dominant one)may be expressed more than another form (the recessive one)allelochemical - a chemical substance produced by one organism that istoxic or inhibitory to the growth or well being of anotherhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (23 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataallelomimetic behavior - behavioral activities that have strongcomponents of social facilitation, imitation, and group coordination;imitation of behavioral habits of another animal, usually of the samespecies; behavior in social animals in which each animal does the samething as those nearby. It is developed to a high degree in schools offishes, flocks of birds, and and herds or pods of mammalsallelopathic substance - a substance produced by one organism thatadversely affects another organismallelopathy - a particular form of amensalism found in plants. In thisinteraction, one species produces and releases chemical substances thatinhibit the growth of another speciesallergen - an antigen that provokes an immune responseallo - - a prefix meaning other, or differing from the normal or usualalloantigen - an antigen that occurs in some but not other members ofthe same speciesallochoric - occurring in two or more communities within a givengeographical regionallochronic speciation - speciation without geographical separationthrough the acquisition of different breeding seasons or behavior patternsallochthonous population - an organism or a population of organismsforeign to a given ecosystem; they have arrived from elsewhereallocryptic - pertaining to organisms that conceal themselves withcoverings of other organisms or with inanimate materialsallogenic - resulting from factors acting from outside a system ormaterial transported into an area from the outside which alters thesystem's habitat; genetically different individuals belonging to the samespecies; when describing transplantation biology, the donating individualis of the same species, but not one's selfallogenic succession - a kind of ecological succession in which one kindof community replaces another because of a change in the environmentwhich was external to and independent of that produced by thecommunity itselfallograft - a piece of tissue or an organ transferred from one individual toanother individual of the same specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (24 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataallometric equation - the general form of the allometric equation is y =bxa where y = measure/process in question, x is size, a is the allometricexponent (which tells you the relationship between x & y), and b = aconstant (the allometric coefficient)allometric growth - type of differential growth in which parts of thesame organism grow at different rates. For example, in humans, the headand body grow at different rates, resulting in a human adult withcompletely different proportions from those of an infantallometry - study of the relative growth relationships between differentparts of an organism; mathematically expressed by the allometricequation y = mx + b, where y = predicted size of body part; x = observedbody weight; m = slope acquired; and b = the value of y where itintercepts the vertical axis. Allometry is studied during the growth of asingle organism, as a comparison between different organisms of thesame species, and between organisms in different species. The allometricequation is graphed on an XY axis, with the body size on the x-axis andthe part size on the y-axis. The scatter produced by the differentmeasurements being compared can then be analyzed for useful dataallomone - a chemical substance that induces a response in an individualof another species that is beneficial to the emitting organism. Manyallomones are essentially chemical deterrents. For example, a chemicalsubstance that is produced by a prey species to repel a predator speciesallomorphosis - allometry based on the comparison of relatedindividuals, rather than upon ontogeny. Systematic change of shapeamong successive adults of a phyletic sequence, for example, isallomorphosis; the rapid development of specialized organs or increase ofspecialization in an organismalloparent - an animal which exhibits parental behavior towards anotheranimal's offspringallopatric speciation - speciation which occurs in populations initiallyisolated geographically, such as by habitat fragmentation or migration. Asnatural selection and genetic drift act independently in isolatedpopulations, separation will eventually produce organisms that cannotinterbreedallopatric species - species occupying mutually exclusive geographicalareasallopolyploid - a type of polyploid species resulting from two differentspecies interbreeding and combining their chromosomesallorecognition - the ability of an individual organism to distinguish itsown tissues from those of another; the recognition of antigens, expressedon the surface of cells of non-self origin. Allorecognition has beendescribed in nearly all multicellular phylahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (25 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataalloresponse - allorecognition, followed by the immune effectormechanisms generated by the recognition processallosome - a chromosome which deviates in size, form or behavior fromother chromosomes. An allosome is usually a sex chromosomeallotopic - refers to species with overlapping ranges but do not occupythe same space. They do not "live together"allotype - in taxonomy, a paratype of the opposite sex to the holotypeallozyme - a form of an enzyme that differs in amino acid sequence fromother forms of the same enzyme and is encoded by one allele at a singlelocusalluvial - relating to mud and/or sand deposited by flowing wateralluvium - sediments deposited by erosional processes, usually bystreamsalmost atoll - an atoll whose rim is less than 75 percent complete as acircle at low tideAlong Track Reef Imaging System (ATRIS) - a boat-mountedinstrument that acquires continuous digital still EXIF-format images ofshallow-marine substrates. Images are acquired via a digital still cameramounted in a waterproof housing that is deployed on a pole attached to asurvey vessel. Images are instantaneously transferred to a shipboardcomputer and stored. ATRIS acquires high resolution, color digital imagesthat are accurately geo-located in real-time. For a typical mission, 1,000ATRIS images are captured per hour at a survey speed of 1 knot. ATRISwas developed by the U.S. Geological Surveyalpha animal - in animal behavior, the individual that takes a lead roleand occupies the dominant position in a groupalpha particle - a particle emitted from the nucleus of an atom,containing two protons and two neutrons, identical to the nucleus (withoutthe electrons) of a helium atomalpha taxonomy - descriptive taxonomy concerned primarily with thediscovery, description, and naming of species, usually on the basis ofmorphological charactersalternation of generations - a life cycle in which a multicellular diploidstage is followed by a haploid stage, and so on; found in land plants andmany algae and fungihttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (26 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataalternative hypothesis - in statistics, the hypothesis that is adoptedwhen the null hypothesis is rejectedaltimeter - an instrument for measuring altitudealtimetry - a technique to measure theheight of the sea surface from radar pulsestransmitted from a satelliteArtist's rendition of asatellite measuringaltimetry.altricial - born or hatched undeveloped; requiring maternal care afterbirth; as opposed to precocialaltruism - a form of behavior in which an individual risks lowering itsfitness for the benefit of another; in evolutionary biology, an organism issaid to behave altruistically when its behavior benefits other organisms, ata cost to itself. The costs and benefits are measured in terms ofreproductive fitness, or expected number of offspringalveolus - one of thousands of tiny air sacs at the end of the bronchiolesin lungs. Alveoli are the sites of gaseous exchange between theatmosphere and the blood. Oxygen passes into the lung capillaries andCO 2 passes from the capillaries into the lungs and is exhaledambient noise - acoustic signalsoriginating from a variety of underwatersources, such as propeller cavitation,engine noises, animal sounds, wind, waves,and rainThe sounds produced bythe spotted boxfish,Ostracion meleagris,contribute to the ambientnoise on Pacific reefs.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (27 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Data(Photo: Hawai'i Coral Reefnetwork)ambient pressure - the pressure surrounding an organism. On land, itresults from the weight of the atmosphere. At depth, it comes from theweight of the water plus the weight of the atmosphereambit - the geographic range or extent in which an organism normallylives or growsambulacrum - a row of tube feet of anechinodermThe ray of a starfishrevealing the ambulacralgroove and tube feet.ambush predator - a predator that hides and waits for prey to pass inclose proximity rather than actively hunting for itamensalism - a type of symbiosis where two (or more) organisms fromdifferent species live in close proximity to one another, and where one ofthe members suffers as a result of the relationship while the other isunaffected by itamino acid - the building block of a protein. Twenty different amino acidsare used to synthesize proteins. The shape and other properties of eachprotein is dictated by its precise sequence of amino acids. Humans mustinclude adequate amounts of 9 of the 20 amino acids in their diet. These"essential" amino acids cannot be synthesized from other precursorsamino acid sequence - the order of amino acids as they occur in apolypeptide chain. This is referred to as the 'primary structure' of proteinsamino group - a nitrogen atom single-bonded to two hydrogen atoms(_NH2); imparts basic properties to an amino acidamitosis - an unusual form of cell division in which the nucleus cleaveswithout change in its component structure (such as the formation ofchromosomes), followed by the division of the cytoplasm. Amitosis mayoccur chiefly in highly specialized cells which are incapable of longcontinuedmultiplication, in transitory structures, and in early stages ofdegenerationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (28 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataammonotelic - having ammonia as the chief excretory product ofnitrogen metabolismamnion - a non-vascular extra-embryonic membrane of amniote embryosthat forms a fluid-filled cavity surrounding the embryo. It protects theembryo by functioning as a shock absorberamniote - a vertebrate whose embryo is surrounded by a fluid-filled sac,the amnion; characteristic of reptiles, birds, and mammalsamoeba - a-naked freshwater or marineprotozoan protist that forms temporarypseudopodia for food and water capture,and locomotion ­An amoeba thrusting outpseudopodia (false feet).(Photo: NASA)amoebocyte - a phagocytic cell found circulating in the body cavity ofcoelomates, particularly annelids and mollusks, or crawling by amoeboidmovement through the interstitial spaces of sponges; an amoeboid cell insponges that transports nutrients and is found in the matrix between theepidermal and collar cells; any cell having the shape or properties of anamoebaamoeboid - amoeba-likeamoeboid movement - a type of motility of a cell in which cytoplasmicstreaming (directional flow of cytoplasm) extrudes outward of the cell toform pseudopodia (false feet) so that the cell can change its locationamorphous - lacking a distinct form or shapehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (29 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAmphibia - a class of vertebrates thatconsists of frogs, toads, newts,salamanders, and caecilians. Theseorganisms live at the land/waterinterface and spend most of their lifecycle in water. With exception of sometree frogs, all must reproduce in wateror otherwise moist conditions.Amphibians are not typically marineThe African Bullfrog,Pyxicephalus adspersus. Thisamphibian is an inhabitant ofNamibia. (Photo: CopyrightMiguel Vences and Frank Glaw,1998)amphiblastula - a sponge larva thatappears as a hollow ball with anteriorflagellated cells and posterior larger andnonflagellated cells (megascleres)Amphiblastula larva of asponge. (Photo: CopyrightBIODIDAC)amphidiploid - an allopolyploid; an organism produced by hybridizationof two species followed by chromosome doublingamphidromous - refers to the migratory behavior of fishes moving fromfresh water to the ocean and vice versa, not for reproductive purposes butoccurring regularly at some stage of the life cycleamphimixis - sexual reproduction involving the fusion of male andfemale gametes and the formation of a zygoteamphipathic - refers to molecules with both hydrophobic and hydrophilicregions. Proteins and lipids may be amphipathicamphophilic - having an affinity for both basic and acidic dyeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (30 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataamplicon - the DNA product of a polymerase chain reaction (PCR),usually an amplified segment of a gene or DNA sequenceamplification - in genomics, the process of increasing the number ofcopies of a particular gene or chromosomal sequenceamplified ribosomal DNA restriction analysis (ARDRA) - DNAfingerprinting based on restriction patterns of ribosomal DNA. The methodconsists of amplification of the 16S rRNA gene (rDNA) and subsequentrestriction digestion of the ampliconampulla - a membranous vesicleampullae of Lorenzini - small vesiclesand pores around the head of a shark thatform part of an extensive subcutaneoussensory network system that detects weakmagnetic fields produced by other fishes, atleast over short ranges. This enables theshark to locate prey that are buried in thesand, or orient to nearby movement. Theampullae may also allow the shark todetect changes in water temperatureThe ampullae of Lorenziniare small vesicles andpores that form part of asubcutaneous sensorynetwork of sharks. Thesevesicles and pores arefound around the head ofthe shark and are visibleto the naked eye. Theyappear as dark spots inthis photograph of aporbeagle shark head.(Photo: Dr. StevenCampana, BedfordInstitute of Oceanography)amural form - a coral growth form in which the corallite walls arepartially or wholly lost; the septa stay unreducedamylopectin - a highly branched polymer of glucose found in plantsamylose - a linear polymer of glucoseanabolism - the metabolic processes that consumes energy and involvethe synthesis of larger, complex molecules from simpler oneshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (31 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataanadromous species - a species thatspends its adult life in the ocean but swimsupriver to freshwater spawning grounds inorder to reproduce, e.g., Pacific salmonThe chinook salmon is ananadromous fish whichspends most of its life inthe ocean, but returns tofresh water streams forspawninganaerobe - an organism that can live in the absence of oxygenanaerobic - deriving energy from a process that does not require freeoxygenanagenesis - the evolutionary process whereby one species evolves intoanother without any splitting of the phylogenetic treeanaglyph - a stereoscopic picture consisting of two images of the sameobject, taken from slightly different angles, in two complementary colors.When viewed through colored spectacles, the images merge to produce astereoscopic sensation, i.e., that appears three-dimensional whensuperimposed; anything carved in low reliefanal fin - the single fin situated on theventral midline of a fish, behind the anus,and anterior to the caudal finAnal fin of a bony fish.(Photo: John Lyons,University of Wisconsin)analgesia - the absence of pain in response to stimulation that wouldnormally be painfulanalgesic - any drug intended to alleviate pain. Analgesics increase apatient's pain threshold, thereby decreasing the sensation of pain.Analgesics range from aspirin and acetaminophen to narcoticsanalogous behavior - behavior exhibited by different species that issimilar in function, but does not originate from a common ancestryhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (32 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataanalogous structure - a body part that serves the same function indifferent organisms, but differs in structure and embryologicaldevelopment, e.g., the wing of an insect and a birdanalysis of covariance - an analysis of variance in which the data areadjusted or controlled for the presence of one or more other variablesanalysis of variance - a statistical technique for testing for differences inthe means of several data populationsanamniote - an aquatic vertebrate whoseembryonic stage is not surrounded by anamnion. Fishes and amphibians areanamniotesFish eggs and larvae.These aquatic vertebratesdo not possess an amnionduring embryonicdevelopment. (Photo:NOAA/National MarineFisheries Service)anaphylaxis - a severe, potentially life-threatening, allergic reaction,which can occur after an animal sting or as a reaction to an injected drug.Less commonly, the reaction occurs after a particular food or drug hasbeen taken by mouth. Symptoms may include vascular collapse, shockand respiratory distress; also called "anaphylactic shock"anastomose - a term that refers to coral branches which grow backtogether after the initial divisionanastomosis - the union or connecting of branches forming a meshworkor a networkanatomy - the science of internal morphology as revealed by dissectionancestor - any organism, population, or species from which some otherorganism, population, or species is descendedancestral - in evolution, a trait that has been inherited unchanged froman ancestorancestral polyp - an anthozoan polyp which develops from a sexuallyproduced larva and gives rise to a colony by asexual buddinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (33 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataancestral trait - a trait shared by a group of organisms as a result ofdescent from a common ancestorancestrula - the first (parental) zooid of a bryozoan colony, formed froma settled and metamorphosed larva. It is often smaller andmorphologically distinct from the zooids that bud from itanchialine cave - a coastal cave formed in limestone or volcanic rockthat is flooded with seawater. These marine or brackish water bodies lacksurface connections to the sea. They include the longest submerged caveson Earthanchialine pool - a land-locked brackishbody of water that displays tidalfluctuations but has no surface connectionto the sea. Anchialine pools are restrictedto highly porous substrates, such asrecently solidified molten rock or limestoneadjacent to the seaAn anchialine pool, HaluaPond, located in the Ühihi­Kïna'u Reserve, Maui(Photo: Hawai'i's NaturalArea Reserves System(NARS))Andavadoaka - a small fishing village located on the southwestern coastof Madagascar. It lies on the edge of a shallow lagoon protected from theopen ocean by a series of fringing and submerged barrier reefs The coralreefs, including patch reefs, in the region are in generally pristine shape,ranging from moderate to excellent. The reefs are not directly threatenedby terrigenous sedimentation, as elsewhere in the country, due to theabsence of major rivers. However, they are at risk from over fishing froma still small but rapidly increasing population of Vezo fishermen.Conservation efforts are currently underway to maintain the presentstatus of these coral reefs, including the establishment of a marineprotected area network encompassing parts of the barrier and patch reefsystemsandrogen - a principal male steroid hormone, such as testosterone,which stimulates the development and maintenance of the malereproductive system and secondary male sexual characteristicsandrogenesis - male parthenogenesis, i.e., the development of a haploidembryo from a male nucleus. The maternal nucleus is eliminated orinactivated subsequent to fertilization of the ovum, and the haploidindividual (referred to as androgenetic) contains the genome of the malegamete only in its cellsanemochory - the dispersal of seeds, fruits, or other plant parts by windhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (34 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataanemometer - an instrument for measuring wind velocityanemone - a cnidarian of the classAnthozoa that possesses a flexiblecylindrical body and a central mouthsurrounded by tentaclesA sea anemone of thePhylum Cnidaria, ClassAnthozoa. The tentaclesbear stinging cells whichare used for food captureand defense.aneuploidy - the condition of having an abnormal number ofchromosomes; a chromosome number that is not an exact multiple of thehaploid numberangelfish - any species of colorful deepbodied,laterally compressed, spiny-rayedfishes in the family Pomacanthidae. Theyresemble the closely related butterflyfishes, but generally possess a more robustbody and a sharp preopercular spine. Thereare other kinds of unrelated fresh waterangelfishes, belonging to the familyCichlidae, which are common homeaquarium fishesThe yellowmask angelfish(Pomacanthusxanthometopon)photographed on a reef inPapua New Guinea (Photo:Tom Doeppner/BrownUniversity)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (35 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataangiogenesis - the growth and proliferation of new blood vessels.Angiogenesis is a normal biological process that occurs in both healthyand disease states. It is essential for the growth of tumors. Tumor cellsrelease chemicals to encourage blood vessel growth for their nourishmentangler - a person catching fish or shell fishwith no intent to sell; includes peoplereleasing the catchA skiff, a guide, and anangler fishing for bonefishin Florida. (Photo:Bonefish and TarponUnlimited)angstrom - a unit of length equal to one ten-thousandth of a micron (10 ­4 micron) or 10 -10 of a meteranimal communication - animals useseveral ways to communicate with oneanother. These include the visual, auditory,and tactile senses, as well as certainchemicals involved in taste and smell.Other possibilities are magnetic fields andelectrical discharges. Communicationamong animals helps them to recognizeeach other, cause reproductive behavior,and to organize social behaviorsThe oyster toadfish,Opsanus tau, producessounds during thereproductive season.Thesesounds facilitate mating.(Photo: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (36 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataannulus - a mark or ring that forms annually on the otoliths, scales, andbones of fishes that correspond to the annual period of growth. Annuli canbe use to determine age and growth rates of fishesanomaly - the deviation of a particular variable (e.g., temperature) fromthe mean or normal over a specified timeanonymous work - according to the International Code of ZoologicalNomenclature, a published work that does not state the name of theauthor(s)anoxic - the absence of free oxygenantagonistic pleiotropy - in genetics, a situation in which a single genecreates multiple competing effects, such that beneficial effects of a traitcreated by the gene are offset by "losses" in other traitsantenna - one of the paired, flexible, andjointed sensory appendages on the head ofa crustacean, an insect, or a myriapod (e.g., a centipede)A spiny lobster displayingits paired uniramousantennae and biramousantennules. (Photo:Copyright CorelCorporation)antennal gland - the main organ in crustaceans used for excretion andosmoregulation; the green glandantennular fosette - in crustaceans, a depression, pit or socketcontaining the basal portion of the antennuleantennule - a small antenna, especially the first pair of antennae incrustaceanshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (38 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataanterior - morphologically, toward thehead or front end of an individual, orproximal portion of a bodily partClose up of the anteriorend of a spotlightparrotfish supermale.anteromesal - in the front and along the midline of a bodyanteroposterior axis - the longitudinal axis of an animal, from head totailanthoblast - in stony corals, a young sessile polyp producing ananthocyathus, the disklike crown that separates from the stalk(anthocaulus)anthocaulus - a polyp that develops asexually on the skeletons of somecoral speciesanthocodium - the free oral end of an anthozoan polyp, the basal portionof which is united with other zooids in a common mass; the uppertentacular part of the polyp that can be retracted into the calyx; It is asite of bioluminescence in some anthozoansanthocyathus - the disklike crown portion of solitary stony corals thatseparates from the stalk (anthocaulus)anthostele - the lower part of a cnidarian polyp, into which the distalportion of the polyp, the anthocodium (which includes the mouth and thetenacles) is withdrawnAnthozoa - a class of Cnidaria thatincludes the stony corals, soft corals, seaanemones, gorgonians, andcorallimorphariansA deep-sea anemonephotographed by the Alvin2001 during a survey ofBlake Ridge off the U.S.Georgia coast (Deep Easthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (39 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataexpedition).anthozooid - any of the individual zooids of a compound anthozoananthropogenic - made by people or resulting from human activitiesanthropomorphism - attributing a human characteristic to an inanimateobject or a non-human speciesanti-codon - a triplet of nucleotide bases (codon) in tRNA (transfer RNA)that pairs with (is complementary to) a triplet in mRNA (messenger RNA).For example, if the codon is UCG, the anticodon is AGCantibiosis - an antagonistic association between two organisms in whichone of the organisms is adversely affected; an association betweenorganisms that is harmful to one of them or between organisms and ametabolic product of another; the inhibition of growth of a microorganismby a substance produced by another microorganismantibiotic - a chemical substance, e.g., penicillin, that kills or inhibits thegrowth of bacteriaantibody - a protein produced by higher animals in response to thepresence of a specific antigenanticryptic coloration - a color or color pattern used for concealment bya predatoranticyclone - an area of high pressure. Circulation is clockwise aroundthe high in the Northern Hemisphere and counterclockwise in theSouthern Hemisphereantigen - a foreign macromolecule introduced into a host organism thatelicits an immune responseantigenicity - the ability of an antigen to induce an immune responseand combine with specific antibodies or T-cell receptorsantihelmintic - a chemical agent used to combat parasitic worms, suchas roundworms and tape wormsAntillean z trap - a common type of fish trap used widely in theCaribbean and elsewhere. It takes the form of a double chevron or "Z"with two down-curving "horse-neck" entrance funnels. Typically, thesemeasure between 180 and 230 cm in length and are 60 cm highhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (40 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAntilles Current - one of the currents of the North Atlantic subtropicalgyre flowing along the northern side of the Greater Antilles. Its water issupplied from the northern branch of the North Equatorial Current, drawnmainly from the Gulf Stream recirculation. The Antilles Current mergeswith the Florida Current east of the Straits of Floridaantinutrient - a compounds that inhibits the normal uptake of nutrientsantioxidant - a molecule that is capable of reacting with free radicals andneutralizing them; a compound that slows the rate of oxidation reactionsantioxidant - a substance that prevents cellular damage caused by freeradicals, which are are highly reactive chemicals that often containoxygen. They are produced when molecules are split to yield products thathave unpaired electrons (oxidation). Antioxidants counteract thedamaging effects of oxidation in body tissuesAntipatharia - an order of corals whichcontains the black and horny coralsBlack coral in the orderAntipatharia.antipathin - a proteinaceous and chitinous material that forms the axis inan antipatharian coralantipodal - diametrically opposite; located on the opposite sideantisense DNA - the strand of chromosomal DNA that is transcribed; aDNA sequence that is complementary to all or part of an mRNA moleculeantisymmetry - a pattern of deviation without a side bias. A sidedifference occurs for a given trait, but the larger side varies at randomamong individualsantitoxin - a substance that neutralizes a toxinhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (41 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataantivenom (or antivenin, or antivenene) - a biological product(antitoxin) used in the treatment of venomous bites and stingsantrum - a hollow space or cavityanus - the posterior opening of the digestive tract, through which wasteproducts of digestion are releasedaperture - an opening in some structure. For example, the opening in asnail's shell through which the snail emergesapex - the tip, top, point, or angular summit of anythingapex predator - a predator which is notitself preyed upon as a species. Theseanimals are often at the end of food chains,where they have a crucial role inmaintaining and determining the health ofecosystemsThis large blue shark is anapex predator in theocean. (Photo: GregSkomal, NOAA/NOSNational MarineSanctuaries)aphorism - a concise statement of a general truth; a short pithyinstructive sayingaphotic zone - that portion of the ocean where light is insufficient forplants to carry on photosynthesisaphrioid form - a coral growth form in which the septa are reduced attheir outer ends so neighbouring corallites are united by a zone ofdissepiments (horizontal partitions within or outside of a corallite)apical - relating to or located at the tip (an apex), or opposite to the baseapiculate - ending in a short, sharp pointhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (42 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAplacophora - a class of Mollusca. They are a small group (less than 300species) of wormlike mollusks that lack a shell. Some are associated withsoft corals. Creeping species feed on cnidarians. Burrowing species aredeposit feeders and carnivoresapobiosis - the local death of a part of an organismapode fish - a fish which lacks pelvic (ventral) fins, such as the Americanor European eelapogee - the point in the orbit of the Moon or man-made satellite farthestfrom the Earth; the point in the orbit of a satellite farthest from itscompanion bodyapomixis - the asexual production of diploid offspring without the fusionof gametes. The embryo develops by mitotic division of the maternal orpaternal gamete, or in the case of plants, by mitotic division of a diploidcell of the ovuleapomixis - in flowering plants, asexual reproduction through seedapomorph - a derived character differing from the ancestral conditionapomorphy - a relatively derived or advanced or unique character stateapopinacocyte - in sponges, an endopinacocyte lining the excurrent canalapopinacoderm - in sponges, a surface lined with apopinacocytesapoptosis - a normal cellular process involving a genetically programmedseries of events leading to the death of a cell; also called "programmedcell death (PCD)" or "cell suicide"apopyle - the opening of a choanocyte chamber of a sponge into anexcurrent canalaporrhysa - the exhalent canals in spongeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (43 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaposematism - conspicuous warningcolorationA venemous lionfish(Pterois volitans) withconspicuous coloration.(Photo: Copyright CorelCorporation)aposymbiosis - loss of a symbiont, such as zooxanthellae in hard coralsapparent shoreline - in areas where the land is obscured by marshgrass, mangrove forests, cypress or similar marine vegetation, the actualshoreline can not be accurately represented. Instead, the outer limit lineof the vegetation area is delineated (where it would appear to the eye asthe shoreline) and is referred to as the apparent shorelineappeasement behavior - any conciliatory behavioral display.Appeasement cues often are exhibited toward threatening conspecificswhen flight is either difficult or impossible; conciliation directed toward anaggressor or potential aggressorappendage - any body part that extends from the main axis or trunk orcephalized portion of an organismappendicular - relating to the appendages, as opposed to axial, whichrefers to the trunk and head of an organismapplet - a small Java program that can be embedded in a web page tocreate special effects. Applets differ from full-fledged Java code. They arenot allowed to access certain resources on the local computer such as filesand serial devices, and are prohibited from communicating with mostother computers across a networkapprehensive behavior - any behavior that indicates an organism' santicipation of an adverse or noxious experience. Some behaviors includehigh level of alertness, defensive postures, and threat displaysapproximate - in morphlogy, placed close togetherhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (44 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataapron reef - the initial stage of a fringing reef. It is discontinuous andcovers a small areaaquaculture - the growing of aquatic organisms in controlledenvironments for any commercial, recreational, or public purpose; sectorof fisheries that includes the rearing or raising under controlled conditionsof aquatic products such as fishes, mollusks, crustaceans, sea weeds andother aquatic resources in sea, lakes and rivers. Examples are fish ponds,fish pens, and fish cages. Aquaculture is widespread, and in tropicalcountries has been a significant source of pollution in coastal waters andalso contributes to the destruction of mangrove forestsaquarist - a hobbiest or professional that keeps organisms in an aquariumAquarius - Aquarius is an underwaterocean laboratory located in the NOAAFlorida Keys National Marine Sanctuary.The laboratory is deployed three and halfmiles offshore, at a depth of 60 feet, nextto spectacular coral reefs. Scientists live inAquarius during ten-day missions usingsaturation diving to study and explore thecoastal ocean. Aquarius is owned by NOAAand is operated by the National UnderseaResearch Center at the University of NorthCarolina at WilmingtonThe Aquarius, anunderwater oceanlaboratory located in theNOAA Florida KeysNational Marine Sanctuary.(Photo: NOAA/OARNational UnderseaResearch Program)aqueous solution - a solution in which water is the solventaquifer - a subterranean layer of porouswater-bearing rock, gravel, or sand capableof storing and conveying water to wells andstreamsDiagram of an aquifersystem. (Diagram: TexasA&M Univ.)aquiferous system - water circulatory system in sponges composed ofchoanoderm, pores and chambershttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (45 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAra-A - an antiviral drug developed from the discovery of particularnucleosides (the basis of synthesis of Ara-A) in the marine spongeCryptotethia cryptaAra-C - an anticancer drug developed from the discovery of particularnucleosides (the basis of synthesis of Ara-C) in the marine spongeCryptotethia cryptaarachnactis - a planktonic larva of tube anemones (Ceriantharia)aragonite - a mineral species of calcium carbonate (CaCO 3 ) with a crystalstructure different from the other two forms of CaCO 3 (vaterite andcalcite). It is precipitated from ocean surface waters mainly by organisms(e.g., coral) that use it to make their shells and skeletonsaragonite saturation horizon - a natural boundary in the oceans belowwhich organisms such as stony corals cannot maintain calcium carbonatestructures. As carbon dioxide levels increase, the aragonite saturationhorizon becomes shallower, severely limiting the distribution of stonycorals in certain parts of the deep ocean; the limit betweenundersaturation and supersaturation of aragonitearagonite skeleton - skeletons primarily composed of the aragonite formof calcium carbonatearborescent - having a large tree-like appearancearborescent colony - a coral colony with a tree-like growth structurearc - in a geographical information system (GIS), an arc is a line thatbegin and end with a node. Intersections of arcs are always connectedwith a node. Arcs also make up part of a polygonArc/INFO - geographical information system (GIS) software developedby ESRI that is used to do more robust GIS operationsarch- - a prefix meaning 'ultimate beginning'Archaea - a group of organisms that resemble bacteria. However, theseorganisms are biochemically and genetically different from bacteria. Somespecies live in the most extreme environments found on EarthArchaebacteria - an ancient group of prokaryotes, over 3.5 billion yearsold; sometimes this group is placed into a separate kingdom, the Archaea.Most biologists currently place it within the Kingdom Monera.Archaebacteria inhabit extreme environmentshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (46 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataarchaeocyte - in sponges, an amoeboid cell capable of phagocytosis.Archaeocytes are totipotent, having the capability of differentiating intoother types of sponge cellsarchenteron - the primitive endoderm-lined gut of an animal embryoformed during gastrulation. It is formed by the invagination of blastulacells (blastomeres) into the blastocoel. The archenteron develops into thedigestive tract of the adult animalarchetype - the plan or fundamental structure on which a group oforganisms, or their systems of organs, are assumed to have beenconstructed; as, for example, the vertebrate archetypearchi- - a prefix meaning primitive, original, or ancestralarchipelago - a cluster of islands usually in the open ocean. Archipelagosare often volcanic, forming along ocean ridges or hotspots. Examples ofarchipelagos are the Japanese islands, the Hawaiian Islands, thePhilippines, and the Malay archipelago,which includes all of the islands ofIndonesiaarciform - bow-shapedArcIMS - ESRI software that allows for centrally hosting and serving GISmaps, data, and applications for use on the Internetarcuate - crescent-shapedArcView - desktop geographical information system (GIS) softwaredeveloped by ESRI used to do some basic GIS operations and print mapsarea cladogram - a dendrogram that displays historical relationshipsamong geographic areas, rather than phylogenetic relationships amongtaxaarenaceous - a condition of skeletal architecture in sponges in whichsand and/or foreign spicule debris partly or completely replaces nativespicules within the sponge skeleton; resembling or containing sand; orgrowing in sandy areasarenicolous - living in sandhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (47 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataareolate - appearance of a surfacecharacterized by circular spots of tissue orareolaea grouper with an areolatepattern of pigment (Photo:Agriculture, Fisheries andConservation Department,Hong Kong)argent - silvery colorARGO Project - Argo is a global array of 3,000 free-drifting profilingfloats that measures the temperature and salinity of the upper 2000 m ofthe ocean. This allows continuous monitoring of the temperature, salinity,and velocity of the upper ocean, with all data being relayed and madepublicly available within hours after collectionAristotle's lantern - a highly developed chewing apparatus used forfeeding in some sea urchinsARKive - a not-for-profit, UK-based organization whose mission is ‘topromote the conservation of nature and public appreciation of biodiversity,through the power of wildlife imagery.' by finding, sorting, cataloging andcopying the key audio-visual records of the world’s animals, plants andfungi, and building them into comprehensive and enduring multi-mediadigital profiles (http://www.arkive.org/coral/Coral/coral.html)ARMDES (AIMS Reef Monitoring Data Entry System) adapteddatabase) - a data entry and analysis program running on MicrosoftAccess, which enables users to input data from line transects, mantatows, and fish visual censuses into a standard access database and tocarry out basic analysis of the data. It was created by AIMS and isdistributed free of chargearomatic - a type of hydrocarbon, such as benzene or toluene, with aspecific type of ring structurearrayed library - in genomics, Individual primary recombinant clones(hosted in phage, cosmid, YAC, or other vector) that are placed in twodimensionalarrays in microtiter dishes. Each primary clone can beidentified by the identity of the plate and the clone location (row andcolumn) on that plate. Arrayed libraries of clones can be used for manyapplications, including screening for a specific gene or genomic region ofinteresthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (48 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataarrhenotoky, arrhenotokous - parthenogenetic production of haploidmales from unfertilized eggs. Fertilized eggs produce viable diploidfemalesarribada - a large aggregation of female sea turtles coming to shore tonest at the same place and at the same timeARS (autonomous replicating sequence) - any eukaryotic DNAsequence that initiates and supports chromosomal replication; also calledautonomous(ly) replicating segmentarterial gas embolism - a hazardous condition for scuba divers that ischaracterized by air bubbles released from ruptured lung air pockets(alveoli) into the pulmonary circulation. The bubbles then travel to thearterial circulation, where they may block blood flow in the small arteriesor capillaries of the brain or heart. The results may be fatal. Arterial gasembolism in divers may be caused by holding one's breath during anascent, wherein the lungs expand to the danger pointArthropoda - an animal phylum thatcontains lobsters, crabs, shrimp, mantisshrimp, barnacles and copepods, fairyshrimp (all crustaceans), insects,centipedes, millipedes, spiders, scorpions,horseshoe crabs, pycnogonids (seaspiders), ticks and mites. Approximatelythree quarters of a million species aredescribed, many more than all the otheranimal phyla combined. The crustaceansare the arthropods associated with coralreefsA spiny lobster (phylumArthropoda).articular - pertaining to a jointarticulated - jointed, as in for example, the soft fin rays of fishesarticulating - united by means of a moveable jointartifact - an object made by human workmanship, usually for somepractical purposeartificial classification - in taxonomy, classification based on convenientor conspicuous diagnostic characters without attention to characters whichindicate phylogenetic relationship; often a classification based on a singlearbitrarily chosen character, rather than an evaluation of the totality ofcharactershttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (49 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataartificial reef - an artificial structureplaced on the ocean floor to provide a hardsubstrate for sea life to colonize. Artificialreefs are constructed by sinking densematerials, such as old ships and barges,concrete ballasted tire units, concrete andsteel demolition debris and dredge rock onthe sea floor within designated reef sitesThese concrete blockswere the first artificialstructures deployed toprovide a substrate forreestablishing colonies ofOculina coral (Oculinavaricosa) and simulatingfish habitat on OculinaBank (central FloridaAtlantic coast), which weredestroyed by bottomtrawling in the 1990s.artificial selection - the practice of choosing individuals from apopulation for reproduction (selective breeding), usually because theseindividuals possess one or more desirable traitsartificial selection - a process in which humans select desireable geneticcharacteristics in plants and animals and selectively breed those animalsand cultivate those plants to ensure that future generations ofdescendents have those specific desireable traitsartisanal fishing - fishing which is typically a small-scale operation thatuses simple fishing methods; fishing for subsistence by coastal or ethnicisland groups using traditional methods; fishing with the purpose ofcatching/collecting aquatic products for saleascidian - a solitary or colonial sea squirtof the phylum Chordata, class Ascidiacea.The adult form does not resemblevertebrate chordate animals but the larvalstage possesses all basic chordatecharacteristics. Adult ascidians aresedentary, filter-feeding, cylindrical orglobular animals, usually found attached toa substrate. The soft body is surrounded bya thick gelatinous to leathery test, or tunic(which also gives them the name oftunicate), often transparent or translucent.The test is secreted by the body wall of theadult animal. It is composed of cellulose, acarbohydrate unique in the animal kingdomThese adult ascideans (seasquirts) resembleinvertebrates, but they areclosely related tovertebrates and othermembers of the phylumChordata.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (50 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataASCII (American Standard Code for Information Interchange) - aset of codes for representing alphanumeric information (e.g., a byte with avalue of 77 represents a capital M). Text files, such as those created withthe text editor of a computer system, are often referred to as ASCII filesasco - a prefix meaning "sack"asconoid - simplest body form of sponges,with canals leading directly from thesurrounding water to the interior spongocoelAsconoid sponges havethe simplest organization.Flagellated choanocytesline the spongocoel,drawing water throughsmall ostia and expelling itthrough the osculum.(Illustration: BIODIDAC)ase - a suffix used for the name of an enzyme, e.g., polymerase, lipase,cellulaseasexual embryogenesis - the sequence of events whereby embryosdevelop from somatic cellsasexual reproduction - reproduction that does not involve the union ofsex cells (gametes) to produce a zygote. Examples in corals are buddingand fragmentationAsia-Pacific-Network for Global Change Research (APN) - an intergovernmentalnetwork for the promotion of global change research andlinks between science and policy making in the Asia-Pacific Regionaspergilliform - brush-shapedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (51 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataaspergillosis - a widespread fungal infection of Caribbean soft corals. Itaffects six species of sea fans and sea whips. The pathogen is Aspergillosissydowii, a terrestrial fungus which infects gorgonia after germination ofspores on the coral surface. This is followed by penetration and spread ofhyphae in coral tissue, resulting in highly visible lesions which may beassociated with complete loss of tissue and skeleton. Lesions often occurat multiple sites across an infected colony.-Purple galls may be producedby the coral host to encapsulate fungal hyphae. For more information andillustrations, see: http://www.coral.noaa.gov/coral_disease/aspergillosis.shtmlasperity - a peak or projection from a surface; pertains to roughness of asurfaceassay - in general, the qualitative or quantitative analysis of a substanceto determine its constituents and the relative proportion of each, or todetermine the biological, chemical, or pharmacological potency of a drugassemblage - a group or association of interacting populations oforganisms in a given area or volumeassimilation - the biological process of absorbing nutrients into anorganism's body after digestionassimilation efficiency - the fraction of ingested food that is absorbedand used in metabolismassociation - a group of species living in the same place at the same timeAssociation of Marine Laboratories of the Caribbean (AMLC) - AMLCis a confederation of more than 30 marine research, education, andresource management institutions endeavoring to encourage theproduction and exchange of research and resource managementinformation, advance the cause of marine and environmental education inthe region, and facilitate cooperation and mutual assistance among itsmembership. It was founded in 1956 by marine researchers with interestsin the marine science of the tropical Atlantic and the Caribbean. Thestrength of AMLC lies in the diversity of its member laboratories and theextensive expertise of its membershipastaxanthin - a carotenoid pigment found in crustaceans. Astaxanthinsmay give a green color to the musculature of fishes which feed oncrustaceansastern - behind the vessel; toward the rear of the vesselasthenosphere - a layer of soft but solid, mobile rock comprising thelower part of the upper mantle from about 100 to 350 km beneath theEarth's surfacehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (52 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataasymmetric competition - competition between two organisms (orspecies) in which one is much more adversely affected than the otherasymmetry - the lack or absence of balanced proportions between partsof a thing; without symmetryata (atmosphere absolute) - one (1) ata is the atmospheric pressure atsea levelatavism - the reapperance of an ancestral character after an interval ofgenerationsatmosphere - a unit of pressure, abbreviated as atm; "one atmosphere"is the pressure of the atmosphere at sea level, i.e., 760 mm Hg. Twoatmospheres is twice this pressure, 1520 mm Hg, etc.; the airsurrounding the earth, from sea level to outer spaceatmospheric pressure - the pressure of the atmosphere at any givenaltitude or location; it is synonymous with barometric pressureatoke - the anterior, nonreproductive part of a marine polychaete worm,as distinct from the posterior, reproductive part (epitoke) during thereproductive seasonatoll - a horseshoe or circular array of reefislets, capping a coral reef system thatencloses a lagoon, and perched around anoceanic volcanic seamountA small Pacific atoll. Notethe coral reef encirclingthe calm and shallowlagoon.atom - the smallest component of an element, made up of neutrons,protons, and electronsATPase - an enzyme that functions in producing or using adenosinetriphosphate (ATP)atresia - an abnormal condition in which a normal opening or tube in thebody is closed or absenthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (53 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataatrial siphon - in tunicates, the opening that carries water, wastes, andgametes from the organism. Also called the excurrent or exhalent siphon/canalatrichous - in Cnidaria, lacking spines or barbsatrichous isorhiza - in hydrozoans, a small cnidocyst (nematocyst) witha smooth tubule.These are only type of cnidocysts found in all the classesof Hydrozoa. they are never very common, but all the classes have somespecies with them .This type of cnidocyst occurs also in the Anthozoa,Cubozoa and Scyphozoaatrium - a cavity or passageway; a heart chamber which receives bloodatrophy - a wasting or decrease in size of a tissue or organ because of areduction in the size or number of its cells. Atrophy may result fromcellular death, reduced cellular division, pressure, ischemia, malnutrition,decreased activity or hormonal changesatrous - jet black colorattachment stage - a stage in an animal's life cycle when it ceases beingfree swimming or motile, and becomes attached to a substrateattendant male - a male fish which is not a member of a spawning pair,but hovers close by; often a sneaky maleattitude - in animal behavior, the posture or expression assumed by anorganismattribute - a measurable component of a biological system; a particularfeature or character possessed by an organismauditory ossicle - one of a series of bones conducting sound in somefishesaulostomatous - having a tubular-shaped mouth, such as a cornetfishaureate - golden yellow in colorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (54 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataauricularia larva - larva of a seacucumber; an early bipennaria larva of astarfishLate-stage auricularia ofStichopus californicus - ca.17-18 days old, raised inculture by T.H.J. Gilmour.(Photo: University ofSaskatchewan Archives)austral - relating to or coming from the south; of the south temperateregion, between the antarctic and tropical regionsAustralian Centre of Excellence for Innovative science forsustainable management of coral reef biodiversity - the primary goalof this Australian Research Council Centre of Excellence is to undertakeresearch programs of international significance (through the establishmentof new collaborative teams of Australia’s leading coral reef researchers)that transcend traditional disciplinary, institutional and geographicboundaries. The Centre of Excellence cements Australia’s leadingcontribution to coral reef sciences, and fosters stronger collaborative linksbetween James Cook University, The Australian National University,University of Queensland, and 28 other leading institutions in ninecountries. Collectively, the JCU-led Centre creates the world’s largestconcentration of coral reef scientists. The aim is to add focus, scale andscope to build an enduring program of innovative research development,leading to world leadership in coral reef science. A key outcome of theCentre of Excellence is to actively transfer scientific knowledge to industrypartners and end-users, to increase their capacity and effectiveness, andprovide benefits to all Australiansautapomorphy - an apomorphy (derived character differing from theancestral condition) possessed by a species or clade that is shared with noother species or clade, i.e., a derived character found only in a terminaltaxonautecology - the ecology of a single specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (55 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataauthor - in taxonomy, the person(s) to whom a work, a scientific name,or a nomenclatural act is attributedauthority - in taxonomy, the name of the author of a taxonomic name,cited after the nameautochory - the process of seeds and fruits dispersal by means of somekind of explosive physical expulsion.The fruit "explodes", propelling itsseeds some distance to the ground surrounding the parent plant; alsocalled "discharge dispersal"autochthonous - native; indigenous; originating or occurring naturally inthe place specifiedautoepizooism - settlement and growth of hydrozoan colonies on olderanimals of the same speciesautoevisceration - ejection of intestines and associated organs, inanimals such as sea cucumbers, caused by adverse environmentalconditions. Regeneration of the organs may occur within weeksautoimmune disease - a disease in which the organism producesantibodies against its own tissuesautoimmunity - a condition in which an organism mounts an immuneresponse against one of its own organs or tissues; i.e., an organism'simmune system attacking its own bodyautologous cells - cells that are taken from an individual, cultured, andpossibly genetically manipulated before being infused back into theoriginal donorautolysis - the spontaneous disintegration of cells or tissues by theorganism's proteolytic enzymes and macrophage activity, as occurs afterdeath and in some pathologic conditionsautomated bleaching early warning system - automated bleachingalerts/warnings directly from satellite and/or in situ derived indicesautomyxis - obligatory self-fertilizationautopolyploid - a polyploid formed from the doubling of a single genomeautoradiography - a technique that uses X-ray film to visualizeradioactively labeled molecules or fragments of molecules; it is used inanalyzing length and number of DNA fragments after they are separatedby gel electrophoresishttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (56 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataautoskeleton - the endoskeleton of sponges, comprised of spicules orspongin fibersautosome - any chromosome that is not a sex chromosome;distinguished from a sex chromosomeautotomy - the voluntary shedding of an appendage by snapping it offthe base; in corals, some, reproduce asexually by autotomy(fragmentation), for example, Fungia spautotrophic - relating to organisms that have a type of nutrition in whichorganic compounds used in metabolism are obtained by synthesis frominorganic compoundsautozooecium - a tube that encloses a bryozoan autozooidautozooid - a feeding polyp of a bryozoan (Ectoprocta). Autozooidscompose the majority of a bryozoan colonyautumnal equinox - the equinox at which the sun approaches theSouthern Hemisphere and passes directly over the equator. It occursaround September 23auxesis - to grow; growth resulting from increase in cell size without celldivisionauxotroph - a polyploid formed from the doubling of a single genomeauxotroph - an organism which is unable to synthesize a particularorganic compound required for its growth. An auxotrophic alga, forexample, is one which requires a few organically derived substances, suchas vitamins, along with dissolved inorganic nutrients for photosynthesis;in microbiology, a mutant strain that requires a new nutrient for growthavailable name - in taxonomy, any name which conforms to allmandatory provisions of the Code. There are general requirements ofpublication and date, language, name formation etc. An available name isnot necessarily a valid name, as an available name may be in synonymy.Conversely a valid name must always be an available oneaversive stimulus - a noxious stimulus in its immmediate environmentthat an organism tends to remove or avoidAves - the name of the class of vertebrates that consists exclusively ofbirds; the Latin word for "bird"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (57 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAVHRR (Advanced Very HighResolution Radiometer) - a broad-band,four or five channel (depending on themodel) scanner, sensing in the visible, nearinfrared,and thermal infrared portions ofthe electromagnetic spectrum. This sensoris carried on NOAA's Polar OrbitingEnvironmental Satellites (POES). AVHRR isused for studying and monitoringvegetation conditions. Applications includeagricultural assessment, land covermapping, producing image maps of largeareas and tracking regional and continentalArtist's rendition of POESsatellite.snow cover. AVHRR data are also used to retrieve various geophysicalparameters such as sea surface temperatures (SST) and energy budgetdataavian - of, relating to, or characteristic of birdsavicularium - a small bryozoanheterozooid in which the zooecium andoperculum form a beak-like, snappingstructure that deters small predatorsA magnified view of anavicularium from themarine colonial bryozoanBugula sp. (Photo: Dr.Rick Gillis, Biol. Dept.,Univ. of Wisconsin)avifauna - the birds of a specific region or periodavirulent - unable to cause diseaseAvogadro's number - a large constant used in chemistry and physics. Itis the number of molecules (6.02214 × 10 23 )in one mole of substance;also called "Avogadro's Constant"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (58 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataAVTAS (AIMS Video Transect Analysis System) - video transects aresystematically sampled by identifying the benthos occurring at fixed pointsalong the transect to the highest taxonomic level possible. The AVTASsoftware is used to analyse the video transects. During analysis the dataare saved into a Microsoft Access¼ database. In order to eliminateconfounding in data analyses due to observer biases, transects from eachsite are analysed by two observers. The observer who actually surveyedthe reef in the field analyses transect one from site one and then everyalternate transect. A second observer analyses the remaining transectsaxenic - a culture containing only one type of microorganism; notcontaminated by or completely free of the presence of other organisms; apure cultureaxial - refers to the head and trunk of an individualaxial corallite - a corallite which forms the tip of a branchaxial cortex - the layer around the central core of the axis of an octocoralaxial polyp - the longest polyp of a group of polyps which producessecondary polyps by buddingaxial sheath - the coenenchyme which surrouds the axis on theGorgonacea and Pennatulaceaaxial skeleton - in a vertebrate skeleton, the skull, vertebral column,ribs, and sternumaxial swimming - the predominant swimming mode of fishes. Thisswimming movement involves lateral bending of the body caused bycontractions of the lateral body musculature and oscillating movements ofthe caudal finaxis - the internal, usually calcium carbonate skeletal rod of sea fans(Gorgonacea) and sea pens (Pennatulacea)axis epithelium - the layer of ectodermally-derived cells which consistsof corticocytes, which produce the axis, and desmocytes, which attachtissues to the axisaxocoel - the most anterior of three coelomic spaces that appear duringlarval development of echinodermsaxon - the single motor branch of a neuron that passes the nervousimpulse away from the cell body to another neuron or effector organaxoneme - a bundle of microtubules and other proteins forming the coreof each cilium or flagellumhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (59 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef Dataazooxanthellate coral - a coral which does not have symbioticzooxanthellae in its tissuesazure - light or sky blue color(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=a (60 of 60) [2/26/2008 9:13:09 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: BThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZB lymphocyte - a type of white blood cell which produces antibodiesbacillus - a bacterium with a rod-like shapeImage of rod-shapedbacterium, Bacillusinfernus, collected fromdeep (20-2800 meters)terrestrial subsurface.(Photo: U.S. Dept. ofEnergy/SubsurfaceMicrobial CultureCollection)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (1 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databack reef - the shoreward side of a reef,including the area and sediments betweenthe reefcrest/algal ridge and the land. Itcorresponds to the reef flat and lagoon of abarrier reef and platform margin reefsystemsEmergent coral heads in aback reef zone. (Photo:Great Barrier Reef MarinePark Authority)backcross - crossing an organism with one of its parents, or with thegenetically equivalent organism. The offspring of such a cross are referredto as the backcross generation or backcross progenybackground extinction - the continuous, low-level extinction of speciesthat has occurred throughout much of biological historybackground level - the concentration or level of a substance or otherfactor in an environment that is not the result of human activities, e.g.,background levels of chemicals, light, sound, etcbackground noise - noise coming from sources other than the noisesource being monitoredbackscatter - the deflection of acoustic radiation in a scattering processthrough an angle greater than 90 degrees. Backscatter is the termcommonly used to describe the return of energy from the seabed to thereceiver in an active sonarbacteria - a major group of living organisms in the kingdom Monera.They are microscopic and mostly unicellular, with a relatively simple cellstructure lacking a cell nucleus, cytoskeleton, and organelles such asmitochondria and chloroplasts. Bacteria are genetically distinct fromprotists, fungi, plants, and animals. Many species of bacteria arepathogenic to other organisms, including humansbacterial bleaching - loss of zooxanthellae with resultant bleachingcaused by a specific bacterial infection, as opposed to environmentalstress. The bacteria (Vibrio sp.) produce a toxin which cause lysis of thezooxanthellae. For additional information and illustrations, see: http://www.coral.noaa.gov/coral_disease/bacterial_bleaching.shtmlbacterial chlorophyll - chlorophylls (bacteriochlorophylls a, b, c, d, e,and g) found in photosynthetic bacteria. They differ from plant chlorophyllin chemical construction and absorption spectra characteristicshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (2 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databacterial generation time - the time interval required for a bacterial cellto divide, or for a population of bacterial cells to double. Generation timesfor bacterial species growing in nature may be as short as 15 minutes oras long as several daysbactericide (bacteriocide) - a substance that kills bacteriabacteriocyte - a cell which harbors symbiotic bacteria in animals asdiverse as insects and marine tube worms living around hydrothermalventsbacteriophage (phage) - a virus that attacks and infects bacterial cells.Phages consist of a protein coat enclosing the genetic material, DNA orRNA, that is injected into the bacterium. Upon infection, synthesis of hostDNA, RNA and proteins ceases and the phage genome is used to direct thesynthesis of phage nucleic acids and proteins using the host'stranscriptional and translational apparatusbacteriophagous - feeding on bacteriabaffling - to impede the force or movement of flowing water, such thatsediment particles may settle from suspensionbailer - an exopod of the maxilla of decapod crustaceans, such aslobsters, that functions in regulating the flow of water in the gill chamberbalanced polymorphism - a type of polymorphism in which thefrequencies of the coexisting forms do not change noticeably over manygenerationsbalanoid - acorn shapedBaldwin effect - a hypothesis in which a characteristic, such as individuallearning, significantly affects the evolution of the species with respect tothat characteristic. The Baldwin effect functions in two steps. First,phenotypic plasticity (the ability of an organism to adjust to itsenvironment during the course of its lifetime) allows an individual toadjust to a partially successful mutation, which might otherwise be utterlyuseless to the individual. If this mutation adds to inclusive fitness, it willsucceed and proliferate in the populationballast - a weight at the bottom of the boat to help keep it stable. Ballastcan be placed inside the hull of the boat or externally in a keel. Waterpicked up as ballast in one location may be released in another, and indoing so, may introduce non-native specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (3 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databamboo coral - an octocoral found in both warm, shallow-water andcold, deep-water marine habitats throughout the world's oceans. Bamboocorals possess a skeletal arrangement which resembles bamboo. Theskeleton is composed of calcareous plates and proteinaceous gorgonin.They can live for centuriesband - a thick, pigmented vertical markingthat encircles the circumference of anorganism's bodyChaetodon striatus, thebanded butterfly fish, hastwo black bands ofpigment encircling itsbody. (Image: NOAA)bank - a broad elevation of the sea floor around which the water isrelatively shallow but not a hazard to surface navigationbank reef - large reef growths, generally having irregular shape, whichdevelop over submerged highs of tectonic or other origin and aresurrounded by deeper watersbank/shelf - deepwater area extending offshore from the seaward edgeof the fore reef to the beginning of the escarpment where the insular shelfdrops off to the deep, oceanic water. If no reef crest is present, it is theflattened platform between the fore reef and the deep ocean waters orbetween the intertidal zone and open oceanbar - a thick, pigmented vertical markingthat does not encircle the body of anorganism; an elongate submarine shoalThe royal gramma,Gramma loreto, has adarkly pigmented baracross its eye.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (4 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databar - unit of pressure of one million dynes per square centimeterbar and spit - a low accumulation of sand or sediments forming anintertidal or subtidal extension of a reef isletbar-built estuary - an estuary formed when a barrier island or sand barseparates a section of the coast where fresh water entersbarb - a type of spine armed with teethpointing backwardsStingrays have whip-liketails, defensively armedwith a venemous barbwhich can inflict a seriouswound on another animal(Photo: Peter Piermarini,Ph.D.)barbel - a slender elongate sensorystructure protruding from the lips or jaws ofcertain fishes, such as catfishes, goatfishes,drums, cods, and many deep-sea fishes.Barbels may appear singly or in groups.They are primarily tactile in function butmay also bear tastebuds, allowing the fishto taste its environmentA yellow goatfish with twoprominent barbelsprotruding from its chin.(Photo: NOAA)Barcode of Life Data System (BOLD) - an online system that aids inthe collection, management, analysis, and use of DNA barcodes. BOLDwas created and is maintained by the University of Guelph in Ontariobarcode; barcoding - a technique for characterizing species oforganisms using a short DNA sequence from a standard and agreed-uponposition in the genome. The cytochrome c oxidase subunit 1 mitochondrialregion is emerging as the standard barcode region for higher animals. It is648 nucleotide base pairs long in most groupsbaroceptor - a sensory organ perceiving changes in pressure; also called"baroreceptor"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (5 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databarometer - an instrument for measuring air pressurebarophile - a microorganism which grows best (or can only grow) in highpressureenvironments, such as deep-sea environmentsbarotrauma - an injury that results from rapid or extreme changes inpressure. Scuba divers may experience ear barotrauma, a condition ofdiscomfort in the ear caused by pressure differences between the insideand the outside of the eardrumbarotropism - a response to pressure stimulibarren zone - the region of a coral reef seaward of the lower palmatazone and just landward of the buttress or mixed zonebarrier island - a long, usually narrowaccumulation of sand, that is separatedfrom the mainland by open water (lagoons,bays, and estuaries) or by salt marshesCape Lookout NationalSeashore currentlyconsists of 4 barrierislands. (Photo: U.S.National Park Service)barrier net - a small-mesh net used to capture coral reef or coastalpelagic fishesbarrier reef - a long, narrow coral reef,roughly parallel to the shore and separatedfrom it by a lagoon of considerable depthand width. It may lie a great distance froma continental coast. It is often interruptedby passes or channelsHealthy Acropora coral inAustralia's Great BarrierReef. (Photo: RayBerkelmans/Great BarrierReef Marine ParkAuthority)basal - of, at or forming a basehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (6 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databasal bud - in bryozoans, the bud arising from the basal wall of theparent zooidbasal plate - lower part of the coral cup, separating the polyp from thesubstratum. A synonym of pedal discbasalt - a dark, fine-grained igneous rock composed of minerals rich inferromagnesian silicatesbase - a substance that reduces the hydrogen ion concentration in asolutionbase - in genomics, a key component of DNA and RNA molecules. Fourdifferent bases are found in DNA: adenine (A), cytosine (C), guanine (G)and thymine (T). In RNA, uracil (U) substitutes for thymine; also knownas nitrogenous bases; a base, a phosphate molecule and a sugar joinedtogether constitute a nucleotidebase pair - two nitrogenous bases whichform a "rung of the DNA ladder." A DNAnucleotide is made of a molecule of sugar,a molecule of phosphoric acid, and a basemolecule. The bases are the "letters" thatspell out the genetic code. In DNA, thecode letters are A, T, G, and C, which standfor the chemicals adenine, thymine,guanine, and cytosine, respectively. In basepairing, adenine always pairs with thymine,and guanine always pairs with cytosine. InRNA, thymine is replaced by uracilDiagram of a DNAmolecule. (Diagram: U.S.NIH/Human GenomeProject)base sequence - the order of nucleotide bases in a DNA moleculebaseline data - a quantitative level or value from which other data andobservations of a comparable nature are referencedbasement rock - a complex of metamorphic and igneous rocks thatunderlies sedimentary deposits. These are the oldest rocks in a given areahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (7 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databasic research - research conducted with the sole goal of obtainingknowledge; in contrast with applied researchbasicaudal - on the base of the caudal fin of fishesbasicaudal spot - a spot on the base of the caudal fin, common in manyunrelated fish speciesbasilar - forming a foundationbasin - any large depression in which sediments are depositedbasionym - In taxonomy, the first name published for a taxon. It remainsthe defining name for the taxon even when the taxon has beentransferred to a new combination. According to priority rules of biologicalnommenclature, after a taxonomic revision that results in a species beingreclassified in another genus, the specific epithet must remain the sameas the one in the basionymbasipinacocyte - a pinacocyte that adheres a sponge to a substrate bythe external secretion of a collagenous matrixbasitrichous isorhiza - an isorhizal cnidocyst (nematocyst) with spinesat the base of the tube only; also called "basitrich"basket star - a basket star is a specializedtype of brittle star (Echinodermata). It hasa series of complexly branched arms whichare used to capture planktonThe spiny arms of thisbasket star branchrepeatedly to form a coiledmass. Unlike other brittlestars,basket stars aresuspension feeders,trapping large particles intheir extended arms.(Photo: NOAA oceanExplorer/ L. Mullineaux)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (8 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataBatesian mimicry - a type of mimicry in which a harmless speciesresembles a different species that is unpalatable, poisonous, or otherwisenoxious or harmful to a predatorbathyal zone - region of the seafloor from the shelf edge (200m) to thestart of the abyssal zone (2,000m)bathymetric map - a map which delineates the form of the bottom of abody of water by the use of depth contours (isobaths)bathymetry - the science of measuring ocean depths to determine thetopography of the sea floorbathypelagic zone - a layer (zone) of the ocean which lies just beneaththe mesopelagic zone. It extends from 1000-4000 meters. Because nolight (except for bioluminescence) penetrates this zone, it is also calledthe midnight zone. The temperature in the bathypelagic zone remainsfairly constantat about 4 degrees Cbattery - a group of nematocysts on the tentacles of hydras and someother hydroid polypsbaud - unit of data transmission speed of one bit per secondBCD (buoyancy control device) - theBCD is a mandatory piece of equipment forSCUBA diving. It is an expandable bladder,most commonly worn as an expandablevest, that can be inflated with air from thetank to increase buoyancy while diving. Todecrease buoyancy, the BCD is deflatedthrough special air-dump valves or hoses.It provides positive buoyancy for resting,swimming or lending assistance to othersunder water. The BCD allows maintenanceof neutral buoyancy at any depth simply byadding or releasing air. It is also called abuoyancy compensator (BC)A buoyancy control devise(BCD). It is a vest-likeexpandable bladder thatcan be inflated with air toincrease or decrease ascuba diver's buoyancywhile diving.beach - an aggregation of unconsolidated sediment, usually sand, thatcovers the shorehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (9 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databeak - in cephalopods, one of two chitinous mandibles (jaws) usedprimarily to cut prey tissues during feedingbeam - the widest part of a vesselBeaufort scale - a scale used to classify wind speeds, devised in 1805 byAdmiral Francis Beaufort of the British Navybeche-de-Mer - commercially harvestedsea cucumbers (Class Holothuroidea). InAsia, it is considered to be a delicacyImage of the commerciallyharvested -beche de mer+.bedload - sedimentary material subject to transport by flowing water, e.g. currents. The size of particles moved is proportional to the strength ofthe water movementbedrock - the solid rock of the earth's crust that lies under the soil andother unconsolidated earth materialsbehavioral isolating mechanism - a difference in behavior (usuallyreproductive behavior) that prevents genetic exchange between membersof different populations or speciesbel - unit of noise intensity equal to ten decibelsBelau - traditional (native) name for Palau (Republic of Palau)belt transect - a linear or circular transect with the observation areabeing a specified distance on either side of the transect linebenchmark - a measurement or standard that serves as a point ofreference by which process performance is measuredbenign introduction - the purposeful introduction of members of aspecies into an appropriate habitat, foreign to the "home" habitat or area,for the purposes of conservation of that speciesbenthic - bottom dwelling; living on or under the sediments or othersubstratehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (10 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databenthic carbon dioxide flux - the amount of carbon dioxide (CO2)released from a unit area of sediment over a specific time interval, duringthe decomposition of organic matter. Part of the benthic CO2 flux mayalso result from the dissolution of calcium carbonatebenthic chamber - an open-bottom container (usually constructed ofacrilic) that encloses an area of sediment/substratum and overlying water.The chamber is deployed to capture gas (e.g., efflux of CO2 fromsediments) and solute movement between the sediment and the watercolumnbenthic organism (benthos) - an organism whose habitat is on or nearthe bottom of a stream, lake, or oceanbenthic region - the bottom layer of abody of waterA benthic crab (phylumArthropoda).benthic-pelagic coupling - the cycling of nutrients between bottomsediments and the overlying water columnberm - a low, incipient, nearly horizontal or landward-sloping area, or thelandward side of a beach, usually composed of sand deposited by waveaction; a mound of earth formed to control the flow of surface water; asloped wall or embankment used to prevent the inflow or outflow ofmaterials into/from an areabeta animal - in animal behavior, the subordinate or second animal in asocial groupbeta particle - a high-speed particle, identical to an electron, emittedfrom an atomic nucleusbeta taxonomy - in taxonomy, the process of arranging taxa into highercategories which reflect the evolutionary history of a group of organisms.bicarbonate - any salt containing the HCO3 anionbicentric distribution - the presence of a species (or other taxonomicunit) in two widely separated geographic areasbicornate - having two horns or horn-shaped structureshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (11 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databicuspid - having two cusps or pointsbiennial - occurring once every two yearsbifacial - having like opposite surfaces; describes plates which havecorallites on both sidesbifid - divided or cleft into two parts or lobesbifurcate - a coral branch that divides into two equal branchesbigeminal - occurring in pairsbigeye - any species of bony fishes in thefamily Priacanthidae. Bigeyes ( also called"catalufas") are most typically coloredbright red, but other coloration patternsexist. The common name of "bigeye" refersto their unusually large eyes which areadapted theirThe short bigeye,Pristigenys alta,photographed at PulleyRidge (Photo: U.S.Geological Survey)bight - an indentation of the coast forming a large open baybilateral symmetry - a bilaterally symmetric organism is one that issymmetric about a plane running from its frontal end to its caudal end(head to tail), and has nearly identical right and left halves. Most animalsare bilaterally symmetrical. The exceptions are sponges (no symmetry),cnidarian polyps and medusae, and ctenophores (radial symmetry), andechinoderms (partial radial symmetry).Bilateria - group containing all multicellular animals with bilateralsymmetry; the name has no taxonomic statusbilineate - having two linesbimaculate - having two spotshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (12 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databimodal - a distribution in which thefrequency curve has two peaks. A singlepeak is called a modeChart showing apopulation of data havinga bimodal distribution.bimodal curve - a frequency curve characterized by two peaksbinary fission - type of cell division foundin prokaryotic cells, in which dividingdaughter cells each receive a copy of theparental chromosomeA bacterial cellreproducing by binaryfission. The two resultantdaughter cells aregenetically identical.(Photo: Dr. Vincent A.Fischetti, Laboratory ofBacterial Pathogenesis andImmunology, RockefellerUniversity)binding - the ability of molecules to stick to each other because of theexact shape and chemical nature of parts of their surfacesbinding site - the reactive part of a macromolecule that directlyparticipates in its specific combination with another moleculebinomen - a two-part name given to a species in which the first part isthe name of the genus and the second is the specific namebinomial nomenclature - a system of nomenclature where each animalhas a dual name consisting of genus and species, e.g., the boulder coral,Montastrea annularisbioaccumulation - the buildup of chemical substances in the cells ortissues of an organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (13 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databioacoustics - a discipline of zoology that is concerned with sounds ofbiological origin: their mechanisms of production, physical properties,receptors and reception physiology, and the role of the sounds in behaviorbioassay - an assay for the activity or potency of a substance thatinvolves testing its activity on living materialsbiochemical - a product produced by chemical reactions in livingorganismsbiochemical cycle - the flow of an element through the living tissue andphysical environment of an ecosystem, e.g., the carbon, hydrogen,oxygen, nitrogen, sulfur, and phosphorus cyclesbiochemical genetics - the study of the relationships between genesand enzymes, specifically the role of genes in controlling the steps inbiochemical pathwaysbiochemical oxygen demand (BOD) - the amount of oxygen taken upby microorganisms that decompose organic waste matter in water. It istherefore used as a measure of the amount of certain types of organicpollutant in water. A high BOD indicates the presence of a large number ofmicroorganisms, which suggests a high level of pollutionbiochip - an electronic device that uses organic molecules to form asemiconductor; a microchip that uses tiny strands of DNA to latch ontoand quickly recognize thousands of genes at a time; collection ofminiaturized test sites (microarrays) arranged on a solid substrate thatpermits many tests to be performed at the same time in order to achievehigher throughput and speed. A biochip can perform thousands ofbiological reactions, such as decoding genes, in a few seconds. Biochipscan also be used to rapidly detect chemical agents used in biologicalwarfare so that defensive measures can be takenbiochore - a group of similar biotopesbioclastic sediment - a sediment type composed of fragments of organicskeletal materialsbiocoenose - an assemblage of diverse organisms inhabiting a commonbiotopebiocoenosis - a community or natural assemblage of organisms. Theterm often is used as an alternative to ecosystem, but strictly it is thefauna/flora association excluding physical aspects of the environmenthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (14 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databiocriteria (biological criteria) - as defined by the U.S. EnvironmentalProtection Agency (EPA), biocriteria are powerful management toolsbecause biological communities are dependable indicators of the health ofan aquatic ecosystem. The criteria are generated as narrative descriptionsor numeric values that represent the biological condition of thecommunity. Rigorous biological assessments are needed to identifymetrics for a monitoring program and to set expectations for the waterbody. These are used to develop a scoring system to indicate the health ofthe water body and to develop biocriteria for each class or designated usebiocycle - a subdivision of the biosphere, e.g., a biochorebiodegradable - capable of undergoing rapid decomposition bymicroorganisms under aerobic and/or anaerobic conditions. Most organicmaterials are biodegradablebiodiversity - the total diversity andvariability of living things and of thesystems of which they are a part. Thisincludes the total range of variation in andvariability among systems and organismsat the bioregional, ecosystem and habitatlevels, at the various organismal levelsdown to species, populations andindividuals and at the level of thepopulation and genesA coral reef contains agreat variety of species ofall major kingdoms ofliving forms. (Photo: Dr.Anthony Picciolo)Biodiversity Conservation Information System (BCIS) - The purposeof the BCIS Framework for Information Sharing is to support BCISMembers and others making decisions on the conservation andsustainable use of living resources. BCIS is a consortium of teninternational conservation organizations and programs of IUCN—TheWorld Conservation Union. BCIS Members collectively represent the singlegreatest global source of biodiversity conservation information in theworld. BCIS is a framework within which the Members’ networks worktogether toward a common goal: to support environmentally sounddecision-making and action by facilitating access to biodiversity data andinformationbiodiversity hot spot - an area that features exceptional concentrationsof species, including many endemics. Many such hot spots also experiencelarge habitat losses, putting these ecosystems at riskbiodiversity indicators - in conservation biology, sets of species or taxawhose presence may indicate areas of high species richnesshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (15 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databioenergy - energy made available by the combustion of materialsderived from biological sourcesbioerosion - erosion of the physical/geological environment by organismactivities such as boring, scraping, etching, etc.biogenesis - a central concept of biology that all living organisms aredescended from predecessor living organismsbiogenic - refers to things which came about as a result of the activitiesof living organismsbiogenic reef - a mound-like layered structure built by andpredominantly composed of organic remains such as shells and skeletonsof sedentary organismsbiogenic rock - an organic rock produced by the physiological activitiesof plants or animalsbiogenous - produced by living organismsbiogenous sediment - sediment that is composed of the skeletons andshells of marine organisms, primarily planktonbiogeochemical cycle - the chemical interactions among theatmosphere, biosphere, hydrosphere, and lithospherebiogeographical filter - a geographic or ecological barrier that restrictssome dispersal between regions and blocks passage of certain forms butnot othersbiogeography - a branch of biology that deals with the geographicaldistribution of organismsbioherm - a body of rock built up by or composed mainly of sedentaryorganisms, e.g., hard corals, calcareous algae or mollusks, and enclosedor surrounded by rock of different originbioinformatics - the analysis of biological information using computersand statistical techniques; the science of developing and utilizingcomputer databases and algorithms to accelerate and enhance biologicalresearch. Bioinformatics is particularly important as an adjunct togenomics research, because of the large volume of complex datageneratedbiolimiting - relating to the environmental factors determining orrestricting the growth of a particular life formhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (16 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databiolistics - a technique to insert DNA into cells. The DNA is mixed withsmall metal particles, usually tungsten or gold, a fraction of a micrometeracross. These are then fired into a cell at very high speed.biological clock - an internal biological mechanism which controls certainbiological rhythms and biocycles, such as metabolism, sleep cycles, andphotosynthesisbiological control - the use of living organisms, such as parasites,disease agents, and predators, to control or eliminate other unwantedliving organisms, rather than by using toxic chemicals or other means ofeliminationBiological Data Profile of the Content Standard for DigitalGeospatial Metadata - provides a common set of terminology anddefinitions for the documentation of biological data through the creation ofextended elements and a profile of the FGDC Content Standard for DigitalGeospatial Metadata. Its purpose is to provide a user-defined or themespecificprofile of the FGDC Content Standard for Digital GeospatialMetadata to increase its utility for documenting biological resources dataand information. This standard can be used to specify metadata contentfor the full range of biological resources data and information. It alsoserves as the metadata content standard for the National BiologicalInformation Infrastructure (NBII)biological half-life - the time required for one-half of the total amount ofa particular substance in a biological system to be consumed or brokendown by biological processes when the rate of removal is approximatelyexponential. Toxic chemicals with a long biological half-life will tend toaccumulate in the body and are more likely to be harmful. A substancewith a short biological half-life may still accumulate if a portion of it itbecomes tightly bound to bone or other tissues, even if most of it isquickly eliminated from the bodybiological indicator - an organism, species or community whosecharacteristics show the presence of specific environmental conditions.Other terms used are indicator organism, indicator plant and indicatorspeciesbiological marker - a measurable and quantifiable biological parameterwhich serves as an index for health and physiology related assessments,such as disease risk, environmental exposure and its effects, diseasediagnosis, metabolic processes, and epidemiologic studies; also called"biomarker"biological navigation - the ability of certain animals to navigate byinstinct to specific sites. Depending upon the species, the cues involvedmay be related to star patterns, sun angle, polarized light, chemicalscents or tastes, or the Earth's magnetic fieldbiological productivity - the amount of organic matter, carbon, orenergy content that is accumulated during a given time periodhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (17 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databiological rank - in animal behavior, when a hierarchy of dominanceexists between different species which compete for food, water or spacebiological rhythm - an overt, measurable activity generated by someinternal oscillator (or ‘clock’)biological survey - collecting, processing, and analyzing a representativeportion of the resident aquatic community to determine its structural and/or functional characteristicsbioluminescence - light produced byorganisms as a result of conversion ofchemical energy to light energyA bioluminescent combjelly of the phylumCtenophora.biomagnification - the accumulation and amplification of chemicalsubstances at each succeeding trophic levelbiomarker - a molecular marker associated with a biological function; aphysical, functional, or biochemical indicator (eg, the presence of aparticular metabolite) of a physiological or disease process; a chemicalcompound produced by a specific organism that can be used as anindicator for the presence of that organismbiomass - an estimate of the amount of living matter per some unitvolume or areabiome - a community of animals and plants occupying a climaticallyuniform area on a continental scalebiometrics - the use of statistics for the study of biological eventsbiopharming - to genetically engineer an organism to produce apharmaceutical drug, vaccine or industrial substancebiophysics - the scientific study of the physics of organisms, theirbiological structure and processesbiopolymer - a macromolecule, including nucleic acids, proteins, andpolysaccharides, which is formed by a living organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (18 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databioregion - any geographical region characterized by a distinctive biotabioremediation - the use of organisms such as plants or microorganismsto aid in removing hazardous substances from an areaBiorockTM - Biorock Technology, or mineral accretion technology is amethod that applies safe, low voltage electrical currents throughseawater, causing dissolved minerals to crystallize on structures, growinginto a white limestone similar to that which naturally makes up coralreefs. This material has a strength similar to concrete. It can be used tomake robust artificial reefs on which corals grow at very rapid rates. TheBiorock Process is owned by Biorock, Inc; see also "mineral accretion" inthis glossarybiosphere - the thin region surrounding the Earth that is capable ofsupporting lifebiosynthesis - a metabolic process where chemical compounds areproduced from simpler reagents. Biosynthesis is a cellular process whichoccurs within living organisms and is generally catalyzed by enzymes. Theprocess is a vital part of metabolismbiota - all life forms of a given areabiotechnology - biological techniques used in applied research researchand product development. In particular, the use by industry ofrecombinant DNA, cell fusion, and new bioprocessing techniques; anytechnology that is applied to living organisms to make them more valuableto humansbiotic potential - the maximum rate a population can increase underideal conditionsbiotope - an area of relatively uniform environmental conditions,occupied by a given plant community and its associated animal communitybiotoxin - any poisonous or venemous substance produced by any livingorganismbioturbation - the rearrangement of sediments by organisms that burrowthrough them and ingest thembioturbator - an organism, mainly a worm or crustacean, that disturbssediments by burrowing or feeding. Its activities mix the sediment layersand may cause substantial resuspensionbiotype - a physiological variety or a group of individuals havingdistinctive genetic characters in commonhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (19 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databiparental - the situation where the young are raised by both parentsbipectinate - having two margins which are toothed, like a comb;descriptive of the gills (ctenidia) of aquatic mollusksbipectinate gill (ctenidium) - in mollusks, refers to having gill lamellaeon both sides of the ctenidial axisbipinnaria larva - an early starfish larvawith ciliated bands running about theperipheryMature bipinnaria ofPisaster ochraceus, ca 24days old, raised in cultureby T.H.J. Gilmour. (Photo:University ofSaskatchewan Archives)biradial symmetry - a body plan in some cnidarians that has two planesof symmetry rather than the several planes of a radially symmetricalanimal, or the single plane of a bilaterally symmetrical one. Both planesof symmetry are longitudinal and are at right angles to each other. Bothinclude the aboral-oral axis, which is the axis of symmetrybiramous appendage - a type ofappendage that is characteristic ofcrustaceans. It forks from the basalprotopodite to form two branches, the innerendopodite and the outer exopodite. Eachof these branches can be composed ofeither one or more segments. There aremany variations on this generalizedstructure; the branches often possesshighly specialized extensionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (20 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataNote the biramousantennules of the spinylobster.bit - the smallest unit of information that a computer can store andprocess. A bit has two possible values, 0 or 1, which can be interpreted asyes/no, true/false, or on/offbitmap - a format for storing graphics in an uncompressed mannerbitmap image - also called raster or paint images. They are made ofindividual dots called pixels (picture elements) that are arranged andcolored differently to form a pattern. Compared to a vector image, bitmapimages are great for photographs because they tend to offer greatersubtleties for shading and texture but require more memory and takelonger to print. Vector images are best for drawings that need sharperlines, more detail, and easy modification. Vector images require far lessprinting resources than bitmap imagesBivalvia (Pelecypoda) - a class ofMollusca that includes clams, oysters andmussels. Bivalves are laterally compressedand possess a shell composed of two valvesthat hinge dorsally and enclose the body.They are common inhabitants of coral reefsA scallop (class Bivalvia)displays its rows of lightsensitiveeyespots.black coral - black corals are colonialcnidarians in the Order Antipatharia. Theyare found throughout the world+s oceans,but are most common in tropical deepwater habitats from 30-80 m depth. Thesespecies of black coral have rigid, erectskeletons that form branched, bush-likecolonies. Black coral is commerciallyharvested primarily for jewelry, and may beglobally threatened in many parts of theworld as a result of over-harvestingBlack coral isn't reallyblack. The name refers tothe black color of theirproteinaceous skeletons.The living colonies aremade up of thousands ofhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (21 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Datatiny coral polyps whosecolors may be yellow,green or orange. (Photo:Dr. A. Bruckner, NOAA)black-band disease - a world-widedisease of corals that is characterized by adark ring, or band, that separatesapparently healthy coral tissue from freshlyexposed coral skeleton. It migrates acrosscoral colonies and completely degradescoral tissue. The infecting agent is asynergestic assortment of photosyntheticand non-photosynthetic bacteria. For moredetails and illustrations, see: http://www.coral.noaa.gov/coral_disease/black_band.shtmBlack band disease.(Photo: Dr. A. Bruckner,NOAA)bladder - any sac or cavity used to store liquids or gasesblade - a leaf-like structureblastocoel - the fluid-filled cavity formed within the mass of cells of theblastula of many animals during the later stages of cleavageblastocyst - a preimplantation embryo. The blastocyst consists of asphere made up of an outer layer of cells (trophectoderm), a fluid-filledcavity (blastocoel), and a cluster of cells on the interior (inner cell mass)blastomere - an undifferentiated cell of a cleaving embryo, and of themorula and blastula stages of embryonic developmentblastopore - the opening into the archenteron (primitive gut) of agastrula. In some animals it develops into the mouth and, in others, intothe anusblastostyle - the axial portion of a modified gonangium, upon whichmedusoid buds are developedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (22 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Datablastula - a stage of embryonicdevelopment of animals near the end ofcleavage (cell division), but beforegastrulation. In animals where cleavageinvolves the whole egg, the blastula usuallyconsists of a hollow ball of cells(blastomeres) surrounding a fluid-filledcentral cavity, the blastocoelA late blastulacharacterized by a singlelayer of cells surroundingthe central hollow area -the blastocoel (B). Theblastomeres at the vegetalpole (VP) are taller thanthose at the animal pole(AP), making the vegetalpole appear slightlythicker. (Photo: Cell andDevelopmental BiologyOnline website (Universityof Guelph); URL: http://www.uoguelph.ca/zoology/devobio/)bleach - to make or become white or colorless by means of chemicals, byexposure to solar radiation, etc. In corals, the reduction in intensity orcomplete absence of coloration within living coral tissues, due to expulsionof symbiotic algae (zooxanthellae)bleaching index - index based on the strength and duration of localHotSpots to monitor bleaching eventsbleaching outbreaks - development of bleaching eventsbleaching stressors - environment-induced stress that results inbleaching, e.g., disease, excessive or insufficient light, increased levels ofultraviolet radiation, sedimentation, pollution, salinity changes, andincreased temperatureshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (23 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Datablenny - the common name of a largegroup of over 800 species within sevenfamilies of bony fishes in the suborderBlennioidei. Blennies are small, usuallyscaleless fishes with comb-like teeth livingin coastal and coral reef areas, includingseagrass beds and tidepools. At least onespecies lives in fresh water. Most are arecharacterized by possessing bluntforeheads, elongated, tapering bodies, anda continuous long dorsal fin. The pelvic finsare usually anterior to the pelvic fins, andin the jugular in position. Many species arecryptic or inhabit the surge zone. Most areherbivoresThe blenny, Blenniellagibbifrons, is common onHawaiian shallow reefsliving in empty vermetidtubes (Photo: Keoki andYuko Stender)blind test - a method of testing or experimentation, in which anindependent observer records the results of any test, drug, placebo, orprocedure without knowing the identity of the samples or what resultmight be expectedblog (weB LOG) - basically a journal that is available on the web. Theactivity of updating a blog is "blogging" and someone who keeps a blog isa "blogger"blood - a circulating tissue composed of afluid portion (plasma) with suspendedformed elements (red blood cells, whiteblood cells, and platelets) that deliversnutrients and hormones to cells andremoves wastes; In some invertebrates,the blood is called the haemolymphRed and white blood cells.The white blood cells arethe larger ones withirregular nuclei.The smallparticles are platelets.(Photo: U.S. NationalInstitutes of Health)blood pigment - a pigment used by an organism to transport oxygenefficiently, usually in a circulatory system (e.g., hemoglobin, hemocyanin)blood sinus - in invertebrates, a space among the muscles and viscerathrough which blood returns to the blood-pumping organ (heart)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (24 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Datablood sinus - a channel, not a blood vessel, which permits the passage ofbloodbloodworm - a marine polychaete worm used as bait in anglingbloom - a sudden increase in the biomassof phytoplankton or benthic algae in agiven areaA SeaWiFS (Sea-viewingWide Field-of-view Sensor)image of a coccolithophorebloom in the Bering Sea.blotch - a patch or a spot of pigment withirregular edgesThe blotch-necked moray(Gymnothoraxmargaritophorus) fromAmerican Samoa bearsdarkly pigmented blotchesalong its body. (Photo:NPS, Copyright Richard C.Wass)blue coral - the blue coral, Helioporacoerulea, is an octocoral that has a massivearagonite skeleton and is an important reefbuilder in some areasBlue coral (Helioporacoerulea) from AmericanSamoa. (Photo: NPS, EvaDiDonato)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (25 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataBlue List species - registers of those Red List species that show anoverall stabilization or increase in abundance in the region considered;Blue List species are considered to be vulnerable and "at risk", but not yetendangered or threatened. Populations of these species may not be indecline, but their habitat requirements are such that they are vulnerableto further disturbances; Blue Lists are mostly a subset of the Red ListsBlue Ventures - a not-for-profit organization (UK) which facilitatesprojects and expeditions that enhance global marine conservation andresearch. It coordinates expeditions consisting of scientists and volunteersworking with local biologists, governmental departments, NGOs and localcommunities, to carry out research, environmental awareness, andconservation programs at threatened marine habitats around the worldblue-green algae - the former name forthe blue-green bacteria, now classified asCyanobacteria. A group of prokaryotic cellsthat use chlorophyll on intracytoplasmicmembranes for photosynthesis. The bluegreen color is due to the presence ofphycobiliproteins. they occur as single cells,colonies or simple filamentsBlue-green algae(Cyanobacteria). (Photo:J. Waterbury, Woods Hole/NASA AstrobiologyInstitute)BOD (Biological (or Biochemical) Oxygen Demand) - the oxygenused in meeting the metabolic needs of aerobic microorganisms in waterrich in organic matter (as water polluted by sewage)body wall - the layers of tissue (epidermis, mesoglea, and gastrodermis)that make up the body of a cidarian polyp. The body wall surrounds thegastrovascular spacesbond - a physicochemical association between atomsbond energy - the energy required to form a particular chemical bondbooby - the common name for large, streamlined sea birds of the familySulidae. Tropical and subtropical members of the family are calledboobies; those of northern waters are called gannets. Gannets havestrong migration tendencies, while the boobies do nothttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (26 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databooties - short "boots" usually made ofneoprene, worn inside open-heeled fins.they protect a scuba diver's feet fromrubbing against the fins while swimming, aswell as protecting the entire foot whilewalking to and from a dive site. Bootiesalso provide warmthA pair of booties worn byscuba divers under anopen-heeled fin.bootstrapping - a statistical technique based on repeated randomsampling with replacement from an original sample to provide a collectionof new pseudoreplicate samples, from which sampling variance can beestimatedborer - an invertebrate that bores into wood, stone, coral, or anotheranimal's shellboring sponge - a sponge that chemically digests the limestoneskeletons of corals during its search for food and living space, whichbreaks down the structure of the reefboss - a columnar, flat-topped coral-algal growth or erosion structureusually found on the upper surfaces of spurs and buttressesbosselated - covered with small, knob-like projectionsBotCam (bottom camera station) - a deep water camera stationsystem that can be used as a cost-effective and non-extractive method toassess and monitor the abundance and size composition of bottomfishpopulations in deepwater habitats.This Bottom Camera ("BotCam")system includes programmable control functions which allow for theactivation of imaging systems, bait release mechanisms, image scalingindicators, and acoustic release to enable recovery of the camerabottlebrush branching - describes a branch with compact radial subbranchesbottleneck - in evolutionary biology, a bottleneck is a brief reduction inthe size of a population which usually leads to random genetic drift whichleads to a loss in genetic (allelic) variationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (27 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databottom trawl - a method of fishing inwhich a large bag-shaped net is draggedalong the bottom, behind the vessel. Themouth of the net is kept open by variousmethods, such as a wooden beam (beamtrawl) or large flat boards (otter trawl).Bottom trawling has been very destructiveto deep water coralsThis image shows thelikely impact of bottomtrawling on the OculinaBanks. Note the linearfeature at the lower right.On this type of bottom,small linear mounds ofcoral rubble are createdimmediately adjacent tothe track of the trawl.(Photo: NOAA)bottom trawler - a fishing vessel thatuses an open-mouthed fishing net drawnalong the sea bottom. This type of fishing isdestructive to shallow water and deep seacoral reef communitiesSmall stern trawler fishing.(Photo: David Comb/NewEngland Biolabs)boundary - in ecology, the edge between different habitat types. Ifdistinctive, a boundary can be considered a separate edge habitat orecotone. Boundaries that are readily crossed by an organism are calledpermeable, those that are crossed reluctantly are called semipermeable,and those that are not crossed are called impermeableboundary current - a large-scale water stream in the upper ocean whichseparates water masseshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (28 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databow - the front part of a vesselThe Facing the bow of theNOAA Ship Ronald H.Brown (Photo: NOAA)Boyle's Law - if the temperature is kept constant, the volume of a givenmass of gas is inversely proportional to the absolute pressurebp (base pairs) - pairs of nucleotide bases in DNAbrachial - pertaining or belonging to the armbrachial canal - a canal in the oral arms of scyphozoan medusaebrachidium - in brachiopods (lamp shells), the internal skeleton (a longribbon or loop-shaped calcified brachial support) for the lophophorebrachiolaria larvae - a starfish larval stage following the bipinnariastage. It has projecting arms and a developed stomachBrachiopoda - a phylum of marineinvertebrates that superficially resemblebivalve mollusks because of their hingedbilaterally symmetrical shells.They arecommonly known as "lampshells"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (29 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataGeneral view of theexternal features of abrachiopod. The valves(shells) are positioneddorsal and ventral. Inbivalve mollusks, thevalves are positioned rightand left. (Photo:BIODIDAC)brachy- - a prefix from the Greek, meaning "short"brackish - mixed fresh and salt waterA brackish water areashowing a mix of salt andfreshwater marsh speciesin the Weeks Bay Nationalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (30 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataEstuarine ResearchReserve, AL. (Photo:NOAA)brady - a prefix meaning "slow"bradyauxesis - a form of heterauxesis in which the growth process of apart is less than that of the wholebradycardia - an unusually slow heart ratebradytelic - an exceedingly slow rate of evolution manifested by slowlyevolving lineages which survive much longer than would be expected.Possibly the best example of bradytelic evolution is the brachiopod,Lingula, which arose in the Cambrian and persists todaybrain coral - species of scleractinian (hard or stony) corals which arecharacterized by their spherical shape and human brain-like appearance,with furrows and grooves. Brain corals are found in warm-water coralreefs in all the world's oceans. There are several species of brain coralsfound in two familiesbranchia - a respiratory organ, such as a gill; a ctenidiumbranchial - pertaining to gillsbranchial aperture - the exterior opening of a gill chamberbranchial chamber - in crustaceans, the area between the body andcarapace which encloses the respiratory organs (gills)branchial cleft - a gill slit, such as is found in sharks, skates, and raysbranchial crown - in marine polychaete worms, a structure surroundingthe mouth composed of ciliated, bipinnate filaments which function insuspension filter feeding and respirationbranchial plume - a respiratory structureor external gills, usually located on thedorsal side toward the posterior of doridnudibranchs. This plume surrounds theanus and in some species, it may beretracted. The branchial plume is the majorrespiratory structure in nudibranchs; inmarine polychaete worms, a structuresurrounding the mouth composed ofciliated, bipinnate filaments which functionin suspension filter feeding and respirationThe feathery structuretoward the posterior ofthis nudibranch gastropod(marine sea slug) is itsrespiratory organ.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (31 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databranchial siphon - the incurrent siphon in some mollusksbranchiform - gill-shapedbranching colony - a coral growth pattern where branches are formedbranchiocardiac groove - in decapod crustaceans, a groove on eachside of the carapace which separates the branchial and cardiac regionsbranchiopallial - pertaining to the gill and mantle of mollusksbranchiostegal - one of the dermal bony or cartilaginous struts thatsupport the branchiostegal membranes of fishes. Sometimes calledbranchiostegal rays, but not to be confused with the fin raysbranchiostegal area - in crustaceans, the part of the carapace whichextends laterally and ventrally over the gillsBraun-Blanquet method - a method for estimating seagrass and otherplant species composition. It involves identifying all species represented ina specific quadrat, then assigning each a code based on its contribution tothe total area. An example of Braun-Blanquet codes is: 0: species notpresent; 1: species 90% of totalBray-Curtis similarity coefficient - a similarity coefficient used todetermine site similarities based on organism abundances. It is widelyemployed in multivariate analysis of assemblage data. It reflectsdifferences between two samples due both to differing communitycomposition and/or differing total abundancebreaker - a wave that approaches shallow water, causing the wave heightto exceed the depth of the water, in effect tripping it. The wave changesfrom a smooth surge in the water to a cresting wave with water tumblingdown the front of it; a wave breaking on the shorebreaker zone - the area of a coral reef most exposed to breaking wavesbreast - in fishes, the anterior ventral surface under the headhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (32 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databreed - a group of organisms, usually infrasubspecific, related by descentfrom common ancestors and visibly similar in most characteristics. Aspecies can have numerous breeds; a population of a species that hasdistinct characteristics that differentiate them from other populations inthat species. Reproduction within the population produces offspring whichare recognizable as members of that population. Breeds can further besubdivided into varieties based on differences within the breedbreeding season - the time of the year during which mating occursbreeding season - that period of a year in which organisms are sexuallyactivebrevilingual - having a short tonguebrine - water that contains a high concentration of saltbrine pool - concentrations of water on the ocean floor which have anextremely high salinity relative to the surrounding water. Brine pools arecaused by salt tectonics, which is the process by which large deposits ofsalt are moved by geological forces. Cold seep activity often coincides withthe location of a brine poolbristle - a stiff, coarse, hair-like structurebrittle star - brittle stars are echinoderms(class Ophiuroidea) which are closelyrelated to sea stars (starfish). They possessradial symmetry with a central body discfrom which five highly flexible snake-likearms protrude. There is no replication ofinternal organs,as in the arms of sea stars,just one set in the central disk. Comparedto starfish, brittle stars have a muchsmaller central disc and no anus. Wastesare eliminated through the mouth, which issituated on the undersideof the disc. Thename is derived from their arms breakingoff as a means of defense. New arms areeasily regenerated. They are also calledserpent stars because of the snakelikemovements of the five armsThis black brittle star(Ophiomastix variabilis) isan inhabitant of Indo-Pacific coral reefs. (Photo:Teresa (Zubi) Zuberbühler(www.starfish.ch))broadcast spawner - an organism that releases gametes directly intothe sea for external fertilizationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (33 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databrood - all of the offspring that hatch from a single clutch of eggs or theoffspring of a single birth that normally mature at about the same time; toincubate eggsbrood pouch - a sac-like cavity in the parent's body in which eggs aredeposited and fertilized and larvae develop, such as in seahorses;marsupium; brood chamberbrooder - a coral which harbors or broods developing larvae within itspolypsbrooding - the development of larvae within the gastrovascular cavity ofan adult coral polypbrooding - parental care of youngbrown algae - brown algae belong to theDivision Phaeophycophyta, whoseapproximately 1,500 species are almostexclusively marine. They include the largestof the seaweeds and the kelps. The brownalgae have chlorophyll a and c, as well ascarotenes and xanthophylls, but the greenchlorophyll coloration is masked by thebrown and yellow pigments. Brown algaeare among the largest photosyntheticorganisms on earth. The largest kelps maygrow to more than 60 meters in length,forming dense underwater forests in colderwaters. Many microscopic brown algaeBrown algae. (Photo:NOAA)grow as epiphytes on underwater vegetation, forming networks ofbranched filaments, or broad encrustations. All species are multicellularand do not form colonies. Their life cycles are complex, involvingalternation of generations. In general, they are not free-floatingorganisms, but are attached to rock, coral, or other firm surfaces.Sargassum weed, however, is a floating brown algae that stays afloat byproducing gas-filled bladdersbrown tree snake - the mildly venemousbrown tree snake (Boiga irregularis) is anintroduced species on some Pacific islandsthat has become a serious pest, especiallyon Guam. In the absence of naturalpopulation controls and with vulnerableprey on Guam, the snakes have become anexceptionally common pest causing majorecological and economic problems. Thesnakes probably arrived on Guam hidden inship cargo from the New Guinea area. By1968, they had dispersed throughout theThe brown tree snake(Boiga irregularis) is aninvasive species that hascaused great ecologicaland economic damage onhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (34 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Dataisland and caused havoc by virtually wiping Guam. (Photo: U. S.Geological Survey)out Guam's native bird species and helpeddecimate their fruit bat populations. Inaddition to Guam, brown tree snakes havebeen sighted on Saipan, Tinian, Rota,Kwajalein, Wake, Oahu, Pohnpei, Okinawa, and Diego Garcia. To date, thissnake is not known to be established on any of these islands except Guambrowser - a software program, such as Netscape Navigator or MicrosoftInternet Explorer, that allows one to view pages on the Internetbrumation - a long period of torpor or rest induced by cold temperaturesin reptiles and other cold-blooded animals. Brumation is similar tohibernation in warm-blooded animalsbrunneous - dark brown colorbrush - a cluster of bristlesbryostatin - a marine pharmaceutical, isolated from bacteria living in thebryozoan Bugula neritina, having anti-cancer and immune systemmodulating propertiesBryozoa - an animal phylum synonymouswith Ectoprocta that contains approximately5,000 living species. They are all sessilecolonial forms composed of zooids. Zooidsare tubular, oval or box-like structures thatcontain a lophophore, which is a circular orhorseshoe-shaped fold of the body wall thatencircles the mouth and bears numerousciliated tentacles. Most species form erector encrusting colonies. They occur in manydifferent habitats, including coral reefsBryzoa colony.bubblegum coral - a deep watergorgonian, Paragorgia arborea, found in theNorth Pacific and North Atlantic Oceans atdepths that may exceed 1400m. It cangrow to 5m in height and 8 m in width. It iscalled the bubblegum coral becausebecause it is usually orange or pink incolor, and has a lumpy surface textureBubble gum coral on Gulfof Alaska Seamounts.(Photo: NOAA OceanExplorer )http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (35 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databuccal - pertaining to the cheek or oral cavitybuccal cavity - the mouth or oral cavitybuccal siphon - in tunicates, the opening through which water entersinto the pharyngeal basket. It is also called the incurrent, inhalant, or oralsiphon/canalbuccopharyngeal - pertaining to the oral cavity and pharynxbudding - a type of asexual reproduction in which new individualsdevelop from the parent organism, forming a swelling similar inappearance to a bud, which separates from the parent as it grows;budding is a form of asexual reproduction in corals where a parentcorallite forms daughter corallitesbuddy - a scuba diving partner. For safediving, a pair of divers (buddies) stay closeto each other in order to offer assistance ifneededNOAA divers working inbuddy pairs. (Photo:NOAA/National UnderseaResearch Program)buddy breathing - two scuba diverssharing air from one second stage regulatorScuba divers practicingbuddy breathing. (Photo:John Buchanan)buffer - a solution or liquid whose chemical makeup neutralizes acids orbases without a great change in pHhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (36 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databuffer species - a species which may serve as an alternate food supplyfor a predator or consumerbuffer zone - the region near the border of a protected area; a transitionzone between areas managed for different objectivesbuffered solution - a chemical solution that resists changes in pHdespite the addition of small amounts of acids or basesbulb - a rounded dilation or expansion in a canal, vessel, or organbulbous - a rounded or swollen shapebullate - describes a blistered or puckeredsurfaceA leaf with bullateappearance (Photo: ShaunL. Winterton)bulliform - blister or boil-shapedbulwark - the side of a ship above the deckbuoy - a floating platform for navigational purposes or supportingscientific instruments that measure environmental conditionsbuoyancy - the tendency of object to float or sink when placed in a liquid.Positively buoyant objects float, negatively buoyant objects sink, andneutrally buoyant objects stay in placeburrow - a hole or excavation dug in the substrate by an animal, usuallyfor shelter, habitation, refuge, or to rear younghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (37 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databurrower - an animal that makes a hole orburrow in the substratum and lives in it.For example, a fidler crabA male fiddler crab (Ucapugnax) lives and matesin a burrow on the beach(Photo: NOAA)bursa - a sac or sac-like cavitybutterflyfish - any species of colorful, ovalshaped,deep-bodied and stronglycompressed spiny-rayed fishes in the familyChaetodontidae. They have small mouthswith flexible, brush or comb-like teeth.They resemble the closely relatedangelfishes. They feed on a variety offoodstuffs from zooplankton to tinycrustaceans and mollusks, soft and hardcorals, anemones, segmented worms, andother soft and encrusting invertebratesassociated with coral reefs. Some speciesare omnivores that primarily feed onmarine algae as well as animals, whileothers are obligate corallivoresThe butterflyfish,Chaetodon vagabundus,photographed in theSolomons Islands (Photo:Photo: Tom Doeppner/Brown University)buttress - see spur and groovebuttress zone - the seaward-sloping area of a coral reef (just beneaththe algal ridge) that consists of alternating ridges and furrowsbycatch - organisms taken in a fishery which are not of the speciesintended for harvest. For example, mammals or turtles captured in trawlor seine fishingbycatch reduction devise - equipment attached to commercial fishingequipment to reduce the amount of bycatch takenhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (38 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef Databyssal thread - one of many thin, hairlikefilaments secreted by certain mollusks forattachment to a substrateThe byssal gland is locatedwithin the foot of themussel. It producessecretions which are usedto form byssal threads forattachment to substrates.(Photo: Great Lakes SeaGrant Network ExoticSpecies Library, OntarioMinistry of NaturalResources)byte - a memory and data storage unit composed of contiguous bits,usually eight. For example, file sizes are measured in bytes or megabytes(one million bytes). Bytes contain values of 0 to 255 and most oftenrepresent integer numbers or ASCII characters(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=b (39 of 39) [2/26/2008 9:13:20 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: CThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zc-card - a scuba diving certification card from scuba certifying agencies,such as NAUI, BSAC, NOAA, PADI, etc.CaCO3 (calcium carbonate) - a moleculeconsisting of calcium, carbon and oxygensecreted by corals to their skeleton. It isalso secreted by mollusks to form theirprotective shellsThis Queen Conch(Strombus gigas) utilizescalcium carbonate informing its protectiveshell. (Photo: AndyBruckner)cacophonous - having a harsh, unpleasant soundcacospongionolide B - an antiinflammatory drug derived from themarine sponge Fasciospongia cavernosahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (1 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacadastral survey - a survey which creates, marks, defines, retraces orreestablishes the boundaries and subdivisions of the public land of theUnited States. It is derived from the word cadastre, meaning a publicrecord, survey, or map of the value, extent, and ownership of land as abasis of taxationcaecum - a blindly ending sac arising from the gut or some other holloworgancalathiform - cup-shapedCalcarea - a class of exclusively marinecalcareous sponges (phylum Porifera) thatpossesses spicules composed of calciumcarbonate. They are predominantly found inshallow, temperate and tropical waters,though at least one species is known froma depth of 4,000 meters. Some inhabitcoral reefs. The Calcarea is thought to bemost primitive group of sponges. It is theonly class with asconoid and syconoidgrades of construction, though somespecies are leuconoid. Generally,they aresmall in size. The different shapes arerelatively simple, either purse, vase, pearor cylindricalThe Calcarea is a class ofsmall, delicate, marinesponges whose spiculesare made up of calciumcarbonate. Most aretubular or vase-shaped,and they can haveasconoid, syconoid, orleuconoid organizations.(Photo: P. Madl and M.Yip)calcareous - composed of or containing a substance made of calciumcarbonatecalcareous algae - algae which deposit calcium carbonate in its tissues.When they die and decompose, their calcium carbonate skeletons are leftbehind to form or contribute to the growth of a reef. Calcareous algae alsoprovide an adhesive function, cementing reef components together; see"coralline algae"calcareous ooze - a biogenous sediment that is made of the calciumcarbonate shells and skeletons of marine organismscalcariform - spur-likecalceolus - complex sensory organelles on the antennules of somedecapod crustaceanscalcification - the process by which corals and calcareous algae extractcalcium from seawater and produce it as calcium carbonatehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (2 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacalcite - a mineral made up of a crystalline form of calcium carbonatecalcite skeleton - a skeleton composed of the calcite form of calciumcarbonatecalibrate - to check or adjust the graduations of a quantitative measuringinstrumentcalice - the oral surface of the corallitecalice relief - the height of a corallite or corallite seriescalicle - one of the small cuplike cavities, often with elevated borders,covering the surface of most corals. Each is formed by a coral polyp; thecalyxcalicoblastic epithelium - a thin squamous epithelial layer of cells instony (hard) corals which deposits the white calcium carbonate skeleton;also called "calicodermis"caliculate - cup-shapedcalipee - a fatty, gelatinous substance in green turtles, traditionally usedin the preparation of green turtle soupcallyspongynic acid - a bioactive compound, isolated from the marinesponge Callyspongia truncata, interferes with glycogen hydrolysis therebykeeping glucose concentrations in the blood at low levels. It can be usedin the treatment of diabetescalm - the condition of the water surface when there are no winds, wavesor swellcalorie - a unit of measurement defined as 4.184 absolute joules or theamount of energy it takes to raise the temperature of one gram of waterfrom 15 to 16 degrees Celsius (or 1/100th the amount of energy neededto raise the temperature of one gram of water at one atmospherepressure from 0 degrees C to 100 degrees C). Food calories are actuallyequal to 1,000 calories (1 food calorie = 1 kilocalorie)calorimetry - measurement of the amounts of heat absorbed or givenout; measurement of heat flowCalvin cycle - a series of biochemical reactions that take place in thestroma of chloroplasts during photosynthesis. It´s main result is theassimilation of carbon. Environmental carbon dioxide is reduced andincorporated into organic molecules, including sugars. It is one of the lightindependentreactions (dark reactions) of photosynthesis; also called theCalvin-Benson cyclehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (3 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacalyciform - goblet or cup-shapedcalyculus - a cavity in a coral which contains polypscalypto - a prefix meaning "covered"calyptoblastic - in hydrozoans, hydroids with complete gonothecal cupsaround the polypscalyx - the upper or open end of the corallite or coral polyp cup; thecentral body of entoprocts (goblet worms) or crinoids (sea lilies andfeather stars)Cambrian - a major division of the geologic timescale that extended fromat least 580 million years ago to 500 million years ago. It marks thebeginning of the Paleozoic Era. The name comes from the CambrianMountains in Wales, where the strata of the Cambrian were first definedCambrian explosion - a burst of evolutionary origins when most of themajor body plans of animals suddenly appeared in a relatively brief timein geological history, approximately 530 to 570 million years ago; theseemingly rapid appearance of most major groups of complex animals inthe fossil record, around 530 million years ago, accompanied by a majordiversification of other organismscamouflage - the use of color patterns, shape, texture, and/or behaviorthat allows an animal to blend in with its surroundings and thus remainconcealed from predators or preyCaMPAM (Caribbean Marine Protected Area Management) - anetwork of managers of marine and coastal protected areas in the widerCaribbean organized to achieve goals of conservation and sustainable useof Caribbean coastal and marine environmental resources. Generalactivities conducted through CaMPAM's membership include sharingexperiences and addressing management challenges by facilitatingtraining opportunities, information exchange, communication, andproblem solvingcampaniform - bell-shapedcampanulate - bell-shapedcanal - a groove, tube, or ductcanaliculus - a very small canalcancellous - possessing a spongy or porous surfacehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (4 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacancellous - reticular, spongy, or lattice-like structure; usually pertainsto bonecancriform - crab-shapedcancroid - resembling a crabcanine tooth - a pointed, conical tooththat is located at the front or edge of thejaw. Canine teeth are used for piercing andgrabbing preyMoray eels are armed withsharp canine teeth usedfor capturing prey and alsofor defense. (Photo: Dr.Tom Doeppner, BrownUniversity)cannibalism - predation of an animal by a member of its own speciescanopy - the more or less continuous cover of branches and foliageformed collectively by the tops, or crowns, of adjacent treescape - a piece of land that that projects out into a large body of watercapillary - a minute blood vessel that connects the arteries and veins.Capillary walls are one-cell thick (endothelium) and act as semipermeablemembranes for the interchange of various substances, including fluids,between the blood and tissue fluids; a tube of small internal diameterwhich holds liquid by capillary actioncapillary action - the means by which liquid moves through the porousspaces in a solid, such as soil, plant roots, and capillary blood vessels dueto the forces of adhesion, cohesion, and surface tension. Capillary actionis essential in carrying substances and nutrients from one place to anotherin plants and animalscapsid - the protein coat of a virus particlecaptaculum - a filamentous tactile organ with an adhesive, sucker-likeend near mouth of a tusk shell (mollusks in the class Scaphopoda).Thecaptacula are used to gather small particles of food in the sand and passthem to the mouthhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (5 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacaptive breeding - raising animals (or plants) in controlled conditions toproduce stock for subsequent release into the wildcapture-recapture method - a procedure involving the distinctivemarking of individuals and their subsequent recapture (or sighting) toestimate population size and other population parameters; also known as"mark-recapture"carapace - a hard shield, or shell covering,found over all or part of the anterior dorsalportion of an animal. In lobsters, shrimps,crayfish, and crabs, the carapace is the partof the exoskeleton that covers the headand thorax and protects the dorsal andlateral surfaces. In many crustaceans, theterm carapace is also used to describe thehard, protective covering of thecephalothorax, as that of the horseshoecrab. The carapace of a turtle's shell iscomposed of expanded ribs and vertebraeoverlain by dermal plates and horny scalesThe carapace is the hardshell covering of thecephalothorax of this spinylobster.carbohydrase - an enzyme that acts upon a carbohydratecarbohydrates - organic compounds composed of carbon, oxygen, andhydrogen; includes the simple sugars, double sugars, and complex sugars(starches)carbon cycle - the cycling of carbon in the form of carbon dioxide,carbonates, organic compounds, etc., between various reservoirs, e.g.,the atmosphere, the oceans, land and marine biota and, on geologicaltime scales, sediments and rockscarbon fixation - the conversion of inorganic carbon into organic carbon,usually by photosynthesiscarbon-14 - a radioactive isotope of carbon with a half life of 5,730±40years that is particularly useful for dating carbonaceous materials; alsocalled 14Carbon or radiocarboncarbonate - a mineral composed mainly of calcium (Ca) and carbonate(CO3) ions. Carbonates may also include magnesium (Mg), iron (Fe) andothers; rock or sediments derived from debris of organic materialscomposed mainly of calcium and carbonate (e.g., shells, corals, etc.) orfrom the inorganic precipitation of calcium (and other ions) and carbonatefrom solution (seawater). For example, limestone or dolomitecarbonate bank - a narrow, fairly flat, shallow, submarine plateau(measured in tens of meters) of composed of limestone (carbonate rock),e.g., the Bahama Bankshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (6 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacarbonate compensation depth - the depth in the ocean below whichmaterial composed of calcium carbonate (CaCO 3 ) is dissolved and doesnot accumulate on the sea floorcarbonate mound - a seabed feature usually constructed from carbonateproducingorganisms and current-controlled sedimentation. Carbonatemounds are a unique combination of cold-water coral framework andrubble, sediment deposition, and local hydrodynamic influencescarbonate platform - a broad, flat, shallow, submarine expanse ofcarbonate rock. Its size is measured in hundreds of meterscarboxyl group - the -COOH functional group, acidic in nature, found inall amino acids; the acid group of organic moleculescarcinogen - a chemical substance that causes cancercarcinology - the study of crabs and other crustaceanscardinal - deep scarlet red colorcardinalfish - any species of bony fishes inthe family Apogonidae. Cardinal fishes areoften brightly colored with attractivepatterns, usually in shades of red or brown.Most are small tropical marine species,although some live in brackish and evenfresh water watersThe cardinalfish, Apogondammermani. (Photo:Richard C. Wass/NationalPark service)Caribbean Coral Reef Institute (CCRI) - NOAA's Caribbean Coral ReefInstitute (CCRI), inaugurated in May, 2005, is located at the theUniversity of Puerto Rico-Mayaguez. The CCRI focuses exclusively on theacute problems of Caribbean coral reefs. Its main objective is to aid in themanagement and conservation of Puerto Rico’s coral reefs by providingtimely, relevant information to the Puerto Rico Department of Natural andEnvironmental Resources and the scientific community at large. CCRIprojects include conducting habitat mapping of the western shelf of PuertoRico, assessing the status of reef resources, and assessing fishery impactshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (7 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCaribbean Decision Support System (CDSS) - a tool developed by theNature Conservancy and its partners to improve the linkage betweenbiodiversity conservation objectives and human development-relatedprograms such as disaster mitigation/response/planning, economic growth(especially tourism and fishing), and land and water use planning. Itrepresents a comprehensive database of biodiversity and socio-economicinformation in existence for the Greater Caribbean basinCaribbean Regional Association (CaRA) - the National Oceanic andAtmospheric Administration, NOAA, has provided funding to the CaRA toestablish and administer a sustained observing system for thenortheastern Caribbean region, the Caribbean Regional Integrated CoastalOcean Observing System (CaRICOOS) to provide observations andproducts for the purposes of detecting and predicting climate variabilityand consequences, preserving and restoring healthy marine ecosystems,ensuring human health, managing resources, facilitating safe and efficientmarine transportation,coastal Hazard Management Response, andpredicting and mitigating against coastal hazardsCARICOMP (Caribbean Coastal Marine Productivity) - a regionalcoral reef, seagrass and mangrove monitoring program and networkinvolving a number of Caribbean laboratories, parks and reserves to studyland-sea interaction processes in the wider Caribbean region. Twentyseveninstitutions in 17 countries participate in CARICOMPcaridean shrimp - caridean shrimps can be distinguished from othershrimp-like creatures by the way in which the plate of the secondabdominal segment overlaps the segments both in front and behind,forming a saddle. They are found in marine, brackish and freshwaterhabitats from the tropics to the polar regions. Carideans are taxonomicallyand ecologically diverse, with many remarkable adaptations for survivaland reproduction.These crustaceans are placed in the infraorder Caridea,order Decapoda, and class Malacostracacarina - any elevated ridge or keel-like structurecarinate - shaped liked a keel or ridgecariniform - keel-shapedcarnivore - an organism that feeds uponanimalsA carnivore (barracuda)caught in the act.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (8 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacarotene - a red, orange, or yellow pigment belonging to the group ofcarotenoids; a precursor of vitamin Acarotenoid - any of a group of red, orange, and yellow accessorypigments of plants or algaecarpogonium - the female gamete-producing reproductive organ in redalgae, consisting of a single cell and its extension, the trichogynecarposporangium - a single-celled structure in red algae that producesdiploid carpospores on the carposporophytecarpospore - a non-motile diploid spore formed on the carposporophytestage of the red algae life cycle which germinates to form thetetrasporophyte stagecarposporophyte - the diploid stage of red algae which develops afterfertilization of the carpogoniumcarrageenan - a water-soluble polysaccharide extracted from redseaweed, mainly Chrondus crispus (Irish moss). It is used in bothcosmetic and food applications as a stabilizer and emulsifier capable ofcontrolling viscosity, maintaining product integrity, and for giving animproved mouthfeel and body to foods. Carrageenan is a commonly usedingredient in toothpaste, ice cream, dry mixes, desserts, milk products,tomato sauces, salad dressings, and cheese productscarrier cell - in sponges, a migratory choanocyte that transports spermto the oocytecarrion - the dead and rotting body of an animal; carrion is food forscavenging animalsCARRUS Alliance (Comparative Analysis of Reef Resilience UnderStress Alliance) - the CARRUS Alliance was organized at the 2004International Coral Reef Symposium held in Okinawa. Its objective is toprovide a basis for better understanding of coral reefs at the scale of thewhole reef system. The Alliance consists of researchers conductingindependently-supported long-term, interdisciplinary research on wholereef systems, including associated social and economic systems, unitedthrough agreements for the exchange of information, methods, expertise,and software. One focus of the Alliance will be on developing commonresearch objectives, including the development of decision supportsystems to facilitate reef management. The Alliance will be linked to avariety of international effortscarrying capacity - the maximum population size that can be regularlysustained by an environment; the point where the population size levelsoff in the logistic growth modelhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (9 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCartagena Convention: Convention for the Protection andDevelopment of the Marine Environment of the Wider CaribbeanRegion - the "Convention area" means the marine environment of theGulf of Mexico, the Caribbean Sea and the areas of the Atlantic Oceanadjacent thereto, south of 30 deg north latitude and within 200 nauticalmiles of the Atlantic coasts of the States referred to in article 25 of theConvention. The Cartagena Convention was adopted on 24 March 1983and entered into force on 11 October 1986 as the legal instrument for theimplementation of the Caribbean Action Program. It is a regionalframework agreement negotiated under the auspices of the Regional SeasProgram of the United Nations Environment Program (UNEP). It sets outgeneral legal obligations to protect the marine environment of the Gulf ofMexico, Straits of Florida, Caribbean Sea, and immediately adjacent areasof the Atlantic Ocean -- collectively known as the Wider Caribbean Region.The United States became a Party to the Cartagena Convention in 1984.The Convention and its three Protocols constitute a legal commitment bythe participating governments to protect, develop and manage theircommon waters individually or jointly. The Convention is a frameworkagreement setting out the political and legal foundations for actions to bedeveloped. These actions are directed by a series of operational Protocolsdesigned to address special issues and to initiate concrete actions. Thethree protocols supporting the Convention are the Oil Spill Protocol, theSpecially Protected Areas and Wildlife Protocol (SPAW), and the LandBased Spills Protocol (LBS). RAC/REMPEITC-Carib is the Regional ActivityCenter established under the Oil Spill Protocolcartilage - a type of connective tissuewhere the functional component is therubbery intercellular matrix that is secretedby cartilage-producing cells calledchondrocytes. Cartilage exists in severalforms, from glassy to fibrous in appearanceA microscopic section ofhyaline cartilage. Thecartilage cells(chondrocytes) exist inlittle cavities (lacunae) inthe smooth, glassycartilaginous matrix.(Photo: NIH/NationalCancer Institute)cartilagenous - pertaining to or composed of cartilage; of theconsistence of cartilage or gristlecartography - the science, technology, and art of making maps andcharts. Cartography includes all the steps necessary to produce a map:planning, aerial photography, drafting, editing, color separation, andmulticolored printinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (10 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacaruncle - a fleshy outgrowthCASI (Compact Airborne Spectrographic Imager) - a digital airbornemultispectral sensorcast net - a circular net with weights attached to the perimetercatabolism - a destructive metabolic process by which organisms convertsubstances into excreted compoundscatadromous species - a species thatspawns in the ocean but lives parts of itslife in fresh water, e.g., American eelThe American eel is acatadromous species thatspawns in the ocean, nearthe Sargasso Sea, butgrows to maturity infreshwater streams.catalysis - the acceleration of a chemical reaction by a catalyst.catalyst - a substance that accelerates a chemical reaction, but is notconsumed or changed in the processcatamaran - a type of boat consisting of two hulls joined by a frame.Catamarans can be sail or motor poweredcatastrophe - an event that causes sudden decreases of population sizeor the entire elimination of subpopulationscatch per unit effort - the number of fish caught by an amount of effort.Typically, effort is a combination of gear type, gear size, and length oftime the gear is used. Catch per unit of effort is often used as ameasurement of relative abundance for a particular fish; the total catchdivided by the total amount of effort used to harvest the catchcatchment - the area drained by a river or body of waterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (11 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacategorical excusion - a category of actions that do not individually,collectively, or cumulatively have a significant effect on the environmentand that have been found to have no such effect in procedures adopted bya federal agency in implementation of these regulations and for which,therefore, neither an environmental assessment nor an environmentalimpact statement is requiredcategory - in taxonomy, any rank within the classification hierarchy, e.g.,family, subfamily, subspeciescatenation - linking of multiple copies of a macromolecule to each othercation - a particle that carries a positive electrical charge. The cation getsthis positive charge from losing negatively charged electronscaudal - pertaining to the tail; denoting aposition more toward the tail of an animal,e.g., the tail fin of a fish is called the caudalfin. Caudal vertebrae are the vertebraewhich extend into the tail of an animalCaudal fin of a shark. Thedorsal lobe of the caudalfin is elongated. (Photo:Copyright CorelCorporation)caudal fan - in crustaceans, a fan-shaped structure formed by thelaterally expanded uropods and telson. The caudal fan functions inswimming, steering and balancing; also called "tailfan"caudal peduncle - the narrowest portionof a fish's body, located just posterior tothe anal fin and just anterior to the caudalfinThe caudal peduncle of thespotted unicorn fish (Nasobrevirostris) is locatedbetween the anal andcaudal fins. (Photo:Copyright Richard C. Wass)cavate - cave-likehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (12 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacay - a small, low coastal island or emergent reef of sand or coral; flatmound of sand and admixed coral fragments built upon a reef flat or justabove high tide level. A synonym of key, as in the Florida KeysCD-ROM (Compact Disk-Read Only Memory) - an optical medium. ACD-ROM 5.25-inch disk can hold about 650 megabytes of informationCDHC (Coral Disease and Health Consortium) - in response to thedramatic increase of coral diseases observed over recent years, the U.S.Coral Reef task force (2002) recommended the creation of the CDHC froma cross-section of internationally recognized experts in coral diseases,biomedical and veterinary sciences, pathology, chemistry, biology,biotechnology, and marine management. It organizes and coordinates thescientific resources of the U.S. and its territories to meet the challenge ofglobally declining coral reefscDNA (complementary DNA) - a strong, cloned DNA copy of otherwisefragile mRNA, made using reverse transcriptase. A cDNA is so-calledbecause its sequence is the complement of the original mRNA sequence.However, when double-stranded cDNA is synthesized, it contains both theoriginal sequence and its complementcDNA library - a collection of cDNA clones that were generated in vitrofrom the mRNA sequences isolated from an organism, or a specific tissueor cell type, or populationcell - the smallest unit of living matter. Allorganisms are composed of cells and cellproducts (Cell Theory). Organisms existeither as single cells (unicellular) or asmulticellular unitsThis example of a singlecelledorganism, thedinoflagellateGambierdiscus toxicus,produces toxins includingciguatoxin and maitotoxin.The toxins are associatedwith ciguatera fishpoisoning.cell adhesion - adherence of cells to surfaces or to other cellscell body - the enlarged portion of a neuron which contains most of theorganelleshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (13 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacell culture - the in vitro growth of cells derived from multicellularorganisms. The cells are usually of one typecell cycle - the period between the formation of a cell by the division ofits parent cell and the formation of two new cells by cell divisioncell division - the separation of one cellinto two daughter cells, involving bothnuclear division (karyokinesis) andsubsequent cytoplasmic division(cytokinesis). Genetically, the daughtercells are identical to the mother cell(mitosis); however, in gametogenesis(meiosis), the resultant daughter cells(gametes) have the chromosome numberreduced by one-halfCell division by mitosis. A­B: Prophase - thereplicated (daughter)chromosomes(chromatids) undergoextensive condensation.They are greatly thickenedand shortened but are stillcontained within thenuclear membrane.Prophase ends with thesudden beakdown of thenuclear membrane. C:Metaphase - the replicatedchromosomes convergetoward the center of thecell. D: Anaphase - sisterchromatids split at theircentromeres. Thesedaughter chromosomesthen begin to separatefrom each other, andmove toward one of thetwo spindle polar regions.E-F: Telophase/Cytokinesis - Chromatidsarrive at opposite poles ofcell, and new membranesform around the daughternuclei. The chromosomesdisperse and are no longervisible. Cytokinesis or thepartitioning of the cell mayalso begin during thisstage. In animal cells,cytokinesis results when afiber ring composed of aprotein (actin) around thecenter of the cell contractsand pinches the cell intotwo daughter cells, eachwith one identical nucleus.Chromosomal replicatonoccurs during theinterphase beween mitoticactivities. (Photo: Dept. ofBiology, University of NewMexico)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (14 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacell fusion - the formation of a hybrid cell produced by the fusion of twodifferent cellscell line - cells that have been extracted from human or animal tissueand now grow and replicate continuously outside the living organismcell membrane - the structure enveloping a cell, enclosing the cytoplasmand forming a selective permeability barrier which permits the passage ofsolvents and solutes into and out of cells. It consists of lipids, proteins andsome carbohydratescell wall - an extracellular material that forms the outer surface of plant,fungus, and certain bacterial cells. It is external to the cell membrane andserves in a structural and supporting role. The cell wall is composedprimarily of cellulose and lignin in plants, chitin in Fungi, andpeptidoglycans in bacteriacellular differentiation - genetically-induced divergence in the structureand function of cells as they become specialized during a multicellularorganism's developmentcellular respiration - the transfer of energy in cells by the catabolism ofmolecules to produce ATP, during which oxygen is consumed and carbondioxide produced. It occurs in the mitochondria of eukaryotescellulolytic enzyme - an enzyme that acts upon cellulosecellulose - a polysaccharide that is composed of unbranched chains ofglucose. It is the major structural carbohydrate of plantscement - the chemically precipitated calcium carbonate present in spaceswithin skeletons or between grains of internal sedimentcenospecies - species that can interbreedCenozoic - the current geologic era, which began 66.4 million years agoand continues to the presentcensus - the enumeration of all the individuals in a populationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (15 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCensus of Marine Life (CoML)/Census of Coral Reefs (CReefs)Project - a research initiative to conduct a taxonomically diversifiedcensus of coral reef ecosystems throughout the globe. This internationalpartnership, led by NOAA’s Pacific Islands Fisheries Science Center, theAustralian Institute of Marine Science, Scripps Institution ofOceanography, and the Hawai´i Institute of Marine Biology, will expandtropical taxonomic knowledge (with a particular focus on understudiedspecies), increase the exchange of coral reef ecosystem data dispersedthroughout the globe, and develop new and innovative technology andsampling strategies, as well as contribute to the CoML barcode initiative.CReefs plans to work closely with the NOAA Coral Reef ConservationProgram (CRCP) and other organizations on outreach and education,collaboration with other existing coral reef efforts, and collection andunification of data into the Ocean Biogeographic Information Center forresearch, management, and preservation purposescenter line - the imaginary line running from bow (front) to stern (rear)along the middle of a vesselcenter of genetic diversity - a region where a particular taxonomicgroup of organisms exhibits greater genetic diversity than it doeselsewherecenter of origin - the area in which a given taxonomic group oforganisms originated and from which it has subsequently spreadCentigrade Temperature Scale - a thermometric scale in which 0degrees C (Celsius) marks the freezing point of water and 100 degrees Cindicates the boiling point of water at sea levelcentiMorgan - the unit of genetic map distance between two loci thatshow one (1) percent recombinationcentrad - toward the center or interiorcentradenia - a spongy mass formed by the coenosarc in some types ofsiphonophore colonies, which is partly hepatic in function, and partlyexcretorycentral chord - the central part of the axis of an octocoral composed ofgorgonin or gorgonin permeated with calcareous materialhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (16 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCentral Dogma (of molecular biology) - the principal statement of themolecular basis of gene action. Genetic information is stored in andtransmitted as DNA. Genes are expressed by being copied as RNA( transcription), which is processed into mRNA (messenger RNA) viasplicing and polyadenylation. The information in mRNA is translated into aprotein sequence using a genetic code to interpret three-base codons asinstructions to add one of twenty amino acids, or to stop translation; ormore simply put, DNA carries the genetic information which is transcribedto RNA and subsequently translated to protein. Francis Crick, the codiscovererof the double helix structure of DNA, coined the term "CentralDogma" in 1958 to characterize the all-important cellular processeswhereby DNA is "transcribed" into RNA and RNA is "translated" into proteincentrifugation - the spinning of a mixtureat very high speeds to separate substancesof different densitiesA centrifuge used to "spindown" materials.centriole - one of two small cylindrical cell organelles composed of ninetriplet microtubules. They form the asters during cell divisioncentrolecithal - a type of egg cell that has its yolk in the very center ofthe cytoplasm, such that the initial meroblastic cleavage of the zygotehappens all around the embryo. Most arthropods have centrolecithal eggscentromere - the center part of a chromosome that appears ‘pinched’, inbetween the short arm (p) and the long arm (q). The centromere holdsthe two chromatids together, and during cell division (mitosis) it is the siteof attachment for the spindle fiberscentrosome - a granular region of a cell which contains two centriolesand is a center of microtubule organization during the division of thenucleuscentrum - a center or central masshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (17 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacephalic - pertaining to the headcephalization - the localization of neural coordinating centers andsensory organs at the anterior end of the bodyCephalopoda - a class of the phylumMollusca that includes squids, octopods,cuttlefishes and nautili. Many species areinhabitants of coral reefsSquid (class Cephalopoda)with egg mass.cephalopodium - in cephalopods (octopi, squids) the head region,consisting of head and tentacles; a muscular mass enabling the mollusk tomove, with brain and sense organs at the front end, which evolved into afoot for gastropods and bivalves, or into tentacles and funnel forcephalopodscephalothorax - the region of the body in decapod crustaceans that iscovered by the carapace, with the boundary between the fused head andthorax indicated by the cervical groove. In lobsters, the cephalothorax iscalled the "body"; in shrimps, it is called the "head"ceras - one of many multifunctional hornor lobe-shaped or leaf-like process on theback or side of a nudibranch mollusk (seaslug). It has a major function as arespiratory organ (a gill), and with a branchof the digestive gland, it also serves as anorgan for the exchange of gases and othermolecules with the blood. The ceras alsostores stinging nematocysts in a structurecalled the cnidosac, from the cnidariansupon which they feed, which gives it adefensive function. Its ability to changecolor also gives it a protective camouflagefunctionCerata (plural of ceras) ofAeolidiella foulisi showingthe brown duct of thedigestive gland and thewhitish cnidosac at the tip.cerebral ganglion - in invertebrates, one of a pair of ganglia (or fusedmedian ganglion) situated in the head or anterior portion of the body;alsocalled the the "dorsal ganglion" or " cerebroganglion"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (18 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacerioid growth form - a coral growth form in which the coral colony iscomposed of corallites united directly to one another by fused walls. Thecorallites are juxtaposedcerulean - dark blue colorcetacean - a marine mammal of the OrderCetacea. The Cetacea includes whales,dolphins and porpoisesThe killer whale is actuallya dolphin in the cetaceanfamily, Delphinidaecf - an abbreviation for the Latin word 'confer', meaning "compare"chaeta - a stiff hair or bristle, made of chitin, characteristic of annelidworms. In the earthworm they occur in small groups projecting from theskin in each segment and function in locomotion. The chaetae of marinepolychaete worms are borne in larger groups on paddle-like appendagescalled parapodiaChaetodontidae - a family of fishes(butterfly fish) whose number and behaviormay serve as indicators of reef healthA pair of butterfly fishes(Chaetodontidae). Theirpresence and behaviorserve as biologicalindicators of reef health.chain transect - a linear transect where a chain is used to mark the lineunder study. By following the surface contour of the reef, chain transectsprovide data that may be used to calculate the estimated spatial index(the ratio of reef surface contour to linear distance of the reef)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (19 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCHAMP (Coral Health And Monitoring Program ) - a NOAA programwhose mission is to provide services to help improve and sustain coralreef health throughout the world. Long term goals are: establish aninternational network of coral reef researchers for the purpose of sharingknowledge and information on coral health and monitoring; provide nearreal-time data products derived from satellite images and monitoringstations at coral reef areas; provide a data repository for historical datacollected from coral reef areas; and add to the general fund of coral reefknowledgechannel - a deep and relatively narrow body of water (as in a river,harbor, or a strait linking two larger bodies) that allows the best passagefor vessels; an open conduit either naturally or artificially created whichperiodically or continuously contains moving water, or which forms aconnecting link between two bodies of water. River, creek, run, branch,and tributary are some of the terms used to describe natural channels.Canal and floodway are some of the terms used to describe artificialchannels.character - in taxonomy, any attribute of organisms used for recognizing,differentiating or classifying taxacharacter displacement - the process by which two closely relatedspecies, with overlapping ecological requirements, interact so as to causeone or both of them to diverge evolutionarily in one or more traits. Theydiffer more when they co-occur than when they do notcharismatic megafauna - large animals (usually vertebrates) that evokesentimental support from the general public, for example, porpoises,sealsand sea lions, marine turtles, and manateesCharles Law - under conditions of constant pressure and quantity, thereis a direct relationship between the volume and absolute temperature foran ideal gaschela - a pinching claw of a decapodcrustacean, composed of a moveablefinger, the dactylus, and a fixed finger, adistal extension of the propodusThe large pinching claw ofthis crustacean is thechela. The entire legbearing the chela istermed the cheliped.(Photo: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (20 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCheliceramorpha - an order of arthropodsthat includes horseshoe crabs, daddylonglegs,and extinct "sea-scorpions,spiders and scorpions, mites and ticks, "Most of its marine representatives areextinct, but were prominent in the PaleozoicThe horseshoe crab is anarthropod in the orderCheliceramorphacheliform - pincer-shapedcheliped - one or more pairs of thoraciclegs of decapod crustaceans that terminatein a chela, or claw. The entire cheliped isoften referred to as a clawA cheliped of thisAmerican lobster(Homarus americanus) is aleg bearing a pinchingclaw.Cheloniidae - a family of hard-shelled turtles that include the greenturtle, loggerhead turtle, hawksbill turtle, leatherback turtle, kemps ridleyturtle, olive ridley turtle, and flatback turtle. The leatherback turtle is theonly sea turtle not in this familychemical bond - the link between two atoms within a molecule. Differenttypes of chemical bonds include hydrogen bonds, covalent bonds, andionic bondschemical equilibrium - the state in which a chemical reaction proceedsat the same rate as its reverse reaction; the rates of the forward andreverse reactions are equal, and the concentration of the reactants andproducts stop changing. When this condition is met, there is no change inthe proportions of the various compounds involved, and the reactionceases to progresschemical evolution - the chemical changes that transformed simpleatoms and molecules into the more complex chemicals needed for theorigin of lifehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (21 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachemiluminescence - a chemical reactionthat gives off energy in the form of lightinstead of heatCommercially availablelight sticks contain asolution in a glass vial.When the vial is broken, asecond solution mixes withthe first and light(chemiluminescence) isgenerated. Different dyesgive off different colorswhen they are caused tofluoresce by the light ofthe chemiluminescentreaction. (Photo: AmericanChemical Society)chemoautotroph - an organism that utilizes oxidation of inorganicchemicals for its energy and carbon from inorganic carbon dioxide for cellgrowth; these organisms are also called chemolithotrophschemocline - a sharp gradient in chemical concentrationchemokinesis - the response by a motile cell to a soluble chemical thatinvolves an increase or decrease in speed, or frequency of movement, or achange in the frequency or magnitude of turning behaviorchemoorganotroph - an organism that obtains energy from theoxidation of organic compounds and cellular carbon from preformedorganic compoundschemoreceptor - a receptor that is stimulated by the presence of certainchemical substanceshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (22 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachemosynthesis - the process wherebychemical energy is used to synthesizeorganic compounds from inorganiccompounds, e.g., the oxidation of ammoniato nitrite by nitrifying bacteriaThe deep-sea hot-springenvironment supportsabundant and bizarre sealife, including tube worms,crabs, giant clams, all ofwhich depend uponchemosynthesis for theirnutrition. (Photo: USGS)chemotaxis - a unidirectional response of motile cells or organisms inwhich the direction of movement is affected by the gradient of a diffusiblesubstancechemotrophs - organisms (usually bacteria) that derive energy frominorganic reactions; also known as chemosynthetic organismschi-square - a statistical technique whereby variables are categorized todetermine whether a distribution of scores is due to chance orexperimental factorschi-square distribution - a distribution in which a variable is distributedlike the sum of the the squares of any given independent random variable,each of which has a normal distribution with a mean of zero and avariance of onechi-square test - a statistical test based on the comparison of a teststatistic to a chi-square distribution. It is used to reject or not reject thehypothesis that two or more population distributions do not differ fromone anotherchimaera - a cartilagenous fish that has a compressed body and rodentliketeeth. Chimaeras are closely related to sharks and rays (classChondrichthyes, subclass Holocephali), but have larger heads and eyes,the mouth is more towards the front of the head, the gills are protectedby a gill cover, the skin is smooth, and most species have a whip-like tail;also called ghost sharks or ratfishchimera - the individual produced by grafting an embryonic part of oneindividual onto an embryo of either the same or of a different specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (23 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachimeric protein - a human-engineered protein that is encoded by anucleotide sequence made by splicing together two or more complete orpartial geneschitin - a polysaccharide made up of chains of N-acetyl-D-glucosamine, aderivative of glucose. Chitin is structurally very similar to cellulose andserves to strengthen the supporting structures of various invertebrates. Italso occurs in fungichiton - a marine mollusk of the SubclassPolyplacophora, which contains about 600species of sedentary animals commonlyknown as chitons.They are found fromshallow waters to depths of about 400 m. Achiton has a broad foot and a shellconsisting of eight overlapping platesA dorsal view of a chitonshell. Chitons aredistinguished from allother mollusks by thepresence of their convexshell, which is divided intoeight articulating plates(valves). (Photo: RickGillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)chlorocruorin - a greenish iron-containing respiratory pigment dissolvedin the blood plasma of certain marine polychaete worms. It may give thegreen color to the blood of these wormschlorofluorocarbons (CFC) - gases that can be dissociated by solarradiation, which release chlorine, which in turn destroys ozonechlorophyll - a green pigment present in green plants and cyanobacteria.Chlorophyll is essential in the transformation of light energy to chemicalenergy in photosynthesischlorophyll a - the major photosynthetic pigment found in all oxygenevolvingphotosynthetic organisms (higher plants, and red and greenalgae)chlorophyll b - the chlorophyll generally characteristic of higher plantsand green algae .It is absent in other types of algaehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (24 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachlorophyll c - the chlorophyll present in brown algae, diatoms, andflagellateschlorophyll d - the chlorophyll present in red algae, together withchlorophyll achloroplast - a disk-like organelle with a double membrane, found insome protists and all green plant cells, that contains chlorophyll and is thesite of photosynthesischlorosis - the yellowing or bleaching ofplant tissues due to the loss of chlorophyllor failure of chlorophyll synthesis. It can becaused by insuffient light or nutrients, andalso by certain diseasesDisease symptoms(necrotic lesionssurrounded by chlorosis)caused by a bacterialinfection. (Photo: Dr.Roger Thilminy and ShengYang He, Michigan StateUniversity)choanocyte (collar cell) - a flagellatedcell that lines the interior of the centralcavity (spongocoel) of a sponge.Choanocytes have a tubular collar with anextended flagellum that faces thespongocoel and creates currents that forcewater into the interstices of the sponge.Suspended food particles, such as plankton,are trapped by the choanocytes and passedto an amoebocyte that carries the food toother cellsDiagram of choanocyte.The flagella create watercurrents that bringnutrients into the interiorof a sponge. (Diagram: U.S. EnvironmentalProtection Agency)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (25 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachoanocyte chamber - in sponges, a cavity lined with choanocytes andlocated between incurrent and excurrent systemschoanoderm - in sponges, a surface lined with choanocyteschoanosome - the internal region of a sponge, including the choanocytechambersChondrichthyes - the class ofcartilaginous fishes that includes sharks,rays, skates, and chimaeras. Their skeletonis composed of cartilage, not boneA manta ray, a member ofthe class Chondrichtyes.(Photo: NOAA)Chordata - an animal phylum that includessea squirts (tunicates), lampreys andhagfishes, fishes, amphibians, reptiles,birds and mammals. Many species ofmarine chordates play prominent roles inthe ecology of coral reef ecosystemsThe phylum Chordataincludes the mammalssuch as this largehumback whale(Megaptera novaeangliae).chorion - a thick, vascularized extra-embryonic membrane of amnioteembryos that forms around the entire undersurface of the eggshell inbirds and reptiles, and in direct contact with the uterine wall in mammals.It unites with the allantois to form the major structure for exchangebetween the embryo and the outside (birds and reptiles) or the maternalcirculation (mammals)chorology - the study of the spatial distribution of organismschory - a suffix meaning plant dispersal by a specified agency (animals,wind, water, etc)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (26 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataChristmas tree coral - a recentlydiscovered (2002) deep water black coral(Antipathes dendrochristos) observed ondeep rocky banks off southern California.The species, which was described in 2005,forms bushy colonies that grow up to tothree meters in height and width, andresembles ornamented Christmas trees.Like many other deep water corals,Christmas tree corals support a diversebiological assemblageChristmas tree coral(Antipathesdendrochristos)photographed duringsurveys of deepwaterrocky banks off southernCalifornia.(Photo: MarkAmend/NOAA)chromatid - each of a pair of identical DNA molecules after DNAreplication, joined at the centromerechromatin - replicated DNA and associated proteins; highly folded ribbonlikecomplexes of deoxyribonucleic acid (DNA) and a class of proteinscalled histones; protein/DNA complex making the chromosomechromatophore - a cell whose cytoplasmcontains pigment granules that can berapidly concentrated or dispersed,producing an overall effect of altering thecolor, color pattern or tone of the whole orpart of an animalThis flounder is rarelynoticed unless disturbedbecause of its remarkableability to change color tomatch the substrate, byconcentating or dispersingpigment granules in itschromatophores.chromocyte - a pigmented cellchromoplast - a plastid containing pigments other than chlorophyll,usually yellow or orange carotenoidshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (27 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachromosomal aberration - any change in chromosome structure ornumber. Although chromosomal abberations can be mechanisms forenhancing genetic diversity, such alterations are usually deleterious or illadaptive;includes deficiency, duplication, inversion, translocation,aneuploidy, polyploidy, or any other change from the normal patternchromosomal deletion - a mutation resulting from the loss of a smallsegment of DNAchromosomal mutation - a mutation involving a long segment of DNA.These mutations can involve deletions, insertions, or inversions of sectionsof DNA. In some cases, deleted sections may attach to otherchromosomes, disrupting both the chromosomes that loses the DNA andthe one that gains it; any type of change in the chromosome structure ornumberchromosome - one of the threadlike"packages" of genes and other DNA in thenucleus of a cell. Different species oforganisms have different numbers ofchromosomes. In sexually reproducingspecies, each parent contributes onechromosome of each pair, so offspring gethalf of their chromosomes from thematernal parent and half from the paternalparent. Bacterial cells do not possess anucleus, therefore their chromosomes arelocated in the cellular cytoplasmHighly magnified view ofcell chromosomes.chromosome aberration - changes in chromosome structure orchromosome numberchronic - long term or frequently recurringchronobiology - the field of biology concerned with the timing ofbiological events, especially repetitive or cyclic phenomena in individualorganisms.chronograph - an instrument for recording the moment of an eventchronology - the age-depth relationship in ice, sediment, or anotherdeposit. Ages are usually measured for discrete samples, and the ages ofintermediate samples are interpolated between samples with measuredageschronometer - an instrument for measuring timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (28 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datachub - any species of bony fishes in thefamily Kyphosidae. Chubs have compressedoval bodies with small heads.They havesmall mouths with fine teeth and feedmainly on algae; some are carnivorous,feeding on benthic invertebrates. Theycongregate in great numbers for pelagicspawning. Kyphosids are distributed in thetemperate and tropical inshore waters ofthe Atlantic, Indian and Pacific Oceans,where they are also known as sea chubs,pilotfishes, rudderfishes, drummers, and byother common namesThe grey chub, Kyphosussandwicensis, is aschooling species that isusually found in shallowrocky areas throughoutthe Indo-Pacific. (Photo:James Watt)ciguatera - a food poisoning of humanscaused by eating some species of tropicalfishes whose flesh is contaminated withtoxins obtained through the food chainCiguatera food poisoningmay be contracted byeating the flesh of acontaminated barracuda.ciguatoxin - a toxin found in flesh ofmarine animals, especially some fishes, atsome times, in some localities. It isprobably of algal origin and causesparesthesia, gastrointestinal symptoms,neuromuscular blockade, and respiratoryparalysis due to interference withmembrane functionBarracuda (Sphyraena sp.)are often the culprits inciguatera food poisoning,caused by ciguatoxin.(Photo: Copyright CorelCorporation)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (29 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacilia - short, motile, generally microscopic, hairlike projections found onmany protists and larvae of some invertebrates. Cilia are used forlocomotion, the generation of a current, or filter feeding; A cilium is madeup of microtubules and has basically the same internal structure as aflagellum. Movement is caused by the interactions of the microtubules. Inhigher animals, cilia are found projecting from cells that line certain tubesand passages, such as the tracheae (windpipe) of mammalsciliary - relating to any cilia or hairlike processes; can relate to musclesconcerned with visual focusingciliated epithelium - any epitheliumhaving motile cilia on the free surfacePseudostratified ciliatedcolumnar epithelium - theciliated epithelium thatlines the trachea(windpipe) of mammals.(Photo courtesy of Dr.Franklin S. Carman III,donated from URL: http://tooldoc.wncc.edu)Ciliophora - a group of protists bearing ciliaThe stalked ciliate,Stentor. (Photo: JonHouseman/BIODIDAC)cinclide - one of many blister-like openings in the lower part of the bodycolumn of some anemones, through which the animal expels long, threadlikeacontiacirca - about; aroundhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (30 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacircadian - being, having, characterized by, or occurring in approximately24 hour periods or cyclescircadian rhythm - the regular recurrence, in cycles of about 24 hours,of biological processes or activitiescircinate - ring-shapedcirculatory system - the system that contains the heart and the bloodvessels (arteries, capillaries, veins) and moves blood and other circulatingfluids throughout an organism's body. This system delivers oxygen andnutrients to the cells, and it helps rid them of waste products. Circulatorysystems can be open or closed. Open systems lack capillaries and theblood perfuses through the tissues of the animal’s body. Closed systemshave capillary beds which connect arteries and veins. The blood is alwayscontained in a vessel.circum - a prefix meaning "around"circumesophageal - pertains to structures encircling the esophaguscircumesophageal commissure - the major commissure (junction) ofthe nervous system of many invertebrates to which are connectedanteriorly and posteriorly directed nerves and nerve chords. It iscomposed largely of nerve fibers and associated ganglia. This structureencircles the esophagus; also called " nerve ring"circumesophageal connective - one of the nerve strand connectives oneach side of the esophagus connecting the supraesophageal ganglia andsubesophageal ganglia of arthropods, annelids and brachiopodscircumesophageal nerve ring - anterior concentration of nervous tissuein several invertebrate groups, such as mollusks, annelid worms,sipunculids (peanut worms), and echiurans (spoon worms or innkeeperworms)cirrus - a slender, flexible appendage or part of an organism, usuallyhaving a tactile functioncistron - a DNA sequence that codes for a specific polypeptide; analternate name for a genehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (31 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCITES (Convention on International Trade in Endangered Species)- the ‘Washington’ Convention on International Trade in EndangeredSpecies of Wild Fauna and Flora, more commonly known as CITES, aimsto protect certain plants and animals by regulating and monitoring theirinternational trade to prevent it reaching unsustainable levels. There aremore than 150 Parties to the Convention. The CITES Secretariat isadministered by the United Nations Environment Programme (UNEP).CITES regulates international trade in over 30,000 species, of whichapproximately 25,000 are plantscitreous - lemon colorcitric acid cycle - see: Krebs cycleclade - a group of species with a common evolutionary ancestrycladist - a systematist who attempts to classify life forms according totheir evolutionary relationships, not just overall similaritycladistic distance - the number of branching points between any twonodes on a phylogenetic treecladistic species - the concept of species in which a species is a lineageof populations between two phylogenetic branch points (speciation events)cladistics - the systematic classification of groups of organisms on thebasis of the order of their assumed divergence from ancestral speciescladogenesis - the evolutionary process whereby one species evolvesinto two or more speciescladogram - a tree-like diagram, resulting from a cladistic analysis, whichdepicts a hypothetical branching sequence of lineages leading to the taxaunder consideration. The points of branching within a cladogram are callednodes. All taxa occur at the endpoints of the cladogramclasper - a rod-like modification of thepelvic fin of a male elasmobranch that isused to transfer sperm into the femaleduring matingNOAA scientist measuringthe length of a rays'sclasper.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (32 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataclass - in taxonomy, a category just beneath the phylum and above theorder; a group of related ordersclass interval - one of the ranges intowhich data in a frequency distribution table(or histogram) are binned. The ends of aclass interval are called class limits, and themiddle of an interval is called a class mark.In plotting a histogram, begin by dividingthe range of all values into non-overlappingclass intervals, in such a way that everypiece of data is contained in some classintervalA histogram in which thepopulation of data aregrouped into nonoverlappingclass intervals.classical conditioning - a form of associative learning, in which ananimal recognizes that two or more events are related. The animalperforms a behavior in response to a substitute stimulus rather than thenormal stimulusclassification - a system of nested hierarchical categories used toefficiently store information about biological diversityclathrate - resembling an open latticework; a chemical substanceconsisting of a lattice of one type of molecule trapping and containing asecond type of molecule. For example, a clathrate hydrate involves aspecial type of gas hydrate that consists of water molecules enclosing atrapped gas, such as methaneclavate - club-shapedClean Water Act (CWA) - an act passed by the U.S. Congress to controlwater pollution. Growing public awareness and concern for controllingwater pollution led to enactment of the Federal Water Pollution Control ActAmendments of 1972. As amended in 1977, this law became commonlyknown as the Clean Water Act. The Act established the basic structure forregulating discharges of pollutants into the waters of the United States. Itgave EPA the authority to implement pollution control programs such assetting wastewater standards for industry. The Clean Water Act alsocontinued requirements to set water quality standards for all contaminantsin surface waters. The Act made it unlawful for any person to dischargeany pollutant from a point source into navigable waters, unless a permitwas obtained under its provisions. It also funded the construction ofsewage treatment plants under the construction grants program andrecognized the need for planning to address the critical problems posed bynonpoint source pollutionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (33 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacleaner wrasse - a small reef fish of the wrasse family (Labridae) thatfeeds on ectoparasites of larger "host" fishes. It establishes a "cleaningstation" at a specific location on the reef where a variety of host fishesassemble and await the cleaner wrasse's servicescleaning behavior - mutualistic behaviorin which larger animals, usually fishes,permit smaller animals, usually otherspecies of fishes or invertebrates, to cleanthem of external parasitesPederson's CleaningShrimp (Periclimenespedersoni) on a reef in theVirgin Islands. This small(to 1 inch) shrimp favorshabitat and a steady foodsupply offered by Ringedand Giant Caribbeananemones.cleaning station - a site visited by fishes where, in a mutually symbioticrelationship, cleaning shrimp or fish remove parasites from their bodiescleavage - the early mitotic cellulardivisions of the fertilized egg (zygote)A four-cell stage of acleaving sea urchinembryo. (Photo: CopyrightDr. Leland Johnson,Augustana College, Illinois)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (34 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCLEO (Coral Literature, Education & Outreach) - the CLEO project isdesigned to provide easy access to gray literature and pre-1990'sliterature on the coral reef environments near the Coral Reef EarlyWarning System (CREWS) monitoring stations to support education,research and management objectives. The Education modules leveragetechniques developed at NOAA/AOML in the Explorer of the Seas, CoralHealth and Monitoring and CREWS programs under which knowledgetransfer of oceanographic instrumentaion and coral reef processes havebeen developed. Education modules for middle school students engage thestudents in oceanographic instrumentation, classroom experiments anduse of data, and the live Coral Cam observationsclient - a software program that is used to contact and obtain data from aserver software program on another computer, often across a greatdistance. Each client program is designed to work with one or morespecific kinds of server programs, and each server requires a specific kindof Client. A web browser is a specific kind of clientclimate - long-term characteristics of weatherclimate change - the long-term fluctuations in temperature,precipitation, wind, and all other aspects of the Earth's climate. It is alsodefined by the United Nations Convention on Climate Change as "changeof climate which is attributed directly or indirectly to human activity thatalters the composition of the global atmosphere and which is in addition tonatural climate variability observed over comparable time periods"climate variability - changes (variability/trends) in the long-termcharacteristics of weatherclimate-induced bleaching - coral bleaching as a result of changingclimate patterns, e.g., temperatureclimax - the final stage in ecological succession that is able to persist inthe absence of environmental changeclinal speciation - a form of allopatric speciation in which a vicariantevent interrupts gene flow in a former clinecline - the gradual variation, in a character of a species, in geographicalspacecloaca - the common passage for fecal, urinary and reproductivedischarge in most lower vertebratesCLOD (Coralline Lethal Orange Disease) - a disease which infectscoralline algaeclone - an individual genetically identical to the parent organism, createdby the splitting off or budding of cells from the parent organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (35 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataclone cells - a group of genetically identical cells all descended from asingle common ancestral cell by mitosis in eukaryotes, or by binary fissionin prokaryotes. Clone cells also include populations of recombinant DNAmolecules all carrying the same inserted sequence of basescloned DNA - exact copies of DNA segments prepared by usingrecombinant DNA technologycloning - the process of asexual reproduction in an otherwise multicellularorganismcloning vector - DNA molecule originating from a virus, a plasmid, or thecell of a higher organism into which another DNA fragment of appropriatesize can be integrated without loss of the vector's capacity for selfreplication;vectors introduce foreign DNA into host cells, where the DNAcan be reproduced in large quantities. Examples are plasmids, cosmids,and yeast artificial chromosomes; vectors are often recombinantmolecules containing DNA sequences from several sourcesclosed circuit scuba - a diving apparatus which allows divers to rebreatheexhaled air after removal of carbon dioxide and addition ofsupplemental oxygen. It is not generally used by recreational scuba diversclosed circulatory system - a circulatory system in which blood flowsthrough blood vessels at all times. Blood flows from arteries to capillariesand through veins, but the tissues surrounding the vessels are not directlybathed by blood. Some invertebrates and all vertebrates have closedcirculatory systemsclosed system - a system in which no matter or energy can leave orenter from the outsideClostridium - a genus of Gram positive anaerobic spore-forming bacteria.Clostridium includes common free-living bacteria as well as importantpathogens of humans and marine animalsclupeoid fish - any soft-rayed, bony fishspecies belonging to the orderClupeiformes. These include herrings,shads, wolf herrings, sardines, andanchoviesA clupeoid fish, theAtlantic thread heringOphisthonema oglinum(Photo: NOAA)clupeoid fish poisoning - a very serious form of fish poisoning causedby eating clupeotoxic fishes; also called clupeotoxismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (36 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataclupeotoxic fish - fishes in the orders Clupeiformes (herrings andherring-like fishes), and Elopiformes (ladyfishes and tarpons) whose fleshmight contain a toxin, clupeotoxin, by ingesting certain dinoflagellateswhich contain the toxinclupeotoxin - the poison in clupeotoxic fishes. It is a neurotoxin,palytoxin, found in marine dinoflagellates and presumably ingested by thefishcluster analysis - a multivariate statistical technique for solvingclassification problems. The object is to sort items into groups such thatthe degree of association is strong between members of the same clusterand weak between members of different clustersclutch - a group of eggs laid at the same timecnida - an organelle located in cnidocytes that is capable of eversion.There are three types of cnidae: nematocysts, spirocysts, and ptychocysts.Cnidaria - a multicellular animal phylum,with a tissue grade of construction, thatcontains the stony (hard) corals,anemones, sea fans, sea pens, hydroids,and jellyfishAn Atlantic coastcnidarian, a dahlia seaanemone (Tealia sp.)(Photo: Andy Bruckner)cnidocyte - a stinging cell of jellyfish, hydroids, sea anemones andcorals. The cnidocyte contains the eversible cnida. The most common typeof cnidocyte is the stinging structure also known as the nematocyst orcnidocyst Cnidocytes are located throughout the epidermis, but areespecially abundant on the tentaclescnidoglandular band - the distal rim or free margin along a cnidarianmesentaryhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (37 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacnidosac - a sac located in a ceras of anudibranch gastropod which containsundischarged nematocysts (obtainedthrough feeding upon cnidarians) passedfrom the slug's digestive system. When apredator attacks the nudibranch, thenematocysts may discharge as a defensivemechanismSection through the cerasof Aeolidiopsis ransonishowing the cnidosac withthree nematocysts.(Photo: Dr. Bill Rudman)co-adaptation - development and maintenance of advantageous traitsbenefiting one or both parties in a two-species interaction; evolution ofcharacteristics of two or more species to their mutual advantage; predatorpreyand cleaning symbioses are examples of such evolving interactions inmarine communitiesco-management - the sharing of authority, responsibility, and benefitsbetween government and local communities in the management of naturalresourcescoacervate - an aggregate of colloidal droplets held together byelectrostatic forces. Coacervate droplets may contain a mixture of organiccompounds. One theory of the evolution of life is that the formation ofcoacervates in the primeval soup was a step towards the development ofcellscoalesce - to come together so as to form one whole; to fusecoarse sediment - a sediment made up of coarse-grained materials,such as sand or gravel particlescoastal area - the areas of land and seabordering the shoreline and extendingseaward through the breaker zone. Coastalareas throughout the world are underenormous environmental stress, which iscaused by a wide range of factors, includingpollution and the destruction anddeterioration of marine habitatsRainbow over Hawaii, HIcoast (Photo: Dr. James P.McVey, NOAA Sea GrantProgram)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (38 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoastal flooding - flooding that occursfrom storms where water is driven ontoland from an adjacent body of waterA coastal storm leavesflooded streets in its wake.(Photo: U.S. Army Corpsof Engineers)coastal margin - the boundary line between land and seacoastal morphology - the form and configuration of a coastcoastal reef - a coral reef occurring near and parallel to a coastlinecoastal waterway - a body of water situated on or near a coast, withsome association with the ocean. Includes embayments, wave-and tidedominatedestuaries, wave-and tide-dominated deltas, coastal lagoons,and tidal creekscoastal zone - coastal waters andadjacent lands that exert a measurableinfluence on the uses of the oceans andtheir living and nonliving resourcesSpectacular Oregoncoastline. (Photo: RearAdmiral Harley D. Nygren,NOAA Corps)Coastal Zone Management Act - passed in 1972, the CZMA provides formanagement of shoreline areas that may include coral reefshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (39 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoat protein - the coating protein thatencloses the nucleic acid core of a viralparticle; the capsidA single coat protein(capsid) of a cypovirussurrounded by a loosepolyhedrin matrix. (Photo:Dr. Hans Ackermann,Medical Faculty, LavalUniversity, Quebec,Canada)Coccidea - a class of parasitic single-celled organisms in the protistanphylum, Apicomplexacoccoid - spherical in shapecoccus - a bacterium with a spherical shapeCoccus bacteria. (Photo:Robert W. Bowker,Glendale CommunityCollege Glendale, AZ)COD (Chemical Oxygen Demand) - a measure of the chemicallyoxidizable material in water which provides an approximation of theamount of organic and reducing material present. The determined valuemay correlate with biochemical oxygen demand (BOD) or withcarbonaceous organic pollution from sewage or industrial wastescod end - the terminal, closed end of a trawl nethttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (40 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCode - in taxonomy, the International Code of Zoological Nomenclature.An authoritative document containing a system of rules andrecommendations to be followed in giving a scientific name to an animalor animal groupcoding - the specification of a peptide sequence by the code contained inDNA moleculescoding region - a sequence of DNA, bounded by start and stop codons,which consists of a series of nucleotide bases that gives rise to mRNA(messenger RNA) that will be translated into the specific amino acids ofthe protein productcoding sequence - that portion of a gene which directly specifies theamino acid sequence of its protein productcoding strand - the strand of duplex DNA which contains the same basesequence (after substituting Uracil for Thymine) found in the mRNAmolecule resulting from transcription of that segment of DNA., known asthe sense strand. The mRNA molecule is transcribed from the otherstrand, known as the template or antisense strandcodon - three bases in a DNA or RNAsequence which specify a single amino acidRNA codons. A = adenine;C = cytosine; G =guanine; U = uracil.(Diagram: NIH/HumanGenome Project)coefficient - a number expressing the amount of some change or effectunder certain conditionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (41 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoefficient of faunal similarity (CFS) - The CFS compares the fauna ofone area with that of another. CFS = 2C/(a+b), where C = the number ofspecies in common between two areas, a = the number of species in thefirst area, and b = the number of species in the second area. The higherthe CFS, the greater the resemblancecoefficient of variation - in statistics, it refers to the standard deviationof a distribution divided by the distribution's mean, providing astandardized measure of the variation in a distribution, which does notincrease simply because the mean itself increases or because the units ofmeasurement changeCoelenterata - an older name for the phylum Cnidariacoelenteron - the gastrovascular (digestive) cavity of a cnidarian orctenophorecoelobite - an organism that lives in pores and spaces within a reefcoeloblastula - a larval form associated with oviparous development,with a cytologically undifferentiated central region, and an evendistribution of small flagella. Coeloblastulae are found in sponges,brachiopods and other invertebrate groupscoelom - an internal fluid-filled body cavity within a coelomate organism.It lies between the gut and the outer body wall, and is lined entirely withtissue (peritoneum) derived from the mesoderm. Most internal organs arelocated within the coelom. The structure and development of the coelom isan important taxonomic character for recognizing major groups of animalscoelozoic - living in the lumen of a hollow organ, such as the intestine,gall bladder, urinary tract, etccoenecium - a branching tubular network inhabited by pterobranch(Hemichordata) colonies that is secreted from glands in the oral shields ofthe zooidscoenenchyme - all of the mesenchymal tissue, perforated with channels,that is common to all polyps of a colonial cnidariancoenocline - a sequence of communities along an environmental gradientcoenosarc - the living tissue of a cnidarian polyp, consisting of the outer,nonciliated epidermis and the inner, ciliated gastrodermis with the thin,acellular meoglea in between. The coenosarc connects the coral polyps ofa coral colony. It spreads along the surface of the calcareous exoskeletoncoenosteum - the common surface of corallum between caliceshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (42 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoenosteum pit - the point of insertion or commencement of septa insome coralscoenzyme - an organic nonprotein molecule that binds with the proteinmolecule to form the active enzymecoevolution - a change in the genetic composition of one species (orinfraspecific group) in response to a genetic change in another, i.e. two ormore species evolving, each in response to the othercofactor - a nonprotein substance required for certain enzymes tofunction. Cofactors can be co-enzymes or metallic ionscohort - individuals all of the same agecohort - in taxonomy, a taxonomic rank between infraclass andsuperordercold front - in meteorology, a mass of cold air moving toward a mass ofwarm air. Strong winds and rain typically accompany a cold frontcold seep - an area of the ocean floor where hydrogen sulfide, methane,and other hydrocarbon-rich fluid seepage occurs. Cold seeps are distinctfrom hydrothermal vents. Cold seep's emissions are of the sametemperature as the surrounding seawater, whereas hydrothermal vent'semissions are super-heated. Cold seeps constitute a biome which supportseveral endemic speciescold water - temperature regime usually between 4º – 13º C, and notexceeding 20° C. This is not an exact definition, and is meant only todistinguish between cold-water and tropical warm-water coralenvironmentscold-water coral ecosystem - a large aggregation of cold-water coralswith their associated fauna in terms of spatial coverage at a given localitycoliform bacteria - bacteria whosepresence in water is an indicator ofpollution and of potentially dangerouscontaminationA coliform-caused fish kill.Fecal coliforms originatefrom sewer overflows,septic tank seepage andanimal defecation. Theyare indicators of fecalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (43 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacontamination which couldalso contain bacteria andviruses responsible forcholera and typhoidinfections, hepatitis andgastroenteritis. (Photo:Pine River ShireEnvironmental Services,Australia)collagen - the protein substance of the collagenous fibers (white fibers)of skin, tendon, bone, cartilage and all other connective tissue. Collagenalso serves as skeletal support in some spongescollagenous - producing or containing collagencollagenous fiber - white connective tissue fiber that occurs in bundles.They possess a high tensile strength and make up the principal element ofirregular connective tissue, tendons, and aponeuroses, and occur in thematrix of cartilage and bone tissuecollar cell - any of the flagellated cells in sponges having a collar ofcytoplasm around the flagellum; they maintain a flow of water throughthe body; a choanocyte; also, a specialized cell found in epithelia ofcnidarian mesenterial filaments and the actinopharynxcollection - an assemblage of specimens compiled and maintained forpurposes of study and/or displaycollection - an assemblage of specimens compiled and maintained forpurposes of study and/or displaycollenchyme - in cnidarians, mesenchyme with sparse cellularcomponentscollencytes - a contractile, collagen-secreting amoebocyte in spongescollinear - lying on the same linecollinear points - three or more points on the same line in a plane or inspacehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (44 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacolloblast - a cell that discharges a stickyfilament upon contact with a preyorganism. Colloblasts are found in thetentacles of ctenophores (comb jellies). Asthe tentacles are dragged through thewater, the colloblasts discharge andcapture preyColloblast discharge organof ctenophorans (combjellies). (Image:Livingstone, CopyrightBIODIDAC)colloid - a stable suspension of particles that, though larger than in a truesolution, do not settle outcolonial - a level of cellular organization intermediate between unicellularand multicellular; refers to organisms that occur in a fixed location, withone generation growing on top previous generations, as in coral reefs;types of animal that are organized into associations of incompletelyseparated individuals; eg, Portuguese man o' war, sponges and corals; inplants, describes cloning by asexual reproduction in which seeminglyseparate plants grew from rhizomes, stolons, or roots of a single orneighboring parent plantcolonial coral - a coral composed of many individualscolonial nester - a species that nests in coloniescolonization - a movement of individuals or propagules of a species to anew territorycolonized hardbottom - a substrate formed by the deposition of calciumcarbonate by reef building and other organisms. Habitats within thiscategory have some colonization by live coralhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (45 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacolony - a group of the same kind of animals, plants, or one-celledorganisms living or growing togethercolor - a quality of light, depending on its wavelength. Perceived color (orvisual color) is the quality of light emission as conveyed by the eye, i.e.,the visual perception of light that enables humans and other organisms todifferentiate between wavelengths of the visible spectrumcolor card - the CoralWatch program(University of Queensland, Brisbane,Australia) developed a method of coralhealth monitoring which uses simple colorcharts, like paint color matching charts. Thecolor charts are based on the actual colorsof bleached and healthy corals. Each colorsquare corresponds to a concentration ofsymbiotic zooxanthellae contained in thecoral tissue. The concentration ofsymbionts is directly linked to the health ofthe coral. The color of the coral is matchedwith one of the colors in the coral healthmonitoring chart, then the the matchingcolor codes, along with coral type (speciesif possible) is recorded on a website datasheet (www.coralwatch.org)The diver is matching thecolor of the coral with acolor on the CoralWatchcolor chart. This healthybrain coral is dark brownand has a color score ofE6. (Photo: University ofQueensland, Australia)colorimeter - an instrument for measuring and determining colorcoloumb - unit of electrical charge of one ampere over period of onesecondcolumella - any small column-likestructure in various plants and animals,often forming the central axis ofdevelopment for the organism as a whole,or an anatomical structure; the thickenedaxial pillar around which the whorls ofgastropods are constructed; the centralaxis of a corallite; the central structure ofthe calyx formed by fusion of the septaThe columella inside aStrombus oyster drill.(Photo: Jesuit DallasMuseum)column - the cylindrical body of an anthozoan polyphttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (46 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacolumnar - column-shapedcolumnar colony - a coral colony formed into one or more columnscomb row - a longitudinal line of ctenes on the epidermis of ctenophores(comb jellies)comb teeth - paddle-shaped projections on the oral pinnules of crinoidsCoML (Census of marine Life) - a global network of researchers inmore than 45 nations engaged in a ten-year initiative to assess andexplain the diversity, distribution,and abundance of marine life in theoceans past, present, and to explain how it changes over timecommensal - having benefit for one member of a two-species associationbut neither positive nor negative effect on the othercommercial extinction - the decline in the population of a wild species,used as a resource, to a level where it is no longer profitable to harvestthe speciescommercial fishing - a term related to the whole process of catching,processing and marketing fishes and shellfish. It also refers to andincludes fisheries resources, fishermen, and related businesses directlyinvolved in harvesting, processing or salesCommission - refers to the International Commission on ZoologicalNomenclature (ICZN)commissure - a juncture or seam; the juncture where two sides of anervous system are joinedcommon ancestor - the most recent ancestral form or species fromwhich two different species evolvedcommon name - a colloquial or vernacular name. For example, "crownof-thornsstarfish" is the common name of Acanthaster plancicommonwealth - an organized United States insular area, which hasestablished with the Federal Government, a more highly developedrelationship, usually embodied in a written mutual agreement. Currently,two United States insular areas are commonwealths, the NorthernMariana Islands and Puerto Rico. A United States insular area from April11, 1899, the Philippine Islands achieved commonwealth status onMarch 24, 1934 (Public Law 73-127), and remained as such until theUnited States recognized the Philippine Islands' independence andsovereignty as of July 4, 1946http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (47 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacommunication network - telecommunications infrastructure thattransfers data from observing systems to data centers, and then to enduserscommunity - a naturally occurring assemblage of organisms that live inthe same environment and are mutually sustaining and interdependent; agroup of populations that interact in time and spacecommunity-based ecosystem management - a process whereby nongovernmentorganizations, community groups, or individuals participate inlong-term management of selected species, habitats, or ecosystemprocesses with the ultimate goal of improving management of ecosystemsand natural resourcescompact branching - a growth pattern where the coral branches areclose togetherCompact of Free Association - the status of free association recognizesan island government as a sovereign, self-governing state with thecapacity to conduct foreign affairs consistent with the terms of theCompact. The Compact places full responsibility for military defense withthe United States. The basic relationship of free association continuesindefinitely; the economic provisions of the Compact are subject torenegotiation at the end of 15 yearscompensation depth - the depth in the ocean at which the differencebetween the oxygen produced by algae through photosynthesis and thatconsumed by them through respiration is zero, i.e., net oxygen productionis zerocompetition - a biological interaction thatcan limit population growth. Competitionoccurs when two or more populations viefor the same limited resourceSweeper tentacles from aGalaxia colony. Thestinging cells killneighboring "non-self"corals in the competion forspace. Mesenterialfilaments which dissolveneighboring non-selfcorals are another meansof competitive tactics byscleractinian corals.(Photo: Copyright 2001Robert C. Michelson)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (48 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacompetitive exclusion - the principle that when the populations of twospecies compete for resources, one will use the resources more efficiently,therefore outcompete and eventually eliminate the other populationcompetitive release - the expansion of a species' ecological niche,associated with the lack of competition with other speciescomplement - the complement of a nucleic acid sequence replaces eachbase by its complementary base: adenine (A) by thymine (T), cytosine (C)by guanine (G), and vice versa. In RNA, adenine is paired not withthymine but with uracil (U)complementarity - the relationship between the two strands of a doublehelix of DNA. Thymine in one strand pairs with adenine in the otherstrand, and cytosine in one strand pairs with guanine in the other strandcomplementary base pair - the specific matching of purine andpyrimidine base pairs in nucleic acids. This matching occurs because thestructure of one base precisely fits with, and bonds to, another specificbase. In DNA, adenine and thymine are complementary and form a basepair, as do cytosine and guanine. In pairing between DNA and RNA,adenine and uracil are complementary, and cytosine and guanine arecomplementarycomplementary nucleotide - a member of the pairs adenine-thymine,adenine-uracil, and guanine-cytosine that have the ability to hydrogenbond to one anothercomplementary resources - a pair of resources for which consumptionby the consumer of one resource reduces its requirement for the othercomplete protein - a protein that has all of the essential amino acids andin the correct proportionscomplex life cycle - a life cycle that consists of several distinct stages (e.g., larva and adult)complexity - in ecology, the number of species at each trophic level andthe number of trophic levels in a community; in molecular genetics, usedto describe a DNA molecule or a mixture of DNA molecules. It is thelength of the nucleotide sequence without including any sequencerepetitioncompound - a material made up of two or more elements combined in afixed ratiocompound chromatophore - a chromatophore that contains more thanone kind of pigmenthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (49 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacompound eye - the eye of arthropods, most highly developed in insectsand crustaceans. It consists of a group of functionally related visualelements (ommatidia), each having its own refractive system and eachforming a portion of an imagecompressed - a body shape which isflattened laterally, bringing the right andleft sides closer together, e.g., a butterflyfish or a flounderThe compressed bodyshape of a garibaldi.(Photo: Copyright CorelCorporation)compressed air - air compressed to a pressure higher than thesurrounding atmospheric pressure (ambient pressure)compression - in information technology, decreasing the size of storedinformation by reducing the representation of the information withoutsignificantly diminishing the information itself, usually by removingredundancies. The information requires decompression upon retrieval.Lossless compression allows the original data to be recreated exactly.Lossy compression sacrifices some accuracy to achieve greatercompressionconchiform - shell-shapedconchology - the study of shellsconciliatory behavior - behavior directed toward other organisms thattends to diminish or eliminate aggression and promote harmonious socialrelationshipsconfidence interval - the probability, based on statistics, that a numberwill be between an upper and lower limithttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (50 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataconfluent - joined togethercongener - a member of the same genusconger eel - any species of eel in thefamily Congridae. Conger eels have a thickcylindrical body and tapering snout. Theypossess a smooth and scaleless skin andlarge pectoral fins. They are much lesscommon than moray eels in coral reefcommunities. During the day they tend tohide in crevices and holes under rocks orcoral, or burrow into sand. They emerge atnight to feedThe conger eel,Congercinereus, is uncommon inHawaiian waters. It hidesunder rocks or in cavernsand emerges at night(Photo: Keoki and Yukostender)conjugated protein - a protein complex combining amino acids withother substancesconjugation - a process of sexualreproduction whereby two cells come incontact and exchange genetic material. Inprokaryotes and unicellular agae, thetransfer is a one-way process. The union oftwo bacterial cells, during whichchromosomal material is transferred fromthe donor to the recipient cell. Conjugationin protozoans is a two-way process, geneticmaterial is passed between each conjugantSpirogyra is a filamentousgreen alga. Certainfilaments in a looseparallel bundle ofSpirogyra assume thefemale role, and othersthe male. The cells ofadjacent filaments developtubular extensions whichgrow towards one anotherand eventually fuse toform a continuous tubebetween the cells.Meanwhile the contents ofeach cell have formed around sphere. The spheresfrom the male filamentsqueeze their way downthe connecting tubes tofuse with a sphere of thefemale cell in the otherfilament. The result of thissexual union is theformation of a zygote(zygospore) within thechambers of the femalehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (51 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datafilament. After a dormantperiod, the zygotesundergo meiosis andgerminate, resulting innew filaments. (Photo:Wappinger Schools)connectivity - natural linkages among reefs including currents, larvaldispersal, spawning patterns, and movements of adult organisms.Connectivity is an important part of dispersal and the replenishment ofbiodiversity on reefs damaged by natural or human-related agents; aqualitative term describing the degree to which ecosystems are linked toone another to form an interconnected network; the movement oforganisms from place to place through dispersal or migrationconopeptide - a family of molecules found in the venom of species ofmarine cone shell snails (Conus sp) that can act as an analgesic andalleviate pain.One particular group, the omega-conopeptides, blockschannels on nerve cells that transport calcium ions and thereby interferingwith the production of neurotransmittors. Synthetic copies of conopeptidesfrom the magician's cone shell, Conus magus, are used to make the drugPrialt, generally known as ziconotideConservation - under the NOAA Coral Reef Conservation program, theterm 'conservation' means the use of methods and procedures necessaryto preserve or sustain corals and associated species as diverse, viable,and self-perpetuating coral reef ecosystems, including all activitiesassociated with resource management, such as assessment, conservation,protection, restoration, sustainable use, and management of habitat;mapping; habitat monitoring; assistance in the development ofmanagement stategies for marine protected areas and marine resoursesconsistent with the National Marine Sanctuaries Act (16 U.S.C. 1431 etseq.) and the Magnuson-Stevens Fishery Conservation and ManagementAct (16 U.S.C. 1801 et seq.); law enforcement; conflict resolutioninitiatives; community outreach and education; and that promote safe andecologically sound navigationconservation - the political/social/economic process by which theenvironment is protected and resources are used wiselyconservation biology - a multidisciplinary science that deals with theconservation of genes, species, populations, communities, and ecosystemsthat make up the Earth's biodiversity. Its goals are to investigate humanimpacts of biodiversity and to develop approaches to prevent extinction ofspecies through stewardship of entire biological communitieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (52 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataConservation Commons - an approach under the World ConservationUnion (IUCN) designed to improve the management of data, information,and knowledge related to conservation.It is a collaborative effort toimprove open access to data, information, and knowledge related to theconservation and sustainable use of biodiversity with the belief that thiswill contribute to improving conservation outcomes. Support for thisinitiative is presently drawn from governments, international and multilateralorganizations, non-governmental organizations, academia, theprivate sector, and many other interested parties who share similar goalsof ensuring the sustainable use of biodiversity while conserving theintegrity of biodiversity for future generations (www.conservationcommons.org)Conservation International (CI) - a nonprofit, U.S.-based,international organization that applies innovations in science, economics,policy and community participation to protect the Earth's richest regions ofplant and animal diversity in the biodiversity hotspots, high-biodiversitywilderness areas, as well as important marine regions around the globe.With headquarters in Washington, D.C., CI works in more than 40countries on four continentsconserved name - in taxonomy, a name otherwise unavailable or invalidthat the International Commission on Zoological Nomenclature, by the useof it Plenary Power, has enabled to be used as a valid name by removal ofthe known obstacles to such useconsexual - of the same sexconspecific - of the same speciesconsumer - an organism which must consume other organisms (living ordead) in order to satisfy its energy needscontaminant - an undesirable substance not normally present, or anusually high concentration of a naturally occurring substance in theenvironment; a substance in water that might adversely affect the healthand welfare of the biotaContent Standard for Digital Geospatial Metadata - provides acommon set of terminology and definitions for the documentation ofdigital geospatial data. The standard establishes the names of dataelements and compound elements (groups of data elements) to be usedfor these purposes, the definitions of these compound elements and dataelements, and information about the values that are to be provided for thedata elementscontiguous - sharing an edge or boundary; touching; neighboring;adjacentcontiguous habitat - a habitat which shares a boundary with anadjacent habitathttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (53 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacontinental margin - the water-covered edges of continents consistingof the continental shelf, the continental slope, and the continental risecontinental rise - the enormous wedge of sediment deposited at thebase of the continental slopecontinental shelf - the shallow, near-horizontal sea floor extending fromthe coast to the upper continental slopecontinental slope - the sloping sea bottom of the continental marginthat begins at a depth of about 100 to 150 m at the shelf edge and endsat the top of the continental rise or in a deep-sea trenchcontinuum - a continuous set of data for which each data point is relatedto the adjacent point; a gradual or imperceptible intergradation betweentwo or more extreme valuescontour - on a map or chart, a line connecting points of equal surfacevaluecontour interval - the difference in surface values between contourscontrolled environment - the environment in which parameters, such aslight, temperature, salinity, etc., are fully controlledcontrolled experiment - a scientific experiment, in which results froman experimental group with variable conditions, is compared with a controlgroup with nonvariable conditionsconule - an empty, somewhat conical elevation on the surface of somespongesconvection - vertical air circulation in which warm air rises and cool airsinks, resulting in vertical transport and mixing of atmospheric properties;transfer of heat by the movement of air or water; the rise of an air masscaused by warming over land or sea that often causes the formation ofcloudsconvection current - a movement of air or water caused by changes indensity or thermal gradientsconvection precipitation - precipitation which occurs from convectiveclouds. It falls as showers with rapidly changing intensity. Convectiveprecipitation falls over a certain area for a relatively short time, asconvective clouds have limited horizontal extent. Most precipitation in thetropics appears to be convectiveconvergence - come together and meet at a pointhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (54 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataconvergence zone - the line where two oceanic water masses meet,resulting in the sinking of the denser oneconvergent evolution - the development of superficially similarstructures in unrelated organisms, e.g., the wings of insects and birdsconvivium - a population differentiated within a species and isolatedgeographically, usually subspecies and/or ecotypes; a population or groupof organisms that is set apart from other related groups by factors otherthan interfertility and are maintained by some isolating mechanism otherthan intersterility. Convivia are usually equivalent to a subspecies orvarietycoordinate taxon - in cladistics, a group within a monophyletic lineage atthe same branching level as another. Therefore, it requires equivalenttaxonomic rank in the Linnean classification hierarchyCoordinating Body on the Seas of East Asia (COBSEA) - theCoordinating Body on the Seas of East Asia (COBSEA) was established in1981 under the framework of the UNEP Regional Seas Programme withthe East Asian Seas (EAS) Action Plan that is basically aimed atestablishing a comprehensive strategy to protect the marine and coastalenvironment of the EAS region and to promote its sustainable developmentcopepod - any of a large subclass(Copepoda) of usually minute freshwaterand marine crustaceans that form animportant element of the zooplankton inthe marine environment and in some freshwaters. A common feature uniting all thecopepod orders is a single simple eye in themiddle of the head, at least in the larvalstage. The cephalosome, a shield over thehead and some thoracic segmentsdistinguishes the free living forms fromparasitic ones. Some species areectoparasites of marine fishesCopepods are veryimportant components ofthe zooplanktoncommunity. Thisillustration show acopepod carrying anumber of eggs (in blue)(Photo: NOAA)copepodid - postnaupliar developmental stages of copepodscoprophagous - pertains to feeding on fecal mattercopulation - the physical act of mating; sexual intercoursehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (55 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoral - a general term used to describe agroup of cnidarians; indicates the presenceof skeletal material that is embedded in theliving tissue or encloses the animalaltogetherFinger coral (Poritescompressa) in Hawaii(Photo: M. White)coral assemblage - a group of coralscoral bank - an undersea mound or ridge that rises above thesurrounding continental shelf or slope and is formed in part from thecarbonate skeletons of coralscoral bleaching - the process in which acoral polyp, under environmental stress,expels its symbiotic zooxanthellae from itsbody. The affected coral colony appearswhitenedBleached Acropora coral inFlorida Keys (Photo: LarryBenvenuti)coral bleaching hotspot - a region of seasurface temperature (SST) that exceedsthe climatological maximum for a region by1 deg C or more. These conditions maycause sufficient stress to coral reefs toresult in coral bleachingSection of a graphicdepicting areas of elevatedocean temperatures thatmay result in coralbleaching events.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (56 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCoral Bleaching HotSpot monitoring program - a NOAA program thatuses satellite and in situ monitoring stations to monitor high sea surfacetemperature events and to analyze conditions that may lead to coralbleachingcoral growth line - a minute growth line on the outer surfaces of coralsthat have a calcified outer wall. The carbonate is produced byzooxanthellae which create a series of diurnal growth incrementscoral holobiont - see "holobiont"coral mining - Corals are mined mainly forthe construction of houses and buildings,groins, solid jetties, breakwaters, sea walls,jewelry, decorative ornaments, householdfurnishings, and aquarium displays. Thecommon species of corals mined aremassive corals, such as Porites, which arecrushed by manual labor into smaller piecesand used as building materials. Anothermajor use of mined coral is in the makingof lime. For many in the tropics, it ischeaper to produce lime locally than buyingimported cement. Coral mining methodsand techniques are usually manual andlabor intensive. Having chosen a suitablereef, miners travel to the site where thecorals are dug and broken up with iron barsCoral stones and blockshave been used for houseconstruction in many partsof the tropical world.(Photo: Bluepeace/Maldives)to manageable sizes, carried to shore, and are left for a period of time todry and clean. In addition to reducing the number of coral colonies, coralmining reduces the wave absorbing properties of coral reefs. Destructionof the reef exposes the shoreline and coastal communities to storm surgesand erosion. Many countries have banned coral mining due to its negativeimpact on coastlinesCoral Parks Program (CPP) - a global initiative that supports existingCoral Parks, assists in the establishment on new Coral Parks, and engagesdivers and the dive industry in coral reef protection. CPP is an initiative ofThe Coral Reef Alliance, a non-profit organization dedicated to keepingcoral reefs alive around the worldCoral Point Count with Excel extensions (CPCe) - a software programthat provides a tool for the estimation of benthic habitat cover usingunderwater images. The coverage can be analyzed using the random pointcount method, and areas can also be traced, digitized, and calculated viaimage calibrationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (57 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoral probiotic hypothesis - a concept which posits that a dynamicrelationship exists between symbiotic microorganisms and environmentalconditions which brings about the selection of the most advantageouscoral holobiont (Reshef et al., 2006). Corals exposed to some type ofstress, such as unusually high water temperatures, expel theirzooxanthellae and then regain a new mixture of zooxanthellae (or othersymbiotic microoganisms) that are better suited to the stress conditionscoral product - any living or dead specimens, parts, or derivatives, orany product containing specimens, parts, or derivatives, of any species ofcoral in the cnidarian Orders: Antipatharia (black corals), Scleractinia(stony corals), Gorgonacea (horny corals), Stolonifera (organpipe coralsand others), Alcyanacea (soft corals), and Coenothecalia (blue coral), ofthe Class Anthozoa; and all species of the Order Hydrocorallina (fire coralsand hydrocorals) of the Class Hydrozoacoral recruit - a coral larva which settles onto a suitable substrate tobecome an addition to the populationcoral reef - a wave-resistant structure resulting from cementationprocesses and the skeletal construction of hermatypic corals, calcareousalgae, and other calcium carbonate-secreting organismsCoral Reef Alliance (CORAL) - CORAL promotes coral reef conservationaround the world by working with the dive industry, governments, localcommunities and other organizations to protect and manage coral reefs,establish marine parks, fund conservation efforts, and raise publicawareness with the mission to keep coral reefs alive for future generationcoral reef bleaching monitoring product - near real-time informationderived from data either from satellite images or in situ monitoringstations at coral reef areas to help improve and sustain coral reef healththroughout the worldCoral Reef Ecosystem Conservation Amendments Act (CRECAA) of2007 - CRECAA reauthorizes the Coral Reef Conservation Act (CRCA) of2000 and adds greater protections for coral reefs while enhancing marinedebris removal and increasing the government’s ability to work throughcooperative partnershipsCoral Reef Ecosystem Research Plan (NOAA) - the NOAA ResearchPlan (FY 2007-2011) provides coastal and ocean managers, scientists, andpolicy makers with the most up-to-date scientific information to addressthe complex nature of the threats facing coral reef ecosystems, andidentifies priority research needed to advance management action. TheResearch Plan is NOAA’s first agency-wide coral reef ecosystem researchplan. Covering all coral reef ecosystems under the jurisdiction of the U.S.and Pacific Freely Associated States, the plan provides a nationalperspective on the research needed to address the range of stressesaffecting the health of coral reef ecosystems, summarizes themanagement and other issues that will drive research at the regionallevel, and focuses on the use of research to guide effectiveimplementation of ecosystem-based management strategieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (58 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCoral Reef Ecosystems Studies- Caribbean Program (CRES) - CRESis a core component of NOAA’s Coral Reef Conservation Program. It wasinitiated in FY 2002 as a science-based, integrated approach tounderstand coral reef dynamics and processes, and to provide tools,ecosystem forecasts and options for coral reef management strategies inthe U.S. Caribbean (Puerto Rico and U.S.Virgin Islands)Coral Reef Targeted Research & Capacity Building for Management(CRTR) Project - The GEF-World Bank Coral Reef Targeted Research andCapacity Building Project has been developed to establish an appliedinvestigative framework to support coral reef management and policy.This project has been designed to coordinate investigations, within alimited number of sites around the world, so that priority unknowns canbe systematically addressed with the intent of applying the results tomanagement and policy. This project will coordinate investigations over anappropriate time-frame (i.e. 15 years) along major themes of inquiry andthen work to appropriately sequence involvement and improve thecapacity of how to use such information in meaningful ways, especiallywithin developing countries and small island states. The project supportssix thematic working groups (Bleaching and Local Ecological Factors,Connectivity and Large-scale ecological processes, Disease, Restorationand Remediation, Remote Sensing for Coral Reefs, and Modeling andDecision Support), and the project's guiding Synthesis Panel. The Projectis executed by a dedicated Project Executing Agency (or PEA)headquartered at the University of Queensland, Australia. However, theproject involves a broad range of international partners, such as TheWorld Bank, The Intergovernmental Oceanographic Commission (IOC),NOAA, The WorldFish Center, and a number of academic institutions fromaround the worldCoral Reef Watch - see CRW (Coral Reef Watch) ProgramCoral Reef Watch experimental doldrums product - NOAA Coral ReefWatch (CRW) developed an Experimental Doldrums Product that identifiesand tracks regions of sustained low wind speed to help coral reefmanagers and scientists better assess conditions that may lead to coralbleaching. Wind is an important physical factor influencing conditionsconducive to coral bleaching. Wind-driven mixing reduces temperaturestress and wind generated waves can scatter harmful levels of incomingsolar radiation. Periods of sustained low wind may therefore promoteenvironmental conditions adverse to corals experiencing thermal and/orUV stresshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (59 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacoral rock - products used in the aquariumtrade. Coral rock is consolidated material,greater than 3 cm in diameter, formed offragments of dead coral and which mayalso contain cemented sand, coralline algaeand other sedimentary rocks. 'Live rock'describes pieces of coral rock to which areattached live specimens of invertebratespecies and coralline algaeCoral rock for sale in themarine aquarium trade.(Photo: Shell Horizons,Inc.)coral rubble - fragments of hard coralCoral Stress Index - an index that indicates the relative accumulatedthermal stress experienced by a given coral reefCorallimorpharia - an order of the subclass Zoantharia (Hexacorallia) ofthe phylum Cnidaria. They are mostly solitary species (some are colonial)that resemble true corals, but lack a calcareous skeletoncoralline algae - algae that form solidcalcium carbonate accretionsCoralline algae removecalcium from water. Thiscalcium carbonate givesthem a coral-like look. Asthey die, they turn white.(Photo: Nancy Sefton)corallite - a coral cup; the skeleton of an individual polyphttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (60 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacorallivore - an organism that eats coralParrotfish are oftencoralliverous, scraping thecoral polyps with beaklikejaws.corallum - a complete coral colony; a coral headcordate - heart-shaped; in the form of two rounded lobesCORDIO (Coral Reef Degradation in the Indian Ocean) - CORDIO isan international program created to respond to the degradation of coralreefs throughout the Indian Ocean. In the western Indian Ocean regioncoral reefs are key ecosystems that support large sectors of the countries'populations and economies, through artisanal fisheries, tourism and largescaleinvestments. Projects within CORDIO focus on determining a) thebiophysical impacts of coral degradation as a result of bleaching and otherdisturbances, and the long term prospects for recovery, b) the socioeconomicimpacts of coral mortality and options for mitigating thesethrough management and development of alternative livelihoods, and c)the prospects of restoration and rehabilitation of reefs to accelerate theecological and economic recovery.core - a cylindrical sample, obtained with ahollow drill, extracted from, inter alia, aseabed, lake bottom, or coral to investigatethe composition and depths of layersA scientist is taking a coralcore using a 1/2 inchpneumatic drill equippedwith a 50 cm long hollowhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (61 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datasteel cutting cylinder. Aconcrete plug is thentapped into the core holeto seal off the hole.(Photo: Daria Siciliano/UCSC)core (geology) - the innermost layer of the Earth, consisting primarily ofpure metals such as iron and nickel. The core is the most dense layer ofthe Earth, and is divided into the outer core, which is believed to be liquid,and the inner core, which is believed to be solidCOREMO 2 - a data entry and analysis program developed by thesouthern Indian Ocean Global Coral Reef Monitoring Program (GCRMN)node. It is based on ARMDES (AIMS Reef Monitoring Data Entry System)but has been extensively modified from COREMO to suit the needs of theGCRMNcornetfish - any species of spiny-rayedfishes in the family Fistulariidae.Cornetfishes are elongated, depressedbodiedfishes with a greatly extendedtubular snout, a very small mouth, and along thin filament extending from themiddle of the caudal fin. They are closelyrelated to the trumpetfishes (Aulostomidae)which are more robust and lack the caudalfilament. At present there areapproximately five known species ofcornetfishesThe red cornetfish,Fistularia petimba,inhabits coastal areas,usually at depths greaterthan 10 m. It feeds onsmall fishes and shrimp.(Photo: Marine Biologicallaboratory, Woods Hole.)cornute - horn or cup-shapedcorrelate - to show a relationship between entitiescorrelation - a relation between a variable and one or more relatedvariablescorrelation coefficient - a measure of the relationship between variablescorrelogram - a graph illustrating the auto-correlations betweenmembers of a time series (vertical axis) for different separations in time(horizontal axis)corridor - a route that allows movement of individuals or taxa from oneregion or place to another; in terms of conservation biology, a connectionbetween habitat fragments in a fragmented landscapehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (62 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacorrugated - having a surface with alternating parallel ridges andgroovescortex - the outer portion (layer) of an organcorticocyte - in octocorals, a cell that secretes gorgonin, which forms theaxis of a gorgonianCoRViL (Coral Reef Virtual Laboratory) - a joint venture of theNational Oceanic and Atmospheric Administration (NOAA), the GreatBarrier Reef Marine Park Authority (GBRMPA), and the Australian Instituteof Marine Science (AIMS). This venture will provide an automated,cooperative exchange of electronic data, computer processing power andremote sensing tools for the purpose of monitoring the coral reefenvironment on the Great Barrier Reef. It is anticipated that this effort willeventually provide a model for monitoring physical processes at othersensitive coral reef areas throughout the worldcorymbose - describes coral colonies with horizontal interlockingbranches and short upright branchescosmid - a DNA vector that allows the insertion of long fragments of DNA(up to 50 kbases)cosmopolitan - having a global distributioncosmopolitan distribution - worldwide distribution within habitat limitscost-benefit analysis - an assessment of the short-term and long-termcosts (losses) and benefits (gains) that arise from an economic decision. Ifthe calculated benefits exceed the calculated costs, the decision to buy aneconomic good or provide a public good is considered profitablecosta - the extension of the septa outside the calyx into the coenosteumcoulombmeter - an instrument for measuring electric chargeCoulter counter - an instrument thatmeasures particle size distribution from thechange in electrical conductivity as particlesflow through a small openingA Coulter counter is aninstrument used tomeasure the distribution ofparticle size.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (63 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacounter current - a secondary current flowing in a direction opposite tothat of the main currentcounter shading - protective bodycoloration where the dorsal surface (above)is dark and the ventral surface (below) islighterCounter shading in a whiteshark. The darker dorsalsurface and lighter ventralsurface allows the shark toblend in with theenvironment when viewedfrom above or below.(Photo: NOAA)counter-illumination - a condition in which an animal hasbioluminescent structures concentrated on its ventral surface so as toincrease the effect of countershadingcourtship behavior - specialized behavior patterns which contribute tothe psychological and physiological synchronization of potential matingpartnerscovalence - the number of pairs of electrons an atom can share withother atomscovalent bond - a bond between two or more atoms that is provided byelectrons that travel between the atoms' nuclei, holding them together butkeeping them a stable distance apartcove - a small sheltered indentation in the shoreline. A cove is smallerthan a bayCRAG (American Samoa Coral Reef Advisory Group) - CRAGadministers American Samoa's Coral Reef Initiative (CRI) and is aninteragency task force representing five agencies in the Territory, all ofwhich have some link to the coral reef environment. CRAG memberagencies work together by mutual consensus to manage coral reefs inAmerican Samoa by planning achievable programs, identifying andcollaborating with other partners, obtaining funding for projects, trackingproject compliance, promoting public awareness, and developing localcapacity for eventual self-sustainabilityhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (64 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacraggy - a surface which is rocky and steepcraterform - massive shape with a broad base and a large, centraldepressioncrateriform - cup-shapedcrawl - tracks and other signs left on a beach by a seaturtleCreefs (Census of Coral Reefs) - a global census of coral reefs, CReefsis one of 17 projects of the Census of Marine Life, an international networkof over 1,700 researchers in more than 70 nations engaged in a 10-yearinitiative to assess and explain the diversity,distribution, and abundanceof marine life in the oceans and how it changes over timecreel survey - a survey of anglers in a particular area to discover thetypes and numbers of fish caughtCREIOS (Coral Reef Ecosystems Integrated Observing System) -NOAA's Coral Reef Ecosystem Integrated Observing System (CREIOS)provides a diverse suite of long-term ecological and environmentalobservations and information products over a broad range of spatial andtemporal scales. The CREIOS goal is to understand the condition andhealth of, and processes influencing, coral reef ecosystems, to assiststakeholders in making improved and timely ecosystem-basedmanagement decisions to conserve coral reefscrenulate - a shape in which the edge is slightly scallopedcrepuscular - most active at low lightlevels during dusk and dawnThe large eyes of asquirrelfish hint about itscrepuscular behavior,allowing it to be active andfeed during periods ofdiminished light. (Photo:Copyright CorelCorporation)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (65 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCREWS (Coral Reef Early WarningSystem) - in situ NOAA meteorological andoceanographic monitoring sites that collectdata continuously which are transmittedhourly via satellite to a data archival site.An automated system (hardware andsoftware) that monitors selectoceanographic and meteorologicalparameters and produces specialized alertswhen conditions may result inenvironmental stresses conducive of coralbleaching. NOAA plans to expand theCREWS from the Florida Keys/Bahamiansites to many remote coral reef sitesthroughout the worldA CREWS station on site.Crinoidea - a small class of ancientechinoderms (sea lillies and feather stars)which number about 600 species. All aresuspension-feeders, occupying deep partsof the oceans to just below the shoreline.Some are common on coral reefs. Crinoidshave long, slender arms arranged radiallyaround a rigid, calcareous, cuplikestructure, the calyx. Two basic adult bodytypes are recognized: the sea lilies, with along, anchored stem vertically supportingthe calyx and arms above the sea bottom;and the stemless featherstars, orcomatulids, with a whorl of flexibleappendages on the calyxA sea lilly (Crinoidea) is astalked, usually sessile,echinoderm. This sea lillywas observed off GrandBahama Island at a depthof about 1200 feet.(Photo: T. K. Baumillerand C. G. Messing/HarborBranch OceanographicInstitution)crinose - hairyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (66 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCRISP (Coral Reef Initiative for the South Pacific) - a French coralreef conservation and sustainable management initiative designed as avector of regional integration between the developed and developingcountries of the Pacific. CRISP pursues the following objectives: gaining abetter understanding of coral ecosystems in terms of their biodiversity,current status and functioning; conducting operations to protect andmanage coral ecosystems on a broad scale; promoting economic potentialbased on the biodiversity and use values of coral ecosystems; and sharinginformation and knowledge, building capacities; and managing local,national and international networks throughout the Pacificcriterion - a standard rule or test on which a judgment or decision can bebased.critical depth - the depth in seawater below which carbon loss throughrespiration by phytoplankton exceeds carbon gain throughphotosynthesis; no net phytoplankton production occurscritical habitat - the ecosystem upon which endangered and threatenedspecies depend; habitat crucial to the survival of the species; TheEndangered Species Act (ESA) defines“critical habitat” as specific areaswithin the geographical area occupied by the species at the time of listing,that contain the physical or biological features essential to the species’conservation and which may require special management considerationsor protection; and specific areas outside the geographical area occupiedby the species if the agency determines that the area is essential forconservationcritical value - in statistics, the value of a test statistic at or beyondwhich the null hypothesis is rejectedcrocodile - in addition to freshwaterenvironments, crocodiles also inhabitbrackish waters and coral reef habitats. TheAmerican crocodile can be found onoffshore cayes and atolls, and in mainlandcoastal habitats. Two endangered speciesof crocodile, the American crocodile(Crocodylus acutus) and Morelet's crocodile Morelet's crocodiles(Crocodylus moreletii), occur in Belize. The(Crocodylus moreletii) livelargest American crocodile population (lessprimarily in freshwaterareas such as swamps andthan 300) in Belize is found in the Turneffemarshes and can also beAtoll, which is one of the largest remainingfound in forested ripariannesting areas in the Caribbean. Morelet'shabitats.(Photo: Jerrycrocodile can be found in brackish water Gingerich )around coastal areas. The saltwatercrocodile (Crocodylus porosus), the world'slargest reptile, can be found in coastal,coral reef-rich waters from eastern India and Bangladesh throughSoutheast Asia to Papua New Guinea and Australia. They occur as far eastas the Solomon Islands and Vanuatuhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (67 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacrocodilefish - any of about 60 species ofbony fishes in the family Platycephalidae.Crocodilefishes have distinct pitsimmediately behind the eyes and a concavehead margin.Their eyes have iris lappetswhich help break up the black pupil andimprove its camouflage. Crocodilefishes areusually found on sandy or rubble bottomsnear mangroves, seagrasses or coralsCrocodilefish (Papillulicepslongiceps) in Hurghada,Red Sea. (Photo: ThomasJundt)cross - in genetics, the mating of two individuals or populationscrossing over - in genetics, the breaking during meiosis of one maternaland one paternal chromosome, the exchange of corresponding sections ofDNA, and the rejoining of the chromosomes. This process can result in anexchange of alleles between chromosomescruciate - cross-shapedcrust (geology) - the outermost layer of the Earth, consisting ofrelatively low-density rocksCrustacea - a subphylum of Arthropodathat includes shrimp, mantis shrimp,lobsters, crabs, water fleas, copepods,crayfish and wood lice. There are almost40,000 described species of crustaceans.The Crustacea are mainly aquatic, butinclude some semi-terrestrial and terrestrialgroupsA marine shrimp(Crustacea).crustose - grows flat along the substrate; crust-likehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (68 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacrustose coralline algae - crustosecoralline algae are red algae of the divisionRhodophyta. They are very importantmembers of a reef community in whichthey cement and bind the reef together.They are particularly common in high waveenergy areas but can also be foundthroughout all reef zones. Crustosecorallines resemble pink or purplepavement. Morphology can range fromsmooth and flat, to rough and knobby, oreven leafyCrustose coralline algaeare very common on reefs.(Photo: http://www.botany.hawaii.edu)CRW (Coral Reef Watch) program - formed in 2000, NOAA's CRWmaximizes NESDIS's coral reef resources by joining and building onexisting NESDIS coral reef strengths under a more coordinated program.It seeks to develop a long-term coral reef monitoring system with theability to predict coral bleaching episodes in all major U.S. coral reef areascrypsis - protective camouflage coloration where the individual resemblesits backgoundcryptic - pertaining to concealment,usually in reference to color pattern orbehavior (e.g., hiding in reef crevices)The viper moray is acryptic fish, concealingitself in crevices and holesin the coral reef. (Photo:Dr. Anthony Picciolo)cryptobiosis - a suspension of life processes when conditions becomeunfavorable. In these resistant states some animals, such nematodes,rotifers and tardigrades, as can survive extreme drying, heat, or cold, andthen return to "life" when favorable conditions returncryptogenic - of obscure or unknown originhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (69 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacryptogenic species - species whose endemic or alien status is unclear.For many species, data are lacking on their original geographicdistribution, and it cannot be determined whether they are native orintroduced into a particular locationctene - the locomotor structure ofctenophores (comb jellies) made up of ciliaarranged into flattened plates. The ctenesare arranged into eight longidutinal bands,from the aboral to the oral surfaceLight refracts off thectenes of the comb-jellyMertensia ovum producingstripes of rainbow color.(Photo: Kevin Raskoff,MBARI.)ctenidium - a comb-like structure; the respiratory organ of a mollusk(ctenidial gill)cteniform - comb-shapedctenoid - comb-shaped; with a comb-likemarginA ctenoid scale of a bonyfish. It is thought that thecombed edge helps toreduce hydrodynamic dragduring swimming. (Photo:Rick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (70 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datactenophore - a member of the animal phylum Ctenophora. A smallphylum (about 50 species) whose members, known as comb jellies andsea walnuts, superficially resemble jelly fishes. These planktonicorganisms are thought to have evolved from a medusoid cnidariancucumiform - cucumber-like formThe sea cucumber(Echinodermata) has acucumiform shape.(Photo:NOAA)cue - in animal behavior, a signal fom one animal which acts as astimulus to elicit a behavioral response in another. The cue may be visual,acoustic, or chemicalcuirass - a protective covering, such as acuticle, plates, scales or shellsThe cuirass is body armor,particulary aimed atprotecting the chest andback. (Photo: Institut etMusée des Suisses dans leMonde)culling - the selective removal of animals from a population forconservation purposeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (71 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Dataculture - a population of plant or animal cells or microorganisms that isgrown under controlled conditionsculture medium - a substance which contains nutrients and a favorableenvironment for the in vitro growth of microorganisms and cellscuneiform - wedge-shapedcurrent - generally, a horizontal movement of water; a body of air,water, etc. that moves in a definite direction; the flow of electricityexpressed in amperescurvilinear regression - the relation between variables when theregression equation is nonlinear. With nonlinear relations, an intrinsicallylinear model may be assumed and then data are fitted to the model usingpolynomial regression i.e., some models are employed that use regressionto fit curves instead of straight linescurvilinear relationship - a situation that is best represented bysomething other than a straight linecusp - a point or projection on a toothcutaneous - pertaining to the skincuticle - an extracellular, protective external body covering, secreted bythe epidermis, of some invertebrate animals, usually composed of fibrousmaterial, such as chitin or collagen; the waxy layer of epidermal cells ofplant parts, such as leaves, stems, and fruitcuticular pore - a minute pore opening at the surface of the cuticlecuttle bone - the internal calcified shell remnant of cuttlefishCuvierian tubules - clusters of stickytubules, located at the base of therespiratory tree, which may be dischargedby some sea cucumbers (holothurians)when mechanically stimulate, as forexample, when being threatened by apredator. Their great adhesivity, combinedwith their high tensile strength, allows theCuvierian tubules to entangle andimmobilize potential predators with whichthey come into contact. After expulsion, thelost tubules are readily regenerated,making them a formidable defensemechanismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (72 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataRespiratory tree and theCuvierian tubules in a seacucumber (Illustration:BIODIDAC)cyanide fishing - a destructive fishing technique in which sodium cyanideor some other cyanide compound is used to stun and capture coral reeffishes for the aquarium and live food tradecyano- - a prefix denoting blue or dark bluecyanobacteria - photosynthetic aquaticbacteria, often called blue-green algae, buthave no relationship to algae.Cyanobacteria get their name from thebluish pigment phycocyanin, which theyuse to capture light for photosynthesis.They also contain chlorophyll a, the samephotosynthetic pigment found in thechloroplasts of plants. Not all "blue-green"bacteria are blue; some common forms arered or pink, resulting from the pigmentphycoerythrinA bloom caused bycyanobacteria (-bluegreenalgae+).cyanocyte - a hemocyte that breaks down and releases hemocyanin intothe hemolymphhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (73 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacyberspace - the whole range of information resources available throughcomputer networkscycloid - having a smooth-edged margincyclomorphosis - cyclical changes in form such as seasonal changes inmorphology, as seen in some planktonic crustaceanscyclone - an area of low pressure. Circulation is counterclockwise arounda low pressure system in the Northern Hemisphere and clockwise in theSouthern Hemispherecyclonic - refers to a region of low atmospheric sea level pressure; or,the wind system around such a low pressure center that has a clockwiserotation in the Northern Hemisphere and a counterclockwise rotation inthe Southern Hemispherecyclosystem - a system of very small tubules that links the polyps ofcalcareous colonial hydrozoanscyclotheonarnide A - a bioactive compound, isolated from a marinesponge Theonella sp., is a potential drug for the treatment of thrombosis,a blood disease in which a blood clot forms in the circulatory systemcydippid larva - a larva of ctenophorescymbiform - boat-shapedcyst - a small, capsule-like sac that encloses an organism in its dormantor larval stage; a fluid-filled sac or vesicle in the body of an animal; athick-walled resting spore, as in certain algae or fungicystid - the exoskeleton and body wall of the stationary trunk ofbryozoanscytochrome - a class of protein, found in mitochondrial membranes,whose main function is oxidative phosphorylation of ADP to form ATP; aniron-containing molecule that transfers electrons in metabolic pathwayscytochrome oxidase - an oxidizing enzyme found in mitochondria ofcells. It contains iron and a porphyrin and is important in cellularrespiration as an agent of electron transfer from certain cytochromemolecules to oxygen molecules. Cytochrome c is a highly conservedprotein found in plants, animals, and many unicellular organisms. This,along with its small size, makes it useful in studies of evolutionarydivergencehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (74 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef Datacytogenetics - the science that links the study of inheritance (genetics)with that of cells (cytology) and is concerned mainly with the study of thestructure, and function of chromosomescytokinesis - the division of the cytoplasm of a cell during cell divisioncytology - the study of the structure and function of cellscytometer - an instrument for counting cellscytoplasm - the protoplasm of a cell exclusive of that of the nucleus. Itconsists of a continuous aqueous solution (cytosol) and the organelles andinclusions suspended in it. The cytoplasm is the site of most of thechemical activities of the cellcytoplasmic genes - DNA-containing bodies in the cell but external tothe nucleuscytoplasmic inheritance - inheritance via genes found in cytoplasmicorganelles, e.g., mitochondria, rather than the nuclear genes; inheritancevia the maternal lineage; extrachromosomal inheritancecytosine - one of the four nitrogenousbases in DNA that make up the lettersATGC. Cytosine is the "C". The others areadenine, guanine, and thymine. Cytosinealways pairs with guanineDiagram of the chemicalstructure of cytosine, oneof the four nitrogenousbases in DNA.cytoskeleton - the network of microtubules, microfilaments, and largerfilaments that provides a eukaryotic cell with its structural support, shape,and its capacity to move and arrange its organelles within the cellcytosol - the fluid, less structured part of the cytoplasm of a cell,excluding organelles and membranous structures; the portion of thecytoplasm which remains after removal of particulate componentscytotoxic - able to cause cell deathhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (75 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataCZCS (Coastal Zone Color Scanner) - a scanning radiometer with sixspectral channels centered at 0.443, 0.520, 0.550, 0.670, 0.750 and 11.5micrometers and selected to allow measurement of ocean color andtemperature, suspended sediment and chlorophyll concentrations, andocean pollutants(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=c (76 of 76) [2/26/2008 9:13:43 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: DThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zdacriform - tear-drop shapeddactyloid - finger-likedactylozooid - a colonial hydrozoan polyp that possesses a large,nematocyst-bearing fishing tentacle, and functions in defense and in foodcaptureDalton's Law - the total pressure exerted by a mixture of gases is thesum of the pressures that would be exerted by each of the gases if italone were present and occupied the total volumedamselfish - a large family(Pomacentridae) of bony fishes which areabundant and common inhabitants of coralreefs. They possess robust, deep, andlaterally compressed bodies. The majorityof damselfishes do not have particularlybrilliant markings or coloration. Exceptionsare the brilliantly colored anemone fishes,the banded sergant major, and the brightorange garibaldi, Many species ofdamselfishes are highly territorialOne of the prettierdamselfishes, the bluechromis (Chromis cyanea),swimming on a hawaiiancoral reef (Photo: Keokiand Yuko stender)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (1 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadark-field microscope - a microscope that has a special condenser andobjective with a diaphragm that scatters light from the observed object.The object appears bright on a dark backgrounddark-spots disease - a coral diseasecharacterized by darkly pigmented areas oftissue on stony corals.-At present, there isno known pathogen. The coral tissueremains intact, although at times lesionsand coral tissue death are observed in thecenters of the pigmented areas. Tissue lossis minimal, if present. This disease iswidespread throughout the Caribbean.-Foradditional information and illustrations,see: http://www.coral.noaa.gov/coral_disease/dark_spots.shtmlDark spots diseaseinfecting Stephanocoeniaintersepta. (Photo: NOAA;image copyrighted)dart - a structure of an invertebrate animal that pierces or wounds; asmall, narrow-pointed missile that is thrown or shotdarwin - a logarithmic unit measuring the rate of evolution incharacteristics of organismsDarwin medal - the most prestigious award given by the InternationalSociety for Reef Studies (ISRS), presented every four years at theInternational Coral Reef Symposium. It is awarded to a senior ISRSmember who is recognized worldwide for major contributions throughouttheir careerDarwin Mounds - two areas of hundreds of sand and cold-water coralmounds at depths of about 1,000 m, in the northeast corner of the RockallTrough, approximately 185 km northwest of the northwest tip of Scotland.The Darwin Mounds cover an area of approximately 100 sq. km. The topsof the mounds are covered with Lophelia pertusa corals and coral rubbleDarwin point - the latitude at which reef growth just equals reefdestruction by various physical forcesDarwinian evolution - evolution of life forms by the process of naturalselection acting on random genetic variationsdata - multiple facts (usually but not necessarily empirical) used as abasis for inference, testing, models, etc.; the word is plural (sing. datum)and takes a plural verbhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (2 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadata management - the act, process, or means by which data aremanaged. This includes the planning, collection, compilation, archival,safe-guarding, listing, organization, extraction, retrieval, manipulation,and dissemination of datadata management and observing system interoperability - theability of two or more systems to exchange and mutually use data,metadata, information, or system parameters using established protocolsor standardsdata management services - a subset of data management andincludes adherence to agreed-upon standards; ingesting data, developingcollections, and creating products; maintaining data bases; ensuringpermanent, secure archival; providing both user-friendly and machineinteroperableaccess; assisting users; migrating services to emergingtechnologies; and responding to user feedbackdata mining - an information extraction activity whose goal is to discoverhidden facts contained in databases. Using a combination of machinelearning, pattern recognition, statistical analysis, modeling techniques anddatabase technology, data mining finds patterns and subtle relationshipsin data and infers rules that allow the prediction of future resultsdata stewardship - a subset of data management and consists of theapplication of rigorous analyses and oversight to ensure that data setsmeet the needs of users. This includes documenting measurementpractices and processing practices (metadata); providing feedback onobserving system performance; inter-comparison of data sets forvalidation; reprocessing (incorporate new data, apply new algorithms,perform bias corrections, integrate/blend data sets from different sourcesor observing systems); and recommending corrective action for errant ornon-optimal operationsdata warehouse - a database, frequently very large, that can accessvast arrays of heterogeneous data, stored within a single logical datarepository, that are accessible to different querying and manipulationmethods . While the warehouse can be distributed over several computersand may contain several databases and information from numeroussources in a variety of formats, it should be accessible through a server.Thus, access to the warehouse is transparent to the user, who can usesimple commands to retrieve and analyze all the information. The datawarehouse also contains data about how the warehouse is organized,where the information can be found, and any connections between data.Frequently used for decision support within an organization, the datawarehouse also allows the organization to organize its data, coordinateupdates, and see relationships between information gathered fromdifferent parts of the organizationdatabase - a structured file of information or a set of logically relateddata stored and retrieved using computer-based meanshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (3 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadatabase management system (DBMS) - a set of computer programsfor organizing the information in a database. A DBMS supports thestructuring of the database in a standard format and provides tools fordata input, verification, storage, retrieval, query, and manipulationdaughter cell - one of the two cells formed by the division of a parent cellDay/Night SST - observations of seasurface temperature obtained during bothdaytime and nighttime orbits from theAdvanced Very High Resolution Radiometer(AVHRR) on NOAA's polar satellite1985-2000 average seasurface temperature fromAVHRR Pathfinder.de facto - in fact; in reality; existing but not officially recognized orlegally establisheddead ahead - a position directly in front of a vesseldecadal - refers to a climatic process that re-occurs every decade or onceevery few decadesdecalcification - the loss of calcium salts from living tissuesdecapod crustacean - a members of theOrder Decapoda, Class Malacostraca,Superclass Crustacea, Phylum Arthropoda;has five pairs of thoracic legs. Examples areshrimps, lobsters, crabs, and hermit crabsA spider crab is a decapodcrustacean.decibel - a logarithmic scale used to denote the intensity (loudness), of asound relative to the threshold of human hearing. A step of 10 dB is a 10­fold increase in intensity or sound energydecibel - unit for measuring sound intensityhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (4 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadeciduous - periodically sheddecomposer - a heterotrophic organism that breaks down dead biologicalmatter and uses some of the products and releases others for use byconsumer organismsdecomposition - the breakdown of organic matter by bacteria and fungidecompression - a change from one ambient pressure to a lowerambient pressure as the scuba diver ascends. Decompression also occursin a decompression chamber. Decompression results in a reduction of gaspressures within the bodydecompression chamber - a hyperbaricsteel enclosure used to treat victims ofdecompression sickness (the "bends") inwhich the air pressure is first graduallyincreased and then gradually decreased.This shrinks the nitrogen bubbles andallows the nitrogen to safely diffuse out ofthe victim's tissuesA NOAA decompressionchamber.decompression dive - any dive where the scuba diver is exposed to ahigher pressure than when the dive began. Decompression occurs as thediver ascendsdecompression diving - scuba diving that requires in-water stops duringascent to the surface to allow off-gassing of nitrogendecompression sickness (the bends) - a dangerous and potentiallylethal condition of divers precipitated by rapid changes in ambientatmospheric pressure, mostly in rapid ascent from underwater, but canalso result from flying in an aircraft too soon after a dive. It occursbecause at high pressures (such as SCUBA divers experience whileunderwater) the blood can contain more dissolved nitrogen than at lowerpressures. When the diver ascends too rapidly, the blood can no longercontain this dissolved nitrogen and tiny gas bubbles begin to form in theblood. Symptoms include: body pain (mainly in the joints), headache,confusion, itchy skin rash, visual disturbances, weakness or paralysis,dizziness, or vertigo. Treatment involves the administration of oxygen andplacing the patient into a decompression chamber until the nitrogenbubbles shrink and safely diffuse from the tissueshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (5 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadecompression stop - a specified timespent at a specific depth as a scuba diverascends from a dive for purposes ofreleasing nitrogen gas from the tissues(nitrogen off-gassing)These NOAA divers aremaking a decompressionstop to allow nitrogen toescape from their tissues.(Photo: NOAA/NationalMarine Fisheries Service)deductive reasoning - an inference in which the conclusion aboutparticulars follows necessarily from general theory. In science, deductivereasoning would involve stating an hypothesis first, and then trying to findfacts that reject the hypothesisdeep fore reef - the deepest seaward part of a coral reef; a vertical cliffbeginning at a depth of about 60 mdeep scattering layer - a thin sound-reflecting layer of zooplankton andnekton that ascends toward the surface at night and descends each day(diurnal vertical migration) in response to changing levels of lightdeep water - the water beneath the permanent thermocline that usuallyhas a low and uniform temperaturedeep-sea corals - stony, soft, gorgonian,black, and horny corals that inhabit thecolder deep waters of continental shelvesand offshore canyons, ranging from 50 ­1000m+ depths. They lack zooxanthellaeand may build reef-like structures or occursolitarilyLophelia pertusa, a deepseastony coral.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (6 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadefinitive host - in a parasite's life cycle, it is the host organism in whichthe parasite reproduces sexuallydeforestation - the removal of trees from a habitat dominated by forestdegeneracy - in relation to the genetic code, more than one codon cancode for the same amino aciddegenerate character - a character, trait or structure that has evolvedto a less developed state from its ancestral form or functiondegenerate code - the genetic code in which more than one triplet ofnucleotides codes for the same amino aciddegeneration - a process by which tissue deteriorates, loses functionalactivity, and may become converted into or replaced by other kinds oftissue; deterioration which causes some degree of loss of originalfunction; the process of declining from a higher to a lower formdegradation - the breaking down of a substance into smaller or simplerpartsDegree Heating Week (DHW) - the NOAA satellite-derived DegreeHeating Week (DHW) is an experimental product designed to indicate theaccumulated thermal stress that coral reefs experience. A DHW isequivalent to one week of sea surface temperature 1 deg C above theexpected summertime maximum. For example, 2 DHWs indicate one weekof 2 deg C above the expected summertime maximumDegree Heating Week accumulation - accumulated thermal stress thatcoral reefs experience over a typical 12-week perioddegrees of freedom - in statistics, the number of independentcomparisons that can be made between the members of a sample; in acontingency table it is one less than the number of row categoriesmultiplied by one less than the number of column categories. The numberof degrees of freedom is defined as the number of observations that canbe chosen freely, i.e., an estimate of the number of independentcategories in a particular statistical test or experimentdeimatic behavior - defensive postures or other visual displays,including color changes, that function to intimidate or frighten anotheranimaldelayed fertilization - when fertilization of an egg does not occurimmediately following introduction of spermatozoa into the femalereproductive tract, but may be delayed for weeks or monthshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (7 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadelta - the fan-shaped area at the mouthor lower end of a river formed by erodedmaterial that has been carried downstreamand dropped in quantities larger than canbe carried off by tides or currentsNile River delta, as seenfrom Earth orbit. (Photo:NASA)delta notation - the absolute abundance of an isotope is difficult tomeasure with accuracy. Therefore, we compare isotopic ratios in a samplewith those in a standard resulting in the delta-notation: d(x) = [{Rx -Rst}/Rst] x 103, where d(x) is the delta-value of a sample, Rx and Rst arethe isotopic ratios in sample (Rx) & standard (Rst). The d-value is therelative difference in the isotopic ratio of the sample and the standard. Itis expressed in part per mille (o/oo); that is why the right-hand side ofthe equation is multiplied by 103 (1000). Carbon and oxygen data fromcarbonates are usually referred to the PDB standard (a belemnite,Belemnitella americana, from the Late Cretaceous PeeDee Formation inSouth Carolina)delta plain - a nearly horizontal portion of a delta which during low tide islargely exposed to the atmospheredeme - a local interbreeding population of a speciesdemersal - pertains to an organism that is essentially bottom living butmay feed and swim in the water columndemography - the rate of growth and the age structure of populations,and the processes that determine these propertiesDemospongiae - a class of asymmetricalsponges (phylum Porifera) which range insize from a few millimeters to over twometers in largest dimension. They arecomposed of spongin fibers alone ortogether with siliceous spicules that aredifferentiated into megascleres (larger size)or microscleres (smaller size) of diverseshapes. The class includes approximately5000 species in 10 orders. They are themost diverse group of sponges and onlyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (8 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Dataexhibit the leuconoid grade of construction.Their geographic distribution in the oceansis from the intertidal to the abyssal zone.Some species inhabit freshwater. Theirshapes include thin encrustations, lumps,finger-like growths, or urns. Pigmentgranules in amoebocytes often makemembers of this class brightly colored,including bright yellow, orange, red, purple,or green. The most economically importantgroup are the bath spongesA yellow barrel sponge inthe class Demospongiae(Photo: Rick Gillis)denaturation - the inducing of structural alterations that disrupt thebiological activity of a molecule. It often refers to breaking hydrogenbonds between base pairs (by heat) in double-stranded nucleic acidmolecules to produce single-stranded polynucleotides, or altering thesecondary and tertiary structure of a protein, destroying its activitydenatured alcohol - ethyl alcohol (ethanol) to which a poisonoussubstance, such as acetone or methanol, has been added to make it unfitfor consumptiondenaturing gradient gel electrophoresis (DGGE) - a method forseparating DNA fragments according to their mobilities under increasinglydenaturing conditionsdendriform - having a structure that resembles a tree or shrubdendrite - a sensory branch of a neuron that carries a nervous inpulse tothe cell bodydendritic - branched like a treeBlack coral is dendritic inshape. (Photo: WaikikiAquarium)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (9 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadendrogram - a branching tree-like diagram used to representphylogenetic paths of evolutiondenitrification - the formation of gaseous nitrogen and/or nitrogenoxides from nitrate or nitrite by denitrifying bacteria during anaerobicrespirationdenitrify - to remove nitrogen from any substance or chemical compounddenitrifying bacteria - anaerobic bacteria in soil or water that use thenitrate ion as a substitute for molecular oxygen during their metabolism.The nitrate is reduced to nitrogen gas (N 2 ), which is lost to theenvironment during the processdentate - having teeth or tooth-like points; serratedenticle - a little toothdenticulate - having an edge with small projecting teethdeoxyribonucleic triphosphates - unreactive nucleotides that closelyresemble the nucleotides that make up DNA. They are 'dummy'nucleotides that act as placeholders when DNA is sequenceddepauperate - an area poor in species richness and/or biodiversity; animpoverished habitatdependent species - a species dependent on another for survival, e.g., apredator on a prey, a commensal or other kind of symbiontdependent variable - the variable being measureddeposit - material left in a new position by a natural transporting agent,such as water, wind, ice, or gravity, or by human activitydeposit feeder - an animal that feeds on nutrients in the sedimentsdepressed - a body shape which is flattened dorso-ventrally, e.g., a ray,skate, monkfishdepth contour - a line on a nautical chart connecting points of equaldepthhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (10 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Dataderived character - in evolution, an advanced trait which only appears insome members of a taxonomic group. For example,a derived character forsome mammals would be the loss of the tail, which occurs in the greatapes and man. Another derived character is the presence of feathers inbirds. Scales are the ancestral feature. Derived characters are also calledapomorphiesdermal - pertaining to or affecting the skindermal flap - a small skin flapdermis - the layer of the skin beneath the epidermis. The dermis islargely fibrous and contains collagen and elastin which are the proteinsresponsible for the support and elasticity of the skin. Depending upon thespecies, the dermis also contains tiny sensory nerve endings, blood andlymph vessels, and sweat and sebaceous glandsdermochelyid sea turtle - a leathery-shelled turtle in the familyDermochelyidae. The leatherback turtle (Dermochelys coriacea) is the onlydermochelyid sea turtle. All other species of sea turtle belong to the familyCheloniidae. Dermochelys coriacea is a federally endangered speciesprotected under the Endangered Species ActDermochelyidae - a family of marine turtle that contains only a singlespecies, the leatherback turtle (Dermochelys coriacea), the largest of allextant turtles. They are carnivorous, feeding almost exclusively on jellyfishdesalinization - the removal of salts from saline water to providefreshwaterdesignated Use - classification specified in water quality standards foreach waterbody or segment describing the level of protection fromperturbation afforded by the regulatory programs. The designated aquaticlife uses established by the state or authorized tribes set forth the goalsfor restoration and/or baseline conditions for maintenance and preventionfrom future degradation of the aquatic life in specific waterbodiesdesmocyte - a connective tissue cell which differentiates into cells whichform the fibrous and supporting tissues of an animals's body; also called a" fibroblast"; in corals, an anchoring cell of the calicoblastic epithelium oraxis epithelium of gorgonianshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (11 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadesmoneme - in hydrozoans, a smallnematocyst with a short, unarmed, spirallycoiled tubule, which functions in entanglingand wrapping around appendages orbristles of prey animalsThe desmoneme of thehydrozoan Hydra vulgaris.(Photo: Alfred H. Gitter)destruction resuspension - the process in which sediment particles onthe substrate are brought back into water column suspension by waves,tides, or winddeterminate cleavage - cleavage resulting in blastomeres each capableof developing only into a particular embryonic structure, not into acomplete organismdetritus - the particulate decomposition ordisintegration products of plankton,including dead cells, cell fragments, fecalpellets, shells, and skeletons, andsometimes mineral particles in coastalwatersLow tide along SouthCarolina shoreline with bitsof sea shells and otherdetritus (Photo: Richard B.Mieremet, NOAA)detritus food chain - a trophic relationship among a variety of speciesthat is sustained at its base by organisms that gather bits of nonlivingorganic materialdetrivore - an animal that eats detritushttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (12 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadeuterostome - one of two distinct evolutionary lines of coelomates,consisting of the echinoderms and chordates and characterized by radialcleavage of the early embryo. The cleaving cells are indeterminate (ifearly embryonic cells are separated, each one develops into a completeorganism). The anus develops from the blastoporedeveloped country - describes nations or countries with social, cultural,industrial and technological advancementdeveloping country - describes regions and countries that are still in theprocess of acquiring modern technology and becoming economicallyproductive. These regions are sometimes called the “Third World”development - the chronological series of changes, from a lower to ahigher state of organization, which multicellular organisms undergo fromthe fertilized egg (zygote) to maturitydevelopmental response - morphological and physiologicalcharacteristics an organism developed in response to prolonged exposureto environmental conditionsdeviation - in statistics, the difference between an actual observation andthe mean of all observationsdewlap - a fold of loose skinFilefishes possessprominent dewlaps ontheir throat-breast region(Photo: NOAA)dextral - right, as opposed to sinistral, or leftdiadromous species - a species which undertakes a spawning migrationfrom ocean to river or vice versadiagenesis - all of the changes that occur to a deposited sediment duringits conversion to rock; includes changes that result from chemical,physical as well as biological processeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (13 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadiagnosis - identifying the nature or cause of some phenomenon; inpathology, (1) the act or process or deciding the nature of a disease byexamination and observation, (2) a careful investigation of the facts todetermine the nature of a thing, and (3) the decision resulting from eitherof thesediagnosis, clinical - a diagnosis based upon signs and laboratoryanalyses while the organism is alivediagnosis, definitive - the name of a disease or pathological condition,as in “white plague”diagnosis, differential - in taxonomy, a statement of the characters thatdistinguish a given taxon from other, specifically mentioned equivalenttaxon; the process of identifying a pathological condition by differentiatingall pathologic processes that may produce similar lesionsdiagnosis, etiological - a diagnosis reflecting identification of the causeor causative agent of a diseasediagnosis, morphological - a diagnosis based upon a description of thealteration of form or structure of the tissues or organs, usually at thegross, histological, cellular or subcellular leveldiagnosis, physical - a diagnosis based on information obtained byinspection or palpation (feeling with the hand)diagnosis, presumptive - an unconfirmed diagnosis based oninterpretation of initial and incomplete informationdiagnostic characters - in taxonomy, the characters, or most importantcharacters, which distinguish a taxon from other similar or closely relatedtaxadiapause - a state of arrested development or growth, accompanied bygreatly decreased metabolismdiaphanous - thin and translucent; semi-transparentdiastema - a space; a gaphttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (14 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadiatom - a unicellular alga that consists oftwo interlocking valves composed of silicaA living diatom(Pleurosigma angulatum)from Arctic seas.diatomaceous - pertaining to diatoms or their fossil remainsdichopatric - pertains to allopatric populations with non-contiguousrangesdichopatric speciation - a type of speciation in which a formerlycontiguous population is split by the rise of some geographical barrier, e.g., a mountain rangedichotomous key - a tool to help identify taxa. It is made up of pairs ofchoices. Each choice is between statements describing specific traits of thetaxa under consideration. Only one statement will be true for each choice.Each choice points to another set of choices until finally only one choiceremainsdiel - a 24-hour period that usually includes a day and its adjoining night;pertaining to the day-night cycledifferential diagnosis - see "diagnosis, differential"diffusion - the movement of particles from a region of higherconcentration to a region of lower concentrationdigestion - the breakdown, by hydrolysis, of complex ingested nutrientcompounds (carbohydrates, fats, proteins) into their building blocks, i.e.,the conversion of food, in the alimentary canal, into soluble and diffusibleproducts, capable of being absorbed into the circulating fluid and the cellsDigital Versatile Disc (DVD) - an advanced type of CD-ROM that holdsa minimum of 4.7 gigabytes (unit of storage) to a maximum of 17gigabytes of information. They are compressed using the MPEG codec,which stores only the changes from one frame to another instead of theentire framehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (15 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadigitiform - finger-shapeddimorphism - having two different distinct forms of individuals within thesame species or two different distinct forms of parts within the sameorganism. It could refer to different colors or color patterns, sizes,anatomical parts, etc. Sexual dimorphism is a common case, where thetwo sexes have different shapes, sizes, etc.dinghy - a small open boatdinoflagellate - a unicellular, generally motile, chiefly marine protist withtwo whip-like flagella. Some autotrophic species, called zooxanthellae, areendosymbionts of corals and other invertebrates. Dinoflagellates areprobably best known as a principal cause of marine bioluminesence, "redtides" and paralytic shellfish poisoningdioecious - having separate sexes. Individuals within the species containonly one or the other of male and female reproductive systemsdiopter - a metric unit used in optics to measure the refractive power of alensdioxin - a chlorinated organic chemical byproduct (dibenzo-p-dioxins),released into the environment from incineration and during industrialprocesses that use chlorine. Dioxins are highly toxic and can haveimmediate and long-term health effects, including skin disease, cancer,and reproductive failuredip net - a small mesh bag, sometimes attached to a handle, shaped andframed in various ways. It is operated by hand or partially by mechanicalpower to capture specimensdiphycercal - a caudal fin shape which is primitively symmetrical andpointed, and with the vertebral column or notochord extending to the tip,as found in primitive fishes, such as lampreys and chimaerasdiploid - the condition in which a cell contains a nucleus with twocomplete sets of chromosomes, one set inherited from each parent. Thediploid condition is often abbreviated as 2n. Most plants and animals arediploid. The term also represents the number of chromosomes in mostcells except the gametes, which are haploid in chromosome numberdirect sun - refers to a measurement based only on direct radiation fromthe sun's disk and excluding indirect radiation from the remainder of theskydirected fishing - fishing that is targeted at a certain species or group ofspecies. This applies to both commercial and sport fishinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (16 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadirectional asymmetry - a pattern of deviation with a side bias. A sidedifference occurs for a given trait, with the larger side generally the sameamong individuals; the right minus the left value of a traitdirectional selection - a type of natural selection that removesindividuals from one end of a phenotypic distribution and thus causes ashift in the distribution. The frequency of an allele is changed in a constantdirection, either toward or away from fixation for that allele. Directionalselection occurs when individuals at one phenotypic extreme have anadvantage over individuals with more common phenotypesdisaccharide - a sugar (carbohydrate) formed by the covalent bonding oftwo monosaccharides. Table sugar, sucrose, is a disaccharidedisciform - round or oval-shapeddiscodermolide - a marine pharmaceutical isolated from deep-watersponges of the genus Discodermia. Discodermolide possesses immunosuppressiveand anticancer properties which inhibit cell division byinterfering with the cell's microtubule networkdiscoidal - disc-shaped; flat and round shapediscrimination - differential response to different stimulidisease - any impairment of an organism'svital functions or systems, includinginterruption, cessation, proliferation, orother malfunctionCoral with yellow banddisease, which results inserious losses of coraltissue.disease vector - an organism which transmits infective organisms fromone host to anotherdisjunct - distinctly separate; disjunct populations are populationsseparated from other potentially interbreeding populations by a distancelarge enough to prevent exchange of genetic materialshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (17 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadisjunct distribution - the discontinuous or separated geographicaldistribution of a species or other taxonomic unitdispersal - the spread of a species to a new location. In many organisms,this happens at a particular stage in the life cycle, and is often critical forthe species' survival. Organisms may disperse as spores, seeds, eggs,larvae, juveniles, or adultsdisphotic zone - the part of the water column that is barely illuminatedby sunlight from above; the "twilight zone" between the photic andaphotic zonesdisplacement behavior - a behavioral response that is appropriate forone situation appears in another situation, for which it is inappropriatedisplay - in animal behavior, visualmessages or body language, used byanimals primarily to communicate anger,fear, and other basic emotions. Displaysare strong indications of an animal'semotional stateAn agonistic display by themale Siamese fightingfish, Betta splendens.(Photo: Jennifer Beavin)Disputed Island - formerly or currently considered U.S. possession bythe U.S. The U.S., through negotiation, has disclaimed ownership of mostislands in favor of another country. Two islands remain contesteddisruptive coloration - a color patternthat breaks up the outline of an organismThe color pattern of thejuvenile spotted drum,Equetus punctatus, is anexample of disruptivecoloration. (Photo: Dr.Tom Doeppner, Brownhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (18 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef DataUniversity)disruptive selection - natural selection that favors individuals thatdeviate from the population average. For example, positive selectionwhich favors individuals that are larger or smaller than averagedissepiment - a horizontal partition within or outside of a corallitedissociation - the temporary or reversible chemical process in which amolecule or ion is broken down into smaller molecules or ionsdissolved oxygen - the concentration of oxygen dissolved in water,expressed in mg/l or as percent saturation, where saturation is themaximum amount of oxygen that can theoretically be dissolved in waterat a given temperature and pressuredistal - the direction away from the midline of the body; the opposite ofproximaldistant linked habitats - connected environments that are intended toconserve "all" biodiversity in an area- typically large and usually includeboth aquatic and terrestrial targetsdistinct - clearly defined and easily recognizeddistinct population segment - "population," or "distinct populationsegment," are terms with specific meaning when used for listing, delisting,and reclassification purposes to describe a discrete vertebrate stock thatmay be added or deleted from the list of endangered and threateneddistribution - the area where a species is known to occurdisturbance - any relatively discrete event in time that disruptsecosystem, community, or population structure and changes resources,substrate availability, or the physical environment; an event or change inthe environment that alters the composition and successional status of abiological communitydisulfide bond - a chemical bond between the sulfur atoms of twodifferent amino acids in a proteindiurnal - active during the day light hourshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (19 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadive computer - a small electronic sensor and calculator, carried by thescuba diver, that calculates and displays the basic information neededduring a dive, i.e., depth, time, decompression status and tank pressure.By constantly monitoring depth and bottom time, dive computersautomatically recalculate the diver's no-decompression status, givinglonger dive times while still keeping the diver within a safe envelope of nodecompressiontime. Computers also monitor ascent rates, logs dives, andmeasures time intervals between divesdive computer algorithm - a suite of equations that compute nitrogenuptake and elimination in tissues from changes in the diver's depth andelapsed time underwaterdive table - dive tables present dive timesfor specific depths, adherence to which, thescuba diver can avoid contractingdecompression sickness (the bends). Thetheory behind dive tables is based on ourunderstanding of how nitrogen is taken upon compression (descent) and given off ondecompression (ascent). The first divetables were devised by John S. Haldane inthe period 1906-1908The PADI (ProfessionalAssociation of DivingInstructors) recreationaldive planner (dive table)has three tables. Table 1gives the maximumamount of time the divercan stay at a certain depthon the first dive, and italso indicates how muchnitrogen the diver has in inthe tissues after a dive.Table 2 is concerned withthe diver's surface intervaltime (how long a divermust remain at thesurface before the nextdive), and Table 3 allowsthe diver to determinesafe diving limits on thenext dive. (Photo: PADI)divergent evolution - the evolution from one species of organism into anumber of different species. As the original population increases in size, itspreads out from its center of origin to exploit other habitats andecological niches. In time, this results in a number of populations, eachadapted to its particular habitat. Eventually these populations, geneticallymay differ from each other sufficiently to become new species. Divergentevolution has also been termed "adaptive radiation"diversity index - a mathematical index of species diversity within acommunityhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (20 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadiverticulum - a blind sac branching off a cavity or canaldiving bell - a hollow, usually invertedvessel, such as one used for diving deep ina body of water. It is open on the bottomand supplied with air under pressure.During the Monitor 2001 Expedition, navydivers utilized a 12-person, two-chambersaturation system with a two-person closeddiving bell. The system can operate as deepas 1,500 ftconsiderably deeper than theMonitor, which rests on the sea floor at adepth of 235 ft. Saturation systems areoften used in deep-water situations (below200 ft) in order to reduce the time lost todecompression during the slow ascent tothe surface required for preventingdecompression sicknessThe SAT system diving bellis raised to the surfaceafter an eight hour dive onthe wreck of the USSMonitor. The bell is thedivers' "taxi" betweentheir topside saturationliving quarters and theirwork site, some 240 ftbelow the surface. (Photo:official U.S. Navy photo byPhotographer’s Mate ChiefPetty Officer (DV/SW)Andrew McKaskle)division - in botanical nomenclature, "division" is used instead of"phylum", and is equal in taxonomic status to the phylumDNA (deoxyribosenucleic acid) - alsotermed deoxyribonucleic acid. The moleculethat encodes genetic information in thecells. It resembles a double helix heldtogether by weak bonds of four nucleotides(adenine, guanine, cytosine, and thymine)that are repeated ad infinitum in varioussequences. These sequences combine intogenes that govern the production ofproteins. The DNA located within thenuclear membrane of eukaryotic cells issometimes referred to as nDNAhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (21 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef DataGraphic of DNA shows thespiral double helixstructure of the molecule.DNA annealling - the reformation of double stranded DNA fromthermally denatured DNA. The rate of reassociation depends upon thedegree of repetition and is slowest for unique sequencesDNA barcode - DNA barcoding is a taxonomic method which uses a shortgenetic marker in an organism's mitochondrial DNA (mtDNA) to quicklyand easily identify it as belonging to a particular species. This approach tospecies identification has its supporters and detractorsDNA chip - a small piece of glass or silicon that has small pieces of DNAarrayed on its surfaceDNA fingerprinting - a method employed to determine differences inamino acid sequences between related proteins. It is used especially foridentification by extracting and identifying the base-pair pattern of anorganism's DNADNA hybridization - the process of joining two complementary strandsof DNA, or one each of DNA and RNA, to form a double-strandedmolecule; a technique in which single stranded nucleic acids are allowedto interact so that complexes or hybrids are formed by molecules withsufficiently similar, complementary sequences. By this means the degreeof sequence identity can be assessed and specific sequences detectedDNA library - a collection of cloned DNA fragments that collectivelyrepresent the genome of an organismDNA ligase - an enzyme that rejoins cut pieces of DNAhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (22 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef DataDNA marker - segments of chromosomal DNA known to be linked withheritable traits or diseases. Although the markers themselves do notproduce the conditions, they exist in concert with the genes responsibleand are passed on with themDNA polymerase - an enzyme that replicates DNA. DNA polymerase isthe basis of PCR ( polymerase chain reaction)DNA probe - in genomics, the DNA affixed to a microarray; a small pieceof nucleic acid that has been labeled with a radioactive isotope, dye, orenzyme that is used to locate a particular nucleotide sequence or gene ona DNA moleculeDNA replication - DNA replication or DNA synthesis is the process ofcopying the double-stranded DNA prior to cell division. The two resultingdouble strands are identical (occasionally errors (mutation) in replicationcan result in a less than perfect copy) and each of them consists of oneoriginal and one newly synthesized strandDNA sequence - the order of nucleotide bases in the DNA moleculeDO (dissolved oxygen) - the concentration of free oxygen dissolved inwater and readily available to aerobic organisms. DO is usually expressedin milligrams per liter, parts per million, or percent of saturationDobson Unit (DU) - the unit of measure for total ozone or other gasesDOC (dissolved organic carbon) - a measure of the organic compoundsthat are dissolved in waterDODS (Distributed Oceanographic Data System) - see "OPeNDAP"Dolastatin 10 - a marine pharmaceutical extracted from the marine seahare (a snail) Dolabella auricularia. It is an anti-cancer drug whichinterferes with cell division processesdolioform - barrel-shapeddoliolaria larva - the larval stage of sea cucumbers immediatelyfollowing the auricularia stage. It is cylindrical in shape and possesses fivetransverse bands of ciliadolomite - a sedimentary rock, similar to limestone, composed largely ofcalcium magnesium carbonate (CaMg (CO3)2)dome shaped - a form that resembles half of a spherehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (23 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadominant species - a species which make up a large proportion of acommunity in terms of its biomass or numbers of individualsdomoic acid - an acidic cyanotoxin found associated with certain diatomblooms. Domoic acid can bioaccumulate in marine organisms that feed onthe phytoplankton, such as shellfish and some fishes. In mammals,including humans, domoic acid is a neurotoxin responsible for AmnesicShellfish Poisoning (ASP) , causing short term memory loss, braindamage, and in severe cases, deathdoppler radar - radar that can measure radial velocity, the instantaneouscomponent of motion parallel to the radar beam (i.e., toward or awayfrom the radar antenna)doppler shift - the change in the tone of a sound caused by the soundsource moving away or towards the listenerdorid nudibranch - a type of nudibranch(order Nudibranchia) possessing a featherlikeexternal gill on the back and arhinophoral sheath. The mantle is thick andextends over the foot. The surface of themantle may bear tubercles which vary insize, shape and number, and are often ataxonomic diagnostic characterThis dorid nudibranch(Chromodoris kunei) feedson sponges and storestheir toxic chemicals in itsbody for protection. Itsstriking colorationadvertise that it is notgood to eat. (Photo:Ocean Futures Society/Richard C. Murphy)dormancy - a period of suspended growth and metabolic activity. Manyplants, seeds, spores, cysts, and some invertebrates become dormantduring unfavorable conditionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (24 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadorsal - refers to the upper or back surfaceof an animalThe upper or back surfaceof this queen angelfish isthe dorsal surface, asopposed to the oppositebelly surface, which is theventral surface. (Photo:Chris Huss, Florida KeysNational Marine Sanctuary)dorsal fin - in fishes, one or more finssituated on the midline of the back, havingspines or rays, sometimes both; excludesthe adipose fin found in some fishes, suchas catfishes and salmonDragonets, such asCallionymus lyra, exhibitstrong sexual dimorphismin the dorsal fin (male[top] and female[bottom]). (Image: NOAA)dorsoventral - an axis extending from the dorsal to ventral surface of ananimal bodydot grid - a technique used to analyze a photograph of a quadrat (photoquadrat),in which a grid of random dots is placed over an image of thephoto-quadrat. It assumes that the proportion of dots that lies on asubstrate is equal to the proportional area of the substratedouble helix - the normal structural configuration of DNA consisting oftwo helices winding about the same axis. The structure of DNA was firstproposed by Watson and Crick (1953) with two interlocking helices joinedby hydrogen bonds between paired basesdoubling time - the length of time required for a population to double insizehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (25 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadownload - transferring data (usually a file) from one computer toanother. The opposite of "upload"downstream - in the direction of the water movementdownwelling - a downward current of surface water in the ocean, usuallycaused by differences in the density of seawaterdrag - the frictional impedance (retarding force) acting on an objectmoving through a fluid parallel and opposite to the direction of motiondredge - a metal collar with an attached collecting bag that is draggedalong the bottom to obtain samples of rock, sediment, or benthicorganismsdredging - a method for deepening streams, swamps or coastal watersby scraping and removing solids from the bottom. The resulting mud isusually deposited in marshes in a process called filling. Dredging andfilling can disturb natural ecological cycles. For example, dredging candestroy coral reefs and other aquatic life; filling can destroy the feedingand breeding grounds for many fish and invertebrate speciesdrift net - a fishing net, often miles inextent, arranged to drift with the tide orcurrent and buoyed-up by floats orattached to a boatA marine turtle is caughtin a drift net. (Photo:NOAA)drop net - a small, usually circular net with weights around the perimeterand a float in the centerdrop root - an adventitious root in mangroves that originates from thebranches, and roots in the surface-sedimentsdrowned river - a former river inundated by a rise in sea level in pasttimesDrupella - a genus of Indopacific muricid gastropod that preys almostexclusively on living coral tissues. Some, if not all of these corallivorousspecies, release a proteolytic enzyme in their saliva that partially digestsits prey. Drupella species may cause considerable damage to reefshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (26 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef Datadry weight - the moisture-free weight of a biological sample obtained bydrying at high (oven-drying) or low (freeze-drying) temperatures for antime sufficient to remove all waterdsRNA (double stranded RNA) - long double-stranded RNAs (dsRNAs;typically >200 nt) can be used to silence the expression of target genes ina variety of organisms and cell typesduct - any tubular structureduplex DNA - double-stranded DNADVD-ram - a high-capacity, high-performance optical disk that allowsdata to be read, written, and erased. It is comparable to a rewritable CD,and can hold up to 2.6 gigabytes of information per sidedychotomic growth - growth of a coral colony in which the corals dividesymmetrically. Since all polyps grow simultaneously, neighboring polypsare the same agedynamic optical demarcation - in animal behavior, a special signallingdevice used by an animal in a stereotypical movement, as for example,the waving of a fiddler crab's claw to attract the attention of othermembers of its speciesdyne - unit of force to accelerate 1 gram to 1 cm per second per seconddysidotronic acid - an antiinflammatory drug derived from marinesponges in the genus Dysidea(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=d (27 of 27) [2/26/2008 9:13:50 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: EThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZEANx ( Enriched Air Nitrox ) - a breathing gas mixture for scuba diverswhich has a percentage of oxygen greater than 21 percent as is found innormal air. This mixture allows longer bottom times at limited depthsearly life history - the stages from egg to juvenile in fish developmentEastern Tropical Pacific Seascape (ETPS) - a coastal and marineregion of 2.1 million square kilometers (roughly 810,815 square miles)that includes the Exclusive Economic Zones (EEZs) of Costa Rica, Panama,Colombia, and Ecuador. The ETPS also encompasses interspersedinternational waters, including the islands of Galapagos, Malpelo,Gorgona, Cocos, and Coibaebb current (ebb) - the movement of a tidal current away from shore ordown a tidal river or estuaryebb strength - phase of the ebb tidal current at the time of maximumspeed; also, the speed at this timeebb tide - that period of tide between a high water and the succeedinglow water; falling tideecad - a non-inheritable plant or animal form produced in response toparticular habitat environmental factors; an environmentally induced formecdysone - a molting hormone of arthropods. It stimulates growth andecdysis (molting)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (1 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef DataEcdysozoa - the ecdyzoans comprise one of the major and largestprotostome groups within the animal kingdom. It includes both thearthropods and the nematodes, as well as lesser groups such as rotifers,cephalorhynchs (which include priapulids, kinorhynchs, and loriciferans),and onychophorans. Ecdysozoans build a cuticle, an outer layer of organicmaterial that functions as a lightweight flexible exoskeleton. The nameEcdysozoa refers to the fact that many members of this group regularlyshed their cuticle, a process called ecdysisEchinodermata - an animal phylum thatcontains starfishes, sea cucumbers, sanddollars, brittlestars, basket stars, sea lilies,feather stars, and sea urchins. Adultsexhibit pentamerous radial symmetry,secondarily derived from a bilateralancestor. They are not at all related to theother radiate phyla, such as the CnidariaA pencil urchin of thephylum Echinodermata.echinopluteus larva - a larval form ofsome echinodermsFree-swimmingechinopluteus sea urchin(Echinocardium cordatum)larva feeds onmicroplankton capturedwith its ciliated arms.(Photo: Jan Parmentier)Echiura - an animal phylum that contains the echiurans or spoonworms.Some species inhabit coral crevices. Echiurans are deposit feedershttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (2 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataecho sounder - an instrument for determining the depth of water bymeasuring the time of travel of a sound-pulse from the surface of a bodyof water to the bottom and backecholocation - the sonar-like ability used by bats, dolphins, somewhales, and two groups of cave-dwelling birds to detect objects in theirenvironment. Using echolocation, the animal emits high-frequency soundsthat reflect off of an object and return to the ears or other sensoryreceptorsecocline - a gradual and continuous change in environmental conditionsof an ecosystem or community; gradual transition between ecotypes; acontinuous change in form as a response to a continuous change in anenvironmentecodeme - an intrabreeding population occupying any specified ecologicalhabitatecological efficiency - the percentage of energy in biomass produced byone trophic level that is incorporated into biomass by the next highesttrophic levelecological equivalent - a different species that occupies a similarecological niche in a similar ecosystem in a different part of the worldecological genetics - the study of genetics in the context of theinteractions among organisms and between the organisms and theirenvironment. It studies phenotypic evolution in natural populations.Thetraits studied are related to those which affect an organism's survival andreproduction (fitness)ecological isolation - a form of reproductive isolation in which twoclosely-related species are separated by what is often a slight difference inthe niches they occupyecological resilience - a measure of resistance to ecological disturbanceand the speed of return to the equilibrium state of an ecosystem; alsocalled "ecosystem resilience"ecological species - a concept of species, in which a species is a set oforganisms adapted to a particular ecological nicheecology - the study of the interrelationships between organisms and theirenvironment, including the biotic and abiotic componentsecomorph - a local population or group whose appearance is determinedby ecological factorshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (3 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataecophenotype - a phenotype showing non-genetic adaptationsassociated with the habitat or environmentecoreach - a subunit of an ecoregion, characterized by distinctivephysical, chemical, and biological conditions within the ecoregionecoregion - a geographic area of relative homogeneity in ecologicalsystems or in relationships between organisms and their environment; arelatively large area of land or water that contains a geographicallydistinct assemblage of natural communitiesecosophy - ecological philosophy; a set of ethics related to ecological andenvironmental matters; It refers to philosophies which have apredominant ecocentric or biocentric perspectiveecospecies - an assemblage of ecotypes which are separated byincomplete sterility barriersecosystem - an ecological community considered together with the nonlivingfactors of its environment as a unitecosystem approach - a strategy or plan to manage ecosystems toprovide for all associated organisms, as opposed to a strategy or plan formanaging individualsecosystem based management (EBM) - EBM integrates knowledge ofecological interrelationships to manage impacts within an ecosystem.Effective implementation of EBM should: (1) consider ecological processesthat operate both inside and outside ecosystem boundaries, (2) recognizethe importance of species and habitat diversity, and (3) accommodatehuman uses and associated benefits within the context of conservationrequirementsecosystem integrity - the ability to support and maintain a balanced,integrated, adaptive biological community having a species composition,diversity and functional organization comparable to that of a naturalhabitat in the regionecosystem restoration - actions taken tomodify an ecosystem for the purpose of reestablishingand maintaining desiredecological structures and processesTwo divers work toreattach a large fragmentof elkhorn coral, Acroporapalmata, at Mona Island,Puerto Rico. The coral inhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (4 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Datathe background has beenattached to the reefframework using stainlesssteel wires. The wire bindsthe coral fragment to theliving coral where it isexpected to reattach tothe live coral. (Photo: ErikZobrist, NOAA RestorationCenter)ecotone - a transitional area between two adjacent ecologicalcommunitiesecotope - the abiotic or non-living part of an ecosystemecotourism - travel undertaken to experience sites or regions of uniquenatural or ecological quality, or the provision of services to facilitate suchtravelecotype - a genetically differentiated subpopulation that is restricted to aspecific habitatecotype - a population in a given ecosystem that is adapted to aparticular set of environmental conditionsecozone - an area at the earth's surface representative of large and verygeneralized ecological units characterized by various abiotic and bioticfactorsecteinascidin - a marine pharmaceutical derived from the sessiletunicate Ecteinascidia turbinata which acts by disrupting the structure ofDNA in the cells of solid tumorsecto- - a prefix meaning 'outside'ectoderm - the outer germ layer of cells in an embryo that gives rise tothe outer layer of skin (epidermis) and neural tissueectodermis - the outer cellular covering of a polyphttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (5 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataectoparasite - a parasite which lives onthe surface of its hostA marine ectoparasitelodged in a fish's mouth.(Photo: NOAA OceanExplorer)ectoplasm - the clear, nongranular portion of the cell cytoplasm justinside the cell membraneEctoprocta - an animal phylum synonymous with the phylum Bryozoa,the "moss animals"ectotherm - a cold-blooded animal, one which cannot internally regulateits body temperature, such as a reptile, fish, or amphibian, whose bodytemperature is mostly determined by the surrounding environment andbehavior; poikiloltherm; cold-blooded organisms maintain their bodytemperatures in ways different from warm-blooded animals, such asmammals and birdsectothermic - having an internal body temperature that is dependent onthe surrounding temperature. Most aquatic animals are ectotherms; alsocaled poikilothermal or "cold blooded"eddy - a circular movement of waterformed on the side of a main currentAVHRR image of eddy inthe Gulf of Mexico.(Image: NOAA-14 PolarOrbiting Satellite/LSUEarth Scan Lab, CoastalStudies Institute)edentate - toothlesshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (6 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataedge effect - habitat conditions created at or near the more-or-less welldefinedboundary between ecosystems (ecotone). Typically there is anincreased richness of organisms resulting from the mixing of twocommunities where they joineelgrass - a common seagrass (Zosteramarina) distributed from Greenland toFlorida that serves as an important habitatfor fishes and shellfish. Unfortunately,approximately 90 percent of all eelgrassthroughout its range along the Atlanticcoast has been destroyedEel grass meadows.(Photo: NOAA)effector - a muscle or gland that receives a stimulus from a neuronefferent - moving or carrying outward or away from a central part. Refersto blood vessels, nerves, etc. For example, blood vessels carrying bloodaway from the heart or nerve fibers conducting impulses from the brain ornerve cordeffluent - a discharge of pollutants into the environment, partially orcompletely treated or in its natural state. Generally used in regard todischarges into waters; in contrast to an emmission, which is generallyused in regard to discharges of pollutants into the airefflux - an outward flow; flux of water, elements or gases out of anecosystem or ecosystem componenteffort - the amount of time and fishing power used to harvest fish.Fishing power includes gear size, boat size, and horsepoweregestion - the elimination of undigested food materials from an organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (7 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataegg - a female sex cell or gamete with the haploid number ofchromosomes. It may be fertilized by a sperm cell to produce a zygotewith the diploid number of chromosomes for that particular species. Theeggs of some species may develop into multicellular individuals withoutbeing fertilized by a sperm cell. This is the process of parthenogenesisegg case - the leathery case whichcontains the developing embryo inhagfishes, sharks, rays, skates andchimaeras; also called a "mermaid's purse"A skate egg case(Mermaid's purse)revealing the skateembryo contained within(Photo: David Siebenaller)egg chamber - a cavity or chamber in the sand, excavated by a nestingseaturtle, into which eggs are deposited for incubationEkman layer - the thin horizontal layer of water riding on top of theocean that is affected by windEl Niño - an irregular variation of oceancurrent that from January to March flowsoff the west coast of South America,carrying warm, low-salinity, nutrient-poorwater to the south. It is associated with theSouthern Oscillation. These two effects areknown as the El Niño Southern Oscillation(ENSO). El Niño usually occurs during theChristmas season when the equatorialcounter current strengthens and flowseastward to overlie the cold, nutrient-richwaters of the Peru current. It does notGraphic of sea surfacetemperatures show ElNiño, May 1997.usually extend farther than a few degrees south of the equator, butoccasionally it does penetrate beyond 12 deg S, displacing the relativelycold Peru Current. The effects of this phenomenon are generally shortlived,and fishing is only slightly disrupted. Occasionally, the effects aremajor and prolongedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (8 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataelasmobranch - a member of the SubclassElasmobranchii of cartilaginous fishes.These include sharks, rays, and skatesThe manta ray is a large,graceful, mostly planktonfeedingelasmobranch.They also feed on smallfishes. (Photo: Jackie Reid/Flower Garden BanksNational Marine Sanctuary)elastic - capable of returning to an initial form or shape afterdeformation; resilientelectric field - the region extending outward in all directions from anelectrically charged material that affects other electrically charged objects;the area around an electrified object where other charges are affectedelectrocyte - a cell that generates electricity. The electric currentsproduced by some species of fishes, such as torpedo rays and electriceels, are generated in stacks or columns of electrocytes.The electrocytesof most 'electric fishes' are modified muscle cells. They are usuallyarranged in columns within electric organs. When an electrocyte isstimulated, a movement of ions (electrically charged atoms) across thecell membrane results in an electric dischargeelectrogenic - capable of generating electric currents and a painfulelectric shock, as in electric rayselectromagnetic radiation - energy that travels through space in theform of waves. The highest frequencies in the spectrum ofelectromagnetic radiation are gamma-rays; the lowest frequencies areradio waves. All electromagnetic radiation travels at the speed of light.Shorter wavelength radiation (eg, ultraviolet) carries more energy and islikely to be more harmful to living tissueelectromagnetic receptor - a neurological receptor that responds tolight, electricity, and magnetism. Photoreceptors respond to light andelectroreceptors detect electrical energyelectron microscope - a microscope which beams electrons, instead oflight beams, at and through the object of interest. This type of microscopeprovides the greatest resolution of extremely small details in thenanometer size range. Magnification may be up to x300,000http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (9 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataelectron spin resonance - a chronometric dating technique thatestimates dates from observation of radioactive atoms trapped in calcitecrystals present in a number of materials, such as limestone, coral, shells,teeth, and bones; also called "Electron Paramagnetic Resonance (EPR)"electrophoresis - a technique for separating different types of moleculesbased on their patterns of movement in an electrical fieldelectroporation - the creation of reversible small holes in a cell wall ormembrane through which foreign DNA can pass. This DNA can thenintegrate into the cell's genomeelectroreceptor - a receptor organ that senses changes in an electricalcurrent in the surrounding water, for example, the ampullae of Lorenziniin sharkselectrotaxis - the movement of organisms in response to an electric fieldeleutherobin - a marine pharmaceutical initially isolated from the softcoral Eleutherobia sp. from Western Australia, and more recently fromErythropodium caribaeorum, an encrusting coral found in South Floridaand the Caribbean. Eleutherobin is a potent cancer cell inhibitorelevation - the height of a geographic location above a fixed referencepoint, often the mean sea levelELISA (enzyme-linked immunosorbent assay) - a rapid test where anantibody or antigen is linked to an enzyme as a means of detecting amatch between the antibody and antigen; a technique for detectingspecific proteins by using antibodies linked to enzymesemarginate - a notched margin, but notso deeply as to be forked. As an example, atrout possesses an emarginate caudal finThe caudal fin of this trouthas an emarginate shape.(Image: U.S. Fish andWildlife Service)embayment - an indentation in the shoreline that forms a bayembryo - the stage of early growth and differentiation of tissues and theformation of primitive organs and organ systems of a multicellularorganism, from fertilization until birth or hatching. In seed plants, it is theyoung sporophyte that resulted from the union of the egg and one of thetwo tube nucleihttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (10 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataemergent vegetation - plants growing in water but emerging from it,usually at the water's edgeemersed - rising above the water surfaceemigration - the movement of individuals out of a population or from onearea to anotheremission - any substance that is discharged into the soil, air or waterempirical - based on experience or observations, as opposed to theory orconjectureemulsion - a suspension of small globules of one liquid in a second liquidwith which the first will not mixencrustation - a crustlike deposit or growth over a substratumencrusting colony - a thin colony whichadheres closely and is attached to thesubstrateEncrusting tunicates atGray's Reef off SapeloIsland, Georgia (Photo:Karen Angle).encryption - a process that transforms plain text or data and makes itunreadable to an outside party. The transformation is made using amathematical formula and a "key," which is a special data item, usuallykept secret, used as input into the formula along with the data. To readthe data from the encrypted version the key and the formula must beknownendangered species - under the Endangered Species Act (ESA), anendangered species is one that is in danger of extinction throughout all ora significant portion of its rangeEndangered Species Act (ESA) - an Act of Congress passed in 1966that establishes a federal program to protect species whose survival isthreatened by habitat destruction, overutilization, disease, etc.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (11 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataendangered taxa - taxa in danger of extinction and whose survival isunlikely if causal factors continue operating. Included are taxa whosenumbers have been drastically reduced to a critical level or whole habitatshave been so drastically impaired that they are deemed to be inimmediate danger of extinction. Also included are those that possibly arealready extinct, in so far as they have not been seen in the wild in thepast 50 yearsendemic species - a species whose distribution is restricted to aparticular areaendergonic reaction - a chemical reaction that requires energy in orderto proceed, so that the products have a higher free energy than thereactantsendo- - a prefix meaning 'inside'endobenthic - refers to meiofaunal-sized organisms that move within thesedimentsendocoel - the space of the cnidarian gastrovascular cavity between twomesenteries belonging to one and the same pairendocrine gland - a gland that manufactures hormones and secretesthem directly into the circulatory system to act at distant sites in the bodyendocrine system - the system of ductless glands in animals thatsecrete hormonesendocytosis - uptake of material into a cell by the formation of amembrane-bound vesicleendoderm - the inner germ layer of diploblastic and triploblastic embryosthat gives rise to internal tissues such as the gut and gut derivatives, e.g.,air bladder, lungs, and the lining of the digestive tractendogenous - having its origin, or produced within the organism or oneof its partsendogenous rhythm - a metabolic or behavioral rhythm that originateswithin the organism and persists regardless of external conditionsendolithic - growing within a rock or any other hard inorganic substratumendolithic algae - algae which burrow into calcareous rocks or coralsendonuclease - a nuclease that cleaves nucleic acids at specific internalsiteshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (12 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataendoparasite - a parasite which lives in the internal organs of its hostendophytic - living within the tissues of a host plant or algaendopinacocyte - in sponges, a pinacocyte lining the incurrent andexcurrent canalsendopinacoderm - in sponges, a surface lined with endopinacocytesendoplasm - the granular portion of the cell cytoplasm between theectoplasm and nuclear membraneendopodite - in crustaceans, the inner branch, or ramus, of a biramousappendage; the main shaft of that appendage; also called "endopod"endoskeleton - skeleton, or supportstructure, which is on the inside of theorganism's body. All vertebrates possess anendoskeleton that is made of either boneand/or cartilageEndoskeleton of a 35-ton,13-m gray whale on thefloor of the Santa CruzBasin.endosymbiont - an organism which lives within the body of anotherorganism as part of a symbiotic relationship. The relationship may bemutualistic or commensalistic; also called an 'endobiont'endosymbiotic - being symbiotic and living within the body of anindividual of the associated speciesendothecal dissepiment - one of many horizontal partitions across thecorallite within the corallite wallhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (13 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataendothermic - an animal that is able tomaintain a body temperature that variesonly within narrow limits by means ofinternal mechanisms. Most birds andmammals are considered endothermic; alsocalled homeothermal or "warm blooded"Whale fat (blubber) aidsthese humpback whales inmaintaining a relativelyconstant bodytemperature. (Photo: DaveMatilla, NOAA/NOSNational MarineSanctuaries)endothermic reaction - a reaction which absorbs heatendozoochory - the dispersal of plant seeds or spores within the body ofan animal, as passing through the animal's digestive system; also called"endochory"endozooic - living inside an animalenergy - the capacity for doing work. Forms of energy include light,thermal, mechanical, electrical, and chemical. Energy may be transformedfrom one form into anotherenergy flow - the movement of energy through a community via feedingwebsenrichment - the addition of nitrogen, phosphorus and carboncompounds or other nutrients into a lake or other waterway that greatlyincreases the growth potential for algae and other aquatic plants. Mostfrequently, enrichment results from the inflow of sewage effluent or fromagricultural runoffENSO (El Niño Southern Oscillation) - see El Niño and SouthernOscillationenterocoelous - the mesoderm and coelom initially develop as pouchesoff of the primitive digestive tract (archenteron) of an embryo.Enterocoelous development of the coelom occurs in deuterostomesenteron - the alimentary canal or the gut of an embryo. Some structuresof the enteron may not be completely developed or differentiated in earlyembryonic growthhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (14 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataentrainment - the synchronisation of one biological rhythm to another orto a zeitgeber cycle, e.g. circadian rhythms are often entrained to thelight-dark cycle; also, the process of small organisms being captured inthe cooling water of a power plantentropy - the measure of the disorder or randomness of energy andmatter in a systemenvironment - everything external to the organismenvironmental impact - a positive or negative effect of any action upona give area or resourceenvironmental impact assessment - detailed studies which predict theeffects of a development project on the environment. They also provideplans for the mitigation of adverse impactsenvironmental impact statement (EIS) - a key component of anenvironmental impact assessment. An EIS provides a summary of theimpact assessment study, including the main project characteristics,environment aspects most likely to be affected, possible alternatives, andsuggested measures and systems to monitor or reduce any harmful effectsenvironmental resistance - the limits set by the environment whichprevent organisms from reproducing indefinitely at an exponential rateenvironmental sensitivity index (ESI)map - ESI maps serve as quick referencesfor oil and chemical spill responders andcoastal zone managers. They contain threekinds of information: (1) Shorelines (colorcodedto indicate their sensitivity to oiling);(2) Sensitive biological resources (such asseabird colonies and marine mammalhauling grounds. They are depicted byspecial symbols on the maps); and (3)A section of anSensitive human-use resources (such asEnvironmental Sensitivitywater intakes, marinas, and swimmingIndex map, showing partbeaches). Project scientists have createdof the Point Reyes NationalSeashore. Shorelines arecollections of ESI maps, called ESI atlases,color-coded to show theirfor most coastal areas in the US, includingsensitivity to oiling.Alaska, Hawaii, the Great Lakes, and the(Photo: NOAA)Trust Territories. Each atlas includes mapsand additional data and information.Starting in 1995 with the outer coast ofCalifornia, ESI project members began using a Geographic InformationSystem (GIS) to produce updated ESI maps that are higher in quality andcan be more readily reproducedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (15 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataenvironmental sex determination (ESD) - the phenomenon in whichthe sex of the offspring is determined by environmental factorsenvironmental stress - severeenvironmental effects on the naturalecosystemA catastrophicenvironmental stress-the1989 grounding of theExxon Valdez, whichspilled an estimated 11million gallons of crude oilover 1,300 miles ofcoastline.environmentalism - advocacy for, or work toward, protecting the naturalenvironment from destruction by human activitiesenzootic - an infectious disease constantly present in an animalpopulation but having low incidenceenzyme - an organic catalystenzyme unit (EU) - a unit to measure enzymatic activity in cells. Oneenzyme unit is the quantity of enzyme needed to cause a reaction toprocess 1 micromole of substance per minute under specified conditionseon - a unit of time equal to 1 billion yearseosinophile - a type of white blood cell(leukocyte) that engulfs and digestsbacteria. Eosinophils, along with othertypes of white blood cells, are important inan organism's internal defense systemA human eosinophile. Thesmaller round cells are redblood cells.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (16 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataephemeral - short-lived, transitoryephyra larva - a jellyfish (Scyphozoa)larval stage that develops into the adultmedusa or jellyfishEphyra larva of thejellyfish Aurelia. (Photo:Rick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)epibenthic (epifaunal or epifloral) - refers to organisms living on thesurface of the substrateepibiont - an organism that lives on the outside of another organismepicenter - the point on the earth's surface directly above thehypocenter, where the energy of an earthquake is first releasedepidemic - the widespread outbreak of a disease, or a large number ofcases of a disease in a single community or relatively small areaepidemic spawning - the simultaneousshedding of gametes by a large number ofindividualsStar coral sheddinggametes in an epidemicspawning event.epidermis - the outer epithelial layer of the bodyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (17 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataepifauna - animals that live upon or are associated with substratumfeaturesepilithic - growing on rock or stone. Epilithic organisms live attached torocksepimeletic behavior - behavioral activities associated with care-giving orhelp to other individualsepipelagic zone - the surface layer of the ocean (also called the sunlightzone) which extends from the surface to 200 meters. Most of the visiblelight exists in this zone. Wide variations in temperature occur in this zone,both latitudinally and seasonallyepipelic - living on or in fine sediments, such as mud or sandepiphyte - microalgal organism living on a surface (e.g., on a seaweedfrond); a plant living on the surface of another plantepipsammic - attached to, or moving through, sand particlesepistasis - the prevention or masking of the expression of an allele atone locus by an allele at another locusepistome - the flap over the mouth of some lophophoratesepitheca - a layer of calcium carbonate that grows outside corallite wallsepitheliomuscular cell - a columnar epithlial cell that containscontractile fibrils in cnidarians. Epitheliomuscular cells facilitate polypmovement and contractionepithelium - a tissue layer of cells which lines body cavities and tubules,or covers surfaces. The cells may be ciliated or non-ciliated, and may besquamous (flat, scale-shaped), cuboidal (cube-shaped), or columnar(column-shaped) in shape. The cells may occur in a single layer, or maybe multi-layered (stratified)epithet - the second name of the binomial given to a species; the speciesname or second part of a Latin binominal. In the name "Homo sapiens,"sapiens is the specific epithethttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (18 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataepitoky - a mode of reproduction unique topolychaete worms in which the wormundergoes a partial or entire transition intoa pelagic, sexually reproductive form,known as an epitoke. In many cases,epitoky involves loss or degeneration ofdigestive structures and enhancement ofswimming, sensory, and reproductivestructures. The epitoke is a considered adelicacy in some islands of the South Pacific.Palolo (Eunice viridis) arepolychaete worms that areabout 12 inches long andlive in burrows dug intothe coral pavement on theouter reef flat. The wormis composed of twodistinct sections. The frontsection is the basicsegmented polychaetewith eyes, mouth, etc.,followed by a string ofsegments, called the“epitoke,” that containreproductive gametes.(Image: www.nps.gov)epizoite - an animal that lives on the surface of another organismepizootic - a temporal pattern of disease occurrence in an animalpopulation in which the disease occurs with a frequency clearly in excessof the expected frequency in that population during a given time interval;an outbreak (epidemic) of disease in an animal populationepizootiology - the study of the factors which determine frequencies anddistributions of infectious diseases among non-human animalsepoch - a division of geologic time next shorter than a period. Example:the Pleistocene epoch is in the Quaternary periodequatorial current - an ocean current which flows westerly near theequator. There are two such currents in both the Atlantic and PacificOceans. The one to the north of the equator is called the North EquatorialCurrent and the one to the south is called the South Equatorial Current.The easterly flowing Equatorial Countercurrent lies between the EquatorialCurrentsequilibrium - the state in which the action of multiple forces produces asteady balance, resulting in no change over timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (19 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataequinox - either of the two times during a year when the sun crosses thecelestial equator and the length of day and night are equalera - a division of geologic time next smaller than the eon and larger thana period. Example: The Paleozoic era is in the Phanerozoic eon andincludes, among others, the Devonian perioderectile - capable of being raised or erected, often referring to spines ofbony fisheserg - unit of work measuring force of one dyne applied over onecentimeterergo - therefore; henceerosion - the wearing away of the land surface naturally by wind orwater, but is often intensified by human's land-clearing practices. Therunoff is harmful to coral reefserrant - motile or free swimmingThe polychaete Nereis sp.is an errant species ofworm. (Photo: U.S.Geological Survey)ERSST (Extended Reconstruction of SST) data set - a globallycomplete reconstruction of of sea surface temperatures (SST) based on insitu measurements and satellite data produced at a monthly, 2 degreeresolutionerythrophore - a chromatophore which contains reddish pigments foundin carotenoids and pteridineshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (20 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataesca - in some fishes, e.g. frogfishes, the first dorsal fin ray is modified tofunction as a fishing pole and lure. The part close to the body is theillicium or fishing pole. The esca is the lure on the end of the illeciumescape reaction - in animal behavior, a response to a predator or otherdangerous situation, in which the threatened animal may flee, hide, orstay motionless in order to avoid contactescarpment - a steep slope or long cliff that results from erosion orfaulting and separates two relatively level areas of differing elevationsESRI (Environmental Systems Research Institute, Inc.) - a worldleader in GIS (geographic information system) software and technologyessential amino acid - an amino acid that cannot be synthesized byanimals and therefore has to be ingested with foodessential fish habitat - under theMagnuson-Stevens Fishery Conservationand Management Act, those waters andsubstrates that fishes require to spawn,breed, feed, or grow to maturityThis tangle of redmangrove roots in theJobos Bay, Puerto RicoNational EstuarineResearch Reserve is anessential fish habitat,serving as a both anursery area andprotection for manymarine animals. (Photo:NOAA)EST (expressed sequence tag) - a small part of the active part of agene, made from cDNA which can be used to fish the rest of the gene outof the chromosome by matching base pairs with part of the gene. The ESTcan be radioactively labeled in order to locate it in a larger segment of DNAestablishment - the subsequent growth and/or reproduction of acolonized species in a new territoryester - a chemical compound formed by the reaction of an organic orinorganic acid with an alcohol, with the elimination of waterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (21 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataesthetasc - a sensory seta covered by cuticle projecting from mostantennules and antennae in crustaceansesthete - a light sensitive organ in a minute vertical canal in the upperlayer of the shell plate of a chitonestimate - the best guess arrived at after considering all the informationgiven in a problemestimator - in statistics, an estimator is a function of the known data thatis used to estimate an unknown parameteret-epimeletic behavior - behavioral activities which solicit attention,care, or help from other individual; care-soliciting behaviorethogram - an inventory or catalog of all of the behavioral patterns of anorganism or a speciesetiology - the science that is concerned with origins and causes of diseaseeuchromatic - containing euchromatin, the extended regions ofchromosomes. These extensions become most dense and thus mostvisible microscopically during the metaphase of the cell cycle; in ahistological preparation, denotes any cell or tissue that stains the color ofthe stain usedeuchromatin - chromosome regions that are loosely packaged and moreaccessible to RNA polymerases than heterochromatin. These regions alsostain differentially in chromosome banding preparationseudistomins - a family of marine pharmaceuticals, produced by thetunicate Eudistoma sp, which holds promise as potent antibiotic and antitumordrugseukaryotic - descriptive of organisms with cells having a distinct nucleuswith nDNA, and intracellular membranes. This includes all protists, fungi,plants and animals. The organisms are termed eucaryoteseumetazoa - all multicellular animals excluding the spongeseuphotic depth - the depth to which significant phytoplanktonphotosynthesis can take place. It is typically taken to be the depth atwhich PAR falls to 1 percent of its value just below the surfaceeuphotic zone - the layer of the ocean that receives sufficient sunlightfor photosynthesis. The depth to which 1% of incident light penetrates(1% is the minimum amount of light required for photosynthesis)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (22 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataeuryhaline - pertaining to an aquatic organism that can withstand abroad salinity rangeeuryokous - adapted to numerous ecological nicheseuryphagous - describes an organism which gains its nourishment froma large variety of foodseurytele - a type of nematocysteurythermal - pertaining to an aquatic organism that can withstand abroad temperature rangeeustatic - pertains to world-wide change in sea level, such as that causedby tectonic movements or expansion or contraction of glacierseutrophic - a situation in which theincreased availability of nutrients such asnitrate and phosphate stimulates thegrowth of plants such that the oxygencontent is depleted and carbon sequesteredEutrophic conditions canresult in large fish kills, asmany fish die fromreduced levels of oxygenin the water.evagination - protrusion of some part or organ from its normal position;the act of turning inside out; an outgrowth or protruded partevanescent - short-lived; temporary; soon disappearingevent - in probability, an event is an occurrence or the possibility of anoccurrence that is being investigatedeverted - turned inside outhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (23 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataevo-devo (evolutionary developmental biology) - a relatively newapproach in biology that seeks to explain the causes biodiversity. Itattempts to integrate every area of biology from molecular geneticsthrough embryology, molecular and population genetics, comparativemorphology, paleontology, molecular evolution, ecology and functionalmorphology. It offers both an account of developmental processes andalso new integrative frameworks for analyzing interactions betweendevelopment and evolution. A major challenge lies in integrating theseapproaches to understand the evolution of biodiversity at a mechanisticlevel. The "evo-devo" community needs access to genomic information ona wide range of organismsevolutionarily significant unit (ESU) - a population or group ofpopulations that is considered distinct (and hence a "species") forpurposes of conservation under the Endangered Species Act. To qualify asan ESU, a population must 1) be reproductively isolated from otherconspecific populations, and 2) represent an important component in theevolutionary legacy of the biological speciesevolutionary significant unit (ESU) - a group of organisms that hasundergone significant genetic divergence from other groups of the samespecies. Identification of ESUs is based on natural history information,range and distribution data, and results from analyses of morphometrics,cytogeneevolutionary tree - a lineage designed to show the evolutionary historyof relationships among groups of organismsex situ conservation - the preservation of components of biologicaldiversity outside their natural habitats, e.g., in zoos, aquaria, botanicgardens and gene banksexaptation - in evolution, a biological adaptation where the biologicalfunction currently performed by the adaptation was not the functionperformed while the adaptation evolved under earlier pressures of naturalselectionexcitotoxin - a toxic molecule that stimulates nerve cells so much thatthey are damaged or killed. For example, domoic acid, a toxin producedby certain species of algae. Domoic acid binds to a receptor that helpsnerve cells control the flow of ions across their cell membranes. Thereceptor no longer works correctly, and the uncontrolled flux of ionsdamages and eventually kills the nerve cellExclusive Economic Zone (EEZ) - the sovereign waters of a nation,recognized internationally under the United Nations Convention on theLaw of the SEA as extending out 200 nautical miles from shore. Within theU.S. the EEZ typically is between three and 200 miles from shoreexcretion - a physiological process, originating in cells, that removeswaste materials produced by the bodyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (24 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataexcurrent canal - in sponges, an excurrent canal discharges waterreceived from the apopyle, into the spongocoel (atrium). The water thenpasses through the osculum or oscula to the outsideExecutive Order - one of a number of official documents, numberedconsecutively, through which the President of the United States managesthe operations of the Federal GovernmentExecutive Order 13089 - on June 11, 1998, President Clinton issuedExecutive Order 13089 directing all agencies to increase their efforts toprotect our nation's coral reef resources. The executive order calls for theestablishment of a U.S. Coral Reef Task Force, cochaired by theSecretaries of the Interior and of Commerce. The Task Force will developand implement a comprehensive program of inventory, monitoring, andresearch to map and identify the major causes and consequences ofdegradation of coral reef ecosystemsExecutive Order 13158 - on May 26, 2000, President Clinton signedExecutive Order 13158 on Marine Protected Areas (MPAs) to strengthenthe protection of U.S. ocean and coastal resources. This significantmilestone in ocean conservation directs the Departments of Commerceand the Interior, and other federal agencies, to strengthen and expand anational system of MPAs by working closely with state, territorial, local,tribal, and other stakeholdersexergonic reaction - a chemical reaction that releases energyexhalant system - in sponges, part of the aquiferous system betweenthe apopyle and the and osculumEXIF format - EXIF stands for Exchangeable Image File Format, and is astandard for storing interchange information in image files, especiallythose using JPEG compression. Most digital cameras now use the EXIFformatexocoel - the spaces of the gastrovascular cavity of cnidarians locatedbetween two mesenteries belonging to different pairsexocrine gland - a gland that secretes its product through a ductexogenous - having its origin external to the organism or ecosystemexogenous deoxyribonucleic acid (DNA) - refers to anydeoxyribonucleic acid (DNA) which originates outside of the organism ofconcern or study; also referred to as foreign DNA or heterologous DNAhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (25 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataexon - a nucleotide sequence (of DNA or RNA) in a gene that codes forpart or all of the gene product or for some control function. In eukaryotes,exons are separated by non-coding sequences called introns; that part ofthe gene (a section of DNA) that is transcribed into messenger RNA andencodes a proteinexopinacoderm - the unicellular external surface of a sponge (ectosomecomposed of pinacocytes)exopodite - in crustaceans, the outer branch, or ramus, of a biramousappendage; also called "exopod"exoskeleton - an external skeleton or supportive covering of an animalformed from the ectoderm, as for example, the shell coverings of acrustacean, the calcium carbonate secretions of stony corals, or the bonyplates of an armadilloexothecal dissepiment - a horizontal partition outside of the corallitewallexothermic reaction - a reaction that gives off heatexotic species - a non-native species that is introduced into an area;also referred to as alien or invasive speciesexozoochory - the dispersal of plant seeds or spores accidentallyattached to the outside of an animal's body; also called "epizoochory"expected value - in statistics, the mean value calculated for a statisticover an infinite number of samplesexplanate coral colony - a colony that spreads horizontally as thebranches fuse into a solid or near solid plateexploitation - the removal of individuals or biomass from a population bypredators or parasitesexponent - an expression of the number of times that a base is used as afactorexponential growth - growth in the size of a population in which therate of growth increases as the size of the population increases; change ina population growth rate that is proportional to the size of the populationexposure - contact with infectious agents such as bacteria or viruses in amanner that promotes transmission and increases the likelihood of diseasehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (26 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataexposure suit - a full or partial garmentthat is worn by scuba divers for protectionagainst heat loss. Water conducts heataway from the body about 20 times fasterthan air. In addition to providing warmth,exposure suits also serve to protect fromminor scrapes, stings and abrasions. Thereare three kinds of exposure suits: wet suits,which allows water to seep in between theinsulated rubber covering and the skin.They come in a variety of thicknessessuitable for insulation in water as cold as50 degrees F; body suits, made from Lycraor nylon.They provide full length abrasionprotection, but only minimal insulation; anddry suits which are water-tight garmentsthat keeps the divers body warm byproviding insulation with a layer of gas,such as air. It is used for diving in watersthat are too cold for comfortable wet suitprotection, usually below 65 degrees FArctic diver withrebreather and heated drysuit prepares to descendinto the ice. (Photo: NOAA/OAR/National UnderseaResearch Program)extant - of a taxon: having living representatives; of a specimen: still inexistenceextant species - species which are now livingexteroreceptor - a neurological receptor that receives information fromthe environment external to the organismextinct - of a taxon: having no living representatives.extinct species - species for which there are no living representativesextinction - the evolutionary terminationof a species caused by the failure toreproduce and the death of all remainingmembers of the species; the natural failureto adapt to environmental changeManatees are threatenedwith extinction from bothhabitat destruction anddirect effects from humanencroachment, such asserious wounds from boatpropellors.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (27 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataextinction coefficient - a coefficient measuring the rate of extinction, ordiminution, with distance of transmitted light in sea waterextirpated species - a species that has been destroyed or removedcompletely from a particular area, region, or habitat. The species,however, may exist elsewhere, e.g., in a zoo or aquariumextra- - outside, beyondextra-embryonic membrane - membranes possessed by amniote(reptiles, birds, and mammals) embryos that allow these classes ofvertebrates to be free of aquatic habitats for reproduction, and in theirevolution, occupy terrestrial habitats. The membranes are the amnion,yolk sac, allantois and chorionextracellular digestion - a form of digestion that takes place within thelumen of the digestive system. The resulting nutrient molecules aretransferred into the blood or body fluids through the process of absorptionextratentacular budding - an asexual form of reproduction wheredaughter corallites grow from the outside wall of the parent corallitesextreme environment - an environmentcharacterized by extremes in growthconditions, including temperature, salinity,pH, among othersCrowded life in an extremeenvironmentRiftiatubeworms, mussels, andscavenging crabs found ata hydrothermal vent sitein the Pacific Ocean. Mosthydrothermal vents arefound at an average depthof about 2,100 meters(7,000 ft) in areas ofseafloor spreading alongthe Mid-Ocean Ridgesystem. (Photo courtesy ofC. Van Dover.)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (28 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef Dataextremophile - a microorganism that lives at extreme levels of pH,temperature, pressure or salinityextrinsic - not forming an essential part of a thing; arising or originatingfrom the outsideextrinsic factor - a biotic or abiotic factor acting on an organism orpopulation from outside the organism or population.These are the physicaland chemical features of the environment, as well as other organismsexumbrella - the upper surface of the bellof a medusa or jellyfishThe rounded upper surfaceof this jellyfish is theexumbrella.Eye-in-the-Sea - a video camera capable of operating in deep water (upto 3,000 ft) for days at a time. It is mounted within a steel structure andanchored to the seafloor by its own weighteyespot - any light-sensing structure insome primitive organisms that consists of apigmented area and light sensitive cells;also called an ocellusEyespots of a free-livingflatworm, Planaria dugesia.(Top)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (29 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef DataRevised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=e (30 of 30) [2/26/2008 9:13:58 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: FThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zfacies - a geographical variant of a community, or a variant whichincludes a conspicuous or abundant species not present in the maincommunity; all of the characteristics of a particular rock unit. Thecharacteristics of the rock unit come from the depositional environment,which puts its own distinctive imprint on the sediment, making a particularfacies. Thus, a facies is a distinct kind of rock for that area or environmentfacultative - able to exist under more than one set of environmentalconditions. For example, a facultative parasite may exist either as aparasite or as a saprotroph (gaining nutrients from dead organic matter)facultative mutualism - mutualism in which one or both species in theassociation may survive and maintain populations in the absence of theother speciesFagatele Bay National MarineSanctuary - Fagatele Bay, located onTutuila, the largest island of AmericanSamoa, was designated as a NationalMarine Sanctuary in 1986. It is the smallestand most remote of all the national marinesanctuaries encompassing only 163 acres(.25 sq. mi.). Fagatele is the only truetropical coral reef in the National MarineSanctuaries ProgramFagatele Bay, a NationalMarine sanctuary inAmerican Samoa. (Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (1 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafaginism - cannibalism by adults on their youngFahrenheit temperature scale - a thermometric scale on which thefreezing point of water is at 32 degrees F (Fahrenheit) above the 0 degree(F) mark on the scale, and the boiling point of water is at 212 degrees Ffalcate - scythe-shapedFalcate-shaped dorsal finof an Orca Whale. (Photo:Robyn Angliss, NOAA/NMML)falciform - curved like a long, narrow scythefalculate - a shape that is curved and sharp-pointed, like a clawfamily - a taxonomic group containing one or more generafan palm - the only species of tree(Pritchardia remota) on the island of Nihoain the Northwestern Hawaiian IslandsThe fan palm is the onlyspecies of tree on theisland of Nihoa, in theNorthwestern HawaiianIslands. (Photo: SheilaConant)FAQ (Frequently Asked Questions) - documents that list and answerthe most common questions on a particular subjecthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (2 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafarctate - a filled or solid structure, as opposed to one that is tubular orhollowfaro - a rhomboid-shaped, steep-sided, continental shelf atollfat - a triglyceride (lipid) that is usually solid at room temperaturefathom - is a unit of length often used to measure depth of water and isequivalent to 6 feet or 1.8 metersfathometer - an instrument for measuring underwater depth using soundfatty acid - any of a class of saturated aliphatic monocarboxylic acidsthat form part of a lipid molecule; a product of fat hydrolysisfault - a crack or fracture in the Earth'scrust accompanied by a displacement ofone side of the fracture. Movement alongthe fault can cause earthquakes or, in theprocess of mountain-building, can releaseunderlying magma and permit it to rise tothe surfaceAn aerial view of the SanAndreas fault in theCarrizo Plain, CentralCalifornia.(Photo: USGeological survey)fault zone - an area in which there are several closely spaced faultsfauna - the entire group of animals found in an areahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (3 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafeather star - feather stars areechinoderms in the class Crinoidea. Thejuveniles attach to the substrate by a stalkwith rootlike branches. The mouth sidefaces upward. In the adult stage they breakaway from the stalk and move about freely.They possess appendages, known as cirri,attached to the underside of the body withwhich they cling to to sponges or corals.Some can swim by undulating movementsof the arms. Some have five arms, othersup to 200Feather stars care verymobile, but usually theycling by their cirri tosponges or corals. Theyare very abundant in areasexposed to strongcurrents, because theyfeed on plankton.(Photo:Teresa (Zubi) Zuberbühler(www.starfish.ch))feces - egested undigested food wastesfecundity - the productiveness or potential productiveness of anorganism, measured in the number of viable offspring it may produce; thenumber of eggs an animal produces each reproductive cycle; the potentialreproductive capacity of an organism or populationFederal Geographic Data Committee (FGDC) - coordinates thedevelopment of the National Spatial Data Infrastructure (NSDI). The NSDIencompasses policies, standards, and procedures for organizations tocooperatively produce and share geographic data. The 17 federal agenciesthat make up the FGDC are developing the NSDI in cooperation withorganizations from state, local and tribal governments, the academiccommunity, and the private sectorFederal Information Processing Standards (FIPS) codes - astandardized set of numeric or alphabetic codes issued by the NationalInstitute of Standards and Technology (NIST) to ensure uniformidentification of geographic entities through all federal governmentagencies. The entities covered include: states and statistically equivalententities, counties and statistically equivalent entities, named populatedand related location entities (such as, places and county subdivisions),and American Indian and Alaska Native areasFederal waters - generally waters from 3 - 200 miles offshorefeeding guild - a group of unrelated fishes that feed on similar foods, e.g., benthivore, detritivore, herbivore, insectivore, omnivore, planktivore,piscivore, etchttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (4 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Dataferal - existing in a wild or untamed state.The term is often used todescribe an animal which has reverted to such a state from domestication.An example of the latter is a once farmed fish, or the progeny of a farmedfish, which is living (but not necessarily breeding) in a wild statefermentation - the anaerobic breakdown by microorganisms of complexorganic substances, especially carbohydrates, to CO2 and alcohol;fermentation is also used to describe the process by which variouschemical or pharmaceutical compounds can be made in large tanks, calledfermenters, that contain microorganisms or plant or animal cells, and thenutrients they require to live and growfermi - unit of length equal to one quadrillionth of a meterferruginous - rust colorfertilization - the process where a spermatozoan (sperm cell) penetratesthe cell membrane of an egg cell and the nuclei of the sperm and egg cellsjoin together and their chromosomes combine to form a diploid zygotefetch - the uninterrupted distance over which the wind blows (measuredin the direction of the wind) without a significant change of directionfibrillose - covered with or containing fibrilsfibropapillomatosis - a fibroepithelial tumor, probably caused by aherpes-type virus, found in juvenile, subadult, and adult sea turtles,causing them to be emaciated, weak, depressed, and anemic. Affectedturtles may have flotation problems resulting from fibrous tumors in thelungs. Fibrous tumors are also found in visceral sites, such as liver, lung,kidney and gastrointestinal tract.fide - on the authority of, according to, with reference to a publication orto a cited published statementfield guide - a pocket-size book or a CD containing taxonomic keys foridentification, illustrations and/or photographs of organisms, distributionmaps, and some natural history notesfield research - the study of organisms in their natural habitatfila - a thread-like structure, a filamentfilamentous - slender and/or threadlikehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (5 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafilefish - any species of bony fishes in thefamily Monacanthidae.The body of filefishesis laterally compressed and roughlydiamond-shaped in profile. The filefish getsits name from its very rough skin.The firstdorsal fin is essentially a single sharp spinewhichThe plainhead filefish,Monacanthus hispidusis, acommon inhabitant o coralreefs and seagrass beds inthe tropical Atlantic.Strays are often found asfar north as New England.(Photo: NOAA)filial - an offspring generationfiliform - thread-shapedfiliform tentacle - a long, thin tentacle of a hydrozoan polyp, usuallyconcentrated toward the basefilter feeder - an organism that feeds by capturing particles suspended inthe water column. A synonym of suspension feeder.fimbriate - a structure that is fringed atthe marginThe papillae of thisscorpion fish possess afimbriate appearance.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (6 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafin - organ of locomotion and balance infishes and some other aquatic animals; infishes, fins are of two types: paired(pectoral and pelvic fins) and unpaired ormedian (dorsal, adipose, anal, and caudalfins and finlets). Fins of bony fishes containhard spines and/or soft rays, which may be Drawing of a bony fishjointed and branched. The spines and raysthat shows the locations ofare covered by integument. Counts ofthe median and pairedspines and rays are used as diagnosticfins. (Graphic: Cristi A.Cave, Stream Biology andcharacters in fish taxonomy; aEcology)membranous, finlike, swimming organ, asin pteropod (having the anterior lobes ofthe foot modified so as to form a pair ofwinglike swimming organs), and heteropod(where the foot developed into a median fin) mollusksfin (scuba) - a rubber or plastic shoe-likedevice attached to the feet to increasesurface area for greater thrust whileswimming; they may be open heeled or fullfooted.Scuba divers prefer the open heelstyle, usually worn with bootiesOpen heel SCUBA fins withmask and snorkel. Thistype of adjustable-strapfin is worn over neoprenebooties.fin membrane - the thin membranebetween and connecting fin rays and spinesof fishesNote the thin finmembrane stretchedbetween the hard spinesand soft rays of thehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (7 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datasergeant major, Abudefdufseptemfasciatus (Photo:John E. Randall, Ph.D.)fin ray - a slender, rod-shaped structurethat supports the membranes of the fins offishes. There are two types of rays, softrays and spines. Soft rays are jointed, oftenbranched, and flexible near their tips.Spines are unjointed, unbranched, andusually sharp at the tip and stiff along theshaftCaudal fin of a fish. The finis stained with the vitaldye calcein which colorscalcium/calcified bonematrix. Note the softsegmented fin rays.(Photo: Dr. M. KathyLovine, WashingtonUniversity, St. Louis, MO)fine sediment - a sediment composed of fine-grained materials, such asclay or mud particlesfingerling - a young or small fishfinlet - one of several small nonretractablefins located dorsally andventrally between the second dorsal andanal fins and the caudal fin of scombroids(mackerals, tuna) and some other fishes, e.g., sauries and snake mackerals. Finletsappear to have a hydrodynamic function infishes that have been studied for thischaracterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (8 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef DataA series of small finletsbetween the dorsal andanal fins and the tail of abluefin tuna. (Photo:NOAA)fire coral - a species of hydroid (Milleporasp.) that frequently is brownish to orangeyellowin color and forms encrustingcolonies that can assume the shape of itssupport structure. Their nematocystsrelease a virulent toxin which causespainful welts on human skin. Fire corals arenot true corals (see Hydrozoa)Fire coral in the FlowerGarden Banks NationalMarine Sanctuary (Photo:Jackie Reid)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (9 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafire wall - a combination of hardware and software that separates anetwork into two or more parts for security purposesfirst revisor - in zoological nomenclature, the person who first selectsone of two or more simultaneously published names that he or shebelieves represent the same taxon, or who selects which one of two ormore taxa the name will apply to for which identical names have beensimultaneously published; also applies to first selection of multiple originalspellingsFirst Revisor (Principal of) - the principle that the relative precedenceof two or more names or nomenclatural acts published on the same date,or of different original spellings of the same name, is determined by thefirst reviserfirst stage regulator - attached to thescuba tank, the first stage regulatorreduces the high tank pressure to anintermediate pressure of 100 to 150 psiabove the surrounding water pressureThe first stage regulator isattached to the scubatank. (Photo: NOAA/National UnderseaResearch Program)firth - a partly land-locked arm of the seaFISH (fluorescence in situ hybridization) - hybridization of clonedDNA to intact chromosomes, where the cloned DNA has been labelled witha fluorescent dye. This is the major method of physical mapping of clonedDNA fragments on chromosomesFish Barcode of Life (Fish-BOL) Initiative - a global effort tocoordinate an assembly of a standardized reference sequence library forall fish species, one that is derived from voucher specimens withauthoritative taxonomic identifications. The benefits of barcoding fishesinclude facilitating species identification for all potential users, includingtaxonomists; highlighting specimens that represent a range expansion ofknown species; flagging previously unrecognized species; and perhapsmost importantly, enabling identifications where traditional methods arenot applicable.This effort is creating a valuable public resource in the formof an electronic database containing DNA barcodes, images, andgeospatial coordinates of examined specimens. The database containslinkages to voucher specimens, information on species distributions,nomenclature, authoritative taxonomic information, collateral naturalhistory information and literature citationshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (10 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafish census - the collection of data over time concerning the species offishes in an area, their relative abundances, and population densitiesfish kill - the sudden death of fishes due to the introduction of pollutants,toxic blooms, or the reduction of the dissolved oxygen concentrationfish louse - a parasitic crustacean on marine and freshwater fishesFishBase - a repository of available information on the taxonomy,biology, ecology, occurrence and utilization of fishes. It holds publishedinformation on almost all of the estimated 25,000 existing fish species.The information is arranged in 55 subject tables. It can be accessedthrough the Internet ( http://www.fishbase.org) or installed on a PC froma CD-ROM. At the heart of FishBase is the authoritative taxonomic fishclassification established by W.N. Eschmeyer (California Academy ofScience). It ensures that all information is assigned to current scientificnames, even if a publication uses an outdated namefisher - anyone involved in the harvesting, processing, or marketing offishes or shellfishfisherman - a person, male or female, who harvests fishes or shellfishfishery - all the activities involved in catching a species of fish (or otheraquatic organisms) or a group of species; the sum of all fishing activitieson a given resource, e.g. a shrimp fishery, or activity of catching fish fromone or more stocks, e.g. the North Sea cod fishery, or it may also refer toa single type or style of fishing, e.g., trawl fisheryfishery closure area - a fishery which is closed or restricted by agovernment entity. Such closure prohibits fishing for commercial,recreational, or subsistence purposesFishery Conservation and Management Act - the federal law thatcreated the regional councils and is the federal government’s basis forfisheries management in the EEZ. Also known as the Magnuson Act after achief sponsor, Senator Warren Magnuson of Washington Statefishery management council - a regional, quasi-governmental groupwith authority to manage fisheries in federal waters, generally from threeto 200 miles offshorefisheye lens - an ultra-wide angle lens giving 180o angle of view. Thewidest fisheye lenses produce a circular and very distorted imagefishing mortality - deaths in a fish stock caused by fishinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (11 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafissure - a deep and narrow depression cutting across the reef front withorigins relating to jointing planes in the reef limestone or non-limestonebedrockfistula - an abnormal passage between two organs or between an organand the outside of the body. Fistulae are caused by ulceration, congenitalmalformation, or when damaged tissues come into contact with eachother and join together while healingfistule - in sponges, a tubular structure on the upper surface, upon whichthe osculum is situated. A fistule is frequently found on species thatburrow into mud or excavate coralfitness - the potential evolutionary success of an allele or genotype,which is defined as the reproductive success or the proportion of genesthat an individual leaves in the gene pool of a population (expectedcontribution to future generations). The individuals with the greatestfitness leave the largest numbers of offspring.The fitness of genes andorganisms is always relative to the other genes and organisms that arepresent in the same populationfitness landscape - in evolutionary biology, fitness landscapes are usedto visualize the relationship between genotypes (or phenotypes) andreproductive success. It is assumed that every genotype has a welldefined replication rate (often referred to as "fitness") This fitness is the"height" of the landscape. Genotypes which are very similar are said to be"close" to each other, while those that are very different are "far" fromeach other. The two concepts of height and distance are sufficient to formthe concept of a "landscape". The set of all possible genotypes, theirdegree of similarity, and their related fitness values is then called a fitnesslandscape; also called "adaptive landscape"five prime and three prime ends (5' and 3' ends) - a double strandedDNA (the double helix) always has an orientation or directionality.Because of this directionality, the nucleotides along one strand areheading in one direction (e.g. the 'ascending strand') and the others areheading the other (e.g. the 'descending strand'). For reasons of chemicalnomenclature, the asymmetric termini of each strand are called the 5' and3' ends (pronounced "five prime" and "three prime"). Nucleotidesequences are read by enzymes in the "5' to 3' direction". In a verticallyoriented double helix, the 3' strand is said to be ascending while the 5'strand is said to be descendingfixed action pattern - in ethology or animal behavior, a complexbehavioral response which once released by a key stimulus, runs tocompletion. It is performed in a very similar way by its individualmembers; also called " modal action pattern" because of individualvariations in behaviorfjord - a deep-water inlet, carved out by glacial action and usuallysurrounded by mountains or steep slopeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (12 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Dataflabellate - fan-shapedA flabelliform Gorgonia(Photo: NOAA)flabelliform - fan-shapedflaccid - limp, flabby, lacking in firmnessflagellate - a unicellular protist with one or more flagella, a whip-likeorganelle often used for propulsion; having or resembling a lash or whip(as does a flagellum)flagellated chamber - in sponges, an internal cavity that is lined withchoanocytesflagelliform - whip-shapedflagellum - a whip-like appendage used forlocomotion in sperm cells and somebacteria, fungi, and protistsA bacterium with a whiplikeflagellum. (Photo: U.S.National Institutes ofHealth)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (13 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Dataflagship species - popular, charismatic, socially appealing species thatserve as symbols and rallying points to evoke public sympathy andstimulate conservation awareness and action. Whales, seals, sea lions,and marine turtles are flagship speciesflange - a projecting rimflaring corallite - a corallite with expanding, trumpet-like curves to theouter corallite wallflat - very shallow and still water, usually with a sand or mud bottomflatfish - any fish species in the order Pleuronectiformes, which includesflounders, flukes, dabs, halibuts, plaice, soles, and turbots. All flatfisheshave an unusualy compressed body form adapted to life on the bottom.As the bilaterally symmetrical immature forms develop, one eye migratesto either the left or right side, depending upon the species. The bodycompresses laterally with changes in the skeletal and internal organsystems, and the animal rests on either its left or right side. The side onthe bottom is pale, while the other side is strongly pigmented. Somespecies are able to change their pigmentation to match the appearance ofthe bottomflavescent - yellowish colorflipper - the phenomenon in which the sex of the offspring is determinedby environmental factorsflock - a socially coordinated group of birdsflood tide - the phase of the tide between low water and the subsequenthigh tide; a rising tidefloodplain - a lowland along a riverbank, lake, and coastline which issubjected to periodic inundationflora - the entire group of plants found in an areaFlorida Current - the segment of current between the Gulf of MexicoLoop Current and the Gulf Stream, from the Dry Tortugas to thesoutheastern tip of Florida, and confined by the 250 meter and 500 meterisobathshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (14 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef DataFlorida Keys National Marine Sanctuary- the Florida Keys National MarineSanctuary was designated as a nationalmarine sanctuary in November of 1990.The Florida reef tract is the most extensiveliving coral reef system in North Americanwaters and the third largest barrier reefsystem in the world. The sanctuary extends220 miles in a northeast to southwest arcbetween the southern tip of Key Biscayne,south of Miami, to beyond, but notincluding the Dry Tortugas IslandsThe Florida Keys NationalMarine Sanctuary.(Graphic: NOAA)Florida Reef Tract - the third largest barrier reef in the world, runningfrom the Miami area southwest to the Dry Tortugasfloridean starch - a carbohydrate which is the chief food reserve in redalgae (Rhodophycota). It is a branched polymer of glucose similar toamylopectin of green plants. It occurs as granules in the cytoplasmfloriform - flower-shapedflotsam - wreckage or discarded material,e.g. garbage, found floating on the surfaceof the ocean or washed up on the beachSeahorses caught inflotsam off the Colombian/Panamanian coast. (Photo:NOAA)flow cytometry - a technique used to sort cells or other biologicalmaterials by means of flow through apertures of defined size or by lasersortinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (15 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef DataFlower Garden Banks National MarineSanctuary - the Flower Garden BanksNational Marine Sanctuary was designatedas a national marine sanctuary on January17, 1992. The sanctuary is located about110 miles off the coasts of Texas andLouisiana, and harbors the northernmostcoral reefs in the United States and servesas a regional reservoir of shallow waterCaribbean reef fishes and invertebrates.The coral reefs rise to within 66 feet of thesurface. The area containing both the Eastand West Banks is 41.7 square nauticalmiles in size and contains 350 acres of reefcrest. In October 1996, Congress expandedthe sanctuary by adding a small third bank,Stetson Bank, located about 70 nauticalmiles south of Galveston, Texas.Environmental conditions at Stetson Bankdo not support the establishment and growth of coral reefsGraphic depicting locationof the Flower GardenBanks National MarineSanctuary in the Gulf ofMexico.fluctuating asymmetry (FA) - a pattern of small, random deviationsbetween sides in the size of a given trait - the random component ofbilateral asymmetry, i.e., subtle random deviations from perfect bilateralsymmetry. It arises when genetic or environmental stressors disruptdevelopmental processes that normally promote symmetrical growth.Fluctuating asymmetry is of particular interest because of its potential asa biomonitor of environmental quality. It is a relatively new tool forassessing the impact of environmental and genetic stresses onpopulations. One of the main advantages of FA is its increased sensitivityrelative to other bioindicators. If effective, this tool could allow biologiststo monitor populations and make recommendations before a severeproblem arises, often without the high cost of other solutionsfluorescence - the emission of light from a substance caused byexposure to radiation from an external sourcefluorescent pigment - a pigment that absorbs light at one wavelengthand emits it at a different wavelength. The emitted light usually has alower energy than the light absorbed by the pigmentfluorometer - an instrument for measuring fluorescenceflushing - the exchange of water between an estuary or coastal waterwayand the oceanflushing time - the time required for a waterbody, e.g., an inlet, estuary,marina, etc. to exchange its water with water from the parent waterbodyfluting - grooves in the shaft of a columnhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (16 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Dataflux - the rate of flow of energy or particles across a given surfaceflyway - a broad-front band or pathway used in bird migrationfocal species - the species that is identified as being most sensitive to athreat in a changing environment. Species are being lost from areas inwhich their habitats are being destroyed, fragmented or simplified. Focalspecies can be used to identify the appropriate spatial and functionalparameters that must be present in an environment if it is to retain thebiota that occurs therefoliaceous - leaf-like; also folioseFoliaceous coral. (Photo:NOAA)foliform - leaf-shapedfoliose coral - a coral whose skeletal form approximates that of a broad,flattened platefood chain / food web - all the interactions of predator and prey,included along with the exchange of nutrients into and out of theecosystem. These interactions connect the various members of anecosystem, and describe how energy is converted and passes from oneorganism to anotherfood pyramid - pyramid-shaped diagram which shows feedingrelationships within a food chain, e.g. that herbivores are smaller, morenumerous and faster breeding than the predators that feed on themfoot - in mollusks, the structure found on the animal's ventral side, thatconsists primarily of muscle, and is modified for locomotion, foodgathering, and diggingforage - to search for foodhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (17 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Dataforage fishes - small fishes which which occur in large numbers andserve as food for predatory fishesforamen - an opening in a structureForaminifera - planktonic and benthicprotozoan protists that have a test (shell)composed of calcium carbonateThese foraminiferans havea test composed ofcalcium carbonate. (Photo:Rick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)fore reef - the portion of a reef seaward of reef crest. A synonym of reefslopefore reef escarpment - a slope or cliff seaward of the fore reef terrace,at a depth of about 25-30mfore reef slope - a sand covered, gradual or sharply descending slope;the next-to-deepest part of the fore reeffore reef terrace - the uppermost portion of the fore reef; a flat plainbeginning at the base of the buttress or mixed zone, at a depth of about60 mforeign DNA - refers to any deoxyribonucleic acid (DNA) which originatesoutside of the organism of concern or study; also referred to asexogenous DNA or heterologous DNAforeign fishing - fishing by a foreign (non-U.S.) fishing vessel(Magnuson-Stevens Fishery Conservation and Management Act)formal metadata - metadata that follows an FGDC approved standardformalin - formaldehyde gas dissolved in water. Formalin is used as afixative and preservative in some collections of biological specimensformenkreis - a group of related allopatric species or subspecieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (18 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafossa - a hole or cavity in the coral skeletonfossorial - adapted for a digging or burrowing life style or behaviorfounder effect - in evolution, the effect of establishing a new populationby a small number of individuals, carrying only a small fraction of theoriginal population's genetic variation. As a result, the new populationmay be distinctively different, genotypically and phenotypically, from theparent population from which it is derived. In extreme cases, the foundereffect is thought to lead to the speciation and subsequent evolution of newspeciesfoveolate corallite - a corallite of some species which is located at thebase of a funnel-shaped depressionFRA (Fish Replenishment Area) - a designated area, within a FisheriesManagement Area (FMA), where certain specified fish harvesting activitiesare prohibitedfractal - the smallest part of a mathematical set of numbers which whenrepeated or scaled will maintain the primary permutation; an object whichis self-similar at all scales. Regardless of scale the same level of detail andappearance is presentfractal geometry - a method to study shapes that are self-similar overmany scalesfragile - easily brokenfragmentation - a type of asexual reproduction common in branchingcorals. Branches break off from the parental colony to establish othercolonies nearbyframework - a rigid, wave resistant calcareous structure constructed bysessile organisms such as sponges, corals, and bryozoans, in a highenergy environmentfree - unconstrained or not chemically bound in a molecule or not fixedand capable of relatively unrestricted motionfree dive - diving without the assistance of any breathing apparatus, suchas scubafree energy - the usable energy in the bonds of a molecule; energy thatis available to do useful work. A decrease in free energy accompanies anyspontaneous processhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (19 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafree radical - an atom or group of atoms possessing an unpairedelectron; free radicals are highly reactive and bind with other molecules,thus disrupting normal cellular processes and causing cellular damage(oxidative stress)free-living coral - a coral which is not attached to a substratefreely associated state - an "associated state" is used to describe a freerelationship between a territory and a larger nation. The details of anassociation are specific to the countries involved. This is also known as"free association." The Federated States of Micronesia, the Republic ofPalau, and the Republic of the Marshall Islands are associated with theUnited States under what is known as the Compact of Free Association.Under this relationship the states possess international sovereignty andultimate control over their territory. However, the governments of thoseareas have agreed to allow the United States to provide defense, fundinggrants, and access to US social services for citizens of these areasFrench Frigate Shoals - an open atoll inthe Northwest Hawaiian Islands (NWHI)that consists of a large, crescent-shapedreef surrounding numerous small, sandyislets. While the land area is only onefourthsquare kilometer (67 acres), thetotal coral reef area of the shoals is over938 square kilometers (232,000 acres).The reef system associated with FrenchFrigate Shoals supports the greatest variety Sponges in French Frigate of coral species in the NWHI, withShoals reef. (Photo: NOAA)41species of stony corals documented. Italso supports more than 600 species ofinvertebrates, many of which are endemicto the area, over 150 species of algae, and many species of fishes.Hundreds of green sea turtles travel to the shoals for safe nesting. Themany small islets of French Frigate Shoals also provide refuge to thelargest sub-population of endangered Hawaiian monk sealsfrequency - the number of items occurring in a given categoryfrequency - the number of cycles of a wave per second. Frequency isexpressed as units of Hertz (Hz)frequency distribution - a graphical, tabular, or mathematicalrepresentation of the manner in which the frequencies of a continuous ordiscrete random variable are distributed over the range of its possiblevaluefrequency of recombination - the number of crossover events observedbetween two linked loci expressed as a proportion of the total number ofmeioses sampledhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (20 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafreshwater lens - an underground pool of freshwater that takes theshape of a lens. Lenses are critical sources of fresh water on manyislands. The freshwater lens is suspended by seawater. For example, whenrain falls on a limestone island, it quickly sinks into the porous calcareousrock, picking up a mineral content from the organic material, soil and rockthat it passes through. This water accumulates within the rock, continuingit’s downward path. Eventually, it meets the layer of salt water thatpermeates limestone platforms at sea level. Because fresh water is lessdense than salt water, the lens of fresh water will float on top of the salinegroundwater. In many areas, this lens is very thin. If the sea levelincreases and/or if the lens becomes depleted because of excesswithdrawals, seawater can intrude and make the water unsuitable formany uses. The size of the lens is directly related to the size of the island.Larger islands have lenses that are less vunerable to tidal mixing andexcessive withdrawalsfriction - the mechanical resistive force offered by one medium or bodyto the relative motion of another medium or body in contact with the first;also called "frictional force"frictional drag - the molecular (viscous) retarding force on an object,such as air, as it moves across the earth's surfacefringing reef - a shelf reef that growsclose to shore. Some develop aroundoceanic islands. A synonym of shore reefA fringing reef off a SouthPacific Island.frogfish - any of over 40 species of bonyfishes in the family Antennariidae. They aresmall globose fishes with loose prickly skin,limb-like pectoral fins with an elbow-likejoint, small round gill openings, and a verylarge upward directed mouth. The firstdorsal spine is modified into a moveablefishing rod (Illicium) tipped with a lure(esca)Closeup of a pink frogfishperched on a purplesponge (Photo: JeffDawson)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (21 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef Datafrond - a leaf-like thallus, such as the body of a kelpfront - a boundary or transition zone between two air or water masses ofdifferent propertiesfrontal threat display - agonistic display behavior in which a fish facesanother fish and flares its gill covers (opercula) and opens its mouth wide.This behavior may indicate aggression, territoriality or self defense (bymaking it appear too large to attack or eat)frugivore - an animal which primarily eats fruitfrustule - a nonciliated, planula-like cnidarian larva. It constricts off froma polyp, creeps along the substrate, settles, and develops into a polyp;the siliceous shell of a diatomfry - newly hatched, active feeding post larval fishes; may include all fishstages from hatching to fingerlingfucoid - seaweed-shapedfucosyltransferase inhibito - a suspected antiinflammation andantitumor compound isolated from marine sponges in the genusSarcotragusfull thickness - in histopathology, a lesion, wound or process thatinvolves all layers of tissues in a structure. For example in the body wall ofa polyp, the epidermis, mesoglea, and gastrodermis ; also called"transmural"fulvous - dark yellow, orange-yellowfulvous - dull yellow colorfundamental niche - the full range of physical, chemical, and biologicalfactors a species could use if there were no competition from other speciesFungi - the Kingdom of usuallymulticellular, heterotrophic eukaryotes thathave multinucleated cells enclosed withincell walls. Nutrition is obtained bydecomposing dead and dying organismsand absorbing the decomposition productsFungi growing in anOregon woodland. (Photo:http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (22 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef DataCarol Baldwin, NOAA/OMAO)fungicide - a chemical compound used to retard or prevent the growth offungifunnel organ - a structure, common in several phyla, that leads from thecoelom to the outside and may be used for waste elimination and/orreproduction (Annelida, Brachiopoda, and other small phyla); the modifiedtubular opening of the mantle cavity in cephalopods used in generating astream of water for use in locomotionfurcate - to divide into branches; to forkfusiform - a shape that is tapered at both ends; spindle-shaped; torpedoshaped,like a mackerel(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=f (23 of 23) [2/26/2008 9:14:04 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: GThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZG1 - phase in the cell cycle between the completion of cell division andthe initiation of DNA synthesisG2 - phase in the cell cycle between the completion of DNA synthesis andthe next cell divisionGa - symbol for one billion (109) years. The a stands for the Latin annus,yearGaia theory - a model in which the organisms on the Earth have radicallyaltered its composition. A stronger position is that the Earth's biosphereeffectively acts as if it is a self-organizing system, which works in such away as to keep its systems in some kind of equilibrium that is conduciveto lifegale - a storm with wind speeds between 34 to 40 knotsgaleiform - helmet-shapedgall - an abnormal outgrowth caused by infection or irritation by certainfungi or bacteriagame species - species of animals that are hunted or fished, forpurposes of sport, recreation, and food capturehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (1 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagamefish - a species of fish considered to possess sporting qualities onfishing tacklegamete - a sex cell, e.g., a spermatozoan or egg cell, produced bysexually reproducing orgnaismsgamete bundle - in coral sexual reproduction, the polyps of manyspecies release bundles of eggs and sperm cells, called gamete bundles,that float to the sea surface. The layers surrounding the egg and spermbundles soon rupture, releasing the gametes at the surface, wherefertilization occursgametocyte - a reproductive cell capable of dividing by meiosis toproduce gametes, e.g., a spermatocyte or oocytegametogenesis - the development and maturation of gametes (sex cells)through meiosis. The process is termed 'spermatogenesis' in thedevelopment of sperm cells and 'oogenesis' in the development of egg cellsgametophyte - a life cycle stage in certain algae that produces male andfemale reproductive organsgamma ray - an electromagnetic wave or photon emitted from thenucleusgamodeme - a deme forming a more or less isolated local intrabreedingcommunityganglion - a cluster of nerve tissue primarily composed of cell bodies ofneurons, usually located outside of the central nervous system; a knotlikeswelling of an invertebrate's nerve cord that contains a concentration ofcoordinating nerve cellsgap analysis - a Geographic Information System (GIS) methodology toidentify the distribution of biodiversity over large spatial areas. It wasdeveloped in 1988 by the U.S. Geological Survey in an effort to ensurethat regions rich in species diversity are conserved with the hope that thiswill eliminate the need to list species as threatened or endangered in thefuture. The gap analysis approach uses maps of vegetation and predictedanimal distributions to locate centers of species richness outside areascurrently managed for biodiversity protection. These are considered the"gaps" of gap analysis. Thus far, its use primarily has been in theterrestrial spheregap dynamics - the formation and replacement of patches or gaps in aseascape or landscape, as in the destruction of corals and growth of newcorals in that openinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (2 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagap formation - the creation of a habitat patch of differentcharacteristics within a larger patch; the generation of patches in aseascape or landscape, such as the generation of openings in a coral reefas a result of storm damage or coral deathgap junction - a junction between certain animal cell types that allowsdifferent molecules and ions (small intracellular signaling molecules) topass freely between cells. The junction connects the cytoplasm of thecells. One gap junction is composed of two hemichannels which connectacross the intercellular space, one from each cell. They are analogous toplasmodesmata that join plant cells; also called "nexus"gap phases - the phases of the cell cycle known as G1 and G2, duringwhich relatively less obvious cellular activity is visiblegape - the measurement of the widest opening of a mouth; to open themouth wide; yawn; an openinggarden eel - a family of eels(Heterocongridae) that occur in colonies inthe sandy bottoms adjacent to coral reefs,where they live individually in burrows fromwhich they protrude to feed on plankton.From a distance these eels resemble a fieldof seagrass. They are very shy anddisappear into their burrows at theapproach of a potential predatorRed Sea garden eels(Gorgasia sillneri) inHurghada, Red Sea.Garden eels live incolonies in sandy bottomsadjacent to coral reefs.They live individually inburrows from which theyprotrude to feed onplankton. (Photo: ThomasJundt)gas - a major state of matter consisting of freely moving atoms andmolecules with no definite shape or volume, like airgas chromatograph/mass spectrometer (GC/MS) - an instrumentthat identifies the molecular composition and concentrations of variouschemicals in water and soil samplesgas chromatography - a method of separating chemical components ofa mixture, which involves the passage of a gaseous sample through acolumn having a fixed adsorbent phasegas hydrate - see "methane hydrate"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (3 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagas laws - laws that predict how gases will behave with changes intemperature, pressure, and volumegastric - pertaining to the stomachgastric filaments - in scyphozoan medusae, a fringe of short, threadlikefilaments whose secretory cells secrete digestive enzymes. They arelocated on the floor of each gastric pouchgastric mill - the grinding apparatus in thecardiac stomach of crustaceans. It isformed by three chitinous teeth that projectinto the stomach; the thick-walledmuscular pouch below the crop in manybirds and reptiles, used for grinding foodGastric mill and teethwithin the stomach of agrooved tanner crab(Chionoecetes tanneri).(Photo: NOAA)gastric pouch - in scyphozoans (jellyfish),one of four sacs is which food in digested.Each pouch contains a conspicuoushorseshoe-shaped gonad on its floorGastric pouch region ofthe jellyfish, Aurelia. Thehorseshoe-shapedstructure is a gonad.(Photo: John Houseman,BIODIDAC)gastrodermis - the epithelial lining of the gastrovascular (digestive)cavity of cnidarians and ctenophores (comb jellies)gastrolith - A deposit of calcium salts made in the stomach of manycrustaceans during the period between molts. It may be used to storecalcium needed in the new exoskeletonhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (4 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef DataGastropoda - a class of the phylumMollusca that includes snails, sea slugs,nudibranchs, limpets, and cone shells.There are approximately 30,000 livingspecies described. Many species areinhabitants of coral reefs and nearbyseagrass bedsA sea slug of the ClassGastropoda, PhylumMollusca.gastropore - a pore in the hard skeleton of a hydrozoan colony whichhouses a gastrozooid (feeding polyp)gastrostyle - a small central support column of the feeding polyps(gastrozooids) of a hydrocoralgastrovascular canal - a canal system, lined with gastrodermis, thatconnects the gastrovascular cavities of colonial coral polypsgastrovascular cavity - the internal digestive cavity of cnidarians andctenophores that is lined with the gastrodermisgastrozooid - a polyp in hydrozoans and other colonial cnidarians whichis specialized for feedinggastrula - the embryonic stage of ananimal that has cells differentiated intogerm layers. Sequentially, It follows theblastula stageAn echinoderm gastrula. Itwas formed by theinvagination ofblastomeres at the vegetalpole area of the blastula toproduce the archenteron,which will become thedigestive system.Theopening into thearchenteron is thehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (5 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datablastopore, which willbecome the anus of theadult. The cavity of thearchenteron is thegastrocoel. The roof of thearchenteron, which formsthe mesoderm, will expandand pinch off mesodermalvessicles with an internalcavity that will become thecoelom (see: mesoderm).A - ectoderm; B -blastocoel; C -archenteron; D -endoderm; E - blastopore.(Photo: Dr. Anna E. Ross,Christian BrothersUniversity, TN)gastrulation - during embryonicdevelopment of most animals, a complexand coordinated series of cellularmovements occurs at the end of cleavage.The details of these movements varyamong species, but usually result in theformation of of an embryonic stage termedthe gastrula. The gastrula has two primarygerm layers, the ectoderm and endodermin diploblastic animals, and three primarygerm layers with the development of themesoderm in triploblastic animalsAn early gastrula. Thecells at the vegetalhemisphere have begun toinvaginate into theblastocoel, forming thearchenteron. (Photo: Dr.Anna E. Ross, ChristianBrothers University, TN)Gause's principle - the principle that "no two species can coexistindefinitely on the same limiting resource." Also called Gause's Law, or the'competitive exclusion principle'gazetteer - a dictionary or index of geographical names with locationsgb (gigabase pairs) - one billion (10 9 ) pairs of nucleotide bases in DNAhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (6 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef DataGBIF (Global Biodiversity Information Facility) - an international nonprofitorganization that provides free and universal access to dataregarding the world's biodiversity. A wide range of countries andorganizations participate in GBIF and have made their data availablethrough the GBIF web site (http://www.gbif.org)GCRMN (Global Coral Reef Monitoring Network) - a global networkwhose aim is to improve management and sustainable conservation ofcoral reefs for people by assessing the status and trends in the reefs andhow people use and value the resources. It does this by providing manypeople with the capacity to assess their own resources, within a globalnetwork, and to spread the word on reef status and trendsgel - a jelly-like substance formed by the coagulation of a colloidal liquid;a cytoplasmic phasegel electrophoresis - a process for separating molecules by forcing themto migrate through a gel under the influence of an electric fieldgelatinous - having the the consistence ofjellythe body of a jellyfish hasa gelatinous consistency.(Photo: Mary Hollinger/NOAA)geminate species - a little differentiated species evolved from a closecommon ancestor; a "twin" species. For example, pairs on either side ofthe Isthmus of Panama who are each other's closest relative and wereprobably one species before the sea level droppedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (7 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagemmule - an asexual, spore-likereproductive unit in sponges, capable ofoverwintering and developing into an adultsponge the following summerA sponge gemmule.Calcareous spiculesprojecting from thecovering of the gemmuleprovide additionalprotection. (Photo credit:Rick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)gen. et sp. nov. - in taxonomy, the abbreviation for genus et speciesnova, meaning new genus and speciesgene - the functional and physical unit of heredity passed from parent tooffspring. Genes are pieces of DNA, and most genes contain theinformation for making a specific proteingene amplification - a selective increase in the number of copies of agene which codes for a specific protein without a proportional increase inother genesgene array - a regular pattern of DNA fragments, or oligonucleotides,spotted onto a solid support and used as a diagnostic tool to measuremany individual gene expression levels simultaneouslygene duplication - gene duplication occurs when an error in DNAreplication leads to the duplication of a region of DNA containing afunctional gene. The duplicated gene is free to mutate and may take onnew functions. The two genes that exists after a gene duplication eventare termed paralogous genes, or paralogs. Gene duplication may have amajor role in evolutiongene expression - the conversion of information from gene to protein viatranscription and translationgene flow - the movement of genes through or between populations asthe result of out-crossing and natural selectionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (8 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagene frequency - the relative occurrence of a gene in a given population,usually expressed as a percentagegene index - a listing of the number, type, label and sequence of all thegenes identified within the genome of a given organismgene locus - the specific place on a chromosome where a gene is locatedgene mapping - determination of the relative locations of genes on achromosomegene pool - the sum total of genes, with all their variations, possessed bya particular species at a particular timegene product - the product, either RNA or protein, that results fromexpression of a gene. The amount of gene product reflects the activity ofthe genegene silencing - the interruption or suppression of the expression of agene at the levels of transcription or translationgene splicing - a cell process by which a gene is cut into different parts,exons and introns. The exons are the coding region and are put backtogether to make the gene that is transcribed and translated into a proteingene therapy - an approach to preventing and/or treating disease byreplacing, removing or introducing genes or otherwise manipulatinggenetic material. In some cases, the material can be injected with agenetic vaccination. In other cases the material is introduced throughharmless bioengineered viruses that carry the therapeutic gene to the cell.Globules known as liposomes can also be used to carry therapeutic genesto specific cellsgene tree - a phylogeny of a gene, which may or may not accuratelyreflect the phylogeny of the organisms possessing that genegene-based medicine - instead of solely replacing defective genes, genebasedmedicine is the application of nucleic acids (DNA, RNA) containinggenetic information as therapeutic reagents in general. Nucleic acids areused to add a therapeutically beneficial function to cells, deletepathological functions from cells, or utilize cells for the production oftherapeutic proteins. This can be either a transient or a permanent effectgenecology - the study of the genetic basis of ecological differentiation;the study of the genetic composition of populations in relation to theirhabitatshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (9 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datageneralist - an organism which can survive under a wide variety ofenvironmental conditions, and does not specialize to exist under anyparticular set of circumstancesgeneration - offspring from the same parental group going through theirlife cycle togethergenetic assimilation - the disappearance of a species as its genes arediluted through crossbreeding with a closely related speciesgenetic code - the chemical code by which genetic information in DNA istranslated into biological function. A set of three nucleotides (codons), thebuilding blocks of DNA, signifies one amino acid. Amino acids are the thebuilding blocks of proteinsgenetic disease - a disease that has its origin in changes to the geneticmaterial. Genetic diseases usually refer to diseases that are inherited in aMendelian fashion, although non-inherited forms may also result fromgenic (DNA) mutationgenetic distance - a measure of the genetic similarity between any pairof populations. Such distance may be based on phenotypic traits, allelefrequencies or DNA sequences; any of several measures of the degree ofgenetic difference between populations, based on differences in allelefrequencies. Genetic distances are used for understanding effects ofgenetic drift and gene flowgenetic distancing - a measure of the genetic similarity between anypair of populations. Such distance may be based on phenotypic traits,allele frequencies or DNA sequences. For example, genetic distancebetween two populations having the same allele frequencies at aparticular locus, and based solely on that locus, is zero. The distance forone locus is maximum when the two populations are fixed for differentalleles. When allele frequencies are estimated for many loci, the geneticdistance is obtained by averaging over these locigenetic diversity - the variety of different types of genes or alleles in aspecies or populationgenetic drift - random changes in the frequency of alleles in apopulation. In small populations, it can lead to the elimination of aparticular allele by chance alone. It is thought to be one cause ofspeciation when a group of organisms is separated from its parentpopulationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (10 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagenetic engineering - the technique of selectively removing, modifying,or adding genes to a DNA molecule by use of recombinant DNA or otherspecific molecular gene transfer or exchange techniques. Thesetechniques produce endogenous proteins with properties different fromthose of the normal, or to produce entirely different proteins altogether.Organisms modified by genetic engineering are sometimes referred to astransgenic, bioengineered, or genetically modifiedgenetic erosion - a process whereby an already limited gene pool of anendangered, sexually reproducing species diminishes even more whenindividuals from the surviving population die off without getting a chanceto breed with others in their endangered low population. Genetic erosionoccurs because each individual organism has many unique alleles whichget lost when it dies without getting a chance to reproduce; the loss ofgenetic diversity within the same species over time, due to humanintervention or environmental changesgenetic expression - the process by which genetic information containedin DNA is converted into proteins within a cell. The gene is said to expressor code for a particular proteingenetic map position - the location of a gene on a genetic map,deduced from recombination frequenciesgenetic marker - a DNA sequence used to "mark" or track a particularlocation (locus) on a particular chromosomegenetic modification - human-designed changes in an organism,whether done through traditional breeding or genetic engineering. Theterms "genetically modified" and "genetically engineered" are sometimesused interchangeablygenetic mutation - a permanent structural alteration in DNA. In mostcases, DNA changes either have no effect or cause harm, but occasionallya mutation can improve an organism's chance of surviving and passingthe beneficial change on to its descendantsgenetic pollution - the uncontrolled and undesirable gene flow into thegenomes of organisms in which such genes are not present in the wildstate. The term is usually associated with the gene flow from a geneticallyengineered or genetically modifed organism to a non-geneticallyengineered or modified organism. In some instances it has also been usedto describe gene flow from an invasive or domesticated species to a wildpopulation; the accidental tranfer of genetic material from a geneticallyengineered organism to one that is not genetically engineeredgenetic stability - a measure of the resistance to change, with time, ofthe sequence of genes within a DNA molecule or of the nucleotidesequence within a genehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (11 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagenetically modified organism - an organism that has been modifiedby the application of recombinant DNA technologygenital bursa - an invagination at the base of an arm of a brittle star.Each bursa is a pouch lined with ciliated epidermis and is the primaryrespiratory surface for the organs of the perivisceral coelom. Theepidermal cilia generate a ventilating current. The bursae have the gonadson the coelomic side of their wallgenome - all the DNA contained in an organism or a cell, which includesboth the chromosomes within the nucleus and the DNA in mitochondriagenome size - the size of a genome (all the genetic material in thechromosomes of a particular organism) is generally given as its totalnumber of base pairsgenomic library - a collection of clones made from a set of randomlygenerated overlapping DNA fragments that represent the entire genomeof an organismgenomics - the comprehensive analysis of all the genes of an organism;molecular characterization of all the genes and gene products of a species,including the study of gene sequences, gene mapping, and gene function;genomics usually involves high speed sequencing of the DNA andcomputer searches for sequences that code for genes. Genomics allowresearchers to identify specific genes responsible for specific proteins withspecific functions in an organismgenotype - the genetic constitution of an individual or group. Intaxonomy, the genotype is the type species of a genusgenus - a taxonomic group containing one or more speciesgeo-referenced data - refers to data with geographic locationinformation included, such as latitude and longitudegeochemistry - the study of the chemical elements, their isotopes, andrelated processes with respect to the abundance and distribution ofmaterials within the Earth's waters, crust, and atmospheregeoecotype - a regional ecotype (a population adapted to a restrictedhabitat as a result of natural selection within a local environment)geographical isolation - a form of reproductive isolation in whichmembers of a population become separated from another population bygeographical barriers that prevent the interchange of genes between theseparated populationshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (12 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datageographical speciation - speciation occurring during a period ofgeographical isolationGeoHab - a joint SCOR-IOC Program of international cooperative researchon harmful algal blooms (HABs) in marine and brackish watersgeoid - the hypothetical surface of the Earth that coincides everywherewith the mean sea levelgeologic time scale - a relative time scale based upon fossil content.Geological time is divided into eons, eras, periods, and epochsgeomorphology - the study of landforms and the processes which shapethemgeostationary satellite - satellite whoseorbit around the equator equals that of theEarth's rotation, making it possible forthem to view the same disc of Earth'ssurface below continuouslyArtist+s rendition of GOESI/M, geostationarysatellites whose missionincludes data collectionand broadcasting, andenvironmental sensing.(Image: NASA/GoddardSpace Flight Center)geostrophic current - a flow that sustains a balance between Coriolisdeflection and a pressure gradientgeotextile - a product used as a soil reinforcement agent and as a filtermedium. It is made of synthetic fibers manufactured in a woven or loosenonwoven manner to form a blanket-like product, e.g., a silt curtainhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (13 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datageothermal vent - a submerged feature consisting of a vent of hot,mineral-rich waters on the ocean floor; geothermal vents are generallylocated on or near spreading oceanic ridges or on the continental marginsof subduction trenchesGeotiff - a file format that embeds image registration information directlyinto a raster file; an industry-neutral raster file format widely used andrecognized by all of the major GIS software vendors. ESRI began supportfor Geotiff at version 7.0 of ARC/INFO and version 3.0 of ArcView. Geotiffrepresents an effort by over 160 different remote sensing, GIS,cartographic, and surveying related companies and organizations toestablish a TIFF-based interchange format for georeferenced rasterimagerygeotropism - a turning or growth movement by a plant in response togravity. Plant parts that grow downward, such as the roots, would bepositive geotropism. A negative geotropism would be the stems growingupwardgerm cell - a gamete; a haploid sperm or egg cell or their precursorsgerm layers - distinct layers of cells, produced during the earlyembryonic developmental process of gastrulation, which gives rise to allcells, tissues, organs, and organ systems of the organism's body. Thethree types of germ layers are the ectoderm, endoderm, and mesoderm.Diploblastic organisms (e.g. cnidarians) have two layers, ectoderm andendoderm; triploblastic organisms (all higher animal groups) havemesoderm between these two layersgerminal epithelium - the tissues of the primary reproductive organsthat produce eggs and sperm cellsgestation period - the period of development of the young in viviparousanimals, from the time of zygote formation (fertilization) until birthghost crab - any of several light-coloredburrowing crabs of the genus Ocypodafrequenting the tide line along sandy shoresfrom the northeast United States to Brazil.Ghost Crabs have a relatively thin, lightexoskeleton and two large black eyes thatstand up like periscopes. They are calledghosts because of their ability to instantlydisappear from sight, moving at speeds atspeeds up to 10 miles per hour, whilemaking sharp directional change anddisappearing into their burrowsThe ghost crab, Ocypodepallidula,gets its namecomes from its ability toblend in with sand, thenalternately “appear” and“disappear" while makingrapid sharp directionalchanges (Photo: Keoki andYuko Stender)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (14 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Dataghost net - a lost or abandoned fishing net that drifts through the oceansposing a danger to fishes and other marine lifegibbosity - swelling or protuberance; a convex hump; something thatbulges out or is protuberant or projects from a formgiesma - in a histological preparation, a stain which contains both basicand acidic dyesGIF (Graphics Interchange Format) - a bit-mapped digital imagegraphics file format suitable for efficiently importing image data intocomputer files or for transmitting or displaying the formatted image on acomputer monitor or printing it out. GIF supports color and variousresolutions. It also includes data compression, making it especiallyeffective for scanned photosgigabyte (gb) - a measurement of storage space equal to a thousandmegabytesgill - a highly vascularized respiratoryorgan with a large surface area in aquaticanimals. Gills are in direct contact with thesurrounding water for gas exchangeThe gill cover (operculum)of this fish is lifted toexpose the gills, which arethe respiratory organs offishes and many otheraquatic animals.gill arch - one of several curved bony or cartilaginous structures locatedon either side of the pharynx that support the gills of fishes andamphibians. Each gill arch is made up of an upper and a lower limb thatare joined posteriorly. The gill filaments and gill rakers are attached to thegill archesgill chamber - in fishes, the cavity containing the gills on each side of therear of the head, enclosed by the operculum and the branchiostegalmembranegill filament - a fingerlike projection from a gill arch through whichrespiratory gases enter and leave the bloodhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (15 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagill net - a net primarily designed to catchfish by entanglement in a mesh thatconsists of a single sheet of webbing whichhangs between cork line and lead line, andwhich is fished from the surface of the waterA fisherman setting out agill net. (Photo: NOAA)gill pouch - an anatomical structure of bivalves used to protectdeveloping embryos; located in the gillsgill raker - one of a series of knob- orcomb-like projections on the front edge ofthe gill arch. Gill rakers aid in the fish'sfeeding. Their shape and number are agood indication of the diet of the fish.Fishes which eat large prey, such as otherfishes, have short, widely spaced gill rakersthat prevent the prey item from escapingbetween the gills. Fishes which eat smallerprey have longer, thinner and morenumerous gill rakers. Species which feed onplankton have the longest, thinnest andmost numerous gill rakers. Gill rakers alsoprotect and clean the gill fillaments. Countsof gill rakers are used as taxonomic charactersGill arch of an almaco jack(Seriola rivoliana) showingthe gill rakers and gillfilaments. (Photo: NOAA)gill tuft - a fluffy cluster of gill filamentsGIS (Geographic Information System) - a system that allowsautomatic location of information suitable for mapping. Usually involves asoftware system that takes geographic position data and other data (e.g.,type of bottom sediment) in order to create a map. Data on processes (e.g., current speed) can be incorporated to make a geographic model of flowglabrous - refers to a smooth surface without hairs or setaegladiate - sword-shapedgland - a group of cells or a single cell in animals or plants that isspecialized to secrete a specific substancehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (16 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagland cell - an epithelial cell that secretes digestive enzymes into thegastrovascular cavity of a cnidarian; also called "granular gland cell" or"zymogen cell"glass sponge - a hexactinellid sponge, found at deeper depths, with askeleton made of four and/or six pointed silaceous spiculesglobal change - a transformation which occurs on a worldwide scale (forexample, an increase in CO 2 in the atmosphere) or exhibits sufficientcumulative effects to have worldwide impact (for example, local speciesextinction resulting in global loss of biodiversity)Global Environment Facility (GEF) - an independent financialorganization that provides grants to developing countries for projects thatbenefit the global environment and promote sustainable livelihoods inlocal communities. GEF funds are contributed by donor countries. GEFgrants support projects related to biodiversity, climate change,international waters, land degradation, the ozone layer, and persistentorganic pollutantsGlobal Taxonomy Initiative (GTI) - initiative established by theConference of the Parties to the Convention on Biological Diversity (CBD)to address the lack of taxonomic information and expertise around theworldglobal temperature - an area-weighted mean of temperatures recordedat ground and sea surface -based observation sites around the globe,supplemented by satellite or model-based records in remote regions;usually referring to sea surface temperatureGlobal Temperature-Salinity Profile Program (GTSPP) - acooperative international program designed to develop and maintain aglobal ocean Temperature-Salinity resource with data that are as up-todateand of the highest quality as possible. The primary goal of the GTSPPis to make these data quickly and easily accessible to users. Both realtimedata transmitted over the Global Telecommunications System (GTS),and delayed-mode data received by the U.S. National Oceanographic DataCenter (NODC) are acquired and incorporated into a continuouslymanaged database. Countries contributing to the project are Australia,Canada, France, Germany, Japan, Russia, and the United States. Canada'sMarine Environmental Data Service (MEDS) leads the project, and has theoperational responsibility to gather and process the real-time dataglobal warming - the gradual increase in global temperatures caused bythe emission of gases that trap the sun's heat in the Earth's atmosphere(greenhouse effect). Gases that contribute to global warming includecarbon dioxide, methane, nitrous oxides, chlorofluorocarbons (CFCs), andhalocarbons (the replacements for CFCs). The carbon dioxide emissionsare primarily caused by the use of fossil fuels for energyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (17 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Dataglobular - globe-shaped; having the formof a sphere, or nearly soThe porcupine fish, whenthreatened, swallowswater and takes on aglobular shape. (Photo:Copyright CorelCorporation)glossary - an alphabetical list of technical terms, with brief definitions forthose terms, in some specialized field of knowledgeglucose - a monosaccharide,C 6 H 12 O 6 , that is the end product ofcarbohydrate metabolism and is the chief source of energy for livingorganismsglutamate - an amino acid neurotransmitter that acts to excite neurons.Glutamate is thought to play an integral role in neural pathwaysassociated with learning and memoryglutamate receptor - a protein molecule that helps gate the flow of ionsacross a neuron's cell membraneglutinous - stickyglycan - a polysaccharide consisting of monosaccharides joined byglycosidic linkagesglycobiology - a field of science that combines carbohydrate (sugar)biochemistry and molecular biology. Glycobiology includes the study of thestructure, chemistry, biosynthesis, and biological functions of glycans andtheir derivatives; also called glycomicsglycomics - see glycobiologyglycosidic bond - a type of covalent bond that joins twomonosaccharides (simple sugars) via an atom of oxygenhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (18 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Dataglycosidic linkage - a bond formed between a hemiacetal group of asugar molecule (such as glucose) and an alcohol functional group to forman acetalgnathic - pertaining to the jawGnathostomata - the group of vertebrates that possess jaws; includesfishes, amphibians, reptiles, birds, and mammalsgoatfish - any species of bony fishes in thefamily Mullidae. Goatfishes, also calledsurmullets, are elongate, moderately sizedfishes which are characterized by a pair oflong, tactile barbels under the chin. Somespecies are brilliantly colored and some arenotedThe yellow goatfish,Mulloidichthys martinicus,uses barbels to dig in sandor coral rubble for food,usually smallinvertebrates. (Photo:NOAA)goby - any species of bony spiny-rayedfishes in the family gobiidae. Gobies aresmall fishes with large heads and elongatedtapering bodies. They comprise the largestfamily of marine fishes, with over 2000species. Gobies range in size from themudskipper (about 15-30 cm) to the tinypygmy goby, Eviota sigillata, a 1-2 cm longcoral reef-dwelling goby which has theshortest lifespan for any known vertebrateThe antitropicalshrimpgoby, Amblyeleotrisogasawarensis. Thisspecies of goby grows to11cm in length. It lives ina burrow with a snappingshrimp(Photo: John E.Randall, Ph.D.)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (19 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef DataGOES (Geostationary OperationalEnvironmental Satellite) - a class ofsatellite operated by NOAA, positioned in anearly stationary orbit over the equator atan altitude of about 22,500 miles. GOES-8is currently the operational "east"spacecraft at 75 degrees West longitude,while GOES-10 is the "west" spacecraftlocated at 135 degrees West. GOES-11 is instandby at 110 degrees WestImage developed by NASAfrom GOES data-HurricaneFloyd at the U.S. coast onSeptember 15, 1999 (HalPierce, NASA GoddardSpace Flight Center)gonads - the primary sex organs of an animal. In males they are thetestes, and in females, the ovariesgonangium - a reproductive polyp of acolonial hydrozoan. It consists of a stalkcontaining medusa buds surrounded by athin membrane, the gonothecaA gonangium of thehydrozoan Obelia. 1=medusa bud; 2= perisarc;3=gonotheca; 4=coenosarc. (Photo: RickGillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)gonochoric - having separate sexes. Individuals within the speciescontain only one or the other of male and female reproductive systemsgonoduct - any duct that generally transfers eggs or sperm cellsgonophore - a sexual zooid produced as a medusa bud upon a hydroid,sometimes becoming a free hydromedusa and sometimes remainingattachedgonopodium - a term given to the anal fin (or the anterior portion of it)of a male fish when it is modified to function as a copulatory organ, e.g.,in guppieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (20 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagonopore - an opening between the reproductive system and the outsideenvironment; the genital pore of many invertebratesgonosome - a collective term for all reproductive structures of a colonialhydrozoangonotheca - a thin membrane covering the body of a gonangium, thereproductive polyp of a colonial hydrozoangonozooid - a reproductive polyp of a colonial hydrozoangorgonian - an anthozoan of the subclassOctocorallia, commonly called sea fans andsea whipsA sea fan, Gorgoniaventalina, in the FloridaKeys.gorgonin - a fibrous protein in the mesoglea which provides skeletalsupport for sea fans and other members of the Order Gorgonaceagovernment document - a publication produced by a governmentagencyGPS (Global Positioning System) - anetwork of satellites and receiving devicesused to compute accurate geographicalpositions on the Earth. A GPS is used innavigation, and its precision supportscadastral surveyingPortable GPS unit utilizedin surveying.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (21 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagradient analysis - an intuitive method to portray variation along asingle or multiple environmental gradients. The plots display species orcommunity abundance in response to a known environmental gradient, i.e., the analysis of species composition along a gradient of environmentalconditionsgradualism - a model of evolution that assumes slow, steady rates ofchange, as contrasted with punctuated equilibrium, an evolutionary modelin which change occurs in relatively rapid burstsgram atom (g-at) - the quantity of an element whose weight in grams isnumerically equal to the atomic weight of the element; represents themass in grams of Avogadro's number of atoms of the elementGram's stain - a method for differential staining of bacteria; Grampositivecells stain purple-black and Gram-negative cells stain pink; usefulin bacterial taxonomy and identificationgrassroots - people or society at a local level, rather than at the centerof major political activity. A grassroots movement is one driven by theconstituents of a communitygravid - pregnant; heavy with young; fullof ripe eggs or distended by such fullnessGravid green crab withegg mass on theabdomen. (Photo: GaryWeber)Gray's Reef National Marine Sanctuary- Gray's Reef comprises one of the largestnearshore sandstone reefs in thesoutheastern United States.It is located 32kilometers (17.5 nautical miles) off SapeloIsland, Georgia. Designated in 1981, theGray's Reef National Marine Sanctuaryboundaries protect 17 square miles of openocean. Sandstone outcroppings and ledgesup to ten feet in height separate the sandy,flat-bottomed troughs in a reef thatcombines temperate and tropical flora andhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (22 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datafauna. The rocky platform, some 60 to 70feet below the surface, is covered by acarpet of attached organisms and is knownlocally as a "live bottom habitat." Gray'sreef is not a coral reef. It is a consolidationof marine and terrestrial sediments (sand,shell, and mud) which was laid down asloose aggregate between 6 and 2 millionyears agoA reef scene showingbiodiversity at Gray's Reef.(Photo: NOAA)grazer - an animal which feeds on plantsSea urchins are importantgrazers on coral reefs.Their diet, however, is nottotally restricted to plantsand algae.Great Barrier Reef - the largest complexbarrier coral reef in the world,approximately 2,000 km (1,250 mi) long, inthe Coral Sea, forming a naturalbreakwater for the northeastern coast ofAustralia. It is separated from the mainlandby a shallow lagoon from 16–161 km (10 to100 mi) wide. It is It is composed of morethan 2,800 individual reefs and in someplaces it is more than 122 m (400 ft) thick.The Great Barrier Reef Marine Park, morethan 340,000 km2 (130,000 mi2),encompasses most of the reefs andinterreef areas as well as the neighboringlagoon and a large section of thecontinental shelf. It is the largest UNESCOWorld Heritage AreaSatellite photograph of theGreat Barrier Reef situatedoff the northerastern coastof Australia.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (23 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagreen algae - green algae belong to theDivision Chlorophycota. These algaecontain photosynthetic pigments similar tothose in higher plants (chlorophylls a and b,as well as secondary pigments: carotenes,lutein, and zeaxanthin) and have a greencolor. Green algae include unicellular forms,filamentous forms, and leaf-like thalluses.The green alga Caulerpataxifolia with feather-likebranches. The leaf is 5-65cm in length. (Photo:NOAA)green fluorescent protein (GFP) - a protein produced by a jellyfishAequorea victoria which fluoresces in the lower green portion of the visiblespectrum when exposed to blue light. GFP has become an invaluable toolin contemporary cell and molecular biology research, because its intrinsicfluorescence can be visualized in living cells. GFP has become wellestablished as a marker of gene expression and protein targeting in intactcells and organisms. Mutagenesis and engineering of GFP into chimericproteins are opening new vistas in physiological indicators, biosensors,and photochemical memoriesgreen gland - in some crustaceans (shrimp, crabs, lobsters), anexcretory gland with ducts opening near the base of the large antennae;also called "antennal gland"green turtle - one of seven extant species of marine turtles. The greenturtle, Chelonia mydas, is herbivorous and feeds on algae and seagrasses.It is in the family Cheloniidaegreenhouse effect - the heating that occurs when gases such as carbondioxide trap heat escaping from the Earth and radiate it back to the surfacegreenhouse gases - atmospheric gases, primarily carbon dioxide,methane, and nitrous oxide restricting some heat-energy from escapingdirectly back into spacegregarious - living or moving in a group with others of its kind, as in aflock of birds or school of fishgrid - a network of uniformly spaced parallel lines intersecting at rightangles. When superimposed on a map, it usually carries the name of theprojection used for the map. For example: Lambert grid, transverseMercator grid, and universal transverse Mercator gridhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (24 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagriseous - blue-grey colorGrocott-Gomori's methenamine silver stain (GMS) - in histology, astain preparation for fungigroin - a solid structure built at an anglefrom a shore prevent erosion fromcurrents, tides and waves, or to trap sandA groin is a relativelyslender permeable orimpermeable barrierstructure aligned andconstructed to trap littoraldrift or retard erosion ofthe shore. This is aphotograph of a timberpile groingross photosynthetic rate - the total rate of CO 2 fixation with noallowance for the CO 2 simultaneously lost during respirationgross primary production - the total amount or weight of organicmatter created by photosynthesis over a defined time period (totalproduct of photosynthesis)ground truthing - measurements conducted on the ground or at sea tocalibrate, compare or verify observations made from satellites or aircraftground water - underground water that is generally found in the porespace of rocks or sediments and that can be collected with wells, tunnels,or drainage galleries, or that flows naturally to the earth's surface viaseeps or springs. The term is not applied to water that is percolating orheld in the top layers of the soil, but to that water in the zone ofsaturation below the water tablegroundfish - fishes, usually of commercial value, that live on or near thebottom; also called "bottom fish"grounding - a ship's striking a shoal or reefgroundwater seep - subsurface water flowing into a coastal body ofwaterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (25 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datagrouper - any species of bony fishes in thesubfamily Epinephelinae of the sea bassfamily, Serranidae. Groupers have a typicalseabass appearance with robust bodies,large mouths and sharp teeth. Some get tobe enormous in size, many feet long andreaching weightsThe Hawaiian grouper,Epinephelus quernus, isendemic to Hawaii. Itattains at least 3 feet and50 pounds (Photo: Keokiand Yuko Stender)growth band - a band formed yearly on coral by the secretion of CaCO 3 ;one yearly growth band contains two smaller bands representing wintergrowth and summer growthgrowth factor - any of various chemicals, particularly polypeptides, thathave a variety of important roles in the stimulation of new cell growth andcell maintenance. They bind to the cell surface on receptors. Specificgrowth factors can cause new cell proliferationgrowth rate - the increase in mass per unit of timegrowth - an increase in cell size or cell number, or bothgrunt - any species of bony spiny-rayedfishes in the family Haemulidae. Grunts aremedium-sized tropical fishes that arecapable of making a grunting sounds by thegrinding of pharyngeal teeth.They inhabitcoral reef or hard bottom areas. Manyforage at night over nearby sand and grassflatsBlue striped grunts(Haemulon sciurus) in theFlorida Keys NationalMarine Sanctuary (Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (26 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Dataguanine - one of the four nitogenousbases in DNA and RNA that make up theletters ATGC, guanine is the "G". Theothers are adenine, cytosine, and thymine.Guanine always pairs with cytosineDiagram of the chemicalstructure of guanine, oneof the four nitrogenousbases in DNA.guano - the manure of birds and bats thatis often used as fertilizerBird droppings form theguano deposits on Gardnerpinnacles, NorthwesternHawaiian Islands. (Photo:NOAA)guild - a group of species that use the same resources in a similar way;an ecological association based on similar roles in a community ratherthan evolutionary descent, as for example, filter feeders or browsersgular - of, relating to, or located on the throatgulf - a portion of an ocean or sea that extends into the land; a partiallyland-locked sea, e.g., the Gulf of OmanGulf of Mannar Marine National Park - a marine national park on thesouth eastern tip of India which consists of 21 Islands approximately eightkm off the coast of Tamil Nadu (a state at the southern tip of India).Spreading over an area of 10,500 km², the area described as the Pambanto-Tuticorinbarrier reef was converted into a Biosphere Reserve in 1989http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (27 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef DataGulf Stream - the warm ocean current ofthe North Atlantic. It originates in thewestward equatorial current and isdeflected northward by the coast of SouthAmerica into the Gulf of Mexico and thenfollows the coast of North America toNantucket, where it is deflected eastwardtoward northern EuropeSea surface temperatureimage of the Gulf Stream,derived from infraredmeasurements of theModerate-resolutionImagingSpectroradiometer(MODIS), May 8, 2000.(Image produced from 11-and 12-micron bands byBob Evans, Peter Minnett,and co-workers, Universityof Miami)gunwale - the upper edge of the side of a shipgustation - pertains to the sense of tastegut - the digestive tube formed between the mouth and anus in whichfood is digested and nutrients absorbed; it consists of the mouth,pharynx, esophagus, stomach, intestine, and anus, though some animalsdo not have all these regionsguyot - a flat-topped submarine mountaingynetype - a female type specimengynogenetic - containing genetic material derived from the femaleparent onlygyre - a large water-circulation system of geostrophic currents rotatingclockwise in the Northern Hemisphere or counterclockwise in the SouthernHemisphere(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (28 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef Datahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=g (29 of 29) [2/26/2008 9:14:11 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: HThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zhabitat - the place or environment where a particular organism,population, or species liveshabitat affinity index - defines habitat affinity based on the relativeconcentration of a species in a particular habitat, compared with theavailability of that habitat in a given study areaHabitat Area of Particular Concern (HAPC) - a habitat areadesignated by a Fishery Management Council under the Magnuson-Stevens Fishery Conservation and Management Act of 1976habitat complexity - the areal extent and number and diversity ofhabitat types and distinct ecological zones within a specified areahabitat distribution - the structure and spatial characterization of allhabitat types in a specified areahabitat diversity - the number of different types of habitats within agiven areahabitat fragmentation - the breaking up of a habitat into unconnectedpatches interspersed with other habitats which may not be inhabitable byspecies occupying the habitat that was disrupted. The breaking up isusually by human actionhabitat patch - an area distinguished from its surroundings byenvironmental discontinuitieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (1 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahabitat sharing - a situation in which species occupy the same habitatwithout competition, either through requiring different resources or beingpresent at different timeshabitat specialist species - species that can only survive in a specificenvironment, such as those that rely on certain specific resourceshabituation - in animal behavior, the temporary waning or disappearanceof an innate response when it is elicited many times in successionhadalpelagic zone - the deepest zone of the ocean, extending fromabout 6000 meters to the very bottom (10,911 meters in the MarianaTrench off the coast of Japan). The temperature is constant at just abovefreezing (about 4 degrees C)hair cell - a mechanoreceptor cell having hair-like processes (stereociliaand kinocilia). Vibrations or pressure deform these processes which relaythe induced nervous impulses to the central nervous system. They areresponsive to sound and other mechanical stimulihalf-life - the time required for a radioactive substance to lose half of itsnucleihalichlorine - a bioactive compound, isolated from the marine spongeHalichondria okadai. It has potential as a drug for the treatment ofatherosclerosishalichondrin B - a marine pharmaceutical, derived from a New Zealanddeep water sponge Lissodendoryx sp., which inhibits cell division byinterfering with the cell's microtubule networkHalimeda - an important genus of calcareous green algae in coral reefenvironmentshalo - in animal coloration, a circle of color around a spot of another colorhalocline - the boundary where there is a marked change in salinitybetween surface fresh water and underlying saltwater in a stratifiedcoastal environmenthalophile - an organism which lives in an environment of high saltconcentration. Halophiles have special adaptations to permit them tosurvive under these conditionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (2 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahalophyte - a plant that grows in soils thathave a high content of various saltsA black mangrove is anexample of a halophyte, aplant that thrives in asaline environment.hamlet - any of about 10 species of smallgrouper in the genus Hypoplectrus (familySerranidae) that inhabit shallow reef areasin the western Atlantic.They feed mostly onsmall benthic crustaceans, and occasionallyon small fishes. The black hamlet is asimultaneous hermaphrodite (both sexesoccurring within the same individual). Amating pair takes turns acting out sex rolesduring courtshipA butter hamletphotographed at Curacao(Photo: Mark Rosenstein /Active Window Productions(markrosenstein.com))hamular - hook-shapedhamulus - a small hook-like projectionhaplodiplontic - having a life history that includes both haploid anddiploid phaseshaploid - a haploid cell contains a nucleus with a single complete set ofchromosomes. The haploid condition is often abbreviated as n. Most fungi,protists, and algae are haploid, as are some insects, bryophytes, and thegametes of all organismshaplotype - a set of closely linked genes that tends to be inheritedtogether as a unit; a particular set of alleles at linked loci that are foundtogether on a single homologhapteron - a single branch within a holdfasthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (3 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahard bottom - a substrate formed by the deposition of calcium carbonateby reef building corals and other organisms or existing as bedrock orvolcanic rock usually of minimal reliefhard coral - a coral in the anthozoan orderScleractinia. Also known as the stonycorals, these organisms possess a hardexternal calcareous skeleton. A synonym ofstony coralSkeleton of a hard coralcolony.hard coral forms - may be conveniently summarized as: encrusting(lichen-like); branched (staghorn-like); massive (rock-like); sub-massive(pillar-like); tabulate (table-like); foliose (scroll-like); and solitaryHardy-Weinberg Law - the frequency of a given genotype will reachequilibrium in a randomly mating population and will stay constant overmany generations in the absence of selection pressuresharem - a social structure whereby several females associate and breedwith a single maleharmful algal bloom (HAB) - an increased abundance of algae that maycause illness in people or marine animals. HAB's can cause massmortalities of marine organisms, are a public health risk, and can causeeconomic damage through declines in tourism, shellfish bed closures, andreductions in the market value of seafoodharmonics - pertaining to sound, harmonics are multiples of thefundamental frequency (a single sine wave)harvest - to capture, catch, collect or harvest organisms by any meanshastate - spear-shapedhatch - the process of an embryo leaving the egg envelopeshatch success - the proportion of eggs in a nest that produce livehatchlingshatchling - A newly hatched bird, reptile, amphibian, or fishhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (4 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahaterumadienone - a bioactive derivative of puupehenone, isolated froma sponge Dysidea sp., which interferes with cell division processesHawaiian Archipelago - the Hawaiian Archipelago consists of eight largeislands and 124 small islands, reefs, and shoals. It stretches for over2,400 km from 19 degrees - 28 degrees N to 155 degrees -178 degrees E.It can be divided into two distinct regions: the Northwestern HawaiianIslands (NWHI), primarily uninhabited atolls, islands, and banksaccounting for the majority of U.S. reefs, and the Main Hawaiian Islands(MHI) largely made up of populated, high, volcanic islands with nonstructuralreef communities, fringing reefs, and two barrier reefshawser - a large rope for mooring or towing a shiphazardous waste - a discarded material which contains substancesknown to be toxic, mutagenic, carcinogenic, or teratogenic to humans orother life; ignitable, corrosive, explosive, or highly reactive alone or withother materialsheading - the direction in which a vessel is pointed at any given momentheat shock proteins (HSPs) - a group of proteins that are present inthe cells of all living organisms. They are induced when a cell is exposedto various types of environmental stresses, e.g.,heat, cold and oxygendeprivation. Heat shock proteins are also present in cells under normalconditions, assisting in other cellular protein functions and behavior. Theyalso trigger immune responses through both intracellular and extracellularactivities; also called stress proteinsheavy metal - a metal having a specific gravity of 5.0 or greater. Heavymetals are generally toxic to organisms in relatively low concentrations,and tend to accumulate in the food web. Examples include arsenic,cadmium, chromium, lead, and mercuryhectare (ha) - a metric unit of measure for area, equal to 2.47 acresheiau - a traditional Hawaiian place of worship; a religious shrinehelicoid - spiral-shapedheliophilous - having an attraction for sunny placesheliotropism - an orienting response to the sunheliox - a breathing gas mixture for scuba divers that contains onlyoxygen and helium, used for deep diving to remove the narcotic effect ofnitrogenhelix - a structure with a spiral shapehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (5 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahelophilous - having an affinity for marshesheme - a complex red organic pigment containing iron and other atoms towhich oxygen bindshemichordate - any of various worm-likemarine animals belonging to the phylumHemichordata, having a primitive notochordand gill slitsAn acorn worm in thephylum Hemichordata.(Photo: BIODIDAC)hemipenis - a hemipenis (plural hemipenes) is one of a pair of copulatoryorgans of male snakes, lizards, and amphisbaenians. Only one is usedduring mating. Hemipenes are usually held inverted within the body andare everted for copulationhemocoel - the extensive spaces of an arthropod's body through whichthe hemolymph (blood) circulateshemocyanin - a bluish, copper-containing respiratory pigment with anoxygen-carrying function similar to that of hemoglobin that is present inthe blood of certain mollusks and arthropodshemocyte - a cellular component of the blood, especially in invertebrateorganisms. There are different types of hemocytes performing a variety offunctions, which include defense and nutrient transporthemoglobin - the iron-containing protein (pigment) found in red bloodcells of vertebrates. Hemoglobin transports oxygen from the respiratorysurface (gills, lungs) to the body's tissues. It is red when oxidizedhemolymph - the circulating and tissue-bathing fluid of the arthropodopen circulatory system. It is composed of cells and plasma and oftenloosely termed as bloodHenry's Law - the amount of gas that will dissolve in a liquid at a giventemperature is almost directly proportional to the partial pressure of thatgashepato- - pertaining to the liverhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (6 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Dataherbivore - an animal that feeds on plantsheredity - the transfer of genetic information from parent cells to progenyhermaphrodite - an animal or plant which is equipped with both maleand female reproductive organshermatypic coral - a reef-building coral with zooxanthellae in its tissuesherpetology - the scientific study ofamphibians and reptilesHerpetologists study thebiology of amphibians andreptiles, such as thisIndopacific sea snake,Laticauda colubrina. Thisspecies lays its eggs onland. Other species arelivebearers and give birthto their young in theocean. (Photo: SohanShetty)hertz - unit of frequency equal to one cycle per secondheterauxesis - disproportionate growth of a structure in relation to therest of the bodyheterocercal - a caudal fin where the upper lobe is larger than the lowerlobe. Most sharks have heterocercal caudal finsheterochromatin - the portion of chromosome material that remainscondensed and is transcriptionally inactive during interphase of the cellcycleheterochrony - a change in the timing of ontogenetic events betweentwo species. These can be the result of relatively small genetic changesbetween an ancestor and its descendant speciesheterodont - a type of dentition where the teeth are not all similar. Forexample, a mixture for special functions, such as canines, incisors andmolars for piercing and tearing, snipping and grindinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (7 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Dataheterogeneous - consisting of dissimilar elements, parts or forms;having non-uniform structure or compositionheterologous - derived from organisms of a different but related speciesheterosis - a situation where crossing two inbred lines yields offspringthat are more healthy/vigorous than their parents; hybrid vigorheterotrichous - pertaining to a nematocyst with spines that vary in sizeheterotroph - an organism that cannot manufacture its own food, andtherefore requires external sources of energyheterotypic school - a well-defined group or school of several kinds offishesheterozooid - a specialized non-feeding bryozoan zooid. Heterozooidsinclude forms specialized for producing and brooding eggs, or, morerarely, spermatozoa. Others are specialized to protect the colony, or havea cleaning function, or strengthen and support the colonyheterozygote - an individual having a heterozygous gene pair. A diploidor polyploid with different alleles at a particular locusheterozygous gene pair - a gene pair having different alleles in the twochromosome sets of the diploid individual, for example, Aaheuristic - problem analysis based on informal judgment or experienceversus data manipulation; a guideline or rule of thumb that is normallyeffective in dealing with a given situationHexactinellida - a class of sponges(phylum Porifera) commonly called glasssponges, as they have distinct siliceousspicules which are united with each otherand form a network. The body is usuallycylindrical or funnel-shaped. MostHexactinellida are syconoid or leuconoid inbody organization. All species are marineand are rarely found at depths less than 50metersA glass sponge in theclass, Hexactinellida.(Illustration: BIODIDAC)hexamerous - having six parts, or parts in multiples of six arrangedradially, as found in anthozoans in which the tentacles and mesenteriesare in multiples of sixhexaxon - in sponges, a spicule with six rayshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (8 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahiatus - a gap, e.g., unoccupied space between the distributions of twospecies or populations; a space between teethhigh tide - the tide at its fullest extent,when the water reaches its highest levelA small island at themouth of the AmazonRiver at high tide. See lowtide for contrast. (Photo:Alessandra and Michael)high-resolution satellite SST climatology - 9 km monthly or yearlyaverages of satellite-derived (see AVHRR) sea surface temperaturesobtained over periods of 10 years or longerhinge - the elastic part of a bivalve (Mollusca) shell that unites the valvesalong the top of the shellhistogram - a bar graph in which the area over each class interval isproportional to the relative frequency of data within this intervalhistology - the branch of biology that studies the microscopic structure ofanimal or plant tissues. The four basic types of animal tissues are:epithelial tissue, nervous tissue, muscular tissue and connective tissue(bone, cartilage, blood, fat, and areolar (fibrous). The three basic planttissues are: dermal tissue, ground tissue, and vascular tissuehistone - a type of protein present in the nucleus of eukaryotic cells thathelps to compact DNA into tightly packed chromosomeshistorical data - data sets from previous studieshistosol - soil with a high organic contenthoa - a channel or pass connecting the atoll lagoon with the open oceanholdfast - a root-like structure for attachment that anchors attachedseaweeds, other algae, and octocorals to the substratumhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (9 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Dataholism - the hypothesis that the properties of a system cannot bedetermined or explained simply by the sum of its components alone, i.e.,the total of a system is greater than the sum of its parts; as opposed toreductionismholobenthic - pertaining to fauna that are confined to a benthic existencethroughout their entire life cycleholobiont (coral) - a collective term referring to the totality of a coralanimal, its endosymbiotic zooxanthellae, and the associated community ofmicroorganismsholoblastic cleavage - complete cleavage of the zygote. The cleavagefurrows pass all the way through the zygote; typical of isolecithal andmesolecithal eggsHolocene epoch - an epoch of the Quaternary period dating from theend of the Pleistocene approximately 8,000 years ago until the presentholoeuryhaline - pertains to organisms that inhabit fresh, brackish andmarine watersholoplankton - planktonic organisms that spend their entire life cycle inthe floating state, as contrasted with organisms, such as fishes, whichspend only a portion of their life cycle (eggs, larvae) as members of theplanktonic communityholothurian - a sea cucumber in theechinoderm class HolothuroideaA holothurian (seacucumber), Holothuriaatra.holothurin - a toxic substance released by some holothuroids (seacucumbers)holotrichous - pertaining to a nematocyst with spines along the wholeshaft or threadholotype - in taxonomy, a single specimen designated or indicated thetype specimen by the original author at the time of publication of theoriginal descriptionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (10 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahome page - the first page that a browser opens when accessing a Webaddress (URL). The home page generally serves as a gateway to the restof the Web site by providing links to the other pageshome range - the area over which an animal normally travels in its dailyactivitieshomeobox - a region of DNA sequence found in genes involved in theregulation of the development (morphogenesis) of fungi, plants andanimals. Genes that have a homeobox are called homeobox genes andform the homeobox gene family. They are also called "HOX genes."Homeobox genes regulates activities of other genes (turns genes 'on' and'off' )homeostasis - the ability to maintain a relatively constant internalenvironmenthomeotic gene - a gene that controls the activity of other genes involvedin the development of a body planhomeotic mutation - a mutation that causes a body part of an organismto develop in an inappropriate positionhoming behavior - a type of behavior where the adult organism returnsto its place of originhomocercal - a caudal fin with upper and lower lobes that areapproximately equal in size; characteristic of most bony fisheshomodont - type of dentition where the teeth are all similar, indicative ofa uniform diethomogeneous - of similar or uniform structure or compositionthroughout; refers to anything which displays a uniform or consistentcompositionhomolog - in genetics, one member of a chromosome pair. Homologouschromosomes have corresponding DNA sequences and come fromseparate parents, i.e., one homolog comes from the maternal parent andthe other comes from the paternal parent; in evolution, a characteristicthat is similar in different species because it evolved from a commonancestorhomologous behavior - a behavior in different species which is similar inits manifestation, but not necessarily in functionhomologous chromosomes - the pair of chromosomes in a diploidindividual that have the same overall genetic content. One member ofeach homologous pair of chromosomes is inherited from each parenthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (11 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahomology - the relationship of any two characters that have descendedfrom a common ancestor. The term can apply to a morphologicalstructure, a chromosome, an individual gene, or a DNA sequencehomonym - in taxonomy, each of two or more identical butindependently proposed names for the same or different taxa. A juniorhomonym is the later published of two homonyms. A senior homonym isthe earlier published of two homonymsHomonymy, Law of (Principle of) - any name that is a juniorhomonym of an available name must be rejected and replaced; theprinciple that the name of each taxon must be uniquehomotypic school - a well-defined school of fish composed of onespecies with individuals all of similar sizehomozygote - an individual having a homozygous gene pair. A diploid ora polyploid with identical alleles at a locushomozygous gene pair - a diploid gene pair having identical alleles inboth copies, for example, AA or aahookah - "hookah" refers to diving where the diver is supplied withbreathable air from the surface via an air compressor and an airline(hose). This type of diving is ideal for shallow water commercialapplicationshorizontal classification - in taxonomy, classification which stressesgrouping together taxa in a similar stage of evolution, rather than locationon the same phyletic linehorn - a bony projection, e.g. the "horns"on the heads of cowfishesthe longspine cowfish,Lactoria cornuta, has apair of horns projectingfrom the top of its head(Photo: Keoki and YukoStender)horny coral - coral species in the Order Gorgonacea that embeds calciumcarbonate in a semi-soft, flexible material called keratin. This allows forthe flexibility sea fans and sea whips require to survive in strong currents;gorgonianshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (12 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahorotelic - pertaining to evolution proceeding at a standard ratehorse latitudes - two belts or regions of subtropical high-pressure areas,located between 30-35 degrees north and south, in which the wind is lightand varied and weather is hot and dryhost - an organism which serves as the habitat for a parasite orsymbiont. The host may provide nutrition to the parasite or symbiont, orsimply a place in which to livehotspot - an environmentally endangered region that is both rich inspecies and found nowhere elseHotSpot animation - animations from HotSpot imagery denoting coralreef bleaching events over timeHotSpot charts - charted regions that highlight sea surface temperature(SST) anomalies that are greater than 1 deg C above the maximummonthly climatological SST. See also coral bleaching and coral bleachinghotspotHox gene - a member of a family of regulatory genes which all contain acommon base pair sequence, the homeobox. In morphogenesis, they areinvolved in spatial patterning along the longitudinal axis of an organism.The genes are activated to define the anterior end, the posterior end, themiddle, etc. Their expression pattern is collinear, that is, the order ofgenes in the cluster reflects the temporal and spatial sequence of geneactivation in the organismhump - the raised area behind the head in certain fish species, usuallymature adults or breeding maleshurricane - an intense tropical cyclone inwhich winds tend to spiral inward toward acore of low pressure, with maximumsurface wind velocities that equal or exceed33.5 m/sec (75 mph or 65 knots) forseveral minutes or longer at some pointInfrared image ofHurricane Hugo makinglandfall September 22,1989. (Image: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (13 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahurricane surge - a rise in the sea surfaceon an open coast, often resulting from ahurricaneSurge from 1969'sHurricane Carol swamps ayacht club. (Photo:Providence Journal Co.,NOAA/NWS HistoricCollection)hyaline - translucent or transparenthyalinization - a form of tissue degeneration in which the tissuesdevelop a homogeneous and glassy appearancehybrid - an individual with parents of different specieshybrid name - in taxonomy, names of progeny of two individualsbelonging to different taxa. Names given to hybrids are not normallyavailable, as they are individuals, not populations, and hence not taxahybridization - the production of offspring (hybrids) from geneticallydissimilar parentshydranth - a feeding polyp of a colonialhydrozoan. It bears tentacles armed withnematocysts, a mouth and a thin outercovering, the hydrothecaHydranth of thehydrozoan, Obelia.1=coenosarc;2=hydrotheca;3=tentacles. (Photo: RickGillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (14 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahydrate - a compound produced when certain substances chemicallycombine with water; as a verb, it means to supply water to somethingthat absorbs ithydraulic hypothesis - the hydraulic hypothesis (or "theory") attemptsto explain the formation and existence of Lophelia coral reefs in deep,cool, Norwegian waters. It states that primary producers (mainly bacteria)are locally formed and concentrated at reef locations due to seepage oflight hydrocarbons (mainly methane) on the continental shelf, andnutrient-rich groundwater in the fjords. The health and proliferation ofthese deep water reefs relies on the assumption that there is a stable,local input of nutrients through the seabed at or near the location wherethe reefs are foundhydrocarbon - an organic molecule, such as methane (CH 4 ), whichconsists only of carbon and hydrogen atomshydrocarbon seep - an area where hydrocarbons seep slowly from thesea floorhydrocaulus - the main stem of a colonialhydrozoan which consists of a cylindricaltube of living tissue (coenosarc) covered bya thin outer membrane (perisarc)Hydrocaulus of thehydrozoan, Obelia. (Photocredit: Rick Gillis, Ph.D.,Biology Dept., Universityof Wisconsin-La Crosse)hydrochory - spread of plant seeds, spores or propagules by waterhydrocoral - a cnidarian, belonging to the class Hydrozoa, which containsan internal skeleton of calcium carbonate, unlike therelated hydroids,whose skeleton is chitinous and external. Hydrocorals, which include firecoral and the precious red coral used for jewelry, form encrusting orbranching skeletons similar to those of anthozoan coralshydrogen bond - a relatively weak chemical bond consisting of ahydrogen atom between two electronegative atoms (e.g., oxygen ornitrogen), with one side being a covalent bond and the other being anionic bondhydrogen ion - an individual atom of hydrogen which is not attached to amolecule and therefore has a positive (+) chargehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (15 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahydrogen sulfide (H2S) - a toxic gas formed by the anaerobicdecomposition of organic matter. It's chemical formula is H2S. It is acommon chemical found in the fluids of hydrothermal vents formed whenseawater is exposed to the sulfate in volcanic rock below the ocean floor.Hydrogen sulfide is colorless with a strong odor of rotten eggshydrogenosome - an organelle found in ciliates, trichomonads, andfungi. Hydrogenosomes are enclosed by a membrane and producemolecular hydrogen and ATP. They are thought to have most likelyevolved from mitochondriahydroid - a body shape of cnidarian polyps. A hydroid has a fleshy centralstalk topped by a ring of tentacles used for catching food. Anemones areone kind of hydroid; many jellyfishes are hydroids for part of their life cyclehydrological cycle - the movement of water in all of its phases (gas,liquid, solid) from the Earth to the atmosphere and back to the Earthhydrology - the science dealing with the properties, distribution andcirculation of water and snowhydrolysis - the breaking down of a compound into fragments by theaddition of a molecule of water. The hydroxyl group is incorporated in onefragment and the hydrogen atom in the otherhydrophilic - having a strong affinity for water; tending to dissolve in,mix with, or be wetted by water ­hydrophobic - refers to molecules that do not interact with water and arenot soluble in water. Hydrophobic compounds do not dissolve easily inwater, and are usually non-polar. Oils and other long hydrocarbons arehydrophobichydrophone - an underwater microphonehydropic - having an excess of water or watery fluidhydrorhiza - all structures by which hydrozoan polyps are attached tothe substratehydrosere - an ecological succession beginning in a habitat withabundant water, typically on the submerged sediments of a standingwater body (e.g. lake or lagoon), and ending on dry landhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (16 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahydrostatic skeleton - a type of skeleton found in many soft-bodiedinvertebrates which consists of a turgid column of liquid within one of thebody spaces that provides support or rigidity to the organism or to one ofits parts. Hydrostatic skeletons are found in echinoderms (starfish, seaurchins), annelids (worms), nematodes (roundworms), and a number ofother wormlike invertebrate phylahydrotheca - a thin outer covering of a hydranth, the feeding polyp, of acolonial hydrozoanhydrothermal plume - a cloud of hot,mineral-rich water that flows out of ahydrothermal vent and disperses into theocean, usually several hundred metersabove the seafloor vent site. Rock particlesand minerals in the plume water oftenmake the plume look smokyA "black smoker" chimneyon the Brothers seamounton the Kermadec Ridge,emitting a hothydrothermal plume ofmineral rich fluid (Photo:Japan Agency for Marine-Earth Science andTechnology (JAMSTEC))hydrothermal vent - a sea floor fissure from which a spring ofgeothermally heated mineral and gas rich seawater issues. Hydrothermalvents are found on some oceanic ridges in zones of active seafloorspreading (plate tectonics)hydroxyl group - an [-OH] or alcohol group on a larger molecule. Theoxygen is single-bonded to the hydrogen and has one free bond to therest of the moleculehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (17 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef DataHydrozoa - a class within the phylumCnidaria. The Hydrozoa contains five ordersthat include: small medusae with no polypgeneration; colonial forms with alternatingpolyp and medusa stages and a chitinousexoskeleton; solitary polyps that lack amedusoid stage; colonial forms withmassive aragonite skeletons (e.g., firecoral); and complex colonial forms, withindividual polyps specialized for feeding,swimming, prey capture, and reproduction.Some, but not all, float by means of a largepneumatophore, or gas bagWhite-tipped mustardcoloredfire coral in theFlower Garden Banks.hyoid - having a "U" shapehyper- - above, exceeding, higher, more than, abnormally increasedhypereosinophilia - a disease characterised by a marked increase in theeosinophil (a type of white blood cell) count in the bloodhyperlink - text or images on a Web page that, when clicked with amouse, causes the browser to load another page of HTML. Because asimple mouse click allows the user to easily go from one page of hypertextto another, these pages are said to be "hyperlinked." Text links areusually, but not always underlined in blue, while hyperlinks that areimages often take the form of "buttons"hyperplasia - abnormal increase in the size/volume of a tissue due tomultiplication of cellshypersaline - referring to water with a salinity higher than that of naturalseawaterHyperspectral AVIRIS (Airborne Visible/Infrared ImagingSpectrometer) - a hyperspectral image is a very high resolution imagewhich was acquired with a hyperspectral scanner. These instrumentsacquire data in 224 contiguous channels of approximately 10nmbandwidth. They are spanning the visible, near-infrared and mid-infraredportion of the electromagnetic spectrumhypertrophy - the over-development of a structurehypertrophy - the excessive enlargement or development of an organ ortissue, with increase in cell size but without increased cell divisionhypha - one of the long, branching filaments that forms the mycelium ofa fungushttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (18 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahypo- - under, below, beneath, lower than, small size, deficiencyhypobranchial gland - a gland in the mantle cavity of mollusks thatsecretes mucushypocenter - the point under the earth's surface where the energy of anearthquake is first released. The point directly above the hypocenter onthe earth's surface is the epicenterhypolithic - living on lower surfaces of rockshyposaline - referring to water with a salinity lower than that of naturalseawaterhypostome - in cnidarians, the circular raised area of a hydrozoan polypthat lies between the tentacles and the mouth. The term is also used todescribe mouthparts in other phylahypothermia - a condition when the body temperature is colder thannormal (37 degrees C/98.6 degrees F in humans)hypothesis - a tentative assumption made for the purpose of empiricalscientific testing. A hypothesis becomes a scientific theory when repeatedtesting and the great body of evidence suggests that the hypothesis has astong probability of being correcthypoxic - deficient in oxygenhypural plate - in fishes, the flattenedbony plate at the posterior end of thevertebral columnThe hypural plate is theexpanded ends of thehypurals that form a wide,fan-like plate onto whichthe caudal fin rays areattached (Illustration:Fishbase)(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (19 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef Datahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=h (20 of 20) [2/26/2008 9:14:16 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: IThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zichno - a prefix meaning "trace"ichnogenus - a genus based on the fossilized work of an organismichnologist - a scientist whose area of study and research is ichnologyichnology - the branch of paleontology that deals with traces oforganismal behavior. The division of ichnology dealing with trace fossils ispaleoichnology, while neoichnology is the study of modern tracesichnospecies - a species based on the fossilized work of an organismichnotaxon - a taxon based on the fossilized work of an animal, includingfossilized trails, burrows, and tubesichthyo- - pertaining to fishesichthyochory - the dispersal of plant seeds or spores by fisheshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (1 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataichthyology - the scientific study of fishesThe diver is studying thebehavior and ecology ofsquirrelfishes on aCaribbean coral reef.(Photo: Dr. Anthony R.Picciolo, NOAA)icon - a small picture displayed on a computer monitor that identifies acommand or file.iconel tag - a metal tag that is attached to the trailing edge of aseaturtle's flipper to provide a means of unique identificationiconotype - in taxonomy, a drawing or photograph of a type specimenicosahedral - a many sided, three dimensional, hexagonal shape madeup of many small trianglesICRI (International Coral Reef Initiative) - an environmentalpartnership and network that brings all the stakeholders together with theobjective of sustainable use and conservation of coral reefs for futuregenerations. ICRI is an informal mechanism that allows representatives ofover 80 developing countries with coral reefs to sit in equal partnershipwith major donor countries and development banks, internationalenvironmental and development agencies, scientific associations, theprivate sector and non-governmental organizations (NGOs) to decide onthe best strategies to conserve the world's coral reef resourcesIcriforum - the official web site of the International Coral Reef Initiative(ICRI). Information relative to ICRI and its secretariat are available underthis section, such as the current secretariat, the ICRI Meetings, the historyof ICRI, and the ICRI Partnersidiopathic - denotes a disease of unknown cause or originIDL (Interactive Data Language) - a commercial array-orientedlanguage with numerical analysis and display features, first released in1977. It supports interactive reduction, analysis, and visualisation ofscientific datahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (2 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataigneous rock - a rock formed by the cooling and crystallization of moltenmagmaIKONOS satellite - high-resolution (1-2meter resolution) imaging satellite; theworld's first commercial satellite forimagery of this typeFour-meter true colorIKONOS image of BuckIsland Reef NationalMonument shows anextensive underwatercoral reef ecosystem.illecium - a "fishing rod-like" appendageon the head of some fishes, usually amodified dorsal fin spineIllustration depicting the"fishing rod-like"appendage on the head ofthe above fishimagery - visible representation of objects and (or) phenomena assensed or detected by cameras, infrared and multispectral scanners,radar, and photometersimbricate - with overlapping parts, such as scalesimitation - a behavior that occurs when an animal immediately mimicsthe actions of another animal while they are in each other's presenceimmature - describes an animal that has not reached sexual maturity,regardless of size or ageimmersed corallite - a corallite that is embedded in the surroundingcoenosteumhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (3 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataimmune system - a system that provides the organism with a defenseagainst infection. In higher organisms it is afforded by the presence ofcirculating antibodies and white blood cells. Antibodies are manufacturedspecifically to deal with the antigens associated with different diseases asthey are encountered. White blood cells attack and destroy foreignparticles in the blood and other tissuesimmunogen - any substance that can elicit an immune responseimmunosuppressive compound - a compound that suppresses thebody's immune system. Immunosuppressive compounds are medicallyimportant in cases of hypersensitivity to certain antigens or organtransplantations. A number of immunosuppressive molecules have beenisolated from marine spongesimpact - a change, caused by external sources, in the chemical, physical(including habitat) or biological quality or condition of a habitat orenvironmentimperforate corals - corals which have solid skeletons with noconnections between the polypsimpermeable - having the property of restricting the passage ofsubstances across a membraneimposex - the imposition of male characteristics on female organisms, ascaused by some pollutants. For example, a pseudo-hermaphroditiccondition in female gastropods (development of a false penis) caused bytributylin (TBT), a biocide used in anti-fouling paintsimprimis - in the first placein adnot. - in an annotation (in adnotatio)in hospite - within the hostin litt. - in correspondence or communicated in writing; used for anunpublished source of information (in litteris)in situ - in the natural or original positionin situ data - measurements made at the actual location of the object ormaterial measured, in contrast to remote sensinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (4 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datain situ hybridization - a method of detecting the presence of specificnucleic acid sequences within a cytological preparation. A DNA or RNAprobe is labeled, radioactively or chemically, and hybridized to acytological preparation to detect RNA, or to a denatured cytologicalpreparation to detect complementary DNA. The hybridization is detectedby autoradiography (for radioactive probes) or by chromogenic reactionsor fluorescence (for chemically-labeled probes)in syn. - in synonymy (in synonymis)in vitro - a laboratory experiment or study performed outside the body ofa living organism in a test tube, petri dish, or other vesselin vivo - studies conducted in intact living organisms or cellsinbreeding - reproduction among closely related individualsinbreeding depression - a reduction in fitness and vigor of individuals asa result of increased homozygosity through inbreedinginc. sed. - of uncertain taxonomic position or affinities (incertae sedis)incidence - pertaining to disease, the number of new cases of a specificdisease occurring during a certain time period, or number of diseasedindividuals in a populationincident command system (ICS) - a management system used toorganize emergency response. ICS offers a scalable response to anemergency (incident) of any magnitude, and provides a commonframework within which people can work togetherincidental parasite - an accidental parasiteincipient population - a small population that is just beginning toreproduce and become established in an area or communityincipient species - a geographically isolated population. With time, theaccumulation of genetic differences in the incipient species populationproduces isolating mechanisms which inhibit the reproductive potential ofthe incipient population and its conspecific parent populationincisiform tooth - a chisel-shaped tooth used for cutting. Typically, itwider than it is thickhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (5 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataincomplete dominance - in genetics, an interaction between alleles inwhich both alleles are expressed more or less equally. The expression fora phenotype for a given trait exhibits a blending of the genetic messagesfrom the allele partners controlling that trait. An example may be a crossbetween a homozygous red trait (AA) and a homozygous white trait (aa),where neither the red (A) nor white (a) trait is dominant. The phenotypicexpression of the offspring is pink (Aa), the intermediate phenotypeincomplete protein - a protein which does not supply all the essentialamino acidsincorporated territory - equivalent to Territory, a United States insulararea, of which only one territory exists currently, Palmyra Atoll, in whichthe United States Congress has applied the full corpus of the UnitedStates Constitution as it applies in the several States. Incorporation isinterpreted as a perpetual state. Once incorporated, the Territory can nolonger be de-incorporatedincubation - the period of time from when an egg is fertilized untilhatching; the maintaining of eggs under conditions favorable for hatching;the time between exposure to an infectious organism and the appearanceof clinical systems of diseaseincurrent canal - in sponges, an inpocket of the epidermis (pinacoderm)which opens into a choanocyte chamber via a small opening, theprosopyleindependent assortment - the random alignment of homologouschromosomes during meiosis. Each member of a pair of homologouschromosomes separates independently of the members of other pairs sothe results are randomindependent variable - a variable controlled by the experimenterindeterminate cleavage - cleavage where the fate of the resultingdaughter cells is not determined after the initial divisionof a fertilized egg.If the cells separate, each has the potential to develop into an entireorganism and the resulting individuals are genetically identical (identicaltwins). Inderterminate cleavage is characteristic of deuterostomesindicator species - any organism that by its presence or absence, itsfrequency, or its vigor, indicates a particular property of its surroundingenvironment; a species whose presence is a sign that certainenvironmental conditions existindigenous - native to a particular country or areaIndo-Pacific - a vast region encompassing the tropical Indian and PacificOceans from Africa in the west to Hawaii and French Polynesia in the east.This area represents the largest marine biogeographic region in the worldhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (6 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainductive reasoning - the process of observing data, recognizingpatterns, and making generalizations from the observations; reasoningfrom particular facts to a general conclusioninert - refers to unmoving or unchanging. In chemistry, a substancewhich does not or rarely combines with other substances. In medicine, itmeans a substance that has little or no effect on the human bodyinfauna - animals that inhabit the sandy or muddy surface layers of theocean bottom, i.e., those that live buried or dig into the substrateinfection - the invasion of an organism's body tissues by disease-causingmicroorganisms, which may produce tissue injuryinfectious - capable of spreading diseaseinfectious agent - an organism capable of spreading diseaseinference - a conclusion derived either by logical reasoning frompremises and/or evidence, or by insight or analogy based on evidenceinferior - anatomically beneath, lower, or toward the bottom (e.g., themouth is inferior to the nose)inflammation - a nonspecific, localized protective immune response oftissues to irritation, injury, or infection, characterized by pain, redness,swelling, and sometimes loss of function. Inflammation may be acute orchronicinflated - swollen or expandedinformatics - the management and analysis of data using advancedcomputing techniquesinformation management - the integration of a variety of activitiesdesigned to manage information and information resources throughouttheir life cycle. Activities include planning, budgeting, organizing,directing, training, promoting, and controlling the information andinformation resources throughout the process of collecting, processing,transmitting, disseminating, and disposing of information; themanipulation, reorganization, analysis, graphing, charting, andpresentation of data for specific management and decision-makingpurposesInformation Technology (IT) - a very general term referring to theentire field of Information Technology - anything from computer hardwareto programming to network managementinfra- - a prefix meaning "below"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (7 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainfrared scanner - an instrument that detects infrared radiation andconverts the detected energy to an electrical signal for recording onanother mediuminfrasonic - sound waves that have a frequency that is lower than whathumans can hear (i.e. below about 20 hertz). Some baleen whales andelephants produce infrasounds to communicate over long distancesinfraspecific name - in taxonomy, a general term for any name belowthe rank of species. The term includes subspecific and infrasubspecificnamesinfrasubspecific - in taxonomy, a category below the subspecies levelinfundibuliform - funnel-shapedingestion - the intake of water or food substances by "swallowing" them,taking them into the body cavity or into a cell vacuoleinhalant system - in sponges, part of the aquiferous system between theostia and prosopyleink sac - a diverticulum of the rectum ofmost cephalopods, where an 'inky" melaninsolution is stored. The ink is ejected from aduct opening at the base of the siphon. Itserves to cloud the water, and enable theseanimals to escape from predatorsVentral view of a dissectedsquid revealing the inksac. (Photo: Biology Dept.,Fairfield University,Fairfield, CT)innate - not established by conditioning or learning; "an unconditionedreflex"; a genetic behavior patterninnate releasing mechanism - in ethology or animal behavior, an innatesystem within an animal that responds to a stimulus in the environment toproduce a genetic stereotyped behavior; a stimulus-response mechanisminner cell mass - the cluster of cells inside the mammalian blastocyst.These cells give rise to the embryonic disk of the later embryo and,ultimately, to the fetushttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (8 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainorganic matter - chemical substances of mineral origin which containno organically produced carboninquilinism - a symbiotic association in which one symbiont lives in closeassociation with another, generally in its shell, tube or burrow, or actuallywithin a body cavity of the hostinquilinism - a symbiotic association in which one symbiont lives in closeassociation with another, generally in the tube or burrow or actually withina body chamber of the hostinserted gene - a gene introduced into the DNA of a recombinantorganism which is not present at the same position in the DNA of theorganism before genetic modificationinsolation - the amount of solar radiation received on a given body or ina given areainstar - a discreet, in-between molt stage, during the metamorphosis ofan arthropod from larva to adultinstinct - an unlearned, genetically coded behavior pattern that isinternally motivated and characteristic of the species; the innate capacityof an animal to respond to a given stimulus in a relatively fixed wayinsular - relating to, or characteristic of, or situated on an islandinsular area - a jurisdiction that is neither a part of one of the severalStates nor a Federal district. This is the current generic term to refer toany commonwealth, freely associated state, possession or territory orTerritory and from July 18, 1947, until October 1, 1994, the TrustTerritory of the Pacific Islands. Unmodified, it may refer not only to ajurisdiction which is under United States sovereignty but also to one whichis not, i.e., a freely associated state or, 1947-94, the Trust Territory of thePacific Islands or one of the districts of the Trust Territory of the PacificIslandsinteger - a number without a decimal (0, 1, 25, 173, 1032, etc.). Integervalues can be less than, equal to, or greater than zerointegrated coastal zone management - the process of combining allaspects of the human, physical and biological aspects of the coastal zonewithin a single management frameworkhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (9 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef DataIntegrated Coral Observing Network (ICON) - As of October 2005,the coral research program at NOAA's Atlantic Oceanographic andMeteorological Laboratory (AOML) was titled the "Integrated CoralObserving Network" (ICON), rather than the Coral Reef Early WarningSystem (CREWS). ICON is focusing upon: (a) Integrating data fromdiverse independent sources into value-added products supportingresearch, modeling and management decisions with respect to MarineProtected Areas and other ecosystem approaches to management issues,(b) Consistency with Integrated Ocean Observing System (IOOS) andCoral Reef Ecosystem Integrated Observing System (CREIOS) goals andobjectives, (c) International partnerships to enhance the global ICONnetwork, (d) Facilitation of development and transition to operations ofpromising relevant in situ instrumentation (e.g., PAM-fluorometry, pCO2,acoustic and optical particle detection and size fractionation, and acoustictelemetry), and (e) The hand-off of responsibility for the in situ coral reefstation network infrastructure to a NOAA operational lineIntegrated Ecosystem Assessment - a critical tool to enable NOAA’secosystem approach to management. An IEA is a synthesis andquantitative analysis of information on relevant physical, chemical,ecological and human processes in relation to specified ecosystemmanagement objectives. IEAs focus not on collecting new observations orconducting new research, but on integrating existing datasets to producemore useful assessments, build ecological forecast models, and developother ecological decision support toolsintegrated observing system - a planned, organized, and structuredsystem of interoperable earth observing systems, which, when networked,provide an expanded range of capabilities satisfying user information andproduct needs. An integrated observing system holds some common goalsand adopts common solutions to achieve themIntegrated Ocean Observing System (IOOS) - IOOS is a system ofsystems that routinely and continuously provides quality controlled dataand information on current and future states of the oceans and GreatLakes from the global scale of ocean basins to local scales of coastalecosystems. It is a multidisciplinary system designed to provide data informs and at rates required by decision makers to address societal goalsintensity - pertaining to sound, the average amount of sound power(sound energy per unit time) which is transmitted through a unit area in aspecified direction. The magnitude of the intensity is often referred to asthe intensity, without specifying the direction from which the sound istravellingintention movement - an incomplete behavior pattern that providesinformation about the activity a particular animal is about to perform, andacts as a signal to othersinterannual - refers to a climatic process that re-occurs every three toten years. El Niño is an example of a climatic process that re-occurs every4-6 yearshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (10 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainterface - the common boundary between two substances such as awater and a solid, water and a gas, or two liquids, such as water and oilinterference competition - competition in which one species preventsanother from having access to a limiting resourceinterferon - a family of small proteins that stimulate viral resistance incellsinterglacial period - a warm period between glacial epochsinterleukin - a family of proteins produced naturally to stimulate anorganism's immune system by stimulating the growth and activities ofcertain kinds of white blood cellsintermediate form - a fossil or modernspecies that possesses characters definitiveof two or more different taxa, or thatdisplays characters morphologicallyintermediate between two different taxaSome experts believe thatthe "living fossil" genusNeopilina, an internallysegmented mollusk in theclass Monoplacophora, isan an evolutionary linkbetween mollusks andother more obviouslysegmented invertebrates,such as annelid worms.(Graphic: BIODIDAC)intermediate host - in a parasite's life cycle, it is a host organism inwhich a parasite undergoes a stage of asexual developmentintermittent spawning - spawning at intervalshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (11 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainternal transcribed spacer (ITS) - a sequence of RNA in a primarytranscript that lies between precursor ribosomal subunits and is removedby splicing when the structural RNA precursor molecule is processed into aribosome. These sequences are coded by ribosomal DNA. Eukaryoticorganisms have two internal transcribed spacers; ITS-1 is locatedbetween the 18S gene and the 5.8S gene, and ITS-2 is located betweenthe 5.8S and the 28S gene. Ribosomal genes and spacers occur in tandemrepeats that are thousands of copies long. The ITS region is widely used inmolecular phylogenetics and taxonomyInternational Code of Botanical nomenclature (ICBN) - the set ofrules and recommendations dealing with the formal scientific names thatare given to plants. The ICBN applies not only to plants, as they are nowdefined, but also to other organisms traditionally studied by botanistInternational Code of Zoological Nomenclature (the Code) - intaxonomy, an authoritative document containing a system of rules andrecommendations to be followed in giving a scientific name to an animalor animal group. It has been adopted by the International Congresses ofZoology (more recently the International Union of Biological Sciences) andis administered by the International Commission on ZoologicalNomenclature. The most recent version of the Code is the Fourth Editionpublished in September 1999 and took effect on January 1, 2000; usuallyreferred to as the "Code"International Commission on Zoological Nomenclature (ICZN) - thejudicial body empowered to enforce and interpret the International Codeof Zoological NomenclatureInternational Committee on Taxonomy of Viruses (ICTV) - acommittee which authorizes and organizes the taxonomic classification ofviruses. They have developed a universal taxonomic scheme for virusesand aim to describe all the viruses of living organismsInternational Coral Reef Action Network (ICRAN) - established in2000, ICRAN is a global partnership of coral reef experts who are workingto halt and reverse the decline of the health of the world's coral reefs.Made up of some of the world's leading coral reef scientists andconservation groups, ICRAN partners have created a globally integratedaction plan to manage and protect coral reefs, based on recommendationsfrom the International Coral Reef Initiative (ICRI). The International CoralReef Action Network is a coordinated response to ICRI's urgent call toprotect coral reefs. There are three main interlinked components ofICRAN: reef management, global coral reef monitoring and assessment ,and communications and knowledge disseminationInternational Zoological Congresses - the legislative bodiesresponsible for the rules of the International Code of ZoologicalNomenclature and for authorization of the activities of the InternationalCommission on Zoological Nomenclaturehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (12 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainternesting - as it pertains to marine turtles, the interval between asuccessful nest and the next nesting attemptInternet Service Provider (ISP) - a company or organization thatprovides access to the Internetinteroperability - the ability of two or more systems to exchange andmutually use informationinterorbital - the space between the eyesinteroreceptor - a neurological receptor that is located within theorganism's body and detects physiological changes, e.g. pH, temperature,chemicals in bloodinterpolated name - in taxonomy, a name placed within parentheses(after a generic name to denote a subgenus; after a genus-group name todenote an aggregate of species, or after a specific name to denote anaggregate of subspecies. Names used in this way are not counted as oneof the names in a binomen or trinomeninterradial - in fishes, between the rays (or spines), e.g. interradialpigment is pigment on the membrane between the rays.interradial canal - one of four branched ciliated canals in scyphozoanmedusae that originates from the gastric pouches and move materialsfrom the ring canal back toward the stomach and gastric pouchesinterradial membrane - in fishes, the tissue between the fin rays orspinesinterradial pigment - in fishes, interradial pigment is pigment on themembrane between the fin raysintersex - an organism which possesses a mixture of male and femalecharacteristicsintersexual - involving both sexes, male and femaleinterspecific - between members of different speciesinterspecific competition - competition between individuals of differentspeciesinterspinous membrane - in fishes, the membrane between fin spineshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (13 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Datainterstices - the openings or pore spaces in a rock, soil, and other suchmaterialinterstitial - refers to the interstices or pore spaces in rock, soil, or othermaterial subject to filling by water; fluid-filled spaces between cells intissuesinterstitial fauna - animals that live in the spaces within sedimentparticles (interstitial spaces)interstitial water - water in the pore spaces of soil or rockintertidal zone - the region between thehighest water line and the mean low tidelevelSea anemones crowd arocky intertidal zone(Photo: Nancy Sefton)intertropical convergence zone - the zone of low pressure near theequator where the trade winds converge and create heavy convectionalprecipitation; also known as "intertropical front (ITF)intolerant organism - an organism (or species) that is not adaptable tohuman alterations to its environment and thus declines in number wherealterations occurintranet - a private network inside an organization that uses the samekinds of software found on the public internet, but which is only forinternal useintrasexual - involving only one of the sexes, male or femaleintraspecific - among members of the same speciesintraspecific competition - competition between individuals of the samespeciesintratentacular budding - a type of asexual reproduction wheredaughter corallites grow from the inside wall of parent corallites, usuallyby division of the parent corallitehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (14 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataintrinsic - belonging to a thing by its very nature; the essential nature orconstitution of a thing; inherent; in and of itselfintrinsic value - a value placed on the inherent qualities of a species,independent of its value to humansintrogression - the movement or incorporation of genes from onepopulation into another through hybridization followed by backcrossing.Usually refers to movement of genes from one species to another oramong sub-species that have been geographically isolated then broughtback together by changes in the species ranges or planting of exoticpopulationsintrogressive hybridization - the spread of genes of one species toanother species through hybridization. The hybrids are able to breed backinto one of the parental populations. This allows the reintroduction ofalleles that may have been lost during the speciation processintromittent organ - a copulatory structure employed by the males ofspecies that practice internal fertilization to transfer sperm cells into thereproductive tube of the female, e.g., the clasper of a shark, skate or ray;penis; modified anal fin (gonopodium) of live-bearer fishesintron - DNA sequences that interrupt the protein-coding sequence of agene; introns are transcribed into mRNA but the sequences are eliminatedfrom the RNA before it is used to make protein; junk DNA; in eukaryoticcells, a sequence of DNA that is contained in the gene but does notencode for protein. The presence of introns "splits" the coding region ofthe gene into segments called exonsinvagination - an inward folding of a layerof cells forming an interior pocketThe cells at the vegetalhemisphere of this starfishblastula have begun topush into the blastocoel(invaginaton), forming adiploblastc embryo with anew cavity, the primitivegut, or archenteron. Thecells lining the archenteronare endodermal cells.(Photo: Dr. Anna E. Ross,Christian Brothershttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (15 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef DataUniversity, TN)invalid name - in taxonomy, any name for a given taxon other than thevalid nameinversion - a chromosomal re-arrangement that reverses the order of alinear array of genes on the chromosomeinvert - to turn inward; turn inside out or upside downinvertebrate - an animal that lacks avertebral column (backbone)Feathery invertebrate tubeworms in the CaribbeanSea (Photo: Dr. AnthonyPicciolo).invertivore - an animal or plant that eats invertebratesinvestigative behavior - the sensory inspection of the environmentinvolute - rolled inwards fom the edgesion - a positively or negatively charged atom produced through loss orgain of one or more electronsion channel - a pore in a cell membrane, formed by an integral protein,that selectively regulates the diffusion of ions into and out of the cell. Anion channel switches between open and closed when the proteinundergoes a conformational change. Ion channels are usually selective fora specific ion type (e.g., Na, or K, or Cl, or Ca)ionic bond - a chemical bond in which one atom loses an electron to forma positive ion and the other atom gains an electron to form a negative ionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (16 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataionizing radiation - high-energy radiation capable of producingionization in substances through which it passes, i.e., radiation that hasenough energy to eject electrons from electrically neutral atoms, leavingbehind charged atoms or ions; examples are alpha particles (heliumnuclei), beta particles (electrons), neutrons, and gamma rays (highfrequency electromagnetic waves, x-rays)ionocyte - a type of cell commonly found in the gills of fishes and somecrustaceans. They play a role in regulating the salt concentration of cellsin relation to the external environment, and differ greatly betweenfreshwater and saltwater organisms; also called "chloride secretory cell"IOOS (Integrated Ocean Observing System) - a “user-driven”integrated system of observations, data management andcommunications, and data analysis and modeling that provides data andinformation required to achieve seven societal goals: 1) Improvepredictions of climate change and variability (weather) and their effects oncoastal communities and the nation; 2) Improve the safety and efficiencyof marine operations; 3) More effectively mitigate the effects of naturalhazards; 4) Improve national and homeland security; 5) Reduce publichealth risks; 6) More effectively protect and restore healthy coastalmarine ecosystems; and 7) Enable the sustained use of marine resourcesIR (infrared) radiation - earth-emitted radiation over thermalwavelengths: 3-15 micrometers. Used for satellite remote sensingbecause it can be used to monitor weather and oceanographic conditions24 hours a dayiridescent - exhibiting rainbow colorsThis deep-sea fish called a"greeneye" (Chlorophthalmidae)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (17 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataexhibits a beautifuliridescent pattern aroundits large eyes and head.(Photo: NOAA OceanExploration)iridiophore - a colorless chromatophore which contains purines, mostlyguanine in the form of large, nonmotile crystalsisauxesis - equality in growth; isometryischemia - a condition in which a tissue or organ does not receive asufficient supply of bloodisland arc - a curved chain of islands that rise from the sea floor, usuallynear a continent. The convex side usually faces the open ocean, while theconcave side usually faces the continent, e.g., the Aleutian Islandsisobath - a line on a map or chart that connects all points having thesame depth below a water surfaceisoenzyme - one of a group of enzymes that are very similar in catalyticproperties, but may be differentiated by variations in physical properties,such as isoelectric point or electrophoretic mobility; also called 'isozyme'isogamous - having haploid gametes that are similar in size, structureand motility. An isogamete can unite with another to form a zygoteisogenic chromosome - in a diploid organism, a chromosome in whichboth alleles at every locus are identical on both copiesisohyetal line - a line drawn on a map or chart joining points that receivethe same amount of precipitationisolecithal - an egg cell in which the total amount of yolk is small and theyolk granules are fairly uniformly distibuted throughout the cytoplasm,and cleavage completely bisects the cell, e.g., the egg of a starfish. Asynonym is "homolecithal"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (18 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef Dataisoline - a line on a surface connectingpoints of equal valueIsobars are utilized todepict NOAA-11 AVHRRSST climatology in thisdiagram.isometric contraction - a muscular contraction in which tensionincreases while the length of the muscle remains constantisometric growth - growth that occurs at the same rate for all parts ofan organism so that its shape is consistent throughout developmentisometry - change in overall size that maintains the same relativeproportional shapeisomorphic - having the same morphology for all stages of a life cycleisopleth - a general term for a line connecting points of equal value ofsome quantity. Isobars, isobaths,isotherms, etc. are all examples ofisopleths; also called an isolineisorhiza - a form of cnidocyst (nematocyst) in which the tube is open andhas the same diameter along its length. It responds to mechanical stimuli,and is also used in anchoring the animal when it walks on its tentaclesisotonic contraction - a muscular contraction in which tension isconstant while the length of the muscle changesisotope - one of two or more species of atoms of the same chemicalelement that have the same atomic number and occupy the same positionin the periodic table. They are nearly identical in chemical behavior, butthey differ in atomic mass or mass number. Therefore, they behavedifferently in the mass spectrograph, in radioactive transformations, andin physical properties, and may be separated or detected by means ofthese differencesisthmus - a narrow strip of land connecting two larger land masses, suchas the isthmus of Panamahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (19 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef DataITCZ (Intertropical Convergence Zone) - the region near the equatorwhere the trade winds of the Northern and Southern Hemispheresconvergeiteroparity - the reproductive condition in which individuals reproduceseveral times during their lifetimeiteroparous - a life history in which individuals reproduce more than oncein a lifetimeITIS (Integrated Taxonomic Information System) - a partnership ofU.S., Canadian, and Mexican agencies, other organizations, andtaxonomic specialists cooperating on the development of an online,scientifically credible, list of biological names. ITIS is also a participatingmember of Species 2000, an international project indexing the world'sknown speciesIUCN (International Union for the Conservation of Nature andNatural Resources) - the world’s largest conservation network. TheUnion brings together 82 States, 111 government agencies, more than800 non-governmental organizations (NGOs), and some 10,000 scientistsand experts from 181 countries in a unique worldwide partnership. TheUnion’s mission is to influence, encourage and assist societies throughoutthe world to conserve the integrity and diversity of nature and to ensurethat any use of natural resources is equitable and ecologically sustainable.IUCN is a multicultural, multilingual organization with 1000 staff located in62 countries. Its headquarters are in Gland, Switzerland. ” Since 1990,the IUCN has been known as the "World Conservation Union" but the fullname and the acronym are often used together as many people still knowthe Union as IUCNIUCN Categories I-VI - in the IUCN classification system for protectedareas, Categories refer to higher levels of protection: Category I - StrictNature Reserve/Wilderness Area: protected area managed mainly forscience or wilderness protection; Category la - Strict Nature Reserve:protected area managed mainly for science; Category Ib - WildernessArea: protected area managed mainly for wilderness protection; CategoryII - National Park: protected area managed mainly for ecosystemprotection and recreation; Category 111 - Natural Monument: protectedarea managed mainly for conservation of specific natural features;Category IV - Habitat/Species Management Area: protected area managedmainly for conservation through management intervention; Category V -Protected Landscape/Seascape: protected area managed mainly forlandscape/seascape conservation and recreation; Category VI - ManagedResource Protected Area: protected area managed mainly for thesustainable use of natural ecosystems(Top)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (20 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef DataRevised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=i (21 of 21) [2/26/2008 9:14:20 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: JThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZJ curve - a J-shaped growth curve that depicts exponential growthJaccard distance - a statistic which measures dissimilarity betweensample sets. It is obtained by dividing the difference of the sizes of theunion and the intersection of two sets by the size of the union, or,simpler, by subtracting the Jaccard coefficient from 1Jaccard index - a statistic used for comparing the similarity and diversityof sample sets; also known as the Jaccard similarity coefficientJack - any species of bony fishes in thefamily Carangidae (which also includes thepompanos). Jacks are cosmopolitan inwarm and temperate marine waters, someeven venturing into brackish and freshwater. As a group, they are swift andstrong predators. Typically, jacks have aseries of lateral scutes along each side ofthe caudal peduncle. In some species,these scutes extend along the lateral line.Some are important game and food fishesA pack of crevalle jacksswimming over aCaribbean reef. Note thecharacteristic line of bonyscutes along the lateralsurface. (Photo: Anthony.R. Picciolo, Ph.D./NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=j (1 of 3) [2/26/2008 9:14:21 AM]

Discover NOAA's Coral Reef DataJaspaquinol - an antiinflammatory drug derived from the marine spongeJaspis splendensJava - a programming language created by Sun Microsystems whichallows the user to create programs which run well in a networkedenvironment (such as the World Wide Web). Java programs are commonlycalled "applets" and can be used to add anything from calculators toanimated images to web sitesjawfish - species of small bony fishes belonging to the familyOpistognathidae. Jawfishes inhabit sandy, rubble-strewn areas on thereefs where they dig burrows into which they retreat when dangerthreatens. They hover over their burrows and feed on small animals thatswim or drift by. The entrances to their burrows are lined with smallpebbles or coral rubble and they are continually "grooming" the burrow byshoveling out mouthfuls of sand. They frequently raid neighboringjawfish's burrows to steal pebbles. Males are mouth breeders, carryingfertilized eggs in their mouths until they hatchjetsam - objects that have been thrown overboard in order to lighten aship when it is in troublejetty - a structure extending into the oceanto influence the current or tide in order toprotect harbors, shores, and banksA jetty protecting theshore line. (Photo: NOAA)Johnson-Sea-Link (JSL) Submersible - the Johnson-Sea-Link (JSL) Iand II submersibles are owned and operated bythe Harbor BranchOceanographic Institution. At 23.6 ft long, 10.9 ft high and 8.3 ft wide,these highly maneuverable submersibles can dive to a depth of 3,000 ftand travel at a maximum speed of one knotjoint - the place where two articulating segments meetjoint probability - the probability of two or more things occurringtogetherJordan's Rule - In general, closely related species do not have identicalranges, but often their ranges are not very far apart. They are usuallyadjacent but separated by some kind of a geographic barrier, such as amountain, desert, or river. A second Jordan's Rule is: fishes develop morevertebrae in cold environments than in warm oneshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=j (2 of 3) [2/26/2008 9:14:21 AM]

Discover NOAA's Coral Reef DataJPEG (Joint Photographic Experts Group) - the original name of thecommittee that wrote the standard. It is a lossy compression technique forcolor images. Although it can reduce files sizes to about 5% of theirnormal size, some detail is lost in the compressionjugostegalia - a basket-like structure formed midventrally by overlappingbranchiostegals in some families of eelsjugular - pertaining to the throat areaBlennies have their pelvicfins in the jugular position,anterior to the pectoralfins. (Photo: South FloridaWater ManagementDistrict)junior homonym - in taxonomy, the younger, or most recentlyestablished taxonomic namejunior synonym - in taxonomy, the younger name of two synonymsjunk DNA - a term used to describe the excess DNA which is present inthe genome beyond that required to encode proteins. The term ismisleading since these regions are likely to be involved in gene regulation,and other not yet known functions; a non-coding sequence of DNA; anintronjuvenile - a young animal that has not reached sexual maturityjuxtaposed - placed near together(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=j (3 of 3) [2/26/2008 9:14:21 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: KThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zkairomone - a class of pheromone which is an interspecific chemicalsecretion that benefits the receiver but not the emitter; also defined as apheromone produced by organisms to attract a mate, though in somecases can also undesirably attract the attention of a predatorKarst - a limestone terrain characterized by sinks, caverns, abrupt ridges,protuberant rocks and drainage characteristics due to greater solubility oflimestone in natural waters than is common. The term is derived from thegeographical name of part of SloveniaKarst cave - a cave caused by dissolutionof limestone by waterA karst cave. Karstecosystems are rich inwater and mineralresources, and provideunique habitats tonumerous fish and wildlife.(Photo: USFWS)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=k (1 of 5) [2/26/2008 9:14:23 AM]

Discover NOAA's Coral Reef Datakaryogamy - a process of fusion of the nuclei of two sex cells orgametes; the second step in syngamykaryokinesis - the cellular process of nuclear divisionkaryology - the study of the nucleus of a cellkaryolysis - the disintegration and dissolution of a cell nucleus upondeath of the cellkaryorrhexis - the rupture of a cell nucleus, releasing disintegratedchromatinkaryotype - the entire chromosome complement of an individual cell, asseen during the mitotic phaseKelvin scale - an absolute scale of temperature in which each degreeequals one kelvin. Water freezes at 273.15 K and boils at 373.15 Kkenozooid - a small bryozoan heterozooid that strengthens and supportsthe colony, as well as fill spaces; long, branching, tubular, transparentstolons which extend above the substratum and to which the feedingindividuals (autozooids) are attachedkeramidine - a bioactive compound isolated from the marine spongeAgelas sp. It is a neurosuppressive compound (a serotonergic receptorantagonist that blocks serotonin-mediated communications amongneurons) which has potential as a drug for treatment of neurologicaldisordersketone - any of a class of organic compounds that is produced during fatmetabolism. Ketones contain a carbonyl group, CO, attached to two alkylgroups, such as CH3COCH3key - a small, low coastal island oremergent reef of sand or coral; flat moundof sand and admixed coral fragments builtupon a reef flat or just above high tidelevel. A synonym of cayA number of small keys(cays) in Jobos Bay,Puerto Rico.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=k (2 of 5) [2/26/2008 9:14:23 AM]

Discover NOAA's Coral Reef Datakey character - in taxonomy, a diagnostic character used in a taxonomickeykey factor analysis - a statistical treatment of population data designedto identify factors most responsible for change in population sizekey stimulus - in ethology or animal behavior, the stimulus whichreleases a fixed action patternkeystone predator - the dominant predator or the top predator that hasa major influence on community structurekeystone species - a species that is disproportionately important in themaintenance and balance of its community integritykilobase (kb) - a length unit equal to 1000 base pairs of a doublestrandednucleic acid molecule; 1000 pairs of nucleotide bases in DNAkinetic energy - energy associated with motionkinetics - the study of acceleration, motion, or rate of changekinetochore - a structure forming at the centromere during mitosis forbinding microtubules; a platelike structure necessary for chromosomalmovement during mitosis; it develops on the centromere and links thechromosomes to the mitotic spindlekingdom - in taxonomy, the highest ranked category in the taxonomichierarchy. All organisms are classified into one of five kingdoms: Monera(the prokarytic Kingdom. Includes archaebacteria, eubacteria andcyanobacteria); Protista (unicellular eukaryotes); Fungi (yeasts andmushrooms); Plantae (plants); and Animalia (animals). Some scientistsrecognize slightly different classification schemeskinocilium - a minute short cellular hair-like process (microvillus)responsible for locomotion in motile unicellular organisms, or in higherforms, generates a current of fluidkleptoparasitism - stealing from one animal by another; also called"piracy"knee root - an aerial root of a mangrove that emerges from the groundthen loops back in. It is also called a peg root. It is not clear whether kneeroots have a role in respirationknob - a circular, rounded projection or protuberance that sticks out froma surface; a projecting structure on the reef margin or reef front whereinthe upper surface flares outward, giving the surface a greater diameterthen the basal sectionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=k (3 of 5) [2/26/2008 9:14:23 AM]

Discover NOAA's Coral Reef Dataknoll - a small reef within the lagoon or on shallow shelvesknot - The unit of speed used in navigation that is equal to 1 nautical mile(6,076.115 ft or 1,852 m) per hourKnowledge Management (KM) - an emerging management disciplineoriented toward creating and applying an organization's knowledgeassets; a new branch of management for achieving breakthroughperformance through the synergy of people, processes, and technology.Its focus is on the management of change, uncertainty, and complexity.KM caters to the critical issues of organizational adaptation, survival, andcompetence in face of increasingly discontinuous environmental change. Itembodies organizational processes that seek synergistic combination ofdata and information processing capacity of information technologies, andthe creative and innovative capacity of human beingsKoch’s Postulates - to establish the specificity of a pathogenicmicroorganism, it must be present in all cases of the disease, inoculationsof its pure cultures must produce disease in animals, and from these itmust be again obtained and be propagated in pure cultureKrebs cycle - a series of enzymatic reactions in mitochondria involvingoxidative metabolism of acetyl compounds to produce high-energyphosphate compounds that are the source of cellular energy ; also knownas the tricarboxylic acid (TCA) cycle and as the citric acid cycleKure Atoll - the most remote of theNorthwestern Hawaiian Islands, and thenorthern-most coral atoll in the world,located at the extreme northwest end ofthe Hawaiian archipelago. The atoll hasalmost 80,000 acres of coral reef habitatwith 28 species of stony corals so fardocumented. Kure Atoll is an importantpupping and resting area for HawaiianMonk seals. The island is also a nestingarea for smany species of sea birds, and awintering area for a variety of migratorybird species from North America and AsiaPhotos: (Left) The KureAtoll Reserve PreservationArea includesapproximately 17 squarenautical miles (57 squarekilometers) of submergedcoral reef habitats; (Right)An endangered Hawaiianmonk seal and her pup.(Photos: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=k (4 of 5) [2/26/2008 9:14:23 AM]

Discover NOAA's Coral Reef DataKwajalein Atoll - the largest atoll in theRepublic of the Marshall Islands. KwajaleinAtoll has the world's largest lagoon (839.30km² ) and is comprised of 97 islets with aland area of 6.33 km² . Kwajalein Atoll hasbeen used as a U.S. military base since1944Kwajalein Atoll - NASA NLTLandsat 7 (Visible Color)Satellite Image. (Photo:NASA)Kyoto Protocol - an agreement made under the United NationsFramework Convention on Climate Change (UNFCCC). Nations that ratifythis protocol make a commitment to reduce their emissions of carbondioxide and and five other greenhouse gases or engage in emissionstrading if they maintain or increase emissions of these gases(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=k (5 of 5) [2/26/2008 9:14:23 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: LThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZLa Niña - a phenomenon characterized byunusually cold ocean temperatures in theeastern Equatorial Pacific, compared to ElNiño, which is characterized by unusuallywarm ocean temperatures in the easternEquatorial PacificGraphic showingDecember 1998 La Niñaevent.label - a compound or atom that is either attached to, or incorporatedinto, a macromolecule and is used to detect the presence of a compound,substance, or macromolecule in a sample; also called a 'tag'labeled - to mark substances in a way that they can easily be identified.In an organism, substances may be labeled using stable isotopes orharmless radioactive components so that they can be traced, analyzed ormeasuredlabial - pertaining to the lipslabium - any lip-like structurehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (1 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataLacey Act - the Lacey Act, passed in 1900, and amended several times,makes it unlawful to import, export, transport, sell, buy, or possess fish,wildlife, or plants taken, possessed, transported, or sold in violation of anyfederal, state, foreign, or Native American tribal law, treaty, or regulationlacriform - tear-drop shaped; also called "dacriform"lacuna - a cavity ("little lake") in a matrix-like substance. For example,cartilage cells (chondrocytes) are located in lacunae in the cartilagenousmatrix; bone cells (osteocytes) are located in lacunae in bone matrixlagoon - a warm, shallow, quiet waterwayseparated from the open sea by a reef crestA lagoon in Bora Bora.(Photo: Dr. AnthonyPicciolo/NOAA)lagoon slope - the back reef on a barrier or atoll reeflambert - unit of brightness of lightlanceolate - spear-shaped, tapered at both endslanceolate - shaped like a lance headlanciform - lance-shapedlander system (benthic lander) - ascientific instrument system designed fortemporary deployment on the sea floor inorder to monitor environmentalparameters. It is an unmanned vehicle thatfalls to the seafloor unattached to a cable,and then operates autonomously on thebottom. At thttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (2 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataA lander system beingdeployed. The part withthe large yellow structuresis the floatation rack(Photo: KC Denmark)Landsat satellite - U.S. satellite used toacquire high-resolution (500-800m)remotely sensed multi-spectral images ofthe earth's land surface and surroundingcoastal regionsArtist's rendition of LANDSAT satellite.langley - unit of solar radiationlappet - a sensory structure in some jellyfish (Scyphozoa), associatedwith a rhopalium, which responds to touch (pressure); a fleshy lobehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (3 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataLarge Marine Ecosystems (LMEs) - Large marine ecosystems arenatural regions of ocean space encompassing coastal waters from riverbasins and estuaries to the seaward boundary of continental shelves andthe outer margins of coastal currents. They are relatively large regions of200,000 km2 or greater, the natural boundaries of which are based onfour ecological criteria: bathymetry, hydrography, productivity, andtrophically related populations.The NOAA-Fisheries Large MarineEcosystems (LMEs) Program has been engaged in the development andimplementation of an ecosystem-based approach to support theassessment and management of marine resources and their habitats. Afive theme modular approach has been developed for monitoring andassessing changes in productivity, fish and fisheries, pollution andecosystem health, socioeconomics and governance of LMEs in relation torecovery, sustainability and management of marine resources and theirhabitats. The 10 United States LMEs are the Northeast Shelf, SoutheastShelf, Gulf of Mexico, California Current, Gulf of Alaska, Chukchi Sea,Beaufort Sea, East Bering Sea, Insular Pacific-Hawaii, and the CaribbeanSea ). A global effort is underway by NOAA in partnership with the WorldConservation Union (IUCN), the Intergovernmental OceanographicCommission of UNESCO (IOC), and other UN agencies to improve the longtermsustainability of resources and environments of the world’s 64 LMEsand linked watershedslarva - a sexually immature juvenile stageof an animal's life cycle. However, there area few exceptions, where the larval formnever metamorphoses into the adult stageand is sexually mature (neoteny)Microscopic photograph ofa crab larva (megalopsstage) from a planktoncollection.laser line scan (LLS) - an electro-optic imaging technique whichprovides the efficiency and spatial coverage of a remote survey system, atan image resolution approaching that of visual observations. LLS produceshigh contrast underwater light field images, at millimeter to centimeterscale resolution and at two to five times the range of conventional videoand photographic systems. Resolution and area covered by the images(swath width) vary with water clarity and tow height above the bottomlasonolide - a marine pharmaceutical, extracted from the spongeForcepia sp., which possesses anti-tumor propertieslateral - refers to the side or flank of an animalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (4 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalateral display - a type of threat or reproductive behavior exhibited bymany species of fishes, in which two male fish align beside each other,spread their dorsal, anal, and pelvic fins, and intensify the coloration oftheir bodies. These threats are usually accompanied by tail beats andbody quiveringlateral line scale - one of a series of scales that bear the pores andtubes of the lateral line systemlateral line system - a series of senseorgans that detect pressure or vibrationsalong the heads and sides of cyclostomes,fishes, and some amphibians. It consists ofa network of sensory hair cell clusters(neuromasts) and small water-filled canalsthat lie immediately beneath the skin andextend along the sides of its body. Thisnetwork is sensitive to external motionNote the lateral line of theCaribbean red snapper(Lutjanus purpureus) with49 to 53 scales, whichextend onto the base ofthe caudal fin. (Photo: U.S. Food and DrugAdministration)latitude - the angular distance between an imaginary line around theEarth, or any spherical body, parallel to its equator and the equatoritself; an imaginary line around the Earth parallel to the equatorlaunch - to start up any computer program by clicking on its icon orselecting it from the Start menuLaw - a description of how a natural phenomenon will occur under certaincircumstances; a statement that summarizes the results observed in anexperiment that is repeated many times by many different scientists. Ascientific law is widely accepted as true or as a fact, such as Newton'sLaws of GravitationLaw of Conservation of Energy - energy can be transferred from onesystem to another in many forms, however, it can not be created nordestroyed. Thus, the total amount of energy available in the universe isconstantLaw of Parsimony (Occam's Razor) - when you have two competingtheories which make exactly the same predictions, the one that is simpleris the better; also called "Occam's Razor"Law of the Minimum - the growth of a population is limited by theresource in shortest supply. Also known as 'Liebig's Law'http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (5 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalaw of tolerance - the presence, number, and distribution of species inan ecosystem are determined by whether the levels of one or morephysical or chemical factors fall within the range tolerated by the speciesleaching - the movement of liquid into another materiallead line - a line with a lead weight on theend used to measure depth. The lead isdropped into the water and marks on theline are read to determine the currentwater depth. The lead usually has a cavityto return a sample of the bottom type(mud, sand, etc.)A lead line on the deck ofa ship (Photo: OceanInstitute)least squares - a statistical criterion for the estimation of the goodnessof fit in correlation analysis. Least squares methods aim to minimize thesum of squared differences between the observations and the predictionsfrom a modellecithotrophic larva - a planktonic larva that gains its nutrition from yolk(semi-crystalline phospholipoprotein granules). In most bony fishes, yolkis supplied by the yolk sac, a bag-like ventral extension of the gutcontaining yolk granuleslectotype - in taxonomy, one of several syntypes, designated by anyauthor after the original publication of a species name as the 'typespecimen' for the taxonomic name. Designated only where there was nooriginal holotypeLED (light emitting diode) - a very small light often used in electronicinstrumentationlee - shelteredleeward - referring to the side of an island or reef that faces away fromthe prevailing windhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (6 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalek - a polygynous mating system where a number of males aggregate ata particular site during the breeding period and engage in courtshipbehavior, especially displays. Females attracted to the site "select " malesfor mating and subsequent fertilization of eggs. Once mated, the femalesusually go elsewhere to lay their eggs or to complete gestation. Lekkingbehavior (also called arena behavior) has been observed among cuttlefish,fishes, birds, antelope, and insects. Lekking species tend to stay at asingle lek throughout a breeding season and to return to the same lek sitefrom breeding period to breeding periodlenticel - aerial roots (pneumatophores) of mangroves contain spongytissue connected to the exterior of the root via small pores called lenticels.During low tide, when lenticels are exposed to the atmosphere, oxygen isabsorbed from the air and transported to and even diffused out of theroots below ground. This diffusion of oxygen maintains an oxygenatedmicrolayer around the roots that enhances nutrient uptake.leptocephalus larva - a long, ribbon-like larval form that is characteristicof eels, tarpons, and bonefisheslepton - a class of subatomic particles that constitute matter which haveno measurable size and do not interact with the strong nuclear force. Thecharged leptons are the electron, the muon, the tau and theirantiparticles. Neutral leptons are called neutrinoslesion - any pathological or traumatic discontinuity of tissue, or loss offunction of a partlesion severity - the semiquantitative, subjective ranking of the degreeof damage or extent of pathological change in the tissues of an organismlethal gene - a mutant form of a gene gene whose phenotypic effecteventually results in the death of the bearing organism. Death fromdifferent lethal genes may occur at any time, from fertilization of the eggto advanced age. Lethal genes may be dominant, incompletely dominant,or recessive; also called a 'lethal allele'leucocyte - a cellular component of blood. Leucocytes help to defend theorganism's body against infectious disease and foreign materials as part ofthe immune system; also called "white blood cell"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (7 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Dataleuconoid - the body form of highestcomplexity in sponges. The leucanoid formis highly irregular, displays the greatestdegree of folding of the body wall, and haslost radial symmetry. The choanocytes linethe pockets formed by the convoluted bodywallLeuconoid spongesrepresent the mostcomplex body form. Thecanal system isextensively branched.Usually there are manyoscula in each sponge.(Illustration: www-biol.paisely.ac.uk)leucophore - a colorless chromatophore which contains purines, usuallyguanine, in the form of small, motile crystals in the cell's cytoplasmlevee - a raised embankment along the edge of a river channel. Naturallevees result from periodic overbank flooding, when coarser sediment isimmediately deposited because of a reduction in river velocity. Levees areoften constructed by humans living in low-lying areas as protectionagainst floodinglibrary - in genomics, an unordered collection of clones (i.e., cloned DNAfrom a particular organism) whose relationship to each other can beestablished by physical mappingLIDAR (Light Detection And Ranging) - a remote-sensing techniquethat uses a laser light source to probe the characteristics of a surfacetarget. A laser emission may be directed downward from a low flyingaircraft. Information about the target is derived from back-scatteredreflectance or fluorescence of the target. Chlorophyll pigments in coralreef organisms (e.g., algae, seagrasses, coral), when excited by shorter(blue or green) wavelength light, emit light at longer (red) wavelengths, i.e., it fluoresceslife - there is no universal definition of life. Different scientists haveproposed a variety of similar definitions which describe life as a processthat exists within cells and has the following attributes: homeostasis,organization, metabolism, growth, reproduction, response to stimuli, andadaptation to the environmentlife cycle - the complete succession of developmental changes undergoneby an organism during its life, from fertilized egg (zygote) to maturitywhen another fertilized egg can be producedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (8 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Dataligand - a molecule, such as a hormone or growth factor, that binds to aspecific site on a receptor proteinligase - an enzyme used to join DNA (DNA ligase) or RNA (RNA ligase)segments togetherlight trap - a stationary or floatingcollecting apparatus that contains a lightsource, e.g., a chemical glow light, whichattracts larval, juvenile, and adult fishes, aswell as invertebrates. The animals enter thetrap through small holes or funnels andthen are unable to find their way outA light trap. At night, adultand larval fishes areattracted to chemical lightsticks or fluorescent lightsinside the traps and areable to enter throughopenings on the sides.They are then unable tofind their way out. (Photo:Australian Museum)limnology - the study of the physical, chemical, meteorological andbiological aspects of fresh waterslimoniform - lemon-shapedlimu - general Hawaiian name for all kinds of aquatic plants and softcorals; also terrestrial algae growing in any damp place on the ground, onrocks, and on other plantslimu kohu - the Hawaiian name for the red alga, Asparagopsis taxiformis,an edible species that is no longer common in the Main Hawaiian Islands,but is relatively abundant the shallow waters of some of the NorthwesternHawaiian Islandsline intercept transect - a linear transect protocol where a tape issecured at each end of the transect with the tape draped over the reef inbetween. Observations are collected on each species and substratecomponent and their length under the tapehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (9 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Dataline precedence - in taxonomy, when two different names for the sametaxon are first published in the same publication, then the one whichappears on the earlier line has line precedence. Line precedence does notnecessarily mean priority as well. This is determined by the action of thefirst reviserlineage - a genetically continuous line of evolutionary descentlinear acceleration - the rate of change of velocity in a linear direction(along a straight line) with respect to timelinear reef - a linear coral formation that is oriented parallel to the shoreor the shelf edgelinear regression - regression in which the relationship is linearlinear relationship - a situation in which the best-fitting regression lineis a straight linelinear transect - a line of specified lengthlaid out within a study site. They aregenerally positioned parallel to the shorealong depth contours. Measurements andobservations may be taken along the entiresurface beneath the line (line intercepttransect) or at specified intervals along theline (point intercept transect)A NOAA scientist layingout a linear transect line.linguiform - tongue-shapedlinkage - the proximity of two or more markers (genes, etc.) on achromosome; the closer together the markers are, the lower theprobability that they will be separated during DNA repair or replicationprocesses, and hence the greater the probability that they will be inheritedtogetherlinked genes - genes that are so closely associated on a chromosomethat the allelic forms found on a chromosome are inherited together by anoffspring at least 80 percent or more of the timeLinnaean tautonymy - in taxonomy,the identical spelling of a new genusgroupname and a pre-Linnaean (i.e., before 1758) one-word name citedas a synonym of only one of the species or subspecies originally includedin that genushttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (10 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataLinnaeus, Carolus - the 18th centurySwedish botanist (1707-1778) whoestablished the modern binomial system ofbiological nomenclature for plants andanimals. His non-latinized name was Carlvon LinneIn the 18th century,Linnaeus made a greatcontribution to science bydeveloping systems ofclassification andnomenclature to organizethe explosion ofinformation on plants andanimals. The tenth edition(1758-59), of Linnaeus'sclassic work, SystemaNaturae, was chosen asthe starting point forzoological nomenclature.(Photo: SmithsonianInstitution Libraries)lionfish - the red lionfish (Pterois volitans)is a venemous coral reef fish belonging tothe scorpion fish family (Scorpaenidae).Native to the Indian and western Pacificoceans, lionfish are now an invasive speciesfound in the western Atlantic Ocean fromsouthern Florida to New York and Bermuda.They appear to be a reproducing along thesoutheastern U.S. coast; Other commonnames are turkeyfish, dragonfish, andfirefishThe lionfish, Pteroisvolitans, is a recentinvasive species in thewestern Atlantic Ocean.Like some other membersof the scorpion fish family,the lionfish is a venomousanimal, possessing venomglands at the base of thedorsal, anal and pelvic finspines. The venom isinjected in a potentialpredator via the spines.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (11 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataThe genus Pterois containseight species variouslyreferred to as lionfishes,turkeyfishes, or firefishes.The lionfish is aninhabitant of near andoffshore coral and rockyreefs. During the day, itseems to prefer shelterunder ledges or in cavesor crevices. (Photo: PaulaWhitfield, NOAA BeaufortLaboratory)lipase - an enzyme, secreted by the pancreas and the glands of the smallintestine, that breaks down fats into glycerol and fatty acids duringdigestionlipid - a group of organic compounds, including the fats, oils, waxes,steroids, and triglycerides, that are insoluble in water but soluble incommon organic solvents, and are oily to the touch. Together withcarbohydrates and proteins, lipids constitute the principal structuralmaterials of cellslipopolysaccharide - a compound containing a lipid bound to apolysaccharideliposome - an artificial, single or multilaminar vesicle, made from a lipid,that is used for the delivery of a variety of biological molecules ormolecular complexes to cells, e.g., drug delivery and gene transfer.Liposomes are also used to study membranes and membrane proteinsListserv ® - the most common kind of maillist found on the internetlithoherm - a type of deep water reef composed of surface hardenedlayers of lithified sandy carbonate sediments supporting a diverse array ofbenthic fauna, including deep water coralslithosphere - the outer solid part of the earth, including the crust anduppermost mantle. The lithosphere is about 80-100 km thick, although itsthickness is age dependent The lithosphere below the crust is brittleenough at some locations to produce earthquakes by faulting, such aswithin a subducted oceanic plateLithothamnion ridge - a synonym for algal ridge. The algal genusLithothamnion is important in maintaining reef integrity by cementingvarious pieces of calcium carbonatehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (12 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalittoral - intertidal; between low and hightide levelsThis sea slug is a denizenof northwest U.S. rockylittoral (intertidal) zones.live rock - calcareous rock which isremoved from the vicinity of a coral reefwith some of the life forms on it still living.These may include bacteria, coralline algae,sponges, worms, crustaceans and otherinvertebrates. Live rock is commonly usedin reef aquaria because it contains bacteriathat can help filter the water throughnitrificationLive rock from Tonga,crated for shipping to anaquarist. (Photo: http://www.reefscience.com)liveaboard - a commercial dive boat withsleeping and eating accommodations.Scuba divers live aboard the boat forseveral days and usually visit dive locationsunaccessible to other diversA liveaboard dive boatdesigned and constructedwith divers andunderwater photographersin mind. A vessel such asthis may accommodate upto 20 passengers inprivate cabins, all with fullbathrooms. It is fully airconditionedwith a state-ofthe-artdive center, andcomplete photo and videolabs with daily E6processing. Wide diveplatforms provide easyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (13 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datawater entries and exits.(Photo: Belize Aggressor)living tag - a type of tagging method for marine turtles in which a smallpiece of tissue is taken from the white plastron of a hatchling andimplanted in one of the dark scutes of the carapace. The white patchgrows with the scute, and the particular scute which has been marked,codes for the year that the turtle was taggedlobate - lobe-shapedThis comb jelly(ctenophore) possesses alobate shape. (Photo:NOAA)lobe - a rounded projectionLocal Action Strategy (LAS) - a U.S. Coral Reef Task Force led initiativeto identify and implement priority actions needed to reduce key threats tovaluable coral reef resources in each U.S. coral reef jurisdiction. In 2002,the Task Force adopted the “Puerto Rico Resolution” which calls for thedevelopment of three-year LAS by each of the seven U.S. jurisdictionscontaining coral reefs: Florida, Puerto Rico, the U.S. Virgin Islands,Hawaii, Guam, American Samoa, and the Commonwealth of the NorthernMariana Islands. These LAS are locally-driven roadmaps for collaborativeand cooperative action among federal, state, territory, and nongovernmentalpartnerslocal extinction - the disappearance of a population from a local area.Local extinctions can accumulate into regional extinctionsLocally-Managed Marine Area (LMMA) - an area of nearshore watersactively being managed by local communities or resource-owning groups,or being collaboratively managed by resident communities with localgovernment and/or partner organizations. An LMMA can vary widely inpurpose and design; however, two aspects remain constant: a welldefinedor designated area; and substantial involvement of communitiesand/or local governments in decision-making and implementationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (14 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataLocally-Managed Marine Area (LMMA) Network - a group of LMMApractitioners involved in various marine conservation projects around theglobe who have joined together to increase the success of their efforts.The LMMA Network is a learning network, meaning that participatingprojects use a common strategy and work together to achieve goals. TheNetwork is interested in learning under what conditions using an LMMAstrategy works, doesn’t work, and why. Network members shareknowledge, skills, resources and information in order to collectively learnhow to improve marine management activities and increase conservationimpactlocomotion - the act of moving, or the ability to move, from place toplaceloculus - the calcified area or fiber-filled space within the axis of agorgonian or an interseptal space within the gastrovascular cavity of ananthozoan; a small cavity or space within an organ of a plant or animallocus - the position of a gene, DNA marker, or genetic marker on achromosomelogarithmic phase - the steepest slope of the growth curve of a culture;the phase of vigorous growth during which cell number doubles every 20­30 minutes; also called 'log or exponential growth phase'logarithmic scale - a constant ratio scale in which equal distances on thescale represent equal ratios of increase. For example, in a logarithmicscale, the distance between 10 and 100 is the same as the distancebetween 100 and 1000, or between 1000 and 10,000. Logarithmic scalesare used when the range of numbers being represented is largelong line fishing - a commercial fishing method which uses hundreds tothousands of baited hooks hanging from a single line, which may bekilometers in lengthlong term monitoring - the repeated surveying of organisms,populations, communities, or environmental parameters over time to helpus understand a variety of natural processeslongitude - an imaginary great circle on the surface of the Earth passingthrough the north and south poles at right angles to the equator; "allpoints on the same meridian have the same longitude"longshore current - a current that flows parallel to the shore just insidethe surf zone. It is also called the littoral currenthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (15 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataLophelia pertusa - the scleractinian species, Lophelia pertusa, is themost important global constituent of deep-water coral reefs, formingmassive complexes hundreds of kilometers long and up to 30 meters high.L. pertusa is a widespread structure-forming deep-water species occurringin the Atlantic, Pacific, Indian, and Southern Oceans, with a latitudinalrange from about 56º S to 71º N and a depth range from 39 to over 1,000metersLophelia reef - a reef formed by Lopheliapertusa, a deep-sea coral found in alloceans except the Arctic OceanThis photo of a Lopheliacoral garden was taken viaa manned submersible onthe ocean floor. (Photo:NOAA)lophocyte - a mobile cell in sponges that produces collagenlophophorate - an informal taxonomic unit that includes coleomaticmetazoans which possess a specialized filter-feeding organ, thelophophore. Almost all lophophorates are marine organisms and all aresuspension feeders. Lophophorates are deutersotomes and are typicallyconsidered relatively closely related to chordates and echinoderms. Thereare three lophophorate phyla: Phoronida, Bryozoa and Brachiopodalophophore - a feeding organ possessed by lophorates. It is a disk orhorseshoe-shaped structure which surrounds the mouth and bears thetentacles of the Bryozoa (moss animals), Brachiopoda (lamp shells) andPhoronida (horseshoe worms). The tentacles are hollow (coelomic) andcovered with cilia which generate water currents that draw food towardthe mouthLORAN (LOng RAnge Navigation) - a navigation system developed inthe 1950's based on the time displacement between signals from two ormore fixed shore based antennaehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (16 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalotic - refers to a flowing or running bodyof fresh water, i.e., streams and riversA peaceful loticenvironment, the PatuxentRiver, eastern Maryland, inDecember 2000. (Photo:Mary Hollinger, NOAA/National OceanographicData Center)low recruitment - a low influx of new members into a population byreproduction or immigrationlow tide - the lowest level of the tide; theminimum height reached by each falling tideA small island at themouth of the AmazonRiver at low tide. See hightide for contrast. (Photo:Alessandra and Michael)lower palmata zone - the part of a reefcrest that is seaward of the palmata zone.It consists primarily of elkhorn coral(Acropora palmata) at a depth of about 3-6m in Caribbean reefsA young Acropora palmatacolony in St. Croix, U.S.Virgin Islands (Photo: J.Halas)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (17 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalower risk - a species or other taxonomic group that has been evaluatedbut does not not face a risk of extinction in the wildlowland - a general term for low-lying land or an extensive region ofrelatively low relief; usually applied to coastal regions that do not rise highabove sea levelluciferase - the enzyme which activates luciferin, in the presence of ATP,to produce bioluminescenceluciferin - a compound whose activated form emits light. In the presenceof the enzyme luciferase and ATP, luciferin is oxidized to produceoxyluciferin and energy given off as cold light (bioluminescence)lumen - the interior space of a tubular organ, such as a blood vessel oran intestinelumen - unit of luminous fluxluminous - emitting light.luminous flux - the rate of flow of light energylumisome - in some cnidarians, a small, intracellular membrane-enclosedvesicle which contains all the proteins necessary for bioluminescencelumper - refers to a taxonomist who focuses more on similarities thandifferences among taxa, discounting the importance of minor variationamong individuals, and who tends to recognize fewer taxalunar tide - the portion of the tide that can be attributed directly toattraction to the moonlunate - crescent-shapedBlue tangs with lunateshapedcaudal fins.(Photo: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (18 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef Datalux - unit of illumination equal to one lumen per square meterlycra - a spandex textile fiber which has unique elastic qualities in that itcan be used in very lightweight, durable fabrics of long-lasting elasticity.It has excellent tensile strength, a long flex life, and high resistance toabrasion and heat degradation. Lycra skin coverings are popular withscuba divers as they give some protecion against abrasions and jellyfishand fire coral stings. They also offer (minimal) protection against coldlysis - the breakdown of a cell caused by rupture of its cell membraneand loss of cytoplasm. Lysis can be caused by viral action, chemical orphysical means; to break downlysosome - an organelle that contains digestive enzymes (acidhydrolases). They digest excess or worn out organelles, food particles,and engulfed viruses or bacteria. The membrane surrounding a lysosomeprevents the digestive enzymes inside from destroying the cell(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=l (19 of 19) [2/26/2008 9:14:28 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: MThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZMAA (mycosporine-like amino acids) - MAAs are a family ofcompounds which act as nature’s sunscreen in the marine environment.Shallow-water environments of tropical coral reefs are characterized byhigh levels of ultraviolet-A and ultraviolet-B radiation. Corals havedeveloped an efficient defence against the potential damage of long-termsolar irradiation, which often includes the production of natural"sunscreen"-type UV-absorbing compounds and related antioxidants.These compounds in shallow-water corals were identified to be a group ofmycosporine-like amino acids (MAAs) having absorption maxima in therange 310-360 nm. MAAs are assumed to be produced by thezooxanthellae in coral tissues, since their biosynthesis involves abiochemical pathway not found in invertebrates. The major distribution ofMAAs, however, resides within the coral tissues, suggesting that the algalpartner of the mutualistic relationship provides UV protection to the wholeof the relationship via MAA translocation. MAAs have been identified in anumber of taxonomically diverse organisms such as fungi, marineheterotrophic bacteria, cyanobacteria, eukaryotic algae, marineinvertebrates, fishes,and a wide variety of other marine organismsMAC (Marine Aquarium Council) - an international, not-for-profitorganization that brings marine aquarium animal collectors, exporters,importers and retailers together with aquarium keepers, public aquariums,conservation organizations, and government agencies. Its mission is toconserve coral reefs and other marine ecosystems by creating standardsand certification for those engaged in the collection and care ofornamental marine life from reef to aquariummacerate - to disintegrate tissues by means of cutting, soaking orenzymatic action to obtain a cell dissociationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (1 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamacro - a text file containing a sequence of commands that can beexecuted as one command.macro lens - in photography, a lens with the ability to focus from infinityto extremely close, allowing it to capture images of very small objects inframe-filling, larger-than-life sizesmacroalgae - algae that project more thanone centimeter above the substratumMacroalgae are importanthabitat on temperate andnorthern reefs.macrobenthos (macrofauna or macroflora) - benthic organisms(animals or plants) whose shortest dimension is greater than or equal to0.5 mmmacroevolution - evolution on the grand scale resulting in the origin ofhigher taxamacrofauna - animals large enough to be seen with the naked eyemacrogamete - the larger of the two gamete types in a heterogameticorganism. It is considered as the the female gametemacroinvertebrate - an invertebrate having a body length greater than2 mmmacromolecule - a large polymer, such as DNA, RNA, protein, lipid orpolysaccharide, made up of thousands of atomsmacronutrient - a nutrient, such as a nitrate or phosphate, that isrequired by plants in relatively large quantities in order to undergophotosynthesis and growthmacrophage - an amoeboid cell capable of moving through tissues,engulfing and destroying dead cells or bacteria. Certain white blood cellsare the most aggressive macrophageshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (2 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamacrophotography - photography of a subject where the image isrecorded in the same or larger than actual size; type of photographyemploying the use of special lenses or attachments allowing close-rangephotos of a given subjectmacrosmatic - pertains to animals with a well developed olfactory(smell) sensemacrotidal - coastal ocean or waterway with a high mean tidal range e.g., greater than 4 metersmacula - a dark spot, blemish; the small, highly sensitive area (of thehuman eye) which is located in the center of the retina. It is responsiblefor near and fine detail visionMadison/Swanson and Steamboat Lumps Marine Reserves - twoprotected areas in the Northeastern Gulf of mexico of slightly over 100nautical square miles each, the Madison-Swanson (high relief area) andSteamboat Lumps (low relief area). Within each area, fishing is prohibitedfor all species except for highly migratory species. These marine reserveswere created primarily to protect a portion of the gag grouper(Mycteroperca microlepis) spawning aggregations and to protect a portionof the offshore population of male gag. The areas are also suitable habitatand provide protection for many other species, such as scamp, redgrouper, warsaw grouper, speckled hind, red snapper, red porgy, andothersmadreporite - a perforated platelikestructure in most echinoderms that formsthe intake for their water vascular systemsThe white spot in themiddle of the central discof the starfish is themadreporite, the openinginto the echinoderm+swater vascular system.magenta - reddish purple colormagma - molten rock that forms naturally within the Earth. Magma maybe either a liquid or a fluid mixture of liquid, crystals, and dissolved gaseshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (3 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamagmatic hotspot - in geology, a hotspot is a location on the Earth'ssurface that has had volcanism for a long period of time. Geologists haveidentified some 40-50 such hotspotsmagnetic north - the direction a compass needle points when there areno local interfering influencesmaillist (mailing list) - a system that allows people to send e-mail toone address, whereupon their message is copied and sent to all of theother subscribers to the maillist. In this way, people who have manydifferent kinds of e-mail access can participate in discussions togethermaitotoxin - a neurotoxic compound which is produced by certain marinedinoglagellates and associated with the digestive tract of herbivorousfishes. It is responsible for a form of seafood poisoning in humans eatingtropical coral reef fishesmakatea - a fossil coral reefmalacology - the scientific study ofmollusksA Pacific octopus(Mollusca) photographedduring the NOAASubmarine Ring of Fireexpedition, 2002. (Photo:NOAA Ocean Explorer)Malacostraca - a class of arthropods in the subphylum Crustacea. Themore than 20,000 described species of Malacostraca can be divided intotwo groups, the Phyllocarida, and the Eumalacostraca. Phyllocaridacontains the oldest crustacean known and includes only one living group.The Eumalacostraca consists of all Malacostracan groups other than thePhyllocarida. Eumalacostracans generally possess a well-developedcarapace and a long, muscular abdomen. It is the group that containsmost of the animals the general public recognize as crustaceans, such asshrimp, crabs, lobstersmalar - pertaining to the cheek region of vertebrateshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (4 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMalthusian Law - when birth and death rates are constant, a populationwill grow (or decline) at an exponential rateMammalia - a class of warm bloodedanimals (mammals) whose commoncharacteristics include the presence of hair,milk-secreting glands, a musculardiaphragm between the abdominal andpleural and mediastinal cavities, a lowerjaw composed of a single pair of bones, amiddle ear containing three bones, and thepresence of only a left systemic archDolphins are among themost recognizable marinemammals; this one floatsserenely in the CaribbeanSea. (Photo: CopyrightCorel Corporation)mammalian dive reflex - the physiological responses, includingbradycardia and shutdown of the peripheral circulation, which occursduring dives by an air-breathing vertebratemammalogy - the scientific study of mammalsmandible - pertains to mouth parts; the lower jawmangal - relating to a shoreline ecosystem dominated by mangrovetrees, with associated mud flats; collective term for a mangrovecommunitymangrove - a general name for severalspecies of halophyte belonging to differentfamilies of plants (including trees, shrubs, apalm tree and a ground fern) occurring inintertidal zones of tropical and subtropicalsheltered coastlines and exceeding one halfmeter in height. The term is applied to boththe individual and the ecosystem, the latterof which is termed mangal. Mangrovesprovide protected nursery areas for juvenilereef fishes, crustaceans, and mollusks.They also provide a feeding ground for amultitude of marine species. Manyorganisms find shelter either in the roots orbranches of mangroves. Mangrovebranches are nesting areas for severalspecies of coastal birds. The root systemsharbor organisms that trap and cyclenutrients, organic materials and otherMangrove nursery area,Puerto Rico.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (5 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Dataimportant chemicals. Mangroves alsocontribute to higher water quality bystabilizing bottom sediments, filtering waterand protecting shorelines from erosion. They protect reefs from landrunoff sedimentation. Conversely, coral reefs protect mangroves andseagrasses from erosion during heavy storms and strong wave actionmanoalide - a marine pharmaceutical isolated from the marineIndopacific sponge Luffariella variabilis. It possesses analgesic and antiinflammatorypropertiesmanta tow technique - a technique used to provide a generaldescription of large areas of reef and to gauge broad changes inabundance and distribution of organisms on coral reefs. The technique,widely used in Australia, involves towing a snorkel diver (observer) at aconstant speed behind a boat. The observer holds on to a 'manta board'attached to a small boat by a 17-meter length of rope. This person makesa visual assessment of specific variables during each manta tow (2minutes duration), and records these data when the boat stops, on a datasheet attached to the manta board. The manta tow technique is used toprovide a general description of large areas of reef and to gauge broadchanges in abundance and distribution of organisms on coral reefs. Theadvantage of manta tow over other survey techniques is that it enableslarge areas of reefs to be surveyed quickly and with minimal equipmentmantle - a membranous or muscularstructure in mollusks that surrounds thevisceral mass and secretes a shell if one ispresentA cowrie, Cypraea sp.,with partially extendedmantle.mantle (geology) - the middle layer of the Earth, lying just below thecrust and consisting of relatively dense rocks. The mantle is divided intothe upper mantle and the lower mantle; the lower mantle has greaterdensity than the upper mantlemantle cavity - the space between the mantle and the rest of the bodyparts of a mollusk, which contains several important respiratory andreproductive organshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (6 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamanubrium - the proboscis of a jellyfish: atubular structure that connects the mouthto the digestive cavityThe mouth of a jellyfish isat the end of themanubrium, whichextends to engulf prey.(Photo: NOAA/Florida KeysNational MarineSanctuaries)Manzamine A - a marine pharmaceutical, extracted from the marinesponge Xestospongia ashmorica, possessing anti-inflammatory,antimalarial, antifungal, and anti-HIV-1 activity. It is also active againstthe Gram-positive bacteria Bacillus subtilis and Staphylococcus aureusmarae - in the Marquesas, a Polynesian sacred enclosure or a place ofworship . In Hawaii, it is called a "heiau"MAREANO - a Norwegian program to survey and perform basic studies ofthe seabed’s physical, biological, and chemical environment and tosystematize the information in a marine area database that will coverNorway’s coastal and marine regionmareogram - a graphic representation of the rise and fall of the sealevel, with time as abscissa and height as ordinate, usually used tomeasured tides; may also show tsunamis; also called 'marigram'MAREPAC (Marine Resources Pacific Consortium) - MAREPAC is aconsortium made up of representatives from nine islands in Micronesia(Marshall Islands, Federated States of Micronesia, Northern Marianas,Guam, Palau, and American Samoa). MAREPAC's mission is to developregional capabilities, foster collaboration, and disseminate accurateinformation in support of sound policy development on sustainable use ofmarine resources of cultural, economic, and scientific valuemargin - a boundary, edge, or border of a structurehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (7 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMarianas Archipelago Reef Assessment and Monitoring Program(MARAMP) - a multi-agency effort that began in 2003 with the firstcruise to the Mariana Archipelago. The objective of MARAMP is to rapidlyevaluate and map the shallow water reef habitats in the MarianaArchipelago. Scientists on board the National Oceanographic andAtmospheric Administration (NOAA) research vessel Oscar Elton Sette usea variety of techniques to study the oceanography and coral, fish, algae,and benthic habitats around most of the islands and offshore banks of thearchipelagomariculture - the cultivation of marineorganisms under controlled conditions; asynonym for marine aquacultureShrimp farms and theirwaste runoff have resultedin the destruction ofcoastal habitats and addedto pollution in criticalestuarine waters.marine - an umbrella term for things relating to the ocean, coastal zones,and tidal areasmarine debris - debris composed primarilyof plastics, nets, lines, other fishing gear,glass, rubber, metal, wood and cloth.Sources of debris are people on beaches,storm drains, fishing boats, wastetreatment sites, and industrial facilities.These materials have damaging effects oncoral reefsMarine debris, such as thisplasic bag, can kill coral.(Photo: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (8 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamarine iguana - the marine iguana(Amblyrhynchus cristatus) inhabits theGalapagos Island, an archipelago on theEquator, 800 kilometers west of theEcuadorian coast. It differs from themainland iguanas by the shape of the snoutand other morphological features. Thespecies probably rafted to the islands manymillions of years ago, and developed a newecological niche.They feed almostexclusively on marine algae and seaweed inthe intertidal zone, and some make shallowdives past the breaker zoneA marine iguana from theGalapagos Islands. (Photo:NOAA)marine insects - insects account for over 75% of all species that havebeen described by science. Of these, only 3 percent are aquatic in any lifestage. Even more rare are the 250 to 350 species (in several orders, thelargest being the Diptera) in this aquatic grouping that haveindependently evolved adaptations to exposure to salt water. Marineinsects include pelagic species, species inhabiting tide pools, and beachand marsh-dwelling species. Just five species of sea skaters (Halobatessp) are pelagic. Marine midges in the genus Pontomyia inhabit tide poolsand lagoons in the Indo-Pacific. Some genera of rove beetles live in sandburrows in beach intertidal zonesmarine lake - a unique ecosystem which forms when a depression in aporous, calcareous landscape is flooded by rising sea-levels. Connected invarious ways to the sea, they form a continuum from complete isolation tolagoon-like. Marine lakes, such as the famous ones of Palau, contain avariety of habitats which foster adaptive radiation and rapid evolution ofthe biological assemblages. Palau's Jellyfish Lake is perhaps the mostfamous of these marine lakes, containing an estimated number of 17million jellyfish (Mastigias medusae) in January 2007. The greatestnumber (estimated) ever recorded was 31 millionMarine Managed Area (MMA) - see: Marine Protected Areamarine pharmaceutical - a bioactive chemical derived from a marineorganism which is used to treat disease and other medical conditionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (9 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMarine Protected Area (MPA) - any area of the marine environmentthat has been reserved by federal, state, territorial, tribal or local laws orregulations to provide lasting protection to part or all of the natural orcultural resources within them. Familiar examples of U.S. MPAs includeNational parks, wildlife refuges, monuments and marine sanctuaries,fisheries closures, critical habitat, habitat areas of particular concern,state parks, conservation areas, estuarine reserves and preserves, andnumerous others. Areas which are not MPAs are areas where access isrestricted for reasons other than conservation (such as security zones,shellfish closures, sewage discharge areas, and pipeline and cablecorridors), or unprotected areas that are logistically inaccessible due toweather, sea state, etc; MPAs are sometimes called Marine ManagedAreas (MMA). However, "marine protected area" is a broad, inclusive termwhich includes both mulit-purpose sites with some restrictions as well asthe more restrictive "no take marine reserves."Marine Protected areas (MPA) Network - a system of individualmarine protected areas operating cooperatively and synergistically, atvarious spatial scales, and with a range of protection levels, in order tofulfill ecological aims more effectively and comprehensively than individualsites could alone. The system will also display social and economicbenefits, although these may only become fully developed over long timeframesmarine reserve - an area in which some or all extractive activities areprohibitedmarine sanctuary - as defined by the U.S. government: Multiple-usemarine protected areas, protected under the National Marine SanctuariesAct, that may include breeding and feeding grounds of whales, sea lions,sharks, and sea turtles; significant coral reefs and kelp forest habitats;and the remains of historic shipwrecks. Some sanctuaries are zoned toinclude no-take areas. (Note: States may have sanctuaries that have adifferent purpose or are defined differently)marine snow - dense concentrations of particulate organic detritus andliving organisms whose downward drift appears similar to a snowfallmarine toxicology - a broad field of study encompassing the production,fate, and effects of natural and synthetic harmful chemical substances,such as pollutants, in the marine environmentmaritime climate - a climate strongly influenced by an oceanicenvironment, found on islands and the windward shores of continents. Itis characterized by small daily and yearly temperature ranges and highrelative humiditymarker gene - in genetic engineering, an easily identified gene that isinserted into an organism, along with a desired gene. The presence of themarker gene demonstrates that the transformation was successfulhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (10 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamarl - fine-grained carbonate-rich mud; a calcareous clay which containsapproximately 30 to 65 percent calcium carbonatemarsh - a soft, wet area periodically orcontinuously flooded to a shallow depth,usually characterized by a particular groupof grasses, cattails and other low plantsCoastal marsh in MontereyBay National MarineSanctuary, CA. (Photo: KipEvans)marsupium - an abdominal pouch where certain animals carry theiryoung, as in some crustaceans and the brood pouch of the male seahorseMascarene Plateau - a submerged volcanic plateau dominating thewestern Indian Ocean, extending approximately 2,000 km betweenSeychelles and Mauritius. It covers an area of over 115,000 squarekilometers of shallow water with depths ranging from 8 m to 150 m on theplateau, plunging to depths of 4000 m at its edges. It is the major marineecosystem of the western Indian Oceanmass coral bleaching - coral bleaching extending over large distances asa result of anomalously high water temperaturesmass extinction - a catastrophic, widespread perturbation where majorgroups of species become extinct in a relatively short timemass spawning - spawning events where many different species spawnsimultaneouslymass spectrometer - a laboratory instrument that measures the massto-chargeratio of individual molecules that have been converted into ions.This information is then used to determine the masses of the moleculesmass spectrometry - an analytical technique where ions are separatedaccording to their ratio of charge to mass. The atomic weight of theparticle can be obtained from the mass spectrum producedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (11 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamassive - having a large compactstructure without a definable shapeScuba divers examine amassive coral colony.(Photo: AustralianInstitute of MarineSciences)massive colony - a coral colony that is solid and typically hemisphericalin shapematernal inheritence - uniparental inheritance in which all offspringhave the genotype and phenotype of the female parentmaternal mRNA - messenger RNA found in oocytes and early embryosthat is derived from the maternal genome during oogenesismaxilla - pertains to mouth parts; the upper jawmaxilliped - one of the mouth appendages of crustaceans, situatedbehind the maxillae. Crabs have three pairs, but many of the lowercrustaceans have only one pairmaximal food chain - a sequence of species running from a basal plantor algal species to another species that feeds on it (a herbivore), and soon to a carnivorous climax predatormaximum sustainable yield - the maximum number of a food or gamepopulation that can be harvested without harming the population's abilityto grow back; the largest average catch or yield that can continuously betaken from a stock under existing environmental conditionsmean - a statistical measure of central tendency. The sum of a set ofobservations divided by the number of observations. It is also referred toas 'arithmetic mean' and 'sample mean'mean high tide - the level to which the water rose on an average dayover a previous period of time (years or decades); the average of all thehigh tides as calculated over a long period of timemean low tide - the average altitude of all low tides recorded at a givenplace over a long period of timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (12 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamean sea level - the level of the surface of the sea between mean highand mean low tide. It is used as a reference point for measuring elevationsmeandroid colony - a massive colony that has corallite mouths alignedin valleys, such that there are no individual polypsmeandroid form - a coral growth form in which the corallites arearranged in multiple series within the same wallsmechanoreceptor - a neurological receptor that responds to mechanicalenergy, e.g. pressure, touch, and gravitymedian - a statistical measure of central tendency. The middle-mostvalue in a set of observations with an equal number of observations lyingabove and below the median valuemedian fin - in fishes, an unpaired fin located on the sagittal plane of thebody, i.e., the dorsal, caudal and anal finsmedusa - the free swimming stage ofsome corals, jellyfish, anemones, hydroidsand comb jellies, shaped like a bell orumbrella and swims by pulsations of thebodyA jellyfish (medusa stage)showing its oral orsubumbrella surface. Thehanging tentacles bearstinging cells, used forfood capture.medusa bud - one of the buds of a hydroid, destined to develop into agonophore or medusa. Medusa buds are released from the gonangiumthrough a central opening, the gonoporemedusoid - a body form resembling a medusa; umbrella shapedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (13 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamegabase (Mb) - unit of DNA or RNA sequence equal to one million (10)pairs of nucleotide bases. Abbreviated Mbmegabyte (mb) - a measure of storage space. One megabyte roughlytranslates to a million characters of text, or 180,000 wordsmegafauna - the largest size category of animals in a communitymegalops larva - the larval stage in brachyuran crabs that follows thezoea larval stagemegasclere - a large spicule in spongesmeio- - smaller; less thanmeiobenthos (meiofauna or meioflora) - benthic organisms whoseshortest dimension is less than 0.5 mm but greater than or equal to 0.1mmmeiosis - a two-stage type of cell divisionin sexually reproducing organisms thatresults in the development of sperm andegg cells . In meiosis, a diploid cell dividesto produce four haploid cells, each with halfthe original chromosome content. Inorganisms with a diploid life cycle, theproducts of meiosis are called gametes. Inorganisms with an alternation ofgenerations, the products of meiosis arecalled sporesDiagram showing themeiotic division of adiploid cell, which in twodivisions, results in theproduction of four haploiddaughter cells. Thisprocess is also termedgametogenesis because itresults in haploid spermand egg cells.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (14 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMelanesia - a large region of volcanicislands which includes New Guinea, theSolomon Islands, Vanuatu, Fiji, Maluku, theTorres Strait Islands, and New Caledonia.The name "Melanesia" means "blackislands", referring to the darkcomplexionedinhabitants these islandsMap showing location ofMelanesia. (Graphic:Melanesian CulturalHeritage ManagementIdentification Study)melanic - very dark or black colormelanin - a pigment in the skin of animals which determines skin andcoat color. It is found in two chemically different forms: eumelanin (whichproduces brown and black) and phaeomelanin (which produces yellow andred). Melanin also provides protection against the damaging effects ofultraviolet radiationmelanistic - dark or blackishmelanocyte - a cell in the inner layer of the epidermis that producemelaninmelanophore - a chromatophore which contains black and brownpigments called melaninmelon - a lens-shaped fatty deposit lying in the facial depression of manytoothed whales, such as the bottle-nosed dolphin. It appears as thebulging forehead just in front of the blowhole. It contains fatty deposits,muscles, and nasal air sacs and passages. The melon is used in focusing awhale's sounds, functioning as an acoustical lens for echolocation.Thefatty deposits change shape as the whale is producing soundsmembrane filter - a thin microporous material of specific pore size usedto filter bacteria, algae, and other very small particles from waterMendel's Laws of Heredity - the Law of Segregation states that eachhereditary characteristic is controlled by two 'factors' (alleles), whichsegregate and pass into separate germ cells (gametes). The Law ofIndependent Assortment states that pairs of 'factors' segregateindependently of each other when germ cells are formedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (15 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMendelian inheritance - one method inwhich genetic traits are passed fromparents to offspring. It is named after theAustrian monk, Gregor Mendel, who firststudied and recognized the existence ofgenes and this method of inheritance; ahereditary process explainable in terms ofthe behavior of chromosomes, e.g.,segregation of chromosomes, independentassortment, and homologous exchange ofpartsGregor Mendel (1822­1884), the "father" of thescience of genetics.Mendelian population - a natural, interbreeding unit of sexuallyreproducing organisms sharing a common gene poolmenisciform - crescent-shapedmeristem - organized, undifferentiated plant tissue with rapidly dividingcells (mitosis) that differentiate to form new tissues or organs; aspecialized area within a plant where rapid cell division occurs, e.g., rootsand shootsmeristic - pertains to serially repeated structures which can be counted,e.g. scales, vertebrae, fin rays, fin spines, other spines, myomeres,photophores, scutes, laterel line pores, etcmermaid's purse - an egg case of a shark or ray, usually oblong inshape with horns or tendrilsmeroblastic cleavage - incomplete cleavage of the zygote, restricted tothe blastodisc, the non-yolky cytoplasm at one end of the egg; typical ofteloblastic eggsmeroplankton - planktonic eggs and larvae which are temporarymembers of the plankton communitymerotrichous - pertaining to a nematocyst with spines confined to onedistal region of its threadhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (16 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamesenchyme - in cnidarians, a primitive "connective tissue" locatedbetween the epidermis and the gastrodermis. If it contains no cellcomponents, it is termed "mesoglea"; undifferentiated cells of an embryo,derived from mesoderm, which give rise to connective tissue and thecirculatory and lymphatics systems; amoebocytic cells often embedded ina gelatinous matrixmesenteric filament - the cord of tissue In sea anemones that runsalong the edge of incomplete mesenteries and which bear glandular cellsand nematocysts; they are used in digestion and become acontia towardthe pedal discmesentery - a sheet of tissue that envelops, separates, or supportsparticular organs or body regions; a vertical sheet of tissue that dividesthe gastrovascular cavity of sea anemonesmesentery, complete - in anthozoans, a mesentery which extends fromthe body wall to attach to the actinopharynxmesentery, directive - in anthozoans, one of a pair of mesenteriesattached to the actinopharynx in which the mesogleal pleats of theretractor muscles face away from one another, toward the exocoelmesentery, incomplete - in anthozoans, a mesentery in which the inneredge does not extend to the actinopharynxmesentery, nondirective - in anthozoans, one of a pair of mesenteriesattached to the actinopharynx in which the mesogleal pleats of theretractor muscles face each other, toward the endocoelmeso- - a prefix meaning 'middle'Mesoamerican Reef - the largest coral reef system in the Atlantic Oceanand the second largest coral reef in the world. It extends nearly 700 milesfrom the northern tip of the Yucatan peninsula to the Bay Islands off thecoast of Hondurasmesocosm - an experimental apparatus or enclosure designed toapproximate natural conditions, and in which environmental factors can bemanipulated. Mesocosms characteristically include both natural speciesassemblages in addition to structured populationshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (17 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamesoderm - the middle of the three germlayers of a triploblastic embryo that givesrise to the skeletal and support, muscular,blood vascular, urogenital and reproductivesystems, and contributions to some glandsLate gastrula. Thisphotograph is a dorsalview of the embryo, withthe anterior being towardthe animal pole and theposterior toward thevegetal pole. Note thebeginning of the formationof enterocoelic(mesodermal) pouches,from which the mesodermis derived, on the rightand left side of theanterior end of thegastrocoel. A - mesoderm;B - coelom; C -archenteron (Photo: Celland DevelopmentalBiology Online website(University of Guelph)http://www.uoguelph.ca/zoology/devobio/)mesoglea - the connective tissue layerbetween the epidermis and gastrodermis ofcnidarians and ctenophores (comb jellies)Inner tissues of this GiantGreen Anemone(Anthopleuraxanthogrammica) areseparated by themesoglea. (Photo: LisaEschenbach)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (18 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamesogleal pleat - in anthozoans, a sheet of longitudinal retractormuscles (myonemes) anchored to the mesoglea and pleated accordianwiseso that the mesoglea is sandwiched between two layers of epitheliumwithin the middle portion of a mesenterymesohyle - the non-cellular gel layer (also called 'mesenchyme') ofsponges. It is located between the epidermis (pinacoderm) and thechoanoderm, the cell layer that lines the spongocoel. The mesohylecontains either spicules (supportive needles made of calcium carbonate)or spongin fibers (a flexible skeletal material made from protein); alsocalled mesohylmesolamella - a collagenous layer that separates the choanochambers ofhexactinellid sponges (glass sponges)mesolecithal - a moderately telolecithal egg, typical of amphibiansmesopelagic zone - a layer (zone) of the ocean which lies just below theepipelagic zone. It extends from 200-1000 meters. The mesopelagic zoneis sometimes referred to as the twilight zone as sunlight this deep is veryfaint. This zone contains the thermocline, where temperature decreasesrapidly with depthmesotidal - coastal ocean or waterway with a moderate mean tidalrange, e.g., between 2 and 4 metersMesozoic - an era of time during the Phanerozoic eon lasting from 245million years ago to 66.4 million agometabolic gas - a gas which is released by the body as a result ofmetabolism. Carbon dioxide is an example of a metabolic gasmetabolic pathway - a set of oriented reactions interacting under givenphysiological conditions via simple or apparently simple intermediates.There are relatively few metabolic pathways, but each of these can bebroken down into many individual, enzyme-specific, catalysed stepsmetabolism - the sum of all the physical and chemical processes bywhich living organised materials are produced and maintained(anabolism), and also the destructive transformation processes by whichenergy is made available for the uses of the organism (catabolism); thesum of all the enzyme-catalysed reactions occurring in a cellmetabolite - a substance that takes part in the process of metabolism,which involves the breakdown of complex organic constituents of theorganism's body with the liberation of energy for use in bodily functioning.The various compounds that take part in, or are formed by, thesereactions are called metaboliteshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (19 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datametadata - information about data or other information. Metadata or"data about data" describe the content, quality, condition, and othercharacteristics of datametagamy - pertains to a reproductive cycle that alternates betweensexual and asexual phasesmetagenesis - an alternation of sexual and asexual generations. Whenmetagenesis occurs in cnidarians, the polyp is the asexual generation andthe medusa is the sexual generation. A generalized life cycle occurs asfollows: medusae produce gametes which unite to form zygotes. Eachzygote divides repeatedly and develops into a free-swimming planulalarva, which eventually settles and develops into a polyp. Each polyp thenasexually produces medusae to complete the life cyclemetamere - in biology, any of the homologous segments lying in alongitudinal series that make up the body of certain animals, such asearthworms and lobsters. A metamere is also called a 'somite'metamerism - in biology, the division ofthe body into a series of more or lesssimilar segments (metameres), as in anannelid worm or a lobsterA polychaete wormexhibiting metamerism.(Photo: Rick Gillis, Ph.D.,Biology Dept., Universityof Wisconsin-La Crosse)metamorphic rock - rock that has been altered physically, chemically,and mineralogically in response to strong changes in temperature,pressure, shearing stress, or by chemical action of fluidsmetamorphosis - change of body shape, e.g., the change from a larvalform to a juvenile or adult formhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (20 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datametanauplius larva - postnaupliar larvaof crustaceans with the same general bodyand limb morphology as the nauplius, buthaving additional appendagesCrustacean metanaupliuslarva. (Photo: Dep.deformation des maitres.Physiologie animale,Universite Pierre & MarieCurie, Paris VI.)metanephridium - a type of excretory tubule in annelid worms. Themetanephridium has internal openings called 'nephrostomes' that collectbody fluids and conducts them to the outside through external openings,the 'nephridiopores'metanephros - the final excretory organ that develops in a vertebrateembryo. In birds, reptiles, and mammals it replaces the mesonephros asthe functional excretory organ, and develops into the adult kidneymetapopulation - a group of populations, usually of the same species,which exist at the same time but in different places. The dispersedpopulation can replenish one another with migrants; a set of partiallyisolated conspecific populations which are able to exchange individualsand recolonize sites in which the species has recently become extinctmetazoa - multicellular animals having cells differentiated into tissuesand organs, and usually a digestive cavity and nervous systemmetecdysis - the final stage in arthropod molting in which the new cuticleis hardenedmeteorology - the science that deals withatmospheric phenomena, especiallyweather and weather conditionsMeteorologists often studyviolent weather. (Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (21 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datameter - a unit of length which constitutes the basis of the Metric System.It is one ten-millionth part of the distance measured on a meridian of theEarth from the equator to the pole. One meter equals 39.37 inchesmethane - an odorless gas produced by the decomposition of organicmattermethane hydrate - ice that contains a large amount of methane withinits crystal structure. Methane hydrates are common constituents of theshallow marine geosphere, huge amounts of which underlie the oceansand polar permafrost. The methane is dominantly generated by bacterialdegradation of organic matter in a low oxygen environment. There is anextraordinary amount of energy locked up in methane hydrate deposits,but no one has yet figured out how to extract the methane inexpensively.Methane is also a greenhouse gas and release of even a small percentageof total deposits could have a serious effect onthe Earth's atmosphere;also called "methane clathrate" and "methane ice"method - a description of how data and information are collectedmetric system - a decimal system of measures and weights with themeter and the gram as basesMHC (Major Histocompatibility Complex) - a complex family ofgenetically inherited proteins that play a critical role in immune responseto foreign organisms. It is also involved in autoimmune disease and intransplant rejection. MHC are located on cell surfaces and work likereceptors that interact with immune cells; molecules expressed on thesurface of cells that identify the cell as being "self" vs "foreign". MHCmolecules also bind foreign antigens and present them to the immunesystemmicroarray - in genomics, a tool for studying how large numbers ofgenes interact with each other and how a cell’s regulatory networkscontrol vast batteries of genes simultaneously. A robot is used to preciselyapply tiny droplets containing functional DNA to glass slides. Researchersthen attach fluorescent labels to DNA from the cell they are studying. Thelabeled probes are allowed to bind to cDNA strands on the slides. Theslides are put into a scanning microscope to measure how much of aspecific DNA fragment is presentmicroatoll - a circular colonial corallum up to 1 m height and 4 mdiameter. Growth is mainly lateral, as upward growth is limited by aerialexposuremicrobe - a nonspecific term for small organisms that can be seen onlywith the aid of a microscope. The term encompasses viruses, bacteria,yeasts, molds,and protists. The term, however, is used most frequently inrefererence to bacteriahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (22 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamicrobenthos (microfauna or microflora) - benthic organisms whoseshortest dimension is less than 0.1 mmmicrobial loop - a micro-food chain that works within (or along side) theclassical food chain. In the microbial loop the smallest organisms, theheterotrophic bacteria and picoplankton, use dissolved inorganic materialdirectly as carbon and energy sources. These organisms are grazed uponby flagellates and ciliates. The flagellates and smaller phytoplankton aretoo small to be preyed on directly by copepods, long considered to be amajor predator of microorganisms. Improved detection methods havedemonstrated that ciliates provide an intermediate predator level in themicrobial loop. These are then consumed by copepods and the processcontinues up the classical food chain (Marine Science Online)microbiology - the study of organisms that can be seen only with the aidof a microscopemicrobiota - organisms which are invisible, or nearly so, to the naked eyemicroclimate - the climate within a very small area or in a particular,often tightly defined, habitatMicrodictyon - a genus of non-calcareous, fleshy green macroalgaewhich can form green mats or turf on the substrate; also an extinct"armored worm" known from the Early Cambrian Maotianshan shale ofYunnan, Chinamicroecology - the study of the interactions between microorganismsand their environmentmicroenvironment - a specific set of physical, biological, and chemicalfactors immediately surrounding the organismmicroevolution - relatively minor change in the composition of a species'gene pool over timemicrofauna - animals which are invisible, or nearly so, to the naked eyemicroflora - plants which are invisible, or nearly so, to the naked eyemicrohabitat - a smaller part of a habitat that has some internalinteractions allowing it to function self-sufficiently within a generally largerhabitat, such as a patch reef in a lagoonmicrometer - an instrument for measuring very small distancesmicron (µ) - a unit of length equivalent to a micrometer (µm), onemillionthof a meter or 0.00003937 inchhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (23 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataMicronesia - a region situated betweenthe Mariana Trench in the west and theLine Islands in the east. The name"Micronesia" means "tiny islands." theFederated States of Micronesia consists ofthe states of Yap, Chuuk, Pohnpei, andKosrae. This region is composed ofthousands of small islands, mostly atollsMap of Micronesia.(Graphic: U.S. CIA)micronutrient - a nutrient, such as iron, copper, or zinc, that is requiredin very small amounts by plants in order to photosynthesize and thrivemicropyle - the minute aperture in the egg membrane for the entry ofthe sperm cellmicrosatellites - loci (or regions within DNA sequences) where shortsequences of DNA nucleotides are repeated in tandem arrays (thesequences are repeated one right after the other). The lengths ofsequences used most often are di-, tri-, or tetra-nucleotides. In theliterature they can also be called simple sequence repeats (SSR), shorttandem repeats (STR), or variable number tandem repeats (VNTR).Microsastellites are inherited in a Mendelian fashion. They are widely usedin the following applications: forensic identification and relatednesstesting; diagnosis and identification of diseases; population studies (bylooking at the variation of microsatellites in populations, inferences can bemade about population structures and differences, genetic drift, geneticbottlenecks and even the date of a last common ancestor); andconservation biology where they can be used to detect sudden changes inpopulation, effects of population fragmentation, and interaction ofdifferent populations. Microsatellites are useful in identification of new andincipient populationsmicrosclere - a small spicule in spongesmicrosmatic - pertains to animals with a poorly developed olfactory(smell) sensemicrotidal - coastal ocean or waterway with a low mean tidal range, e.g.,less than 2 metersmicrotubule - a long, hollow rod composed of the protein, tubulin.Microtubule networks make up portions of the cytoskeleton of alleukaryotic cells, aiding in cell structure and shape. They also function inintracellular transport of materials and organelles and are maincomponents of cilia and flagella. Microtubules also participate in theformation of spindle fibers during cell division (mitosis)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (24 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamicrovillus - any of the minute hairlike structures projecting from thesurface of certain types of cellsmicrowave - any electromagnetic radiation having a wavelength in theapproximate range from one millimeter to one meter, the region betweeninfrared and short-wave radio wavelengthsmidlittoral zone - the portion of theintertidal zone that is covered anduncovered by water each dayTidal pools in themidlittoral zone. (Photo:Susan Scott)midnight zone - the layer of the ocean beneath the twilight zone,extending from 1000-4000 meters. No light penetrates this zone; see"bathypelagic zone"midocean ridge - an uplifting of the ocean floor that occurs whenconvection currents beneath the ocean bed force magma up where twotectonic plates meet at a divergent boundary. The mid-ocean ridges of theworld are connected and form a single global mid-oceanic ridge systemthat is part of every ocean and also by far the longest mountain range onEarthmigrant - an animal that makes seasonal trips between breeding and nonbreedingareashttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (25 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamigration - the large-scale movement of apopulation for some specific purposeHumpback whales(Megaptera novaeangliae)migrate from near thepoles to tropical waters.(Photo: R Wicklund)milliammeter - an instrument for recording very small electrical currentsmillipore filter - a thin membrane composed of cellulose fibers that isused, for example, as a filter in the bacteriological examination of watermilt - the testes of fishes when filled withsemen; fish seminal fluidThe testes of this maleadult salmon produce miltwhen ready to spawn. Themilt becomes a liquid,containing sperm cells,and exits through the ventopening to fertilize eggs.(Photo: PacificStreamkeepers Federation)mimicry - the appearance or characteristics of one organism that copiesor "mimics" another in order to gain some advantage; the organism mayresemble some other natural object as an aid in concealmentMinamata disease - mercury poisoning of humans from eatingcontaminated seafoodhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (26 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamineral accretion - a technique used togrow corals on artificial reefs usingelectricity to accrete minerals therebycementing coral colonies to the substrate.Applying a low voltage to a metallicstructure causes calcium carbonate(CaCO3) to build on the metal, upon whichcoral larvae can attach, settle and feed.This greatly speeds the coral reef growthprocess. The voltage is low enough that itcan easily be generated by floating solarpanels or from wave actionThis effective method ofgrowing corals withelectricity,currently usedin worldwide research andholds high potential forrestoring coral reefsdamaged by causes of reefdestruction(Photo:GreatBarrier Reef Marine ParkAuthority)mineral deposit - an accumulation of naturally occurring mineralsmineralization - the process in which organic compounds (e.g., deadplant or animal materials) are converted to inorganic compoundsmini-atoll - a ring-shaped patch reef with a central area (lagoon)containing sandminimum viable population (mvp) - the smallest isolated populationhaving a good chance of remaining extant for a given number of yearsdespite the foreseeable effects of demographic, environmental, andrandom genetic events and natural catastrophesminisatellites - segments of repeated DNA often used as geneticmarkers for individual identificationMinor Outlying Islands - United States Minor Outlying Islands are:Baker Island, Howland Island, Jarvis Island, Johnston Atoll, Kingman Reef,Midway Islands, Wake Island, Palmyra Atoll, and Navassa Island (disputedwith Haiti)misspelling - in zoological nomenclature, a citation of a name in theliterature that is incorrectly spelledmitigation - the act of making less severe or intense; measures taken toreduce adverse impacts on the environmentmitigation plan - a proposal to reduce or alleviate potentially harmfulimpactshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (27 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamitochondrial DNA (mtDNA) - DNA that is located in the mitochondriaof cells. Mitochondrial DNA is maternally inherited and is a powerful toolfor tracking matrilineagemitochondrial genome - the genetic material of the mitochondria. It issimilar in structure to that of the prokaryotic genetic material, formed of asingle circular DNA molecule. The mitochondria of sexually-reproducinganimals usually comes only from the maternal side, and is essentially thesame as that of the mother. Sometimes mitochondria from spermatozoaare also passed on to offspring. Mitochondrial DNA has been studied totrace lineage far back in timemitochondrial RNA (mtRNA) - RNA that is located in the mitochondriaof cellsmitochondrion - an organelle found in thecells of most eukaryotes. Mitochondria aresometimes described as cellular "powerplants" because their primary function is tomanufacture adenosine triphosphate (ATP),which is used as a major source of cellularenergyElectron micrograph of asingle mitochondrionshowing the organizedarrangement of theprotein matrix and theinner mitochondrialmembranes. (Photo: U.S.Dept. of Health andHuman Services/NationalInstitutes of Health)mitogen - any substance that causes cells to begin dividing by mitosismitosis - the process of nuclear division in eukaryotic cells that producestwo daughter cells from one mother cell, all of which are geneticallyidentical to each other. See cell division ­mitotic spindle - a network of fiber-like microtubules that forms in acell's nucleus during mitosis (nuclear division) which connects thecentrosomes to the kinetochores and helps move the chromosomesaroundhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (28 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef Datamixed layer - near-surface waters subject to mixing by the action ofwind and waves. There is little variation in salinity or temperature atdepths below the mixed layermixed zone - the populous region of most bank/barrier reefs seaward ofthe lower palmata zone. It begins at a depth of 6-8 mMJO (Madden Julian Oscillation) - a major perturbation of tropicalconvection which moves and completes a global circuit every 30 to 60days. It is a dominant cause of intraseasonal variability in tropicalequatorial regionsMLCD (Marine Life Conservation District) - a designated area for theconservation and replenishment of marine resources. MLCDs allow onlylimited fishing and other consumptive uses, or prohibit such uses entirely.They provide fishes and other aquatic life with a protected area in whichto grow and reproduce, and are home to a great variety of speciesMMM (Maximum Monthly Mean SST climatology) - the highestexpected (climatological) monthly SST expected at all ocean locationsbased on 15 years of monthly mean SST data (serves as the inputthreshold for the Coral Bleaching HotSpot charts)mode - a statistical measure of central tendency. The number thatappears most in a sequence of numbers. A list of numbers can have morethan one modemodel - a mathematical approximation or simulation of a real system,process, or object that omits all but the most essential variables,developed to understand its behavior or to make predictionsModern Synthesis - the synthesis of natural selection and mendelianinheritancemodifier gene - a gene that modifies the effect produced by anothergenemoiety - a component part of a complex moleculemolar - a large flat or ridged-topped toothadapted for crushing or grindinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (29 of 40) [2/26/2008 9:14:38 AM]

Discover NOAA's Coral Reef DataThe teeth of this fish(Colossoma nigripinnis)are molar-like. Althoughthey may have cusps, theyare designed to crush foodmaterials (Photo: FloridaFish and WildlifeCommission)molar solution - an aqueous solution that contains one mole (grammolecularweight) of solute per litermolariform - shaped like a molar tooth, being rounded and flattened. Infishes, molariform teeth are used for crushing mollusks and crustaceansmole - the mass of a compound in grams numerically equal to itsmolecular weight. Also, the mass of a compound containing Avogadro’snumber of moleculesmolecular biology - a branch of biology that studies the biology of a cellat the molecular level. Molecular biological studies are directed at studyingthe structure and function of biological macromolecules and therelationship of their functioning to the structure of a cell and its internalcomponents. Great attention is given to genetic aspects such asreplication, transcription and translationmolecular clock - a technique in genetics, based on the molecular clockhypothesis (MCH), which is used to date when two species diverged. Itdeduces elapsed time from the number of minor differences between theirDNA sequencesmolecular clock hypothesis (MCH) - the principle that any gene orprotein has a near-constant rate of evolution in all branches of a clade,which means that the amount of sequence divergence between twosequences will be proportional to the amount of time elapsed since theirshared ancestor existedmolecular evolution - the process of evolution at the scale of nucleicacids (DNA and RNA) and proteinsmolecular genetics - the study of how genes function to control cellularactivitieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (30 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamolecular phylogeny - the use of the structure of molecules to gaininformation on an organism's evolutionary relationships. The result of amolecular phylogenetic analysis is expressed in a phylogenetic treemolecular systematics - the process of using data on the molecularconstitution of of organisms' DNA and/or RNA (nucleotide sequencing) inorder to resolve questions in systematics and phylogenymolecular weight - the sum of the atomic weights of the atoms in amoleculemolecule - a small particle composed of two or more atoms. Moleculesare a stable configuration of atomic nuclei and electrons bound togetherby electrostatic and electromagnetic forces. They have characteristicphysical and chemical properties, different from the atoms of which theyare composedMollusca - an animal phylum that includesbivalves, squids, octopuses and snails.They are distinguished by a muscular foot,a calcareous shell secreted by theunderlying body wall (the mantle) and afeeding organ (the radula). Many speciesare common inhabitants of coral reefsAtlantic deer cowrie(Cypraea cervus) grazingin the Flower GardenBanks National MarineSanctuary. (Photo: Frankand Joyce Burek)molt - to shed part or all of a coat or outer covering, such as, shell,feathers, cuticle or skin, which is replaced periodically by a new growthmonaxon - a linear spicule in sponges; a single rod or ray with a pointed,hooked, or knobbed endMonera - the Kingdom composed of prokaryotic organisms. They have acell wall, and lack both membrane-bound organelles and multicellularforms. The Archaebacteria, the most ancient of this Kingdom, are sodifferent that they may belong to a separate kingdom. Monera include thecyanobacteria and eubacteriamoniliform - contracted at short, regular intervals like a string of beads;bead-likemonitoring - the systematic collection of data over timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (31 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamonk seal - an endangered species of seal(Monachus schauinslandi) normally foundon the leeward (southwest) sides of theNorthwestern Hawaiian Islands, andoccasionally sighted in the Main HawaiianIslands. It is estimated that fewer than1500 Hawaiian monk seals exist today. TheHawaiian monk seal was officiallydesignated endangered 1976 and isprotected by the Endangered Species Actand the Marine Mammal Protection Act. It isillegal to kill, capture or harass monk seals.A critically endangered species of monkseal (Monachus monachus) is found in theA Hawaiian monk sealforaging on a coral reef inthe NorthwesternHawaiian islands. (Photo:NOAA/NMFS)Mediterranean Sea. The Caribbean monk seal (Monachus tropicalis) isthought to be extinctmono- - a prefix meaning onemonocarpic - refers to plants that flower and bear fruit only once;semelparousmonoecious - having combined sexes. Individuals of monoecious speciescontain the reproductive systems of both males and femalesmonofilament - a single large filament or threadlike structure of asynthetic fiber, such as a monofilament fishing linemonogamy - a male and a female mating only with each othermonomer - in chemistry, a single molecule that is the subunit of apolymer; in genetics, a character determined by a gene or genes at aparticular locusmonomorphic - occurring in only one formmonopectinate gill (ctenidium) - in mollusks, refers to having gilllamellae on one side of the ctenidial axismonophagous - eating one kind of food onlymonophyletic group - a group of organisms descended from a commonancestormonopodial growth - growth of a coral colony in which the trunk of thecolony is made by the oldest polyp. The trunk grows during growth of newpolyps. The oldest polyp is always on top of the colonyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (32 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamonosaccharide - a sugar that does not hydrolyse to produce othersugars; the simplest group of carbohydratesmonotype - in taxonomy, a situation where a genus group taxon isestablished with only one immediately subordinate taxon, e.g., a genuscontaining only one speciesmonsoon - a periodic wind caused by the effects of differential heating,with the largest being the Indian monsoon found in the Indian Ocean andsouthern AsiaMontastraea - a genus of hard (stony)coral that includes the boulder coral andthe great star coralGreat star coral(Montastraea cavernosa)is one of four species ofMontastraea found at theFlower Garden Banks inthe Gulf of Mexico. (Photo:Dr. Stephen Gittings)montiform - mountain-shapedMontreal Protocol on Substances that Deplete the Ozone Layer - aninternational treaty designed to protect the ozone layer by phasing out theproduction of a number of substances believed to be responsible for ozonedepletionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (33 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamoorish idol - a bony fish species(Zanclus cornutus) in the family Zanclidae.The moorish idol is the only species in thefamily. It has a long, white, sickle-shapeddorsal fin, two broad vertical black bars onthe body, and a yellow-orange saddleacross the sA Moorish Idol (Zancluscornutus) on anIndopacific reef (Photo:NOAA)moray eel - any of numerous chieflytropical, brightly colored marine eels of thefamily Muraenidae that commonly inhabitcoral reefsA spotted moray(Gymnothorax moringa)with a cleaning shrimp(Lysmata grabhami)(Photo:Tom Doeppner, Ph.D./ Brown University)morbidity - illness or disease; the incidence and prevalence of a specificdiseasemorgan - unit of inferred distance between genes on a chromosomemorph - a distinct genetic form or variant of a particular species. Forexample, a distinct color phase of a species that exhibits more than onecolor; a specific form, shape, or structuremorphogenesis - a change in the shape or structure of an organismthrough growth and differentiationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (34 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamorphological species - a typological species distinguished solely on thebasis of morphology; also called "morphospecies"morphology - a branch of biology that deals with the form and structureof organisms, apart from their functions (physiology)morphometric character - a measurement of a body part, e.g., headlength or eye diametermorphospecies - the traditional way to distinguish one species fromanother is to use differences in morphology which could involve size,shape, body part proportions, or color of external and/or internal bodystructures. Species named in this way may be referred to as"morphospecies." Different morphospecies, however, may not conform tothe usual definition of a biological species. Many geographically isolatedmorphospecies that are viewed as being closely related may be justgenetic varieties within a speciesmortality - the death rate; the ratio of the total number of deaths to thepopulation of a specified area in a given time periodmorula - a stage of embryonic development in which the cleaving cells(blastomeres) appear as a cluster of blastomeres without a cavity;precedes the blastula stage of embryonic developmentmosaic evolution - the evolution of different characters within a lineageor clade at different rates, hence more or less independently of oneanothermosaic teeth - the series of rows of flat teeth found in rays,skates andsome sharks. They are used for crushing hard foods as mollusks andcrustaceans; also called "pavement teeth"motile - capable of self-locomotion in organismsmotu - a coral island in the lagoon of an atollMOU (Memorandum of Understanding) - an interagency agreementdefining the role and responsibility which each agency has in dealing withparticular issuesmound - an elongate offshore ridge of unconsolidated substrate; rockyremnants of eroding headlands (bars; shallow masses of limestonedeposited by corals and coralline algae (shallow reefs)mouth brooder (oral brooder) - a fish which broods or protects theeggs or young by taking them into the mouth cavityhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (35 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamouthparts - a collective term for the appendages around the mouth ofcrustaceans which are concerned with feeding: mandibles, maxillae andmaxillipedsMPRSA (Marine Protection, Research, and Sanctuaries Act) - theMPRSA (1972) provides protection for many coral reefs by authorizingNOAA to designate areas as marine sanctuaries and promulgateregulations for the conservation and management of those areas. Sincethe Act was passed, thirteen sanctuaries have been designated, several ofwhich contain coral reef communities. Coral research, monitoring, andmanagement activities are conducted in these sanctuaries, as well as inthe Northwestern Hawaiian Islands Coral Reef Ecosystem Reserve, whichis currently (June 2004) under consideration to become the nation’sfourteenth sanctuarymRNA (messenger RNA) - an RNA molecule that encodes the aminoacid sequence of a protein. It is the mediating template between DNA andproteins. The encoded information from a particular gene is transferredfrom a strand of DNA by the construction of a complementary templatestrand of RNA (mRNA) through the transcription process. Next, threenucleotide segments of RNA, called tRNA (transfer RNA), which areattached to specific amino acids, match up with the template strand ofmRNA to order the correct sequence of amino acids. These amino acidsare then bonded together to form a protein a in a process, calledtranslation. Translation occurs in the ribosomes, which are composed ofproteins and a third kind of RNA, rRNA (ribosomal RNA)MSS (Multispectral Scanner) - a scanner system that simultaneouslyacquires images of the same scene in various wavelength bandsmuciferous - producing or containing mucusmucocyte - a mucus-secreting cellmucophagy - feeding on the mucus of fishes or invertebratesmucus - a gelatinous material secreted by specialized mucous cells. Incorals, it functions in protection from bacterial invasion, food capture, andremoval of sediment particles. Mucus is usually moved by cilia (motile hairlikeextensions of the cell membrane)mucus cell - a cell which secretes mucin, which, when mixed with waterforms mucusmud - a fine sediment often associated with river discharge and buildupof organic material in areas sheltered from high-energy waves andcurrentshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (36 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamud flat - a relatively level area of fine siltalong a shore (as in a sheltered estuary) oraround an island, alternately covered anduncovered by the tide, or covered byshallow waterNutrient-rich mudflats atthe Gulf of the FarallonesNational Marine Sanctuaryin California. (Photo: DanHoward)Muller's ratchet - a term given to the process by which the genomes ofan asexually reproducing population accumulate deleterious mutations inan irreversible manner because of the lack of genetic recombinationMullerian mimicry - a form of protective mimicry in which noxiousspecies evolve through convergent evolution to resemble each othermultibeam sonar - sonar signals arrivingat a target, or the towfish, from a singlesource but along different paths. Themultibeam sonar system consist of atransducer, motion sensor, gyrocompass,and navigation system. When collected inslightly overlapping swaths (fanlikecoverages from sonar scans), multibeamsonars can produce a sonar data set thatrepresents nearly 100 percent acousticcoverage of the seafloorHull-mounted multibeamsonar (left) and towed sidescan sonar (right)(Graphic: NOAA)multicellular - refers to organisms that are made up of more than onecell. Multicellular organisms have differentiated cells that performspecialized functionsmultienzyme - a protein possessing more than one catalytic functioncontributed by distinct parts of a polypeptide chain, or by distinctsubunits, or bothmultimedia - the use of computers to present video, sound, graphics,and texthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (37 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamultimodal distribution - a distribution with more than one modemultiple use MPA - often employed over larger areas, multiple-use areasallow for integrated management of complete marine ecosystems, usuallythrough a zoning processmultispecies fish spawning aggregation - a fish spawning aggregationcontaining multiple species spawning in the same area over timemultivariate - a term that describes statistical, mathematical, orgraphical procedures that involves two or more variables simultaneouslymultivariate analysis of variance - an analysis of variance with two ormore dependent variablesmultivariate community analyses - statistical methods for analyzingphysical and biological community data using multiple variablesmunicipal discharge - discharge of effluent from waste water treatmentplants, which receive waste water from households, commercialestablishments, and industries in the coastal drainage basinmunicipal Sewage - wastes (mostly liquid) originating from acommunity; may be composed of domestic wastewaters and/or industrialdischargesmuon - a charged lepton about 200 times more massive than anelectron; an elementary particle with a negative charge and a half-life of 2microsecond; decays to electron and neutrino, and antineutrinomutagen - an agent that causes a permanent genetic change in a cellother than that which occurs during normal genetic recombinationmutation - changes in the nature of single genes or segments ofchromosomes, which are then inherited by successive generationsmuton - the smallest mutable site within a cistron; the smallest part of agene ( a single nucleotide pair) that can be involved in a mutation eventmutualism - a symbiotic interaction between two species in which bothderive some benefitMYA - an acronym for "million years ago"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (38 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamycelium - the mass of filamentousgrowth (hyphae) from which the vegetativepart of a fungus developsDrawing of the myceliumof a fungus. (Photo: JonHouseman\BIODIDAC)mycobacteriosis - in fishes, mycobacteriosis is a disease caused bybacteria within the genus Mycobacterium. There are many differentspecies of Mycobacterium that also cause diseases in birds, reptiles, andmammals. Some also cause important diseases in humans. theMycobacterim species in fishes are referred to as non-tuberculousmycobacteria and do not cause major disease in healthy humans.However, while rare, transmission from infected fishes to humans ispossible and may cause a skin infection referred to as "fish handler'sdisease" or "fish tank granuloma"mycophage - an animal which primarily eats fungimycosis - any disease caused by a fungusmyocin - one of two proteins responsible for muscle cell contraction (theother is the globular protein, actin). Myosin bundles intermesh with actinbundles, and contraction occurs when the two protein bundles slide overeach othermyoepithelial cell - a contractile cell in cnidariansmyoglobin - an oxygen-binding protein found in the muscle cells ofanimals. It functions as an oxygen storage unit, providing oxygen to themuscles. Diving marine mammals, such as seals and whales are able toremain submerged for long periods because they have greater amounts ofmyoglobin in their muscles than other animals do. There is a closechemical similarity between myoglobin and hemoglobin, the oxygenbindingprotein of red blood cellshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (39 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef Datamyoneme - a contractile fibril found in the cytoplasm of certainprotozoans; a contractle fibril of epitheliomuscular cells of anthozoansmyotome - any segment of embryonic mesoderm that develops intoskeletal (voluntary) muscle in the adult; any of the segmentally arrangedblocks of muscle in lower vertebrates, such as fishesmytiliform - in the shape of the mussel shell (genus Mytilus)myxopterygium (clasper) - the copulatory organ or clasper of sharks,rays, skates and chimaeras(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=m (40 of 40) [2/26/2008 9:14:39 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: NThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Znacre - the irridescent innermost layer of amolluscan shell that is secreted by themantle. It is also called the mother-of-pearllayerA mussel shell showing thenacre or mother-of-pearllayer.NACRI (Netherlands Antilles Coral Reef Initiative) - NACRI wasestablished in 2000 as part of an effort to improve nature conservationand management in the Netherlands Antilles in general, and specificallytargeting coral reefs in order to give more attention to, and bettercoordinate protection of the coral reefs of the islands. Beginning in 2004,NACRI plans to establish a central monitoring node and database for theNetherlands Antilles as part of the Global Coral Reef Monitoring Network(GCRMN), to complement other existing sub-regional nodes in theCaribbean. A catch survey of reef fisheries in all islands is also planned.The Netherlands Antilles consists of five islands in the Caribbean: Bonaireand Curacao just over 100 km off the Venezuelan mainland, and Saba, St.Eustatius and St. Maarten about 900 km to the north-east in the arc ofthe Lesser Antilles. The Netherlands Antilles is a so-called territory of theKingdom of the Netherlands, although it is an independent statehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (1 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanaked skin - pertains to a fish whose body lacks scales; scalelessnanobiology - biological studies at the extremely small to molecularlevels. Many fundamental biological functions are carried out at the levelof molecular machineries that have the sizes of 1-100 nm. The emergenceof nanobiology allowed understanding of the functions of thesemachineries, with the invention of nano- technology, e.g., scanning probemicroscopy, modern optical techniques, and micro- manipulatingtechniquesnanometer - a unit of length equal to 0.001 microns (one thousandth ofa micron), 0.000001 millimeters, or 0.000000001 meters; also called amillimicronnanoplankton - minute phytoplankton organisms with a body diameterbetween 0.2 and 20 micrometersnanoscience - the extension of existing sciences into the realms of theextremely small, as in nanomaterials, nanochemistry, nanobiology,nanophysics, nanoengineering, etcnanozooid - a small zooid in tubuliporid bryozoans which bears a singletentacle and a reduced alimentary sacnape - the area behind the head of a fish, extending from the back of theskull to the origin of the dorsal finnare - nostril; an opening, external and internal, of the nasal passage.Nares (pl) in fishes lead to blind olfactory sacs and do not connect with aninternal passageway. There is an incurrent aperture and an excurrentaperture. Movement of water into the olfactory sacs is for smelling ratherthan respirationNARS (Natural Area Reserve System) - the State of Hawai‘i createdthe Natural Area Reserves System, or NARS, to preserve and protectrepresentative samples of Hawaiian biological ecosystems and geologicalformations. The diverse areas found in the NARS range from marine andcoastal environments to lava flows, tropical rainforests, and even analpine desert. One can find rare plants and animals within these areas,many of which are on the edge of extinction. The reserves also protectsome of the major watershed areas which provide vital sources of freshwaternasal - pertains to the nosenascent - commencing development; immature; coming into existence;emerginghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (2 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanatal homing - the behavior by which an animal returns, for reproductivepurposes, to the place where it was born or hatchednatant - swimming or floatingNational Benthic Inventory (NBI) - a quantitative database on benthicspecies distributions and a corresponding taxonomic voucher collection ofpreserved benthic specimens obtained from studies conducted by theNational Oceanic and Atmospheric Administration (NOAA) and partneringinstitutions in estuarine and other coastal areas of the United States. Boththe NBI and the reference collection are maintained in the Benthic EcologyLaboratory of the Coastal Ecology Program at NOAA's Center for CoastalEnvironmental Health and Biomolecular Research in Charleston, SCNational Biological Information Infrastructure (NBII) - a broad,collaborative program to provide increased access to data and informationon the nation's biological resources. The NBII links diverse, high-qualitybiological databases, information products, and analytical toolsmaintainedby NBII partners and other contributors in government agencies,academic institutions, non-government organizations, and private industryNational Estuary Restoration Inventory (NERI) - a NOAA onlinedatabase of habitat restoration projects. The purpose of the inventory isto: provide information on monitoring and restoration techniques in orderto advance the science of restoration, track acres of habitat restoredtoward the million acre goal of the Estuary Resoration Act (ERA), andprovide information for reports transmitted to CongressNational Marine Protected Areas Center - the National MarineProtected Areas (MPA) Center’s mission is to facilitate the effective use ofscience, technology, training, and information in the planning,management, and evaluation of the nation’s system of marine protectedareas. The MPA Center, located within the National Oceanic andAtmospheric Administration (NOAA), develops operational and programpolicy, supports the MPA Federal Advisory Committee, manages national,regional, and international MPA coordination, conducts outreach andeducation, consults with federal agencies, state agencies, tribal agencies,fishery management councils, and others, maintains the U.S. MPAwebsite, and oversees the collection of data for the marine managed areasinventoryNational Monument - a protected area of the United States that issimilar to a U.S. national park. The President of the United States canquickly declare an area of the United States to be a national monumentwithout Congressional approval. On June 15, 2006, President George W.Bush declared the Northwestern Hawaiian Islands a National Monument,creating the largest protected marine reserve in the worldNational Oceanographic Partnership Program (NOPP) - acollaboration of fifteen U.S. federal agencies to provide leadership andcoordination of national oceanographic research and education initiativeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (3 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNational Priorities List (NPL) - locations throughout the U.S. wherehazardous wastes have been found in the environment and the initialevaluation shows a significant risk of harm to human health or theenvironment. NPL sites are frequently called "Superfund" sites, becauseSuperfund money can be used by the U.S. Environmental ProtectionAgency (USEPA) to investigate and clean up these sitesnative species - a species that occurs naturally in a given area.Therefore, one that has not been introduced by humans either accidentallyor intentionally; also called an indigenous speciesnatural climate record - a record of climatic events found by examiningthe natural environment (e.g., coral growth bands, tree rings, layers of icein glaciers)Natural Heritage Network - the network of Conservation Data Centersand Natural Heritage Programs throughout the Americas. All networkmembers use the same methodology and database to track the rareelements of biodiversity in their jurisdictionsnatural occurrence - the presence of a substance in nature, as distinctfrom presence resulting from inputs from human activitiesnatural selection - a natural process by which organisms (and theirgenes) that adapt to their environment survive while those that do notadapt become eliminated progressivelyNature Conservancy, The - a private, international conservation groupwhose mission is to preserve plants, animals, and natural communitiesthat represent the diversity of life on earth by protecting the lands andwaters they need to surviveNatureServe - an organization dedicated to providing reliable informationon species and ecological communities for use in conservation and landuse planning. NatureServe is an independent nonprofit organizationcreated in collaboration with the network of Natural Heritage Programsand Conservation Data Centers and The Nature ConservancyNAUI ( National Association of Underwater Instructors) - a scubadiving certifying and instruction agencynauplius larva - a free-swimming, planktonic larval stage of manycrustaceansnautical chart - a chart used to navigate bodies of waternautical mile - the length of a minute of arc, 1/21,600 of an averagegreat circle of the Earth. Generally one minute of latitude is consideredequal to one nautical mile. The accepted United States value as of 1 July1959 is 1,852 meters (6,076.115 feet)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (4 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNavassa - a small (35 km2) isolated and uninhabited island located at18o25'N, 75o05'W, approximately 55 km west of the Tiburon Peninsula ofHaiti and 220 km northeast of Jamaica. Navassa was designated as aUnited States National Wildlife Refuge in 1999. Corals and sponges growon large underwater rocks that have broken off from the cliffsnavicular - boat-shapednaviform - boat-shapedNCBI (National Center for Biotechnology Information) - establishedin 1988 as a national resource for molecular biology information, NCBIcreates public databases, conducts research in computational biology,develops software tools for analyzing genome data, and disseminatesbiomedical information - all for the better understanding of molecularprocesses affecting human health and disease. NCBI is a division of theNational Library of Medicine (NLM) at the National Institutes of Health(NIH)neap tide - a tide that occurs when the difference between high and lowtide is least; the lowest level of high tide. Neap tide comes twice a month,in the first and third quarters of the moonnear threatened - a species or other taxon likely to become CriticallyEndangered, Endangered or Vulnerable in the near futurenecrolysis - the decomposition of an organism's body after it diesnecromass - the weight of dead organisms, usually expressed pervolume of water or per unit of land surface or volumenecrophagy - feeding on dead animals or carrionnecropsy - an examination and dissection of a body of a dead organismin order to determine the cause of death or changes produced by diseasenecrosis - the death of living tissues dueto infection or injuryElkhorn coral, sufferingfrom recent necrosis.(Photo: U.S. GeologicalSurvey)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (5 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanectophore - a highly modified medusa that remains with a floatinghydrozoan colony and pulsates for locomotion of the colonynectosome - the region of a siphonophore colony that bears nectophores(medusae specialized for propulsion)Needham's sac - a sac that stores spermatophores in cephalopodsnegative binomial regression model - a useful empirical methodologywhen data are overdispersed, that is, when the variance of the distributionis considerably larger than the meannegative charge - an electrical charge created by having more electronsthan protons.negative phototropism - the tendency to move away from a light sourcenekton - organisms with swimmingabilities that allow them to move activelythrough the water column and to moveagainst currentsFish are a largecomponent of marinenekton. (Photo: Dr.Anthony Picciolo)nematocyst - a specialized stinging cell (cnida) found in cnidarians.It is adouble-walled capsule containing an elongated tubule which everts uponmechanical or chemical stimulation to deliver a toxin or entangle prey orpredators.There are several different morphological types of nematocystsnematode - any unsegmented roundworm of the phylum Nemata, havinga tough outer cuticle. The phylum includes free-living forms and diseasecausingparasitesnematozooid - a hydrozoan defense polyphttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (6 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNemertea - a phylum of elongated, oftenflattened marine worm-like animalscomprising nearly 1000 species whichrange in size from less than an inch tonearly 30 m. They are carnivorous and feedupon annelid worms as well as othermarine animals. Their most distinctivestructure is a proboscis which is used forfood capture, defense, and burrowing intothe soft substrate. The sexes are separatein most species and fertilzation is external.Many are capable of reproducing asexuallyby fragmentation of the body. They are alsocalled "ribbon worms"The Nemertea arevoracious carnivores, andits body wall musculatureis not well developed;when picked up they canstretch to many timestheir original length (Photo:Bill Rudman, Ph.D.)neo-Darwinism - the unification of natural selection and Mendeliangenetics; also called the Modern Synthesisneocotype - in taxonomy, a replacement syntype, q.v., designated in theabsence of the original type or type seriesneonate - a newborn animalneoplasia - the pathological process that results in a neoplasm, anabnormal tissue whose cells proliferate more rapidly than normal andwhich may become malignantneoplasm - a cancerous growthneoprene - a synthetic rubber with good resistance to oil, chemical, andfire. Wet suits and other "rubber" diving accessories used by scuba diversare made of neoprenehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (7 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Dataneotype - in taxonomy, a specimen selected as type specimensubsequent to the original description in cases where the originalholotype, or lectotype, or all paratypes, or all syntypes are lost ordestroyed, or suppressed by the Commission (Zoology)NEPA (National Environmental Policy Act) - passed in 1969, thepurposes of NEPA are: to declare a national policy which will encourageproductive and enjoyable harmony between man and his environment; topromote efforts which will prevent or eliminate damage to theenvironment and biosphere and stimulate the health and welfare of man;to enrich the understanding of the ecological systems and naturalresources important to the Nation; and to establish a Council onEnvironmental Qualitynephelometer - an instrument for measuring the turbidity of a fluid bymeasuring the scattering function of particles suspended in the fluidnephelometric turbidity unit (NTU) - unit of measure for the turbidityof water. Essentially, a measure of the cloudiness of water as measuredby a nephelometernephridium - a simple excretory organ of many invertebrates, consistingof a tube through which waste products pass to the exteriornepionotype - in taxonomy, the type larva of a speciesneritic - refers to the ocean environment landward of the shelf-slopebreakneritic zone - the relatively shallow water zone that extends from thehigh tide mark to the edge of the continental shelfnerve - a bundle of neurons (nerve cells); specifically, a bundle of axonswhich are the motor processes of neurons which carry nervous impulses inthe direction away from the cell bodiesnerve net - the non-centralized, disorganized network of nerve cellsunder the epidermis, and sometimes the gastrodermis, of cnidarians. It iscomprised of multipolar cells with multiple synaptic junctions, but nopolarization. Impulses pass either way across the synapse. Both neuronendings of a synapse have secretory vesiclesnerve net - a diffuse, two-dimensional plexus of interconnected bipolar ormultipolar neurons with no central control organ; found in cnidariansnerve ring - the center of the nervous system of some higherinvertebrates that encircles the esophagus.It is composed largely of nervefibers and associated ganglia; also called the "supraesophagealcommissure"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (8 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNESDIS (National Environmental Satellite, Data and InformationService) - the NOAA agency that operates and manages the U.S. civilianweather satellites and the national environmental data centers, such asthe National Oceanographic Data Center (NODC), the National ClimaticData Center (NCDC), and the National Geophysical Data Center (NGDC)nest - a structure in which animals lay eggs or give birth to their youngand/or provide a place to raise their offspringnest fauna - the invertebrate inhabitants of bird's nestsnesting - the act of constructing a nestnet photosynthetic rate - the total rate of photosynthetic CO 2 fixationminus the rate of loss of CO 2 during respirationnet plankton - plankton captured in a 80 µm netnet primary productivity - the total amount of chemical energy fixed bythe processes of photosynthesis minus the chemical energy lost throughrespiration; same as 'net photosynthetic rate'network - a wide variety of systems of interconnected components; twoor more computers connected together so that they can share resources.Two or more networks connected together is an internetNetwork for Endangered Sea Turtles (N.E.S.T.) - a non-profitorganization dedicated to the preservation and protection of the habitatsand migration routes of sea turtles and other marine animals on the OuterBanks of North Carolina from the Virginia border to Oregon Inletneural - pertains to the nervous system of an organismneuritis - inflammation of the nervesneuromast - a sensory cell with a hair-like process capable of detectingmotion or vibrations in waterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (9 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Dataneuron - a nerve cell; a specialized cellthat can react to stimuli and transmitimpulses. A neuron consists of a cell bodywhich contains the nucleus; dendrites,which are usually short sensory branchesoff the cell body that receive incomingimpulses; and a single, long axon whichcarries impulses away from the body(motor function) and to the next neuron,gland or muscleA neuron in a mammalianbrain. (Photo: Universityof Kansas Medical Center)neurophysiology - the branch of neuroscience that studies thephysiology of the nervous systemneuropodium - a lobe of the parapodium closer to the ventral side inpolychaete wormsneuroscience - the scientific disciplines concerned with the development,structure, function, chemistry, pharmacology, clinical assessments andpathology of the nervous systemneurotoxin - a toxic substance which interferes with the electricalactivities of nerves and inhibits, damages or destroys the tissues of thenervous system, especially neurons (nerve cells)neurotransmitter - a chemical substance ("messenger") produced in andreleased by one neuron that carries a nervous impulse across a synapse(the small gap between the axon and dendrite of communicatingneurons). They relay nervous impulses among neurons and betweenneurons and other types of cells, such as in muscle and glandular tissues.Neurotransmitters can excite or inhibit another neuron or receptor organ.There are more than 300 known neurotransmitters. A few of the morecommon ones are acetylcholine, dopamine, norepinephrine, and serotoninneuston - planktonic organisms associated with the air-water interfaceneutralism - the lack of any interaction between two organisms orspecies in a shared habitat. Neither has any effect on the otherneutrino - a lepton with no electric charge. Neutrinos participate only inweak (and gravitational) interactions and therefore are very difficult todetect. There are three known types of neutrino, all of which have verylow or possibly even zero massnew combination - in taxonomy, when a species is transferred to adifferent genus for the first timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (10 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNGO (Non-governmental Organization ) - a non-profit group orassociation organized outside of institutionalized political structures toobtain particular social objectives (such as environmental protection) orserve particular constituenciesniche - the role of an organism in an ecological community; theenvironmental requirements and tolerances of a species; sometimes seenas a species' "profession" or what it does to surviveniche overlap - an overlap in resource requirements by at least twospeciesNicotinamide adenine dinucleotide phosphate (NADP) - NADP is areducing agent (electron donor) important in the preliminary reactions ofphotosynthesis. NADPH is the reduced form of NADPnictitating eyelid - a movable eyelid found in sharks that can be closedover the eye to protect it from damage. Sharks also have non-movingupper and lower eyelidsnictitating membrane - a semi-transparent membrane which can bedrawn across the eye in birds, reptiles and many mammals. It functions toeither moderate the effects of strong light or to sweep away dust andsimilar particles from the surface of the eyenidifugous - pertaining to an animal that leaves its nest shortly afterbirth or hatchingnitrogen narcosis - a hazardous condition that scuba divers mayexperience at depths usually in excess of 80 ft (24.38 m). It occurs whennitrogen builds up in the body tissues and replaces some of the oxygenrequired by the brain. The longer a diver with conventional scuba stays ata deep depth, the more nitrogen accumulates. As the brain is deprived ofoxygen, the ability to think and function clearly diminishes. It mayprogress from a slightly confused feeling to an almost intoxicated state,where thinking and judgement is severely impaired. If the diver does notascend to a shallower depth and off-gas nitrogen, nitrogen narcossis mayeventually cause death. Although this can happen at any depth, it isespecially a problem with dives in excess of 80 feet. Nitrogen narcossis isalso called 'rapture of the deep'nitrox - any mixture of nitrogen and oxygen that contains less than the78 percent nitrogen as found in ordinary airno take zone - a marine protected area that is completely (or seasonally)free of all extractive or non-extractive human uses that contribute impact(some exceptions may be permitted for scientific activities); also called"marine reserve" or "fully protected area"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (11 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNOAA (National Oceanic andAtmospheric Administration) - theNational Oceanic and AtmosphericAdministration (NOAA) is a federal agencywithin the US Department of Commercethat is dedicated to predicting andprotecting the environment. NOAA's overallmission is to understand and predictchanges in the Earth+s environment,protect life and property, provide decisionmakers with reliable scientific information,conserve and manage the Nation+s livingmarine and coastal resources to meet ourNation+s economic, social, andenvironmental needs, and foster globalenvironmental stewardship. To achieve itsmission, NOAA+s focus through 2008 willbe on four mission goals:1. Protect, restore, and manage the use ofcoastal and ocean resources throughecosystem-based management2. Understand climate variability andchange to enhance society+s ability to planand respond3. Serve society+s needs for weather andwater information4. Support the Nation+s commerce with The National Oceanic andinformation for safe, efficient, andAtmosphericenvironmentally sound transportationAdministration (NOAA) is afederal agency within theU.S. Department ofCommerce that isdedicated to predicting,protecting, and providinginformation about themarine environment.NOAA Coral Reef Conservation Program - a NOAA program whosepurposes are: (1) to preserve, sustain, and restore the condition of coralreef ecosystems; (2) to promote the wise management and sustainableuse of coral reefs; (3) to develop sound scientific information on thecondition of coral reef ecosystems and the threats to such ecosystems;(4) to assist in the preservation of coral reefs by supporting conservationprograms, including projects that involve affected local communities andnongovernmental organizations; (5) to provide financial resources forthose programs and projects; and (6) to establish a formal mechanism forcollecting and allocating monetary donations from the private sector to beused for coral reef conservation projectshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (12 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataNOAA Diving Program - the NOAA Diving Program is administered byNOAA and is headquartered at the NOAA Diving Center in Seattle, WA.The Program trains and certifies scientists, engineers and technicians toperform the variety of tasks carried out underwater to support NOAA'smission. With more than 300 divers, NOAA has the largest complement ofdivers of any civilian federal agency. In addition, NOAA's reputation as aleader in diving and safety training has led to frequent requests fromother governmental agencies to participate in NOAA diver training coursesNOAA's Center for Sponsored Coastal Ocean Research (CSCOR) -NOAA's Center for Sponsored Coastal Ocean Research (CSCOR) developsand improves predictive capabilities for managing the Nation's use of itscoastal resources through competitive research programs. CSCOR alsosupports efforts to translate the results of its research investments, andthose of others, into accessible and useful information for coastalmanagers, planners, lawmakers, and the public to help balance the needsof economic growth with those of conserving the resources of our Nation'sGreat Lakes, estuaries, and coastal ocean. Its mission is to provide thehighest quality research in support of coastal management decisionsthrough competitive, peer-reviewed research and holistic ecosystemstudiesNOAA's Coral Reef Conservation Grant Program - each year, subjectto the availability of funds, NOAA publishes its Coral Reef ConservationGrant Program Funding Guidance, as authorized by the Coral ReefConservation Act of 2000, to solicit proposals for coral reef conservationactivities. The Act authorizes the Secretary of Commerce, through theNOAA administrator and subject to the availability of funds, to issuematching grants of financial assistance for broad-based coral reefconservation activities, consistent with the purposes of the ActNOAA's Coral Reef Watch (CRW) Satellite Bleaching Alert (SBA)system - an automated coral bleaching e-mail alert system designed tomonitor the status of thermal stress conducive to coral bleaching via theuse of the CRW global satellite near-real time HotSpot suite of products.The SBA was developed by the NOAA as a tool for coral reef managers,scientists and other interested people. The SBA became operational in July2005NOAA's National Marine Fisheries Service (NOAA Fisheries) - NOAAFisheries is the federal agency responsible for the stewardship of thenation’s living marine resources and their habitat. It is responsible for themanagement, conservation and protection of living marine resourceswithin the United States’ Exclusive Economic Zone (water three to 200miles offshore). Using the tools provided by the Magnuson-Stevens Act,NOAA Fisheries assesses and predicts the status of fish stocks, ensurescompliance with fisheries regulations and works to reduce wasteful fishingpractices. Under the Marine Mammal Protection Act and the EndangeredSpecies Act, it recovers protected marine species (i.e. whales, turtles)without unnecessarily impeding economic and recreational opportunities.With the help of the six regional offices and eight councils, NOAA Fisheriesis able to work with communities on fishery management issues. NOAAFisheries works to promote sustainable fisheries and to promotesustainable fisheries and to prevent lost economic potential associatedwith overfishing, declining species and degraded habitats. It strives tobalance competing public needs and interest in the use and enjoyment ofhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (13 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Dataour oceans’ resources. For more information, see: http://www.nmfs.noaa.gov/NOAA's National Ocean Service (NOS) - NOS is a scientific andtechnical organization of NOAA whose mission is to preserve and enhancethe nation’s coastal resources and ecosystems along 95,000 miles ofshoreline and 3.5 million square miles of coastal ocean. At the same time,it works to support economic growth for the long-term benefit of thenation. This theme is central to the sustainable development agenda ofboth NOAA and the U. S. Department of Commerce (DOC). For detailedinformation, see: http://www.oceanservice.noaa.gov/about/welcome.htmlNOAA's Office of Ocean Exploration (OOE) - NOAA's center for newactivities to explore and better understand our oceans. This office (OOE)supports expeditions, exploration projects, and a number of related fieldcampaigns for the purpose of discovery and documentation of oceanvoyages. Bringing scientists to ocean frontiers requires rigorous planning,mission staging, and well coordinated marine operations. Education andoutreach rank high as office priorities. Through ocean exploration, NOAA iscommitted to raising America's science literacy and developing the nextgeneration of ocean explorers, scientists and educators. Four crucialcomponents comprise the NOAA Ocean Exploration Mission: (1) Mappingthe physical, biological, chemical and archaeological aspects of the ocean;(2) Understanding ocean dynamics at new levels to describe the complexinteractions of the living ocean; (3) Developing new sensors and systemsto regain U.S. leadership in ocean technology, and; (4) Reaching out tothe public to communicate how and why unlocking the secrets of theocean is well worth the commitment of time and resources, and to benefitcurrent and future generations. OOE is a major program office withinNOAA's Office of Oceanographic and Atmospheric ResearchNOAA's Office of Oceanic and Atmospheric Research (NOAAResearch) - the Office of Oceanic and Atmospheric Research (OAR) or“NOAA Research” works in partnership with NOAA’s National WeatherService, National Ocean Service, National Environmental Satellite DataInformation Service and National Marine Fisheries Service as the researchand development organization of the agency. It is through NOAA Researchthat work results in better weather forecasts, longer warnings for naturaldisasters and an overall greater understanding of our oceans, climate andatmosphere. NOAA Research explores the Earth and atmosphere from thevery surface of the sun to the depths of the ocean. Its role within NOAA isto provide products and services that describe and predict changes in theenvironment. NOAA Research results allow decision makers to makeeffective judgments in order to prevent the loss of human life andconserve and manage natural resources. Research is conducted, with itspartners in academia, in three major areas: atmosphere, climate, andocean and coastal resources. For more information, see: http://www.research.noaa.gov/nociceptor - a sensory receptor which responds to potentially harmfulstimuli; produces a sensation of painnocturnal - being primarily active at nighthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (14 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanode - a knob or swelling; a branching point on a dendrogram(phylogenetic tree); any single computer connected to a network; in ageographical information system (GIS), a node is the beginning,connecting and ending point of an arcnodular - having small knobs, protuberances or nodule-like projectionsnodule - a swollen, knob-like structurenodulose - with small nodules, knobs or swellingsnoise - unwanted soundnomen illegitimum - in taxonomy, an illegitimate name; a validlypublished name that must be rejected for the purposes of priority inaccordance with the International Code of Zoological Nomenclaturenomen negatum - in taxonomy, a denied name: an unavailable namewhich has incorrect original spellings as defined by the International Codeof Zoological Nomenclaturenomen novum - in taxonomy, a new name which is published to replacean earlier name (and valid only if the latter is preoccupied) and which isexpressly proposed as a replacement name; a new name, not to beconfused with a new species, or a new genus, etc., which represent newtaxa. It is commonly applied to names proposed to replace juniorhomonymsnomen nudum - in taxonomy, a naked name, i.e., a name that, ifpublished before 1931, was not accompanied by a description, definition,or indication, or if published after 1930, is not accompanied by astatement that purports to give characters differentiating the taxon; or isnot accompanied by a definite bibliographic reference to such astatement; or is not proposed expressly as a replacement for a preexistingavailable name. A nomen nudum is not an available namenomen nullum - in taxonomy, a null name, i.e.,an unavailable namewhich, as defined by the International Code of Zoological Nomenclature, isa non-demonstrably intentional change of an original spelling, i.e. a formof incorrect subsequent spellingnomen oblitum - in taxonomy, a forgotten name; an unused seniorsynonym rejected under the provisions of the International Code ofZoological Nomenclaturenomen oblitum - in taxonomy, a forgotten taxonomic namehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (15 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanomen vetitum - in taxonomy, an impermissible name; an unavailablename published for divisions of the genus group other than genus andsubgenus, which are not accepted by the International Code of ZoologicalNomenclaturenomenclature - the description of new taxa or alterations to the conceptof previously described taxa which involve changes in the names of taxanominal taxon - in taxonomy, a named taxon, objectively defined by itstype taxon. Thus the nominal family Chaetodontidae is always the one towhich its nominal type genus, Chaetodon, belongsnominate subordinate taxon - in taxonomy, a subordinate taxon whichbears the same names as its immediate higher taxon. Thus Badis badis isthe nominate species of the genus Badisnon-coding linker sequences - short pieces of DNA between geneswhich do not direct protein synthesis or perform a regulatory functionnon-coding RNA (ncRNA) - any RNA molecule that is not translated intoa protein. Examples of non-coding RNAs are transfer RNA (tRNA) andribosomal RNA (rRNA)non-extant - no longer existingnon-point source pollution - a pollution source without a single point oforigin, or not introduced into a receiving stream from a specific outlet. Itoccurs when rainfall, snowmelt, or irrigation runs over land or through theground, picks up pollutants, and deposits them into rivers, lakes, andcoastal waters or introduces them into ground water. Common nonpointsources are agriculture, forestry, mining, construction, dams, channels,land disposal, saltwater intrusion, and city streetsnonallele - a gene that is not a competitor at the same locus (specificlocation on the chromosome)nonbiodegradable material - a material that cannot be broken intosimpler chemicals by living organismssnoncoding DNA - DNA that does not encode any product (RNA orprotein). The majority of the DNA in plants and animals is noncodingnondegradable pollutant - a polluting substance that is not brokendown by natural processesnonessential amino acid - an amino acid which can be synthesized bythe organism's body, and not required in the nourishment source. Humanscan make 13 nonessential amino acidshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (16 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanonindigeneous organism - an organism which is not native to the areain which it occurs. it was either purposely or accidentally introduced; alsocalled exotic, nonnative, introduced, and aliennonionizing radiation - radiation that carries enough energy to excitean atom or molecule, but not enough energy to remove an electron fromthe atom or molecule. This type of radiation does not cause damage tocells and tissues; examples include radio waves, microwaves, infraredlight, and ordinary lightnonpoint - not from a single, well-defined sitenonrenewable resource - an environment resource which is notreplaced or replenished by natural processes at a rate comparable to theuse of the resource; a resource depleted or exhausted by usenonseptate - lacking cross walls (septa); also termed "aseptate"nonsynonymous substitution - in molecular biology, a nucleotidesubstitution that results in a replacement of an amino acidnonvascular plant - a plant which lacks tissues to conduct water andnutrients. Nonvascular plants do not produce flowers or seedsNorth Star - Polaris, the North Star, is visible in the northern hemisphereand indicates the direction of north. In the southern hemisphere theSouthern Cross is used to find the direction of southNorthwestern Hawaiian Islands Marine National Monument - OnJune 15, 2006, The President of the United States declared theNorthwestern Hawaiian Islands a National Monument, enabling nearly140,000 square miles of the Northwestern Hawaiian Islands to receive theNation's highest form of marine environmental protection. The monumentwill preserve access for Native Hawaiian cultural activities; provide forcarefully regulated educational and scientific activities; enhance visitationin a special area around Midway Island; prohibit unauthorized access tothe monument; phase out commercial fishing over a five-year period; andban other types of resource extraction and dumping of waste. This marinenational monument is the largest single area dedicated to conservation inthe history of the United States and the largest protected marine area inthe worldnot evaluated - a species or other taxon whose conservation status inthe wild has not been evaluatednotch - an indentationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (17 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanotochord - a flexible rodlike structure that forms the supporting axis ofthe body in the lowest chordates, (e.g., tunicates and lancelets) andlowest vertebrates (e.g., lampreys), and in the embryos of all highervertebrates, where it is replaced by the vertebral column; a prime definingcharacteristic of the phylum Chordatanotopodium - a lobe of the parapodium closer to the dorsal side inpolychaete wormsnotum - the dorsal portion of an arthropod's thoracic segmentnowCOAST - a web mapping portal that provides spatially referencedlinks to thousands of real-time coastal observations and NOAA forecasts ofinterest to the marine community. The portal serves as a "one-stop"website to real-time coastal meteorological, oceanographic, andhydrologic observations from a variety of Internet sites within and outsideof NOAA, along with NOAA forecasts. NowCOAST is designed as a planningaid for recreational and commercial mariners, coastal managers, HAZMATresponders, marine educators, and researchers, who can discover anddisplay real-time information for their particular needs and geographicarea of interest. NowCOAST covers all U.S. coastal waters including theGreat Lakes; NowCOAST URL: http://nowcoast.noaa.gov/NOWRAMP (Northwestern Hawaiian Islands Coral ReefAssessment and Monitoring Program) - a multi-agency, multi-yeareffort that began in 2000. NOWRAMP's objective is to rapidly evaluate andmap the shallow water reef habitats in the NWHI. The agencies whichcontribute to NOWRAMP are: NOAA, the U.S. Fish and Wildlife Service, theState of Hawai‘i Department of Land and natural Resources, the Universityof Hawai‘i, the Bishop Museum, the Hawai‘i Maritime Service, the U.S.National Park Service, and scientists from the University of California atSanta CruzNPDES (National Pollutant Discharge Elimination System) - aprovision of the Clean Water Act (CWA) which prohibits discharge ofpollutants into waters of the United States unless a special permit isissued by EPA, a state, or where delegated, a tribal government on anIndian reservationnuchal - pertaining to the necknuchal organ - a sense organ on upper side of head in manybranchiopods; photoreceptor-like sensory cells in the nuchal region(posterodorsal region of the head) of some cephalopods; pairedchemosensory structures in some annelidsnuclear family - a monogamous mating pair where both male andfemale partner share in caring for the eggs and younghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (18 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanuclease - one of the several classes of enzymes that degrade nucleicacid; an enzyme that can degrade DNA or RNA by breakingphosphodiester bonds that link adjacent nucleotidesnucleic acid - a large molecule found in biological cells composed ofnucleotide subunitsnucleic acid isolation - a prerequisite for molecular genetic studies is,by definition, the ability to isolate nucleic acids (DNA and RNA)nucleoprotein - a conjugated protein composed of nucleic acid andprotein; chromosomes are composed of nucleoproteinsnucleoside - a nucleotide without the phosphate group; a purine orpyrimidine base linked to ribose or deoxyribosenucleosome - the basic unit of eukaryotic chromosome structure; a ballof eight histone molecules wrapped around by two coils of about 220 basepairs of DNAnucleotide - one of the structuralcomponents, or building blocks, of DNA andRNA. A nucleotide consists of a base (oneof four nitrogenous bases: adenine,thymine, guanine, and cytosine) plus amolecule of sugar and one of phosphoricacidDiagram of DNA showsnucleotide structure.(Diagram: NIH/HumanGenome Project)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (19 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanucleus - a central cell structure thatcontains the chromosomes, and as such,controls the activities of the cell; the centerof an atom, containing protons, neutrons,and most of the massA cell with a large centralnucleus. The dark masswithin the nucleus are thechromosomes.nudibranch - a opisthobranchiate mollusk(sea slugs), having no shell except whilevery young. The gills are naked andsituated upon the back or sidesA Pacific nudibranch.(Photo: Dr. Bill Rudman)null hypothesis (Ho) - the statistical hypothesis that states that thereare no differences between observed and expected data. The nullhypothesis is used in experimental research. It asserts arbitrarily thatthere is no relationship among the variables being studied. Then statisticaltests are used to determine if any relationship shown by the research datais due to chance alone or to alternative hypothesesnumerical prediction model - a computer program designed torepresent, in mathematical terms, processes that occur in naturenumerical taxonomy - study of the relationships of taxa by theapplication of numerical similarity values to characters so as to rank intocategories based on degree of overall similarityhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (20 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datanumericlature - an attempt to express the natural order (i.e.classification) of organisms in numbers, so that each taxon name isrepresented by a numerical code, the structure of which indicates itstaxonomic position, rank and affinitiesnuptial - a term associated with reproductive or breeding behavior, e.g.,nuptial coloration, nuptial tubercles (in fishes)NURP (NOAA National Undersea Research Program) - a uniquenational service that provides undersea scientists with tools and expertisethat they need to work in the undersea environment. Each year, theprogram supports 200 or more undersea research projects related toNOAA's mission as steward of oceanic resources and environments. A keystrength of NURP is its partnership with the nation's science community,carried out primarily through six regional NURP Centersnursery - an area favored for birth or egg deposition and where juvenilesand immature members of a community feed and grow. For example,mangrove root areas serve as nursery grounds for many coral reef fishesnutrient - any substance assimilated by organisms that promotes growth.Marine scientists typically measure nitrites, nitrates, phosphates, andsilicates as nutrients for plant growthnutrient cycle - the cyclic conversion of nutrients from one form toanother within biological communitiesnutrient cycling - all the processes by which nutrients are transferredfrom one organism to another. For instance, the carbon cycle includesuptake of carbon dioxide by plants, ingestion by animals, and respirationand decay of the animalnutrient pollution - contamination of water resources by excessiveinputs of nutrients. In surface waters, excess algal production is a majorconcernnutrient regeneration - the release of nutrients from organic matter bydecomposer organismsNWHI (Northwestern HawaiianIslands) - the Northwestern HawaiianIslands (NWHI) are a chain of small islands,atolls, submerged banks, and reefsbeginning approximately 120 nautical mileswest of the main Hawaiian islands, andstretching northwest for more than 1,079nautical miles or 2,000 kilometers. Thisvast archipelago is uninhabited (except forMidway Island) and is surrounded by someof the most extensive and pristine coralhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (21 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef Datareefs in U.S. waters. On June 15, 2006,President George W. Bush declared theNorthwestern Hawaiian Islands a NationalMonument, creating the largest protectedmarine reserve in the worldGraphic showing locationof Northwest HawaiianIslandsNWHI Coral Reef Ecosystem Reserve -the Northwestern Hawaiian Islands CoralReef Ecosystem Reserve was established byExecutive Order 13178 in December 2000,and January 2001(Executive Order 13196).It was established to conserve and protectthe NWHI coral reef ecosystem and relatednatural and cultural resources of the areaReference map of theNorthwestern HawaiianIslands EcosystemReserve. (1) Nihoa Island,(2) Necker Island, (3)French Frigate Shoals, (4)Gardner Pinnacles, (5)Maro Reef, (6) LaysanIsland, (7) LisianskiIsland, (8) Pearl andHermes Atoll, (9) KureAtoll, (10) The First Bankimmediately east ofFrench Frigate Shoals,(11) Southeast BrooksBank (the first bankimmediately west ofFrench Frigate Shoals),(12) St. Rogatien Bank,(13) The First Bankimmediately west of St.Rogatien Bank, (14) RaitaBank, and (15) PioneerBank. (Graphic: NOAA)(Top)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (22 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataRevised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=n (23 of 23) [2/26/2008 9:14:44 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: OThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZOak Foundation - a group of charitable and philanthropic organizationsestablished in various countries. The Oak Foundation commits itsresources to address issues of global social and environmental concern,particularly those that have a major impact on the lives of thedisadvantaged. It’s marine environment program focuses on three mainareas: the Mesoamerican reef ecosystem; European marine conservation;and Bering Sea and North Pacific conservationOBIS (Ocean Biogeographic Information System) - the marinecomponent of the Global Biodiversity Information Facility. It links marinedatabases around the world to provide an internet accessible, dynamicinterface for comparing species level, geo-referenced biodiversity data inrelation to ocean habitats. All Census of Marine Life (CoML) field projectdata will be managed in and accessible through OBIS (www.iobis.org)obligate mutualism - a mutualistic relationship where one speciescannot survive without the presence of the otherobligatory - obligate or required. For example, an obligatory cleaner fishrelies entirely on this feeding mode to obtain nutrients; opposite offacultativeoblong - elongated (stretched) from a square or circular shapeobservational learning - a learning process where an animal learns bycopying the behavior of other animalshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (1 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef Dataobserving system - a collection of one or more sensing elements(human and/or instrument) that reside on fixed or mobile platforms;directly or indirectly measuring environmental parameters on a definedbasis meeting data user objectivesobtuse - blunt or rounded at the endocean - the salt water surrounding the great land masses, and divided bythe land masses into several distinct portions, each of which is called anocean; the entire body of salt water that covers more than 70 percent ofthe earth's surface. There are five oceans: the Pacific, Atlantic, Indian,Arctic and Antarctic (Southern Ocean)ocean acidification - the decrease in the ocean's pH and the resultingincrease in acidity as the oceans absorb carbon dioxide released into theatmosphere by human activitiesocean color - a term that refers to thespectral dependence of the radiance leavinga water bodySeaWiFS (Sea-viewingWide Field-of-view Sensor)ocean color image ofchlorophyll-a in the Gulf ofMexico.ocean color sensor - an instrument forthe remote sensing of ocean color, usuallyfrom aircraft or satelliteThis SeaWiFS (SeaviewingWide Field-of-viewSensor) is an ocean colorsensor.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (2 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef DataOcean.US - Ocean.US, the National Office for Integrated and SustainedOcean Observations, was established by the Congressionally-createdNational Oceanographic Partnership Program (NOPP). Since itsestablishment on 2000, Ocean.US has catalyzed the coordinateddevelopment of an Integrated Ocean Observing System (IOOS), the U.S.contribution to a Global Ocean Observing System (GOOS) and to theGlobal Earth Observation System of Systems (GEOSS). Ocean.US is afederal interagency office supported by ten agenciesOceania - a region of the world that usually includes Australia, NewZealand, and Pacific Ocean islands, such as Micronesia, Melanesia andPolynesiaoceanic - associated with sea-water environment seaward of the shelfslopebreakoceanic crust - that part of the Earth's crust underlying the oceanbasins. It is composed of basalt and has a thickness of about 5 kmoceanic island - an island in the ocean formed by breaking away from acontinental landmass, volcanic action, coral formation, or a combination ofsourcesoceanic reef - a reef that develops adjacent to deeper waters, often inassociation with oceanic islandsoceanic zone - the pelagic marine environment beyond the shelf-slopebreak with a depth greater than 200 moceanodromous - used to describe organisms that migrate only withinthe ocean, usually from spawning grounds to feeding groundsoceanography - the study of the earth's oceans and their interlinkedecosystems and chemical and physical processes. There are five majordivisions within the science: physical oceanography, chemicaloceanography, biological oceanography, geological oceanography, andmeteorological oceanographyocellus - an eye-like spot, usuallysurrounded with a ring of a lighter color, e.g. the ocellus toward the caudal peduncleof some butterflyfish. It may function todeflect attacks to the eyes in agonisticencounters.Ocelli are also present in otheranimal groups, especially insectsThese butterflyfish have aprominent ocellus (pl.ocelli), which may serve todeflect predator attacksfrom the head region ofhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (3 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef Datathe fish.ochre - yellowish or yellow-brown colorOctocorallia - a subclass of the Anthozoathat contains the sea pens, sea pansies,sea fans, whip corals, and pipe corals.Octocorals always possess 8 tentacles and8 complete septa (hard corals andanemones possess 12 or more tentaclesand septa). They are colonial cnidarianswhose polyps are connected by a tissuemass called the coenenchyme. This tissueconnects the gastrovascular (digestive)cavities of all the polyps in the colonyAn octocorallian (sea fan)with brain coral(sceractinian) in theforeground.octopus - in scuba, a backup second stage regulator connected to thefirst stage, intended for the benefit of other scuba divers in case their airsupply should fail. It is the alternate air source that forms the basis for the"buddy" systemocular - pertains to the eyeOculina Banks - a series of deepwatercoral pinnacles and ridges, 15 to 30 milesoff the east coast of Florida, extending fromFt. Pierce to Cape Canaveral. Formed by asingle species of coral, the Ivory TreeCoral, Oculina varicosa, they form pinnaclesof up to 100 feet tall, growing below theGulf Stream at depths of approximately 70to 100 meters. This is a slow-growing,branching coral often associated with highbiodiversity because they provide idealhabitats and spawning sites for numerousspecies of fishes and invertebratesThe Oculina Banks aredeep water coral reefsoccurring along the shelfedge off the central eastcoast of Florida. TheOculina varicosa habitathosts a diverse array ofmacroinvertebrates andfishes. The habitat alsocomprises significantspawning grounds foreconomically importantspecies of reef fishes.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (4 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef DataOculina varicosa - an important deep water coral reef-building speciesthat forms thickets of large branched colonies along the eastern Floridashelf. O.varicosa is restricted to the western Atlantic, including theCaribbean and Gulf of Mexico, Florida to North Carolina and Bermuda. Thedeep-water Oculina reefs, however, are only known off the east coast ofcentral Florida at depths of 70-100 modontophore - a tooth-bearing structure found in most mollusks, exceptbivalves. It consists of several muscles and a cartilage which support theradula and radula sac; the term is also applied to the radula aloneoff-reef - a synonym of reef slopeOffice of Insular Affairs (OIA) - The Office of Insular Affairs (OIA)carries out the Secretary of the Interior s responsibilities for the insularaffairs. OIA coordinates Federal policy in the territories of AmericanSamoa, Guam, the U.S. Virgin Islands, and the Commonwealth of theNorthern Mariana Islands. With the majority of U.S. coral reefs located inthe insular areas, OIA plays an important role in improving themanagement and protection of the Nations coral reefs. OIA also providestechnical and financial assistance to the Federated States of Micronesia,the Republic of the Marshall Islands, and the Republic of Palau whichshare financial, diplomatic and military ties with the United States througha special relationship known as the Compact of Free Association. Thefreely associated states have some of the richest coral reef resources inthe world and some of the oldest and most effective traditionalmanagement systemsofficial index - in taxonomy, a list of names or works suppressed ordeclared invalid by action of the International Commission on ZoologicalNomenclatureofficial list - in taxonomy, a list of names or works which have beenconserved or declared valid by action of the International Commission onZoological Nomenclatureoffshore current - any current flowing away from shoreoffshore wind - a wind blowing seaward from the land in the coastalarea.olfaction - the sense of smellolfactory - pertaining to the sense of smell (olfaction)oligo - a prefix meaning "few"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (5 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef Dataoligomer - a molecule of intermediate relative molecular mass, thestructure of which essentially comprises a small plurality of units derived,actually or conceptually, from molecules of lower relative molecular mass;a polymer that consists of two, three, or four monomersoligonucleotide - a short sequence (usually 2-50 bases) of DNA.Oligonucleotides of up to 30 bases are routinely synthesized for use asPCR primers or as probes for their sequence compliments in a complexmixture of DNAoligopeptide - a peptide which consists of a small number of amino acidslinked together, as opposed to a polypeptideoligosaccharide - a carbohydrate which consists of three to tenmonosaccharide molecules joined by glycosidic linkagesoligotrophic - refers to water bodies with low concentrations of nutrientsomega animal - in animal behavior, the animal which has the lowestsocial rank in its linear hierarchical groupomega-conotoxin MVIIA - a marine pharmaceutical extracted from thecone snail, Conus magnus. It is a potent pain-killer (analgesic) which actsby interfering with calcium ion flux, thereby reducing the release ofneurotransmittersomegoid - horse shoe-shapedomnivore - an organism whose diet consists of a wide variety offoodstuffs, including plants and animalsoncogene - a gene thought to be capable of causing canceroncology - the science dealing with the physical, chemical and biologicalproperties and features of cancer, including the causes and progression ofthe diseaseone-gene--one-polypeptide hypothesis - the concept that one gene inDNA codes for a sequence of amino acids in a specific polypeptideonline - a general term for when one computer is interacting directly withanother computerhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (6 of 17) [2/26/2008 9:14:47 AM]

Discover NOAA's Coral Reef DataOnline Positioning User Service (OPUS) - OPUS provides GlobalPositioning System (GPS) users, such as scientists, engineers, andprofessional surveyors, the ability to obtain highly accurate positioningcoordinates for the purposes of transportation, construction, navigation,surveying, and other activities. OPUS allows GPS users to submit theirGPS data files via the Internet to NOAA, where the data are processed todetermine a position using NOAA’s computers, software and nationalcoordinate system. OPUS is managed and operated by NOAA's NationalGeodetic Survey (NGS), which defines and manages a national coordinatesystem. This network, the National Spatial Reference System (NSRS),provides the foundation for transportation and communication; mappingand charting; and a multitude of scientific and engineering applicationsonomatophore - in taxonomy, a specimen which acts as the namebearer; a nomenclatural type (holotype, syntype, lectotype, neotype)onshore - a direction landward from the seaonshore wind - a wind blowing landward from the sea in the coastal areaontogenesis - the entire development of an individual organism fromfertilization to completion of its life historyontogeny - the development, growth, and maturation of an individualoocyte - a female gametocyte that develops into an ovum after twomeiotic divisions; the female reproductive cell, also called an egg or ovumooecium - a brood chamber for developing embryos in the Ectoprocta(bryozoans); one of the special zooids of ectoprocts destined to receiveand develop ova; an ovicell.oogamous - characterized by reproducing by the fusion of small motilemale gametes and large nonmotile female gametesoogamy - the union of a large nonmotile egg with a small motile ornonmotile male sperm celloogenesis - the process of ovum (egg) development in female animals,in which the diploid number of chromosomes is reduced by half to thehaploid number in the ovumoolitic limestone - rock composed primarily of petrified corals or theskeletons of other calcareous animalsopen circuit scuba - a diving apparatus in which exhaled air is expelledinto the water as bubbles; no part is rebreathed by the diver. It is mostcommonly used in recreational scuba divinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (7 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataopen circulatory system - a circulatory system, characteristic of someinvertebrates, e.g., arthropods, in which blood flows through aninterconnected system of open sinuses rather than blood vessels. Thetissues and cells are directly bathed by the blood for gaseous exchangeand nutrient uptake. The circulatory fluid is called the hemolymphopen coast - an unenclosed and exposed coastal marginopen sea - that part of the ocean that extends outward from thecontinental shelfopen system - a system that exchanges energy and matter with itsenvironmentOPeNDAP (Open-source Project for a Network Data AccessProtocol) - OPeNDAP is a framework that simplifies all aspects ofscientific data networking, allowing simple access to remote data.OPeNDAP provides software which makes local data accessible to remotelocations regardless of local storage format by using OPeNDAP servers.OPeNDAP also provides tools for transforming existing applications intoOPeNDAP clients (i.e., enabling them to remotely access OPeNDAP serveddata); a protocol for requesting and transporting data across the web. Thecurrent OPeNDAP Data Access Protocol (DAP) uses HTTP to frame therequests and responses; a community of users working together to use,improve, and extend the OPeNDAP protocol and software; AlthoughOPeNDAP was originally designed and developed by oceanographers andcomputer scientists for oceanographic data, there is nothing in the designof OPeNDAP that constrains its use to oceanography. It has been adoptedby the High Altitude Observatory community and is being considered bysegments of the meteorological and space science communities;previously known as "DODS"operant conditioning - a learning process where an animal learns byconnecting its own behavior with a response from its environmentoperational taxonomic unit (OTU) - a terminal taxon; a group oforganisms used in a taxonomic study without designation of taxonomicrankoperator gene - a region of the chromosome, adjacent to the operon,where a repressor protein binds to prevent transcription of the operonopercular spine - in fishes, a spine projecting from the operculum (gillcover)operculate - having an operculumhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (8 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataoperculum - a lid or flap covering anaperture, such as the gill cover in mostbony fishes; the gill cover; also the hornylid closing the aperture of various species ofmollusksA ventral view of the gillchamber and opercularchamber of a fish. Notethe gill (branchial) arches,each with a large numberof gill filaments. (Photo:University of California atDavis)operon - a sequence of genes responsible for synthesizing the enzymesneeded for biosynthesis of a molecule. An operon is controlled by anoperator gene and a repressor geneophiopluteus larva - larva of a brittle star (phylum Echinodermata)opisthobranch - a marine gastropod, many of which have lost or reducedtheir shell, mantle and gillsopisthosoma - a short, posterior multi-segmented region of avestimentiferan polychaete tube worm. The anterior segments of theopisthosoma have rows of hook-like structures that act as anchors for theworm to retract into the tubeopportunistic feeder - a species adapted for utilizing variable,unpredictable or transient environments to obtain foodoptical oceanography - the subdiscipline of oceanography concernedwith the propagation and interaction of radiation, typically at wavelengthsbetween about 350 and 750 nm, with seawateroptimum - a state that is the best fit for the current situation. All minorchanges make the situation worse; in biology, it is the level of someenvironmental factor, within a species' or population's tolerance range, atwhich the species or population can function most efficiently or with thegreatest positive effect to its physiological or reproductive fitnesshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (9 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataoral - pertaining to the mouthThe oral surface of somesea urchins. The centralopening is the mouth.oral cavity - the cavity within the mouthoral disc - the area around the mouth of an anthozoan polyp that bearsfrom eight to several hundred tentaclesoral pinnule - arms of feather stars (Echinodermata-Crinoidea) bearnumerous pinnately arranged branches called "pinnules ." Those pinnulesclosest to the disk are the proximal, or oral pinnules. They are larger thanother types of pinnules and respond to mechanical stimulation. Theyguard the disk and can arch over it and almost completely cover it. Theydo not have ambulacra or tube feet. A few pairs of oral pinnules are at thebase of each arm. Moving distally from the disc are the genital pinnuleswhich contain the gonads, followed by the the distal pinnules whichoccupy the outer end of the arm. They are the major feeding structuresand always have ambulacra and tube feetorbit - a bony or cartilaginous eye socketorder - a taxonomic group containing one or more familiesorgan - a collection of tissues which performs a particular function or setof functions in an animal's body. Organs are composed of tissues, andmay be organized into larger organ systemsorgan system - collection of organs which have related roles in anorganism's functioning. The nervous system, circulatory system, andmuscle system are all organ systemshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (10 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataorgan-pipe coral - the organ-pipe coral,Tubipora musica, is a reef-building(hermatypic) octocoralThe organ-pipe coral, areef-building octocoral.(Photo: A. Bruckner,NOAA)organelle - a structurally discrete component of a cell, e.g., the nucleusor a mitochondrionorganic - refers to those substances produced by the metabolism of aliving organism, especially carbon-containing compoundsorganic act - the body of laws that the United Congress has enacted forthe government of a United States insular area; it usually includes a bill ofrights and the establishment and conditions of the insular area's tripartitegovernmentorganic enrichment - the addition of nutrients from organic matterorganic molecule - a molecule that contains one or more carbon atomsorganically polluted - made unfit for living organisms by excess additionof organic matterorganism - any form of unicellular or multicellular life; a living thing thathas (or can develop) the ability to act or function independentlyorganized territory - a United States insular area for which the UnitedStates Congress has enacted an organic actorganogenesis - the process of formation of specific organs in a plant oranimal involving morphogenesis and differentiationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (11 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataorganophosphate - organophosphate compounds are a diverse group ofchemicals used in both domestic and industrial settings. Examples includeinsecticides, nerve gases, ophthalmic agents, and antihelmintics.Organophosphate pollution may adversely effect coral healthorientation - the way an organism positions itself in relation toenvironmental cues; the ability of an animal to be aware of itsenvironment and its position within that environment with reference totime and spaceoriginal description - in taxonomy, the description of a taxonomic groupwhen first establishedoriginal diagnosis - in taxonomy, a formal statement of characterswhich distinguish a taxon from other similar or closely related taxa,published at the time of proposal of a new taxonomic nameoriginal spelling - in taxonomy, the spelling of an available name whenfirst published. The original spelling of a name is to be kept as the "correctoriginal spelling" unless it does not meet the requirements of theInternational Code of Zoological Nomenclature. An incorrect originalspelling is an original spelling that is incorrect. Multiple original spellingsare two or more different original spellings for the same nameornamental - a non-food species that is produced and maintained solelyfor exhibit purposes in home or public aquaria, or in ornamental gardenpondsornithology - the scientific study of birdsA white tern from LaysanIsland, HawaiianArchipelago. (Photo:NOAA)oroidin - a cytotoxic family of alkaloids isolated from sponges whichpossesses anti-tumor propertieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (12 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataorphan receptor - a potential receptor gene identified on the basis ofnucleotide sequence similarities with known steroid hormone receptorsortholog - a gene found in different species that evolved from a commonancestral gene by speciation. Normally, orthologs retain the same functionin the course of evolutionorthologous genes - genes that have evolved directly from an ancestralgene. This is in contrast to paralogous genes; two genes are to beorthologous if they diverged after a speciation event, i.e., if a gene existsin a species, and that species diverges into two species, then the copies ofthis gene in the resulting species are orthologousorthology - homology (similarity of features based on common descent)that arises via speciationoscillation - any steady back and forth movementsoscillator - the internal biological clock mechanism that produces ameasurable biological rhythm in an organismosculum - a large opening through whichwater flows out of a sponge. Sponges mayhave more than one osculumDistinct osculi of someCaribbean sponges.(Photo: Copyright DigitalStock Corp.)osmole (Osm) - a unit of osmotic pressure used in cell biology andphysical chemistry. One osmole is the osmotic pressure of a one molarsolution (a solution with a concentration of one mole per liter of solvent)of a substance that does not dissociate, such as glucose, in water. Inpractice, most measurements are in milliosmoles (mOsm)osmoregulation - the process of controlling the amount of water intissues and cellshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (13 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataosmosis - the passage of water through a semipermeable membranefrom a solution with a lower concentration of solute to one with a higherconcentration of soluteosmotic pressure - the pressure that is needed to counteract theosmotic passage of water molecules across a semipermeable membraneinto the more concentrated soluteosmotroph - an organism that obtains nutrients through the activeuptake of soluble materials across the cell membraneosseus - bonyossicle - one of numerous small calcareous structures that form theexoskeleton of certain echinoderms. Their size,shape and location arehighly variable, and they may be movable or fixed in position. They mayappear as thin fused plates. In brittle stars they form "vertebrae" in thearms, which with together with their attached muscles, gives the brittlestar its serpentine ophiuroid motion. Sea cucumbers hve microscopicossicles embedded in their dermis. The small, sound transmitting bones inthe vertebrate middle ear are also called 'ossicles'ossified - made or converted into boneostium - in sponges, a microscopic pore through which water enters thesponge bodyostracitoxin - a toxin, discharged with mucus into the water, bytrunkfishes of the genus Ostracion when they are stressedotolith - a calcareous structure of the innerear of some animals, such as fishes, thatfunctions in the detection of changes ingravitational forces relative to orientation.Otoliths are used to determine the age offishes by counting the number of annualrings depositedA section of an otolithfrom an early life stagefish. Growth rings arecounted and a daily age isdetermined, thisinformation can be appliedto understanding theeffects of changes in theenvironment on growthand survival. (Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (14 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataoutbreak - the sudden appearance of a disease in a specific geographicarea or populationoutbreak - a sudden appearance or increase in something, such as anoutbreak of a particular disease in a coral communityoutcrop - an exposure of bedrock that can be seen on the surface, i.e.,that is not covered by soil or waterouter slope - a synonym of reef slope. It is sometimes used to representthe lower reef slopeoutfall - the place where a sewer, drain, or stream dischargesoutlying area - the term 'outlying area' refers to the United States VirginIslands, Guam, American Samoa, and the Commonwealth of the NorthernMariana Islands. It also may include the freely associated states of theRepublic of the Marshall Islands, the Federated States of Micronesia, andthe Republic of Palauoutrigger - a floatation device attached to one or both sides of the hull ofa boat to help prevent a capsizeoverexploitation - the removal of individuals or biomass from apopulation at a rate greater than the population is able to compensate forwith its own recruitmentoverfishing - a level of fishing effort or fishing mortality such that areduction of this level would, in the medium term, lead to an increase inthe total catch; harvesting at a rate greater than the population cansustainoverwash - a deposit of marine-derived sediments landward of a barriersystem, often formed during large storms; transport of sediment landwardof the active beach by coastal flooding during a tsunami, hurricane, orother event with extreme wave actionovicell - the brood chamber of a bryozoan (Ectoprocta), usually located atthe distal end of the maternal zooid. Embryos are brooded until theydevelop into non-feeding larvae, which swim briefly, then settle andmetamorphose to found a new colonyovigerous - carrying eggs or modified for carrying eggsoviparity - the reproductive mode where eggs are released from the bodyand later hatchhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (15 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataoviposition - the process of depositingeggsA marine turtledepositiong eggs(oviposition) on a tropicalbeach. (Photo: SeaturtlePreservation Society ofBrevard County, FL)ovoid - egg-shapedovoviviparity - the reproductive mode where the eggs hatch and developin the female's reproductive tract (or a specialized pouch in the males ofsome species), are not nourished in any way by the female, and are freeswimmingwhen released from the parentovulation - the release of an egg from the ovaryovum - the mature female germ cell (egg; female gamete)oxidant - an oxidizing agentoxidation - the combination of a substance with oxygen. Oxidation canalso describe a type of reaction in which the atoms in an element loseelectrons and the valence is correspondingly increasedoxidative stress - a process whereby the metabolic balance of a cell isdisrupted by exposure to environmental substances, resulting in theaccumulation of free radicals, which can damage components of cells'membranes, proteins or genetic material by "oxidizing" themoxygen isotope ratio (18O) - an expression for the ratio of the 18 O to16 O atoms in a sample relative to a standard, defined as: δ 18 O = ( 18 O/ 16 Osample - 18 O/ 18 O standard)/ 18 O/ 16 O standardoxygen isotopes - oxygen atoms that have the same atomic number(protons) but different mass numbers (and different numbers ofneutrons). The two stable isotopes of oxygen are 16 O and 18 Ooyster reef - a dense, highly structured community of individual oystersgrowing on the shells of dead oystershttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (16 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef Dataozone - a gaseous molecule that contains three oxygen atoms (O3),instead of the usual two (O2). Ozone can exist either high in theatmosphere (stratosphere), where it shields the Earth against harmfulultraviolet rays from the sun, or close to the ground (troposhere), where itis the main component of smog. Ground-level ozone is a product ofreactions involving hydrocarbons and nitrogen oxides in the presence ofsunlight. Ozone is a potent irritant that causes lung damage and a varietyof respiratory problemsozone shield - the ozone (O3) layer in the stratosphere that givesprotection to the Earth's surface because of intense absorption of harmfulsolar ultraviolet radiation by the gas(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=o (17 of 17) [2/26/2008 9:14:48 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: PThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZP-value - in a statistical hypothesis test, the P value is the probability ofobserving a test statistic at least as extreme as the value actuallyobserved, assuming that the null hypothesis is true. This probability isthen compared to the pre-selected significance level of the test. If the Pvalue is smaller than the significance level, the null hypothesis is rejected,and the test result is termed significant; the significance of a statisticaltest. P-values of less than 0.05 are generally considered to be an indicatorthat a statistical model is significant; a quantitative estimate of theprobability that the observed difference between two groups could havehappened by chance alonePacific Plate - the largest of the tectonic plates of the earth's crust. ThePacific Plate comprises most of the rock beneath the Pacific Ocean andcontains the hot spot that has formed the Hawaiian IslandsPADI ( Professional Association of Diving Instructors ) - the world'slargest scuba diving certification agencypaedogenic - sexual reproduction by larval or immature formspaedomorphosis - phylogenetic retention of juvenile or larval charactersin the adulthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (1 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapaedomorphy - the retention of juvenilefeatures in an adult organismCope's giant salamander(Dicamptodon copei) is anexample of paedomorphy.The adult retains thejuvenile external gills.(Photo: U.S.D.A. ForestService)paedophagous - larvae or embryo eating; larvivorouspage precedence - in taxonomy, when two names for the same taxonare first published in the same publication, the one which appears on theearlier page has precedencePAH (polycylic aromatic hydrocarbon) - a class of stable organicmolecules made up of only carbon and hydrogen. These molecules arehighly carcinogenic, but also very common in the enviropnment. PAHs areformed during the incomplete burning of coal, oil and gas, garbage, andother organic substances, such as tobacco or even charcoal broiled meat.PAHs enter water through discharges from industrial and wastewatertreatment plants or through the release of boat engine exhausts.Ultraviolet light (UV) transforms the PAHs into toxic forms that killcrustaceans, polychaetes, and coral larvaepair bond - the temporary or permanent association formed between afemale and male animal during courtship and mating. Pair bonding ischaracteristic of monogamous speciespaired fins - the pectoral and pelvic fins offishesNote the paired fins onthis Townsend angelfish.The pelvic fins (and pelvicgirdle) are in the thoracicposition. (Photo: Jackiehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (2 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataReid, NOAA)Palancar Reef - a Caribbean coral reef located on the southwest side ofthe Mexican island of Cozumel, off the Yucatan Peninsula. Palancar Reef ispart of the Mesoamerican Reef systempalate - roof of the mouth cavitypalatine - a bone in the roof of the mouth of fishes. The palatine iscartilaginous in some primitive bony fishespaleobiogeography - the distribution of organisms as revealed by thefossil recordpaleoclimatology - the study of past climates throughout geologicalhistory, and the causes of the variations among thempaleoecology - the study of therelationship of extinct organisms or groupsof organisms to their environmentsA paleoecolgicalmicrofossil, this rotifer(Callindina angusticollis) isfrom the Beringia region ofthe Arctic. (Photo: WendyEisner)paleoenvironmental proxy - an environmental remnant of the past(pollen grains, tree rings, lake sediments, pack rat middens, ice cores,coral skeletons) used to assist researchers in deciphering past climaticconditionspaleopathology - the study of sickness, injuries and other abnormalitiesin the health of ancient organismspaleothermometer - a proxy that provides absolute estimates of pasttemperature. An example is the Sr/Ca ratio found in coral skeletonsPaleozoic - an era of geologic time lasting from 570 to 245 million yearsagohttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (3 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapaliform crown - a circle of paliform lobes that surround the columellapaliform lobe - an upright skeletal rod or plate at the inner margin ofsepta formed by upward growth of the septumpallial - of or pertaining to a mantle, especially to the mantle of molluskspallial chamber - the cavity enclosed by the mantle in molluskspallial line - a linear impression whichmarks the attachment of the mantle on theinner surface of a bivalve shellOne side of a bivalve shellshowing muscle scars,pallial line created by themantle, hinge and hingeteeth. (Graphic: Biodidac)palmata zone - the region of a reef crestof a bank or barrier reef that is closest tothe water surface. It is composed almostcompletely of elkhorn coral (Acroporapalmata) in the CaribbeanAcropora palmata in ashallow reef zone.palmate - hand-shapedpalolo - a polychaete worm (Palola viridis)that burrows in the coral reefs of somePacific Islands. Just before the last quarterof the moon in October and November,they swarm and breed in vast numbers atthe sea surface. They are gathered andhighly esteemed as food by the islanders.An allied species inhabits the tropicalAtlantic and swarms in June or Julyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (4 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataThe portion containing thereproductive gametes (theepitoke) of the paloloworm, Palolo viridis, isconsidered a delicacy inSamoa and other Pacificislands. (Photo:Smithsonian Institution)palus - one of several upright slender calcareous processes whichsurround the central part of the calicle of certain corals; vertical radiallyarranged plates forming one or more cycles between the septa and thecentral axis in the scleractinian skeletonpalustrine - pertaining to swamps ormarshy habitatsPalustrine habitat in theJobos Bay NationalEstuarine ResearchReserve. (Photo: NOAA)palynology - the scientific study of pollen, pollen stratigraphy,paleobotany, and paleoclimatology of plantshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (5 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapalytoxin - an extremely powerfulneurotoxin naturally found within thebodies of certain soft corals in the genusPalythoa (family Zoanthidae)a soft-bodied hexacoral,Palythoa sp, fromAmerican Samoa. Theextremely potent toxin,palytoxin, has beenisolated from Palythoa spfrom Hawaii. (Photo:National park Service/EvaDiDonato)pan-tropical - throughout the tropicspandemic - an epidemic that is geographically widespread; occurringthroughout a region or even throughout the worldPangea - a supercontinent that existed from about 300 to 200 millionyears ago. It included most of the continental crust of the Earthpanmictic - refers to random-mating populations; one in which allmembers are equally likely to interbreedpanmixis - random mating in a populationPapahanaumokuakea - Hawaiian name for the Northwestern HawaiianIslands Marine National Monument. It refers to Hawaiian genealogy andthe formation of the Hawaiian archipelago. The name was adoptedthrough consultation with the Native Hawaiian Cultural Working Group,whose members have a longstanding interest and involvement in theregion and come from relevant backgrounds including academic scholars,teachers, cultural practitioners, community activists, and resourcemanagersPapahanaumokuakea Marine National Monument - the Hawaiianname for the Northwestern Hawaiian Islands Marine National Monumentpapilla - a raised bump or nipple-like projection on a tissue surface; acellular outgrowth. Papillae have the appearance of little bumps or fingerson the surface of cellspapilliform - slender, elongate and pointedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (6 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapapilliform - nipple-shapedpapillose - covered with papillaePapuan Bird's Head Seascape - a coastal and marine region of 183,000square kilometers (approximately 70,657 square miles) located innorthwest Papua Province of Indonesia, that stretches from TelukCenderawasih in its eastern reaches to the Raja Ampat archipelago in thewest and the FakFak-Kaimana coastline in the south. It is home to morethan 1,200 types of reef fishes and nearly 600 species of hard corals, pluswhales, sea turtles, crocodiles, giant clams, manta rays, and dugongs.Bird's Head is perhaps one of Earth's richest seascapesPAR (Photosynthetically Active Radiation) - those wavelengths oflight that can be absorbed by chlorophyll or other light harvestingpigmentspara - a prefix meaning "beside"parabolic reflector - a portable, disk-like device used to gather,magnify, and focus the sounds of birds and other organisms for thepurpose of making high-quality, electronic recordingsparadigm - a pattern or model that provides a framework for interpretingobservationsparadox - a statement that seems self-contradictory, yet maynevertheless be trueparalectotype - in taxonomy, any one of the original syntypic seriesremaining after the selection of a lectotypeparallel evolution - the development of similar forms by related butdistinct phylogenetic lineagesparalogous genes - two genes or clusters of genes at differentchromosomal locations in the same organism that have structuralsimilarities indicating that they derived from a common ancestral geneand have since diverged from the parent copy by mutation and selectionor drift. Two genes are said to be paralogous if they diverged after a geneduplication eventparamagnetism - magnetic property in certain iron-bearing mineralsthat cause them to be weakly attracted to magnetic fieldsparameter - a particular physical, chemical, or biological property that isbeing measuredhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (7 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataparapatric - pertains to the ranges of species that are contiguous but notoverlapping; adjacent but non-overlapping distributionsparapatric speciation - speciation in which the new species forms froma population contiguous with the ancestral species' geographic rangeparapatric speciation - speciation in which the new species forms froma population contiguous with the ancestral species' geographic range. Theevolution of reproductive isolating mechanisms occurred when thepopulation entered a new niche or habitat within the range of the parentspeciesparaphyletic - a group of taxa that includes an ancestral taxon but notall descendants of that taxonparapodium - one of the shortunsegmented processes located on eachside of most of the body segments in manyannelid worms. Parapodia (pl) function inlocomotion and often also as tactile orbranchial organs. In some marine snails (e.g., sea hares and pteropods) it is a broadlateral expansion of either side of the foot,forming a broad swimming organA polychaete wormshowing a pair ofparapodia per segment.Note the bristle-likechaetae borne by eachparapodium. (Photo: Dr.Anthony Picciolo)parasite - an organism that lives in or on the living tissue of a hostorganism. It gives its host nothing beneficial in return, and often isinjurious and even lethal to the hostparasitic spawning - fertilization of eggs by a subordinate male whilethe female and dominant male are spawningparataxonomist - a field-trained biodiversity collection and inventoryspecialist recruited from local areas. Parataxonomists are specialists,locally trained by professional biologists, that collect specimens, preparethem, sort them into morphospecies, and organize associated informationinto a databaseparatype - in taxonomy, every specimen in a type series, other than theholotype, which were before the author at the time of preparation of theoriginal description, and were so designated and indicated therehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (8 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataparenchyma - the primary tissue of higher plants composed of thinwalledcells that remain capable of cell division, even when mature.Parenchyma constitutes the greater part of leaves, roots, the pulp offruits, and the pith of stems. They are fundamental plant tissues asopposed to more highly differentiated tissues. In animals, the parenchymaconstitutes the essential functional part of an organ, as contrasted withthe organ's connective tissue, nerves, and blood vesselsparenchyme - in cnidarians, mesenchyme with dense cellular componentsparenchymula - a sponge larva which appears as a solid ball withexterior flagellated cells (except at the "posterior end")parent population - any population considered as the source or originfor the population under study or analysisparesthesia - abnormal neurological sensations which include:numbness, tingling, burning, prickling and hyperesthesia (increasedsensitivity); one possible symptom of ciguatera poisoningparology - homology (similarity of features based on common descent)that arises via gene duplicationparrotfish - any species of tropical bonyfishes in the family Scaridae. Parrotfishesare abundant and common inhabitants ofcoral reef communities. Their teeth arefused into a sharp "parrot-like" beak strongenough to bite off pieces of stony corals.Some parrotfishes produce an envelopingmucous envelope that surrounds andpresumably protects the body at nightParrotfish are verycommon inhabitants ofcoral reef communities(Photo: Keoki and YukoStender)parsimony - the principle that the simplest explanation, the one thatrequires the fewest hypotheses, is the one most likely to be correct; sameas Occam's Razor: the simplest of two competing theories is to bepreferredparthenogenesis - reproduction without fertilization; the development ofan unfertilized ovum, seed, or spore. It occurs naturally in several speciesand may also be induced artificially by chemical or mechanical meanspartial pressure - the pressure exerted by a single component of a gaswithin a gas mixture, or dissolved in a liquidhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (9 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataparticulate - a very small solid suspended in waterparticulate organic matter - particulate material of biological origin thatis suspended in waterpartim - in partparts per million (ppm) - number of parts of a substance found in onemillion parts of a particular gas, liquid, or solidparts per thousand (ppt) - number of parts of a substance found in onethousand parts of a particular gas, liquid, or solidparturition - the process of giving birthpassive integrated transponder (PIT) - a small microprocessorenclosed in glass which is injected into the shoulder muscle or flipper ofsea turtles as a method of identifying individuals. The PIT tag transmits aunique number to a hand held scanner when activated by the scannerpassive search - a feeding strategy where the predator remains more orless stationary and ambushes the prey animal when it comes within rangepatch - a nonlinear surface area differing in appearance from itssurroundingspatch reef - a coral boulder or clump of corals formed on a shelf, usuallyof less than 70 m depth, often in the lagoon of a barrier reef or atoll. It isunattached to a major reef structurepatchiness - the condition where organisms occur in aggregationspatchy necrosis - a disease of corals.Colonies with this condition have small (2­10 cm diameter) circular to irregularpatches of denuded skeleton that willincrease in diameter an additional 1-10 cmover a period of 5-7 days. The diseasetypically affects the top surface of elkhorncoral (Acropora palmata) branches. In mostcases most of the affected tissue diesrapidly, and subsequent enlargement of thebare skeletal areas slows after a few daysand eventually stops. A bacterium has beenidentified as a causal agentElkhorn coral with patchynecrosis in two locations(Photo: Andy Bruckner/http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (10 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataNOAA)Pathfinder - a program that focuses on the processing, reprocessing,maintenance, archiving, and distribution of existing Earth science datasets to make them more useful to researchers. NASA, NOAA, and USGSare involved in specific Pathfinder effortspathogen - an organism which causes a disease within another organismpathogenesis - the origin and development of diseasepathogenicity - the quality of producing or having the ability to producepathologic changes or diseasepathognomonic - a sign or symptom that is so characteristic of adisease, and not found in any other condition, that it makes the diagnosispatronym - a taxonomic name derived from the name of a personpavement - rock exposed at the Earth's surface in the form of a more orless horizontal surface, usually with crevices or jointsPCR (polymerase chain reaction) - a method of creating copies ofspecific fragments of DNA. PCR rapidly amplifies a single DNA moleculeinto many billions of moleculespdf (portable document format) - a file format created by Adobe,initially to provide a standard form for storing and editing printedpublishable documents. Because documents in .pdf format can easily beseen and printed by users on a variety of computer and platform types,they are very common on the World Wide Webpectinate - comb-like; in mollusks, it refers to the comb-like lamellae ofthe ctenidia (gills)pectiniform - comb-shapedpectoral - pertaining to the chest areahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (11 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapectoral fin - the farthest forward oruppermost of the paired fins of most fishes,usually located in the thoracic positionA flying fish with hugepectoral fins. (Photo:NOAA)pedal disc - a disc at the aboral end of thebody trunk used for attachment. Asynonym of basal plateAn anemone maintains itsgrip on substrate with itspedal disc. (Photo:Copyright Digital StockCorp.)pedal laceration - a type of asexual reproduction in some sea anemonesin which parts of the pedal disc break off and are left behind as theanemone movespedicellarium - a forceps-like organ whichoccurs in large numbers on starfishes andsea urchins. Pedicellariae, in general, aremultifunctional appendages involved indefense, feeding, and cleaning. They aremainly used to keep small organisms fromsettling on the aboral surface, to capturesmall prey, and to discourage predatorsfrom feeding on soft tissue. The basicstructure of pedicellariae consists of ahead, neck, and stalk. The head usually hasthree jaws and, in some pedicellariae,contains poison glandsA single pedicellariumfrom a starfish. (Photo:http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (12 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataRick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)pedunculate - having a stem or stalkpeeler crab - a crab that has just recently shed its exoskeleton, i.e., arecently-molted crabPEET (Partnerships for Enhancing Expertise in Taxonomy) - theNational Science Foundation in partnership with academic institutions,botanical gardens, freshwater and marine institutes, and natural historymuseums, seeks to enhance and stimulate taxonomic research and helpprepare future generations of experts. NSF announces a specialcompetition, Partnerships for Enhancing Expertise in Taxonomy (PEET), tosupport competitively reviewed research projects that target groups ofpoorly known organisms. This effort is designed to encourage the trainingof new generations of taxonomists and to translate current expertise intoelectronic databases and other formats with broad accessibility to thescientific communitypelagic - refers to organisms that inhabitopen water, as opposed to benthicAn ocean sunfish, Molamola, is a pelagic species,frequently seen basking atthe surface of the water.Pelecypoda (Bivalvia orLamellibranchia) - a class of Molluscathat includes clams, oysters and musselsA member of thePelecypoda, a live scallop(Placopectenmagellanicus) in theStellwagen Bank NationalMarine Sanctuary. (Photo:http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (13 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataDann Blackwood and PageValentine, USGS)pellucid - transparentpelvic fin - the paired fin located ventrally beneath, in front of, or behind,the pectoral finpenicillate - brush-like; having or resembling a tuft or brush of fine hairspenis fencing - a type of reproductive behavior found in hermaphroditicflatworms (some have two penises and one or more genital pores forreceiving sperm cells delivered during copulation). During penis fencing,each flatworm tries to pierce the skin of the other using one of its penises.The first to succeed becomes the de facto male, delivering its sperm intothe other, the de facto femalePennatulacea - an order of soft corals which includes the sea pens andsea pansies. See "sea pen" and "sea pansy"penniform - feather-shapedpentamerous - divided into five parts; acharacteristic of the body plan ofechinodermsBright orange seastar(Pseudarchastermyobrachius) with atypical pentamerous bodyshape.penultimate - the one before the last; the second from the endpeppered - used to describe a pigment pattern of dark stipplingpeptide - two or more amino acids joined by a peptide bondpeptide bond - the bond between two amino acids formed when acarboxyl (-COOH) group of one amino acid joins an amino (-NH 2 ) group ofanother amino acid, releasing water in the processhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (14 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapercentile - one of the division points that divides a set of ranked datainto one hundred equal points; a value on a scale of zero to one hundredthat indicates the percent of a distribution that is equal to or below it. Ascore in the 95th percentile is a score equal to or better than 95 percentof all other scoresperennial - referring to an organism that lives for more than one yearperforate corals - corals which have porous skeletons with connectionsbetween the polyps through the skeletonperi - a prefix meaning "around"perianal - near or surrounding the anusperiderm - an external layer of secreted cuticular material in manyAnthozoa. The term is synonymous with "cuticle." In woody plants, theperiderm is a protective secondary tissue produced by the cork cambiumperigee - the point in the orbit of the Moon or man-made satellite nearestto the Earth; the point in the orbit of a satellite nearest to its companionbodyPeriod - in the geologic time scale, a unit of time less than an era andgreater than an epochPeriodic Table - a chart of the known chemical elements, arrangedaccording to their atomic numbers. Elements with similar physical andchemical properties and similar electron arrangements are in the samecolumnperiostracum - the outside layer or covering of a bivalve (Mollusca) shellperipatric speciation - speciation which occurs when small populationsof organisms become isolated in a new environment. This differs fromallopatric speciation in that the isolated populations are numerically muchsmaller than the parental population. In peripatric speciation, the foundereffect causes rapid speciation through both rapid genetic drift and naturalselection on a small gene pool; a type of speciation in which a founder orsink population is isolated from the parent or metapopulation, usually viacolonization of some new regionperiphery - the outermost part or region within a precise boundaryperisarc - the chitinous outer coat of common tissue connectingindividuals in some colonial hydrozoansperistome - the region around the mouth in various invertebrates; incnidarians, it is the portion of the oral disc surrounding the mouthhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (15 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataperitheca - same as the coenosteum, which is the skeleton betweencorallites within a colony; the living tissue surrounding or betweencorallites (the coenosarc)peritoneum - the mesodermally-derived membrane that lines the coelomand covers the coelomic visceraperitoneum - a membrane lining the body cavity (coelomic cavity) andcovering the viscerapermeable - having pores or openings that permit liquids or gasses topass throughperradial canal - one of four branched ciliated canals that originatesdirectly from the stomach of scyphozoan medusae and moves partiallydigested food materials from the ring canal to the stomachPersistent organic pollutant (POP) - an organic chemical that remainsintact in the environment for a long period of timepersonal communication - unpublished information communicated tothe author verballyperturbation - a disturbance or abnormalitypetabyte - a measure of data size. One petabyte is equivalent to 1,000terabytespetaloid - describes a form that is similar to a flower petalpetaloid septa - primary septa which have a tapered or curved shapebecause they are enclosed by other septapetrel - seabirds in the bird order Procellariiformes. They occur in fourfamilies within that group, which also includes the Albatross family,Diomedeidae. The family Procellariidae is the main radiation of mediumsized'true petrels', characterised by united nostrils with medium septum,and a long outer functional primary. It is dominant in the SouthernOceans, but not so in the Northern Hemispherepetrochemical - a chemical derived from petroleum or natural gaspetrosaspongiolides M-R - an antiinflammatory drug derived from themarine sponge Petrosaspongia nigrahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (16 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DatapH - the logarithm of the reciprocal of hydrogen-ion concentration in gramatoms per liter; provides a measure on a scale from 0 to 14 of the acidityor alkalinity of a solution (where 7 is neutral and 7 isbasic)phaceloid coral - a coral that hascorallites of uniform height which areadjoined toward their baseEusmilia fastigiata is aphaceloid coral with onecorallite per branch.(Photo: University ofPuerto Rico/Morelock)phage - a virus that infects bacteria; also called a bacteriophagephagocyte - a cell that engulfs and digests debris and invadingmicroorganismsphagocytosis - "cell eating." A process in which phagocytes engulf anddigest microorganisms and cellular debris; an important defense againstinfectionpharmaceutical - refers to man-made and natural drugs used to treatdiseases, disorders, and illnessespharmaco- - pertaining to drugspharyngeal arch - one of several columns of mesenchyme found in theneck region of the developing vertebrate embryo. In lower vertebrates,blood vessels formed here become part of the gills; in higher vertebratesderivatives include portions of the jaw and middle ear; also known asbranchial arches, gill arches, or visceral archeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (17 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapharyngeal basket - a feeding structurein tunicates (sea squirts) which is a type ofpharyngeal gill formed into a mesh-likebasket. Cilia on the gill draw water into themouth, through the basket mesh, and outthe excurrent siphonWater entering this seasquirt carries particulatematter which is filtered aswater passes throughopenings in thepharyngeal basket. Foodparticles are carried to thebottom in mucus andenter the digestive tract.Water that has passedthrough basket is expelledvia the excurrent siphonopening, on right in thisillustration. The anusopens at the excurrentsiphon so fecal material iscarried away. (Photo:Houseman at U. Ottawa;BIODIDAC)pharyngeal teeth - in fishes, teeth located on the bones in the pharynx,which is the posterior part of the oral cavitypharyngeal teeth - in fishes, teeth located behind the gills and beforethe esophagus, and anchored in bone or gill arches. Fishes may use theirpharyngeal teeth for sound productionpharynx - the part of the digestive system of many animals immediatelybehind the mouth and in front of the esophagus; the throatphenetic classification - classification based on degree of overallsimilarityphenetic species - a concept of species in which a species is a set oforganisms that are phenotypically similar to one anotherphenetics - classification based on grouping by overall similarity, notrecency of common descentphenocopy - an organism whose phenotype (but not genotype) has beenchanged by the environment to resemble the phenotype usuallyassociated with a mutant organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (18 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataphenology - the science dealing with the relationships between climateand periodic biological phenomena that are related to or caused byclimatic conditions, such as the seasonal budding of trees and migration ofbirdsphenotype - the total characteristics of an individual, i.e., its appearance,resulting from interaction between its genotype (genetic constitution) andits environmentphenotypic plasticity - an alteration of phenotype as an organismadapts from one micro-environment to another and as the localenvironment changes; when an organism activates different phenotypes inresponse to its environment. Phenotypic plasticity may cause someorganisms to look different from each other even though they aregenetically identicalpheromone - a hormone-like substance that is secreted by an organisminto the environment as a specific signal to another organism, usually ofthe same speciesphilopatry - refers to the drive or tendency of an individual to return to,or stay in, its home areaphoenix coral - regeneration of a coral colony from live deep tissuesPhoenix Islands Protected Area (PIPA) - established in 2006 by theRepublic of Kiribati, the PIPA is the largest marine protected area in thePacific Islands and the third largest in the world. Surpassed in size only byAustralia's Great Barrier Reef and the Northwestern Hawaiian Islands, thePIPA represents 8 percent of all marine protected areas on Earth andhelps safeguard more than 71,300 square miles of nearly pristine marinewilderness. The PIPA encompasses eight atolls, each with a 60 nauticalmile protected perimeter, and two submerged reef systems. More than120 species of coral and 520 species of reef fishes have been identified inthe areaphoretic behavior - the use of one organism by another organism as ameans of transportationphospho-diester bond - a bond in which a phosphate group joinsadjacent carbons through ester linkagesphospholipase A2 inhibitor - a drug that acts as an antiinflammatoryagent by inhibiting the release of arachidonic acid from cell membranephospholipids. It prevents the enzyme phospholipase A2 from binding tothe membranes. Phospholipase A2 inhibition mode of protection has beenrecorded from many marine spongesphosphorylation - the addition of a phosphate group to a compoundhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (19 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataphotic zone - the vertical zone in the ocean extending from the surfaceto that depth permitting photosynthetic activityphoto-quadrat - a quadrat that is photographed for purposes of lateranalysis and permanent record for species monitoring or measurementphotocyte - a light-producing cellphotogenesis - light productionphotogrammetry - the process of making surveys and maps usingphotographsphotometer - an instrument for measuring light intensityphotometric - of or relating to photometry; a more precise measurementof the brightness (intensity) of light, which can be digitized and calibratedphotometry - the quantitative measurement of visible radiation, primarilyintensity (brightness), from light sourcesphotomicrograph - a photograph taken through a microscopephotomosaic - an assemblage ofphotographs, each of which shows part of aregion, and put together in such a way thateach point in the region appears once andonly once in the assemblage, and scalevariation is minimizedPhotomosaic of St. John, U.S. Virgin Islands. Imagessuch as these are valuablein studying and managingcoral reefs and otherhabitats. (Courtesy ofNOAA National OceanService)photon - a quantum of light energy, or, more generally, of any form ofelectromagnetic energy having a single wavelength, direction, andpolarizationphotophile - an organism which grows or thrives in lighted conditionsphotophilous - thriving in conditions of strong lighthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (20 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataphotophore - a light-producing organ,found especially in marine fishes andcephalopods. Photophores emit light fromintrinsic structures, or derive lightextrinsically from symbiotic luminescentbacteriaThis bright bluish lightsare given off byphotophores on this blackdragonfish (Photo: E.Widder, Harbor BranchOceanographic Institution)photophosphorylation - the process during photosynthesis in whichlight energy captured by photosynthetic organisms is transformed into thephosphate bond energy of ATPphotoreceptor - a nerve ending, cell, or group of cells specialized tosense or receive lightphotosynthesis - process by which autotrophic chlorophyll-containingorganisms manufacture their own energy sources (simple sugars) fromthe intracellular chemical reaction of carbon dioxide and water in thepresence of sunlight and chlorophyll. Oxygen is a photochemicalbyproduct of photosynthesisphotosynthetic capacity - the maximum photosynthetic rate per unit ofbiomassphotosynthetic pigment - a pigment that efficiently absorbs light withinthe 400-700 nm range and is essential for photosynthesisphototropism - the response of an organism to light, usually expressedas movement of a part of an organism toward or away from the lightstimulus, as when plants grow toward sunlightphototype - in taxonomy, a photograph of the type or a photographserving as the typephreatic water - water below the level at which all voids in the rock arecompletely filled with waterphycocyanin - a blue, water soluble pigment found in red algae andcyanobacteriahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (21 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataphycoerythrin - a red, water soluble pigment found in red algae andcyanobacteriaphycology - the scientific study of algaephylesis - evolutionary events that modify a taxon without causingspeciation, i.e., daughter species are not producedphyletic extinction - the evolution of an ancestral species into one ormore daughter species, none of which resembles the ancestorphylliform - leaf-shapedphyllopod - any of various branchiopod crustaceans having swimmingand respiratory appendages that resemble leavesphyllosoma larva - a larval stage of aspiny lobster. The body is thin, flat, andtransparentEarly stage of a rocklobster phyllosoma larva.(Photo: Russell Bradford/CSIRO)PhyloCode - a proposed alternative to the Linnaean system of biologicalclassification. The PhyloCode is based explicitly on phylogeny, theevolutionary history of a species or higher taxon. It would name andorganize living things based on common ancestry and the branching of theevolutionary family tree. The Linneaean hierarchical system impliesevolutionary relationships, but does not formally incorporate phylogeny.The PhyloCode would abandon Linnaean hierarchical ranks and recognizeonly species and clades (a group of organisms that share a particularcommon ancestor)phylogenetic tree - a branching tree-like diagram (dendrogram) used torepresent the evolutionary history of a set of taxa, with the leaves (orterminal branches) representing contemporary taxa and the internalbranches representing hypothesized ancestorsphylogenetics - the field of biology that deals with the relationshipsamong organismshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (22 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataphylogeny - the evolutionary relationships among organismsphylogeography - the study of the geographic distribution ofphylogenetic lineages, usually within species and to reconstruct the originsand diffusion of lineages; the attempt to take into account the geographicdistribution of species in establishing their phylogeny, and to understandthe geographic patterns that may result from divergence, ultimatelyleading to the evolution of new speciesphylogram - a phylogenetic tree that depicts inferred historicalrelationships among entities. A phylogram differs from a cladogram in thatthe branches are drawn proportional to the amount of inferred characterchangephylum - a major division of a biological kingdom, consisting of closelyrelatedclasses; represents a basic fundamental pattern of organizationand, presumably, a common descentphysical change - a change from one state to another, as when waterchanges from ice to its liquid statephysiology - the branch of biology that is concerned with the study offunctions of particular structures or organs of organismsphysoclistous - in fishes having the swim bladder closed, with noconnection to the gutphysostomous - in fishes having the swim bladder connected by a tubeto the gutphytoplankton - microscopic green plantcomponent of the plankton which isresponsible for most of the photosyntheticactivity in the oceanA phytoplankon species ofthe genus Ceratium.phytotoxin - a substance similar in its properties to an extracellularbacterial toxinhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (23 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapicture element - in a digitized image, this is the area on the groundrepresented by each digital value. Because the analogue signal from thedetector of a scanner may be sampled at any desired interval, the pictureelement may be smaller that the ground resolution cell of the detector. Itis commonly abbreviated as pixelpiebald - with two colors irregularly arranged, usually black and whitepiezometer - an instrument for measuring pressure or compressibilitypigment - a wide variety of organic compounds found in organisms whichhave color (or are colorless in some cases) and perform various functions(e.g., chlorophyll, which aids in the conversion of light energy to chemicalenery during photosynthesis; hemoglobin, which carries oxygen in thecirculatory system of many animals)pileated - having a cap or crestpileiform - umbrella-shapedpiliform - hair-shapedpinacocyte - a cell type which forms the surface layer (pinacoderm orepidermis) of a sponge. Pinacocytes are capable of synthesising collagenpinacoderm - the external surface of a sponge, lined with pinacocytes ina single cellular layerping - a single output pulse of a sonar systempinna - a small lateral branchlet on atentacle of an octocorallian (soft coral); themost visible portion of the outer ear ofmammalsThe presence of an outerear flap, or pinna, is onecharacteristic thatseparates sea lions fromseals. The photograph is ofa Steller sea lion pup withmother's milk still on it'sface. (Photo: Mike Etnier,NMML/ NOAA )http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (24 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapinnacle reef - a nearly cylindrical reef with vertical sides; may be up to200 m diameter and 50 m in heightpinnate - having side branchespinniped - an aquatic mammal in the order Carnivora, such as seals, sealions and walruses, whose front limbs have evolved to become "flippers"pinnule - a side branch structure on the tentacle of soft corals, givingthem a feathery appearancepisciform - having the shape of a fishpisciform - fish-shapedpiscivore - an animal that feeds on fishespit plug - a small cytoplasm connection between cells in many red algaewhich may help with nutrient exchangepixel - abbreviation of picture elementplacode - a thickened or plate-like region within an epitheliumPlacozoa - a phylum of extremely simpleand cryptic marine animals, for which onlytwo species have been described,Trichoplax adhaerens and Treptoplaxreptans. These tiny animals werediscovered in Europe in the late 1800'sliving on the glass walls of an aquarium.Since then, most of what has been learnedabout their biology has come from studyingcultures kept in various laboratories aroundthe world. Their bodies are made up of onlya few thousand cells of just four types.They also have the smallest amount of DNAA drawing of theplacozoan, Trichoplaxadhaerens. These tinymarine animals are crypticinhabitants of tropical andsubtropical seas.(Photo:BIODIDAC )measured for any type of animal. They lacktissues, organs and organ systems.Theyreproduce asexually, but it is not known ifthey can also reproduce sexually.Practically nothing is known about them innature. Some scientists believe they emerged early in metazoanevolution, either before or just after the sponges (Porifera). However,recent DNA studies lead others to believe they emerged after the Cnidaria.Of the two species described, Treptoplax reptans has never been seensince its description in 1896, causing some to doubt its existence.However Trichoplax adhaerens has been reported from the Mediterraneanand many tropical and subtropical locations around the world. It may bethat Trichoplax adhaerens actually consists of more than a single specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (25 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataplague (white plague disease) - a coraldisease characterized by a sharp linebetween apparently healthy coral tissueand freshly exposed coral skeleton.-Thereis no obvious microbial band present.-Theinfective pathogen is a bacterium. Plague iscurrently epidemic throughout theCaribbean, and affects stony corals. Formore information and illustrations, see:http://www.coral.noaa.gov/coral_disease/white_plague.shtmlWhite plague disease.(Photo: Dr. A. Bruckner,NOAA)plain - uniformly colored or unadorned with structures or other featuresplanktivorous - feeding on planktonic organismsplankton - the passively floating or weaklymotile aquatic plants (phytoplankton) andanimals (zooplankton)This large copepod(Neocalanus sp.) is part ofthe Arctic marine planktoncommunity.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (26 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataPlantae - the kingdom of immobilemulticellular eukaryotes that obtain energythrough photosynthesis, and have cellsencased in cell walls composed of celluloseGreen plants in a Hawaiianintertidal community.planula - a ciliated planktonic larval form produced by some anthozoans.It undergoes metamorphosis into the adult stage upon settlement on asuitable substrateplasmid - an autonomous (self-replicating)circular piece of DNA found outside thechromosome in bacteria. Plasmids carryinformation that give the bacteriaresistance to antibiotics. They are oftenused in genetic engineering as cloningvectors to carry desired genes intoorganismsA super coiled plasmid isthe predominant in vivoform in which the plasmidis coiled around histonelikeproteins. Supportingproteins are stripped awayduring extraction from thehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (27 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Databacterial cell, causing theplasmid molecule tosupercoil around itself invitro. (Photo: StanleyMaloy, Ph.D., Director,Center for MicrobialSciences, San Diego StateUniversity)plasmogamy - a process of fusion of the cytoplasm of two sex cells orgametes; the first step in syngamy (fertilization)plastid - a membrane-bound organelle in plant cells that functions instorage (of food or pigments) or food production. Chloroplasts contain thepigments for photosynthesisplastron - the ventral (belly) shield or shell of a turtle or tortoiseplate - a rigid part of the Earth's crust and part of the Earth's uppermantle that moves and adjoins another one along a zone of seismicactivityplate like - resembling thin, flat sheets of uniform thicknessplate tectonics - the theory that the Earth's lithosphere consists of large,rigid plates that move horizontally in response to the flow of theasthenosphere beneath them, and that interactions among the plates attheir borders cause most major geologic activity, including the creation ofoceans, continents, mountains, volcanoes, and earthquakesplatform reef - a large reef of variable shape lacking a lagoon, seawardof a fringing reef and/or a barrier reef, for which the width is more thanhalf its lengthplatform terminal transmitter (PTT) - a small satellite transmitterattached to a sea turtle, bird, bear, etc in order to monitor its movementsand/or behavior. For example, a PTT sends a message to a satellite eachtime a turtle comes to the surface to breathe. Messages are then receivedvia the satellite regarding the turtle's locationPlatyhelminthes - an animal phylumcontaining four classes of flatworms. Threeare parasitic (tapeworms, flukes) and one,the Turbellaria, is free-living and containscoral reef inhabiting specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (28 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataA free-living polycladflatworm.pleiotrophy - in genetics, the condition in which a single gene influencesmultiple phenotypic traits. Should a new mutation occur in that gene, alltraits will be effected simultaneouslyPleistocene epoch - an interval of the Quaternary period, from 1.8million years before present to 10 thousand years before presentplenary power - in taxonomy, power of the International Commission onZoological Nomenclature to suspend articles of the Code to settleparticular casesplenary powers - in taxonomy, the International Commission onZoological Nomenclature (Commission) is empowered by use of its PlenaryPowers to prevent the application of a rule of the International Code ofZoological Nomenclature (Code) where such application in a particularcase would disturb the stability or universality or cause confusion inzoological nomenclaturepleomorphic - variable in size and shape; polymorphic, occurring in morethan one morphological formpleopod - one of the five paired abdominal appendages used forswimming by shrimps; used for attachment of eggs by female shrimps,lobsters and crabs; also called a swimmeretplesiomorphy - an ancestral character stateplesiotype - of the same sex as the holotypepleurite - one of the external lateral processes of a somite (bodysegment) of a crustacean; also called a 'pleuron'pleurodont - teeth implanted in the side of a bone, e.g. in parrotfishesand triggerfishesplexus - a group or network of intersecting nerves and/or blood vesselshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (29 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataplica - a small fold in the skinplicate - having plicae or a series of folds, grooves or wrinkles in theskin; plaitedplication - a foldPliocene epoch - an interval of the late Neogene period, from 5.3 to 1.8million years before presentplocoid colony - a coral colony which hasconical corallites with their own walls; acoral growth form in which the coral colonyis composed of more or less cylindricalcorallites having distinct walls. Thecoenosteum separates the corallites withina colonyPlocoid crust coral,Leptastrea bottae. (Photo:Dave Krupp/Windward)Community Collegeploidy - refers to the number of sets of chromosomesplug-in - a small piece of software that adds features to a larger piece ofsoftwareplumage - the collective term for all the feathers that cover a bird's bodyplume - in hydrodynamics, a plume is a column of one fluid movingthrough another; a long, feather-shaped cloud of steam or gases; avolume of a substance that moves from its source to places farther awayfrom the source; the fluid formation that is created as hydrothermal ventwaters are injected into the ocean from the sea floor; an area of chemicalsin a particular medium, such as air or groundwater, moving away from itssource in a long band or column; the anterior portion of the body of avestmentiferan tube worm which extends out of the tube into the water.The plume is comprised of hundreds of branchial filaments which are filledwith blood vessels. The red hemoglobin in the blood gives the plumestheir bright colorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (30 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapluripotent - ability of a single stem cell to develop into many differentcell types of the body of an organismpluteus larva - a free-swimming,bilaterally symmetrical, ciliated larva ofsome echinoderms, such as sea urchins andbrittlestarsPluteus larva of anAustralian sea urchin.(Photo: Ellen Popodi andRudolf A. Raff)pneumatocyst - one of many gas-filledbladders found in some algae that act as abuoys. In some large brown algae, such askelp, they act to raise the blades closer tothe surface where photosynthesis canoccur. Pneumatocysts keep the brown alga,Sargassum, afloat in the Sargasso SeaThe pneumatocysts arethe swellings at the basesof the blades in this kelp.(Photo: Monterey BayAquarium ResearchInstitute)pneumatophore - a modified aerial rootrising above ground that may function as arespiratory organ in plant species such asmangroves, which are subjected toinundation or soil saturation. Suchevolutionary adaptations enable trees toobtain oxygen directly from the air and alsohelps consolidate swamp sediments. Theyhave special air channels (lenticels) for gasexchange in the atmosphere and there isan internal pathway for getting oxygen intohttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (31 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datathe root and to supply submerged roots.The aerial loop of a mangrove root issometimes called a "knee" or "peg root"Mangrovepneumatophores emergingfrom the sediments. Thesestructures, also known asrhizophores, have barkrich in lenticels to functionin gas exchange for rootsthat are constantly inwater-saturated soil.­(Photo: Copyright Dr.Joseph E. Armstrong,Illinois State University)poacher - a person who hunts or fishes illegally; a family (Agonidae) ofsmall bottom-dwelling cold-water marine fishespod - a group of aquatic mammalsA pod of spinner dolphinsin the lagoon of MidwayAtoll. (Photo: OceanFutures Society)point intercept transect - a linear transect protocol where a tape issecured at each end of the transect with the tape draped over the reef inbetween. Observations are collected on each species and substratecomponent at specified points along the linepoint mutation - a mutation in which a single nucleotide in a DNAsequence is substituted by another nucleotidepoint source pollution - origin of a pollutant discharge from a discreteconveyance, such as an effluent from the end of a pipehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (32 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataPointCount - PointCount for Coral Reefs is a Windows/Win95-basedprogram developed to utilize the random point count method to accuratelyestimate percent coverage of corals, sponges, and associated substratefrom frame grabbed underwater video imagery. See also "Coral PointCount with Excel extensions (CPCe)"poisonous - an organism that containspoison in its tissues that can be harmful ifthe organism is ingestedThe liver, gonads,intestines, and skin ofpuffer fish (and otherrelated and unrelatedanimals) contain highconcentrations oftetrodotoxin, a powerfulneurotoxin that can causerespiratory paralysis anddeath, in approximately60% of persons whoingest it. (Photo: NOAA)Poisson distribution - a probability distribution of random occurrencesin which one occurrence has no influence on any other occurrence. Thevariance of a poisson distribution is equal to its mean and therefore thestandard deviation is equal to the square root of the mean of thedistributionpolar-orbiting satellite - a satellitetraveling in a near-polar orbit around theglobe; civilian satellite program managedand operated by NESDISPolar-orbiting satellite datawas used to derive thisimage of Hurricane Erin,September 2001.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (33 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapolarimeter - an instrument for measuring polarized lightPolaris - see North Starpolariscope - an instrument for detecting polarized lightpolarized light - light waves which vibrate in one plane only as opposedto the multi-directional vibrations of normal rayspollen - the male reproductive cells of flowering plantspoly - a prefix meaning "many"polyadenylation - the process by which the 3' ends of most eukaryoticmRNAs are formed; the covalent modification of a macromolecule (e.g.,mRNA) by the formation of a polyadenyl moiety covalent linked to themacromolecule; post-transcriptional addition of a polyadenylic acid tail tothe 3' end of eukaryotic mRNAs; also called 'poly-(A) tailing'polyadenylic acid - a polymer of adenylic acid that is sometimesattached to eukaryotic mRNA (messenger RNA) and stabilizes themolecule before transport from the nucleus into the cytoplasmpolyandry - a female mating with more than one malepolycarpic - refers to plants that have repeated periods of reproduction;iteroparouspolycentric distribution - the establishment of a population, species orother taxonomic unit in several widely separated geographic placesPolychaeta - a class of the segmentedworm phylum Anellida. There areapproximately 8,000 species of polychaeteswhich include errant (free-moving) formsand sedentary ones that live in stabilizedburrows, galleries or tubes of variousdegrees of complexity. Some burrow intocoral. Many species are commoninhabitants of coral reefs, such as theChristmas tree worms, feather dusterworms, fanworms, fireworms, scaleworms,threadworms, and othersA marine polychaete wormgrazing on the surface of acoral head. (Photo: Dr.Anthony Picciolo)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (34 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapolyclad flatworm - a free-living flatworm belonging to the orderPolycladida (Class Turbellaria; Phylum Platyhelminthes). Many species arecoral reef inhabitantspolyculture - the cultivation of more than one species of organism in anaquaculture systempolygamy - both sexes mating with more than one other individualpolygene - one of many genes of small effect that influence thedevelopment of a quantitative trait; results in continuous variation and inquantitative inheritancepolygenic trait - a phenotype controlled by many genes of small effect(polygenes)polygyny - the mating of a single male with several femalespolymer - a compound of high molecular weight consisting of up tomillions of repeated linked light and simple moleculespolymerase - a general term for enzymes that carry out the synthesis ofnucleic acidsPolymerase chain reaction (PCR) - a technique for quickly makingmany copies of a specific segment of DNApolymorphic species - species which have a variety of morphologicaltypesPolynesia - scattered islands of the centraland southern Pacific Ocean roughlybetween New Zealand in the southwest,Hawaii in the north, and Easter Island inthe southeast. The larger islands arevolcanic, the smaller ones are generallycoral formationsThe island of Bora Bora inFrench Polynesia. (Photo:Anthony R. Picciolo, NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (35 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapolyp - an individual of a solitary cnidarianor one member of a cnidarian colonyCnidarian polyp.polyp bail-out - nonsexual coral reproduction in which a polyp abandonsa corallite and reestablishes itself on a new substrate; the dissociation anddispersal of coral polyps from adult coloniespolypeptide - a long chain of amino acidsjoined by peptide bondsAmino acids in proteins (orpolypeptides) are joinedtogether by peptide bonds.polyphydont - a type of dentition where the teeth are continuouslyreplacedpolyphyletic group - a group of species that resemble each other butare evolved from different ancestors. A polyphyletic group is composed ofmembers that originated, independently, from more than one evolutionarylinepolyploid - cells or organisms having more than twice the haploidnumber of chromosomespolypoid - polyp-shapedpolysaccharide - any of a class of carbohydrates whose moleculescontain chains of monosaccharide molecules ­http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (36 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapolytypic - a taxon including several subordinate taxa, e.g. a polytypicgenus is one containing several speciespony bottle - a small, but independentalternate air supply for scuba divers, to beused in case of main air failure. It is a smallscuba tank with an attached regulatorA pony bottle attached tothe main size cylinder.(Photo: Aqua Explorers)population - a group of individuals of the same species living in the samearea at the same time and sharing a common gene pool; a group ofpotentially interbreeding organisms in a geographic areapopulation (statistics) - any entire collection of animals, plants, people,or things from which we may draw a sample and collect data. It is theentire group we are interested in, which we wish to describe or drawconclusions about. In order to make any generalizations about apopulation, a sample, that is meant to be representative of the population,is often studied. For each population there are many possible samples. Asample statistic gives information about a corresponding populationparameter. For example, the sample mean for a set of data would giveinformation about the overall population meanpopulation crash - sudden decline in the number of individuals found ina population because of a scarcity of required environmental resourcespopulation density - the number of organisms per unit area or volumehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (37 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapopulation dynamics - the study of the factors that affect the growth,stability, and decline of populations, as well as the interactions of thosefactorspopulation explosion - sudden increase in the number of individualsfound in a population because of an abundance of useable environmentalresourcespopulation genetics - the study of the allele frequency distribution andchange in populations under the influence of the four evolutionary forces:(1) natural selection, (2) genetic drift, (3) mutation, and (4) gene flowpopulation sink - a portion of a species' geographic range where thedeath rate exceeds the birth rate for a local populationpopulation viability - the probability that a population will persist for aspecified period across its range despite normal fluctuations in populationand environmental conditionspopulation viability analysis - an analysis that estimates minimumviable populationspore water - water between the grains of a sediment; also calledinterstitial waterporgy - species of bony fishes in the familySparidae. Porgies are found in temperateand tropical coastal areas of the Atlantic,Indian, and Pacific Oceans. They areespecially abundant in the Mediterraneanand Red Seas. Porgies have an ovalshaped,deep body with a blunt snout andsmall, nearly horizontal mouth. Theypossess strong teeth adapted for crushingtheir food of hard-shelled benthicinvertebrates. Many species arehermaphroditic. Some are simultaneoushermaphrodites, having male and femalegonads simultaneously. Others change sexA porgy photographed atBimini (Photo: MarkRosenstein / ActiveWindow Productions(markrosenstein.com))as they get larger. Porgies are importantfood and game fishes. Other common names of fishes in the familySparidae are sea breams and sheepsheadshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (38 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataPorifera - an animal phylum that containsthe sponges. They are the most primitive ofthe multicellular animals. Sponges assumemany sessile body forms, such as finger,branching, bushy, spherical, tubular, vaseand tube-like, encrusting, amorphous andmassive. Some bore into coral and molluskshells. Many of the 5,000 species arecolorful and prominent inhabitants of coralreefsA barrel sponge (Porifera).(Photo: Dr. AnthonyPicciolo)Porites - an important and dominant genus of hermatypic coral. Poritesbrood or release live young rather than sperm and egg packets like mostcoralsporocyte - in sponges, a cell surrounding a pore (ostium)porphyrous - purple colorport - the left side of a vessel to someone facing the bow or frontportunid crab - any member of the crab family Portunidae (orderDecapoda, class Malacostraca). In these crabs, the hindmost pair of legs(5th pair) are flattened into paddles for swimming. The family includes theblue crab (Callinectes sapidus), an edible crab of the Atlantic coast ofNorth America; the velvet crab, Portunus sp of the Atlantic and Pacificoceans and the Mediterranean Sea; and Scylla serrata (mangrove crab) ofthe Indo-Pacific region; also called swimming crabPOSIDIN (Portal for Oceanographic Services for IOOS Data andinformation) - an oceanographic observation web portal for theexchange of information for NOAA’s Center for Operational OceanographicProducts and Services and National Data Buoy Center IOOS participantsposit - a proposition that is accepted as true in order to provide a basisfor logical reasoning; take as a given; assume as a postulate or axiompositive allometry - allometric relationship in which the slope of the linecomparing two variables is greater than unitypossession - equivalent to 'territory.' Although it still appears in Federalstatutes and regulations, "possession" is no longer current colloquialusagepost-emergent nest - a seaturtle nest in which the majority ofhatchlings have emerged through the surface of the sandhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (39 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataposterior - morphologically, toward therear or back end of an individual, or distalportion of a bodily partThe prehensile tail at theposterior end of theseahorse+s body allows itto hold on to aquatic plantsposting - a single message entered into a network communicationssystempostlarva - in fishes, a larva following the yolk sac stage; the term isapplied only when the post larva's morphology continues to be strikinglydifferent from that of the juvenilepostulate - a statement accepted without proof; a fundamentalassumptionpotable water - water that is safe for drinking by humans. Specifically,freshwater that generally meets the standards in quality as established inthe U.S. Environmental Protection Agency (EPA) Drinking Water Standardspotential coral reef bleaching episode - potential for coral bleachingoccurs when the sea surface temperature is at least 1 degree C above themaximum expected summertime temperaturepotentiation - the effect of an initial stimulus in evoking a strongerresponse the next time it is received; the synergistic effect of two drugsgiven simultaneously; the ability of one chemical to increase the effect ofanother chemicalPowerPoint: - a program in the Microsoft Office suite which allows usersto create presentations and handouts. By creating PowerPoint "slides,"users can add color, images, sounds, and movies to their textpresentationshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (40 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapractical salinity unit (psu) - a unit of measurement of salinity similarto part per thousand (ppt)prebiotic - a food substance intended to promote the growth of certainbacteria; also refers to the state of matter before life existed, but wasconducive to the origin of life. The prebiotic 'soup' is the mixture oforganic molecules in the primeval ocean that are thought to havespontaneous, self-assembly properties for the first formation of an organiccomplex with self-replicating qualities; Oparin's organic soupprecautionary approach - measures intended to reduce risk to abiological resource and its environmentprecipitation - any form of water that falls from the atmosphere to thesurface of the earth, i.e., rain, snow, sleet, and hailprecision - the ability of an instrument to measure a variable and torepeatedly obtain the same resultprecocial - born or hatched in a fully-developed state; relatively matureand mobile from the moment of birth or hatching; the opposite of altricialprehensile - capable of or adapted forgrasping, such as the prehensile tail of aseahorseThis seahorse keeps itsposition by anchoring itselfwith its prehensile tail.(Photo: Dr. TomDoeppner, BrownUniversity)preprint - an article printed especially for private distribution in advanceof the actual publicationpressure gradient - a graded change in the level of water or air pressurethat occurs over distanceprevailing winds - winds that blow consistently from one direction; thetypical winds for a particular region and time of yearhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (41 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprevalence - the number of disease cases within a population over agiven period of timeprialt - an analgesic drug made from the venom of a species of cone shellsnail, Conus magus. The particular anagesic substance in the venom is aconopeptide, one of the first pharmaceuticals that demonstrate thepromise of "drugs from the sea"PRIAs (Pacific Remote Island Areas) - waters of the U.S. exclusiveeconomic zone (U.S. EEZ) around Howland Island, Baker Island, JarvisIsland, Johnston Atoll, Kingman Reef, Palmyra Atoll, Wake Island andMidway AtollPrimary male or female - a male or female that is geneticallydetermined at birth or hatching and is not the result of sex changeprimary polyp - in colonial octocorals, e.g., sea pens, one polyp growsvery large and loses its tentacles, forming the central supporting axis. Thisis the primary polyp. The base of this primary polyp forms a bulb, whichanchors it to the substratum. Branching off this primary polyp are varioussecondary polyps. Some are specialized for feeding (autozoids). Others(siphonozooids) serve as intakes for water, which circulates within thecolony and help keep it uprightprimary production - a synonym of primary productivityprimary productivity - the rate at which new plant biomass is formed byphotosynthesis. Gross primary productivity is the total rate ofphotosynthetic production of biomass; net primary productivity is grossprimary productivity minus the respiration rateprime meridian - an imaginary line running from north to south throughGreenwich, England, used as the reference point for longitudeprimer - in genomics, a short pre-existing single-stranded polynucleotidechain to which new deoxyribonucleotides can be added by DNApolymerase. It anneals to a nucleic acid template and promotes copying ofthe template starting from the primer site; a single-stranded nucleic acidthat can "prime" replication of a templateprimeval soup - Soviet biologist, Aleksandr Ivanovich Oparin, in 1924,put forward a theory of life on Earth developing in the oceans throughgradual chemical evolution of carbon-based molecules in a rich organicbroth or "primeval soup." He hypothesized that the early oceans were richin organic compoundsprimitive character - in evolution, an attribute of taxonomic group whichall members of the group possess, i.e., the more common sharedcharacters of a given group of organisms. Primitive characters are alsocalled 'plesiomorphies'http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (42 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprion (proteinaceous infectious particle -on) - an infectious agentcomposed only of protein. Prions cause a number of neurological diseasesin a variety of animals, and all are currently untreatable and fatalpriority - in taxonomy, the seniority of a taxonomic name fixed by thedate of publication; the earliest published name has prioritypristine - an area having its original purity, not contaminated orcorrupted by human intervention; the original or pure condition or state ofsomething; unspoiledprobability - a quantitative description of the likely occurrence of aparticular event. Probability is conventionally expressed on a scale from 0to 1; a rare event has a probability close to 0; a very common event has aprobability close to 1probe - in genetics, a DNA or RNA sequence that is labelled or markedwith a radioactive isotope. It is used to detect the presence of acomplementary sequence by hybridization with a nucleic acid sampleprobiotic - a dietary supplement containing potentially beneficial bacteriaor yeastproboscis - an elongated tubular organ of varying use and form, usuallyassociated with the oral region of many invertebratesprochlorobacteria - a distinct group of Eubacteriophyta which possessboth chlorophylls a and b of higher plants. The prochlorobacteria alsoproduce oxygen like the cyanobacteria, but unlike the cyanobacteria, theydo not have phycobilin accessary pigmentsproduced water - water associated with oil and gas reservoirs that isproduced along with the oil and gas; also called “brine” (and may containhigh mineral or salt content) or “formation water"producers - the first level in a food pyramid; usually consist ofphotosynthetic organisms that generate the food used by all otherorganisms in the ecosystemprogenitor - an ancestor or precursorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (43 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataproglottid - one of the segments of atapeworm, containing both male andfemale reproductive organsGravid proglottid of thetapeworm Taeniasaginata. The darkbranched structure is theuterus. Note the midlateralgenital pore.(Photo: U.S. Center forDisease Control)programmed cell death (PCD) - a form of cell death in which agenetically programmed sequence of events leads to the destruction ofcells without releasing harmful substances into the surrounding areas.PCD plays an important role in the health of an organism by eliminatingaged cells, unnecessary cells, and unhealthy cells; also called "apoptosis"or "cell suicide"prohibited species - with respect to a foreign (non-U.S.) fishing vessel,any species of fish that that vessel is not specifically allocated orauthorized to retain, including fish caught or received in excess of anyallocation or authorization (Magnuson-Stevens Fishery Conservation andManagement Act)Project Seahorse - an international team of biologists, developmentspecialists, and other professionals committed to conserving andmanaging seahorses, their relatives and habitats, while respecting humanneedsprokaryote - an organism whose chromosomes are not enclosed within anuclear membrane, e.g., a bacterium or cyanobacteriumprokaryotic - descriptive of organisms with cells possessing no distinctnucleus. Prokaryotes include bacteria and cyanobacteriaproliferation - to reproduce or increase rapidly and repeatedlypromiscuous - refers to animals that copulate with several differentpartners within a short time spanpromoter - a DNA sequence that is located in front of a gene and controlsgene expression. Promoters are required for binding of RNA polymerase toinitiate transcriptionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (44 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprop root - an adventitious root thatgrows from and supports the trunk abovethe ground in plants, such as mangrovesThe intertidal understoryof a mangrove forestshows the muddy soil, thefairly high density ofstems, and the tangle ofprop and drop roots.(Photo: Copyright Dr.Joseph E. Armstrong,Illinois State University)propagule - a structure for mangrovereproduction. After a mangrove ispollinated, it produces a propagule, whichgrows on a parent plant and requirescarbon dioxide and water from the parent,but produces its own sugars fromphotosynthesis. After a while, it separatesfrom the parent tree and falls into thewater where it can be transported greatdistances. Propagules can resist dessicationand survive for long periods of time untilthey root in a suitable environment.Cigar-shaped propagule ofthe red mangrove,Rhizophora mangle. Itmay reach 15 cm inlength. (Photo: Bill Keogh)proprioceptor - a specialized sensory nerve ending that monitors internalchanges in the body brought about by movement and muscular activity.Proprioceptors are located in muscles, tendons, and joint capsules andwhen stimulated, transmit information concerning movements andposition of the body; also called "proprioreceptor"prosopinacocyte - in sponges, an endopinacocyte lining an incurrentcanalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (45 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprosopinacoderm - in sponges, a surface lined with prosopinacocytesprosopyle - the opening into the excurrent canal in spongesprostaglandin - a fatty acid compound that has many effects throughoutthe body, including activity in inflammation, contraction of smoothmuscles, regulation of body temperature, and effects on certainhormones. Sea fans contain high concentrations of prostaglandinsprosthetic group - a specific nonpolypeptide unit in a proteindetermining and involved in its biological activityprostomium - the anteriormost, presegmental region of the body of anannelid worm, sometimes bearing eyes and antennae; the portion of thehead in annelids that is situated anterior to the mouthprostrate - lying horizontally or flat on the substrateprostrate colony - a coral colony which sprawls horizontally over thesubstrateprotandry - a state in hermaphroditic systems characterized by thedevelopment of male reproductive organs, or maturation of their gametes,before the appearance of the corresponding female product, thus insuringagainst self-fertilizationprotease - an enzyme that hydrolyzes proteins, cleaving the peptidebonds that link amino acids in protein moleculesprotected area - a legally established landor water area under either public or privateownership that is regulated and managedto achieve specific conservation objectivesThis brilliant sea anemoneis from the protected Gulfof the Farallones NationalMarine Sanctuary.protected species - species which are protected by federal legislationsuch as the Endangered Species Act, Mammal Protection Act, andMigratory Bird Treaty Acthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (46 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprotein - a large complex molecule made up of one or more chains ofamino acids. A typical protein contains 200-300 amino acids but some aremuch smaller and some much larger, e.g., titin, a protein found in skeletalmuscle contains approximately 27,000 amino acids in a single chain.Proteins perform a wide variety of essential activities in cells: they largelyform the physical structure of cells and cellular matrices; catalysts for allbiochemical reactions are enzymes, which contain protein; the transportof materials in body fluids depends of proteins; the receptors forhormones and other signaling molecules are proteins; motion andlocomotion of cells and organisms depends on contractile proteins; thetranscription factors that turn genes on and off are proteins; proteins arean essential nutrient for heterotrophs; and many more - the activities ofcells and organisms are largely reflections of the activities of their proteinsprotein kinase C (PKC) inhibitor - an antitumor compound, isolatedfrom marine sponges, which inhibits protein kinase C (PKC). PKC isbelieved to be the receptor protein of tumor-promoting phorbol estersprotein sequencing - the process of determining the amino acidsequence of a protein, or its component polypeptidesprotein synthesis - the creation of proteins from their constituent aminoacids, in accordance with the genetic information carried in the DNA of thechromosomesproteinaceous - any structure composed of proteinsproteolysis - the breaking down by hydrolysis of proteins into peptidesand amino acids by cleavage of their peptide bondsproteolytic enzyme - a term referring to any enzyme which acceleratesthe breaking down or digestive hydrolysis of proteins into smallerproteins, polypeptides, peptides, or amino acidsproteome - all of the proteins produced from all the genes of a genomeProtista - earliest evolved eukaryotic kingdom. It includes theprotozoans, the slime molds, the unicellular algae, and the multicellularalgae. However, some consider the multicellular marine algae (seaweeds)as belonging to the kingdom Plantaeprotocols - the selections of methods and how they are used to gain dataand information at a siteprotogynous - pertains to a sequential hermaphrodite in which theorganism first functions as a female and later as a malehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (47 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataprotogyny - a state in hermaphroditic systems characterized by thedevelopment of female reproductive organs, or maturation of theirgametes, before the appearance of the corresponding male product, thusinsuring against self-fertilizationprotonephridium - a simple type of excretory organ of simpleinvertebrates, such as flatworms and rotifers. It is also called a 'flamebulb.' Protonephridia are primarily concerned with removing excess waterfrom the animalprotoplasm - the complex colloidal substance which constitutes the livingmatter of cells and performs the life process functions. The protoplasmfound between the cell (plasma) membrane and the nuclear membrane istermed the cytoplasm; the protoplasm within the nucleus and separatedfrom the cytoplasm by the nuclear membrane is termed the nucleoplasmprotostome - an evolutionary line of coelomates that include mollusks,annelids, and arthropods. They develop their embryo by spiral cleavage,and the blastopore of the gastrula develops into the mouth. The groupexhibits bilateral symmetryprototroch - the main girdle of cilia in larvae of polychaete wormsProtozoa - heterotrophic eukaryotic unicellular organisms that belong tothe kingdom Protistaprotractile - capable of being protruded or thrust outprotrusible - capable of being protruded,extended or thrust out, e.g., the tongue orthe jaws in some fishesThe protrusible jaw of asouth Florida mojarra(family Gerreidae)proximal - the direction towards center of the body; opposite of distalproximate - immediate or nearest; closest in degree or order (space ortime); very close in space or timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (48 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Dataproxy - in climate research, a proxy variable is something from which avariable of interest can be obtained. For example, temperature proxiessuch as tree ring widths and ice core layering are used bypaleoclimatologists to create a past temperature record. Tree ring widthscan also be used to infer precipitation changes. Variations in Beryllium 10can be used to infer past solar irradianceproxy signal - paleoclimatic evidence that can be used to indirectly inferor estimate some aspect of the paleoenvironment, such as precipitation ortemperaturepsammon - organisms growing on, in, or moving through sand;interstitial organismspseudocoelom - a closed fluid-filled cavity that acts as a hydrostaticskeleton to maintain body shape, circulate nutrients, and hold the majororgans in roundworms, rotifers, spiny-headed worms, and horsehair wormspseudocoelomate - any of a group oftriploblastic invertebrates that has a fluidfilledbody cavity, the pseudocoelom, lyingbetween the endoderm and the mesodermThe pseudocoelom is contrasted with thecoelom of mollusks, annelid worms, and themore complex animals, includingvertebrates, by lacking an endotheliallining. Pseudocoelomates lack a circulatorysystem, using the pseudocoelom totransport nutrients. The hydrostaticpressure of the pseudocoelom gives thebody a supportive framework that acts as askeleton. Nematodes (roundworms),rotifers, acanthocephalans (spiny-headedworms), kinorhynchs, and nematomorphs(horsehair worms) are pseudocoelomategroupsSpiny-headed worms(Acanthocephala) attachedto the intestinal lining of ofa fish. This parasiticpseudocoelomate uses aspiny attachment organ tosecure itself to theintestine. (Photo: MaineDepartment of InlandFisheries and Wildlife)pseudopodium (pseudopod) - aprotoplasmic filament or irregular processthat can project from any unicellularorganism. Formation of pseudopodia (orpseudopods) assist in feeding andlocomotionAn amoeba thrusting outpseudopodia (false feet).http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (49 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Data(Photo: NASA)pseudopterosin - a compound isolated from species ofPseudopterogorgia (soft gorgonacean corals) that may act as a marinepharmaceutical with, inter alia, anti-inflammatory and analgesic propertiespsi (pounds per square inch) - a unit of air or water pressureexpressed as pounds per square inch (psi)pterygiophore - in fishes, one of several bones or cartilage with whichthe base of the rays of the median fins articulateptychocyst - a type of cnida used in tube construction by tube anemones(Ceriantharia). Tube anemones build a tube almost entirely from theeverted tubules of the ptychocystspublic domain - a work is said to be in the public domain if it is notprotected by copyright, or if the copyright for it has expiredpublished name - in taxonomy, any name which is printed andcirculated, i.e., meets the criteria of publication as stated by theInternational Code of Zoological Nomenclature; it may be available,unavailable, valid or invalidPuerto Rico Plateau - a shallow-water geological platform comprisingthe easternmost part of the Greater Antilles in the Caribbean. Theemergent portion of the plateau is composed of Puerto Rico, Culebra,Vieques, St. Thomas, St. John, Tortola, Virgin Gorda, Anegada, andassorted smaller islandspuffer - any species of marine bony fishesbelonging to the families Tetraodontidae(puffers, blowfishes), or Diodontidae(burrfishes, porcupinefishes, spiny puffers).These fishes are able to inflate their bodieswith water or air to form a globe as aprotection against predation. The flesh andorgans of some blowfishes contain anextremely potent toxin which can be fatalto humans when ingestedA spotted puffer (Arothronmeleagris) from MidwayIsland. When threatened,puffers can inflate theirbody by swallowing waterto increase their bodyvolume as a deterrent topredators.(Photo. Dr. JohnE. Randall)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (50 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataPulley Ridge - the deepest known reef off the continental United States,Pulley Reef is a 100+ km-long series of North-South trending, drowned,barrier islands located in the Southeastern Gulf of Mexico, near the edgeof the Florida Continental Shelf. The reef is located approximately 150miles southwest of Naples Florida and 60 miles northwest of the DryTortugas Ecological Reserve. It lies approximately 84 m below the oceansurface. The shallowest parts of the ridge are about 60 m deep. Even atthese depths, there are many species of zooxanthellate scleractiniancorals, green, red and brown macro algae, and shallow and deep waterreef fishespulse amplitude modulation (PAM) fluorometer - a portablesubmersible fluorometer. Fluorometers that use the PAM technique workby rapidly sending brief pulses of light to a plant or other organism Ahealthy organism responds to this light very quickly (within microseconds)by re-emitting some of thepulse-chase isotope labeling experiment - In this protocol, a cellsample is exposed to a radio-labeled compound for only a brief period oftime (the 'pulse'), then it is washed with a buffer solution to remove theisotope, and finally incubated with a non-labeled form of compound (the'chase').punctate - describes a surface stippled with tiny porespunctuated equilibrium - an evolutionary model in which change occursin relatively rapid bursts, followed by little or no discernible change in alineage (stasis)punctule - a minute dot, pit or aperturepungent - sharp, biting or acrid sensation, especially in taste or smellpure line - a genetically uniform strain in which all members havedescended by self-fertilization or close inbreedingpure tone - a sound which consists of one single frequencypurine - a nitrogen-containing, double-ring, basic compound that occursin nucleic acids. The purines in DNA and RNA are adenine and guaninepurse seine - a fishing net used to encircle surface schooling fish. Duringretrieval the bottom of the net is closed or pursed by drawing a purse linethrough a series of rings to prevent the fish from escaping. The catch isdeposited on the fishing boat. The purse seine is operated by two boats, alarge boat that surrounds the catch with the net and a smaller boat whichanchors the net. Purse seines may be of up to 1 km length and 300 mdepthhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (51 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapustule - a pimple- or wart-like projection; a bump or raised knob on theoutside surface of a mollusk shellpuupehenone - a bioactive marine natural product, obtained fromsponges of the genus Hyrtios, which possesses antitubercular, anticancer,and antibacterial propertiespycnogonid - pycnogonids, or sea spiders,are benthic, marine arthropods, with asuperficial resemblance to true spiders, towhich they are probably only distantlyrelated. They are carnivores and use amuscular pharynx to suck soft food into thegut. The mouth is at the end of a largeproboscis. Digestion is intracellular andmost feed on sponges, cnidarians, orbryozoans from which they suck fluids.There are no excretory organs, respiratoryorgans, or body cavity (coelom)The pycnogonidAnoplodactylus evansi is apredator of small marinegastropods as well asother soft bodiedinvertebrates. (Photo: Dr.Bill Rudman)pygmy goby - the pygmy goby, Eviotasigillata, has the shortest life span of anyknown vertebrate on Earth, with amaximum life expectancy of 59 days.Eviota sigillata is a small cryptic coral reeffish distributed in the Indo-West Pacific:Seychelles to the Great Barrier Reef andMicronesia, north to the Ogasawara IslandsThe pygmy goby, Eviotasigillata, has the shortestlife span of any knownvertebrate on Earth, with amaximum life expectancyof 59 days. (Photo:Dr.John E.Randall)pyknosis - degeneration of a cell in which the nucleus shrinks in size andthe chromatin condenses to a solid, structureless masspyknotic - characterized by pyknosishttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (52 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Datapyloric caecum - in fishes, a finger-likepouch connected with the pyloric stomachof the digestive canal. Pyloric caecae mayhave a digestive and/or absorptivefunction. They range in number from two orthree in some species to thousands in There are 4-6othersintermediate-length pyloriccaecae in this specimen(Photo:John Lyons/Wisconsin DNR, theWisconsin Sea Grant, andthe Unviversity ofWisconsin)pyramid of biomass - in ecology, the total biomass of all organisms ateach trophic level in a food chain; typically biomass declines withsuccessively higher trophic levelspyramid of energy - in ecology, the total energy content of all organismsat each trophic level in a food chain; the energy content declines atsuccessively higher trophic levelspyramid of numbers - in ecology, the number of organisms supported ateach trophic level in a food chain; typically, fewer organisms aresupported at successively higher trophic levelspyranometer - an instrument that measures the amount of radiation.pyrenoid - pyrenoids are proteinaceous centers of carbon dioxide fixationwithin the chloroplasts of zooxanthellae, other algae, and somebryophytes. Pyrenoids are not membrane-bound organelles, butspecialized areas of the plastid that contain high levels of ribulose-1,5­bisphosphate carboxylase/oxygenase and are associated with theformation or storage of polysaccharide food reserves.pyriform - pear-shapedpyrimidine - a nitrogen-containing, double-ring, basic compound thatoccurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine.The pyrimidines in RNA are cytosine and uracilpyrolysis - the destruction of a chemical compound by heating or burningpyrosome - a large barrel-shaped colony of colonial pelagic tunicatesbelonging to the genus Pyrosoma. The colony propels itself through thewater by means of cilia that pump water through the individual tunicates.It responds to mechanical, chemical, and light stimuli by moving and byspectacular blue-green bioluminescent displayshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (53 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef Data(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=p (54 of 54) [2/26/2008 9:15:01 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: QThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zq. v. - which see (quod vide)q.e. - which is (quod est)quadrat - a square or rectangularsampling unit of known area (e.g.,1 m 2 )within which organisms are counted ormeasured. Quadrats can be used toestimate the percent cover of each speciesor other reef components and obtaininformation about density, abundance,colony size, and biodiversityScientist conducting aquadrat survey.quadrate - square-shapedqualitative analysis - the analysis of a phenomenon to determine itsqualitative characteristics versus its quantitative characteristics, i.e.,characteristics for which precise numerical characterization is notappropriatequanta meter - an instrument used to measure the number of photonshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=q (1 of 2) [2/26/2008 9:15:02 AM]

Discover NOAA's Coral Reef Dataquantitative analysis - the analysis of a phenomenon that usesenvironmental variables represented by numbers or ranges, oftenaccomplished by numerical modelling or statistical analysisquantitative inheritance - inheritance of measurable traits (height,weight, color intensity, etc.) that depend on the cumulative action ofmany genes.quantitative polymerase chain reaction (QPCR) - real-timequantitative PCR is a highly sensitive method that utilizes small samplesizes and short experimental time frames for quantifying RNA, DNA andproteins. QPCR is especially useful for evaluating "RNA fingerprints"obtained from microarray or siRNA experiments. It allows quantification ofstarting amounts of DNA, cDNA, or RNA templates. QPCR is based on thedetection of a fluorescent reporter molecule that increases as PCR productaccumulates with each cycle of amplification. Fluorescent reportermolecules include dyes that bind double-stranded DNA (i.e. SYBR Green I)or sequence–specific probes (i.e. Molecular Beacons or TaqMan® Probes)quantum - the smallest ‘unit’ of energy. The amount of energy in aquantum depends on the frequency of the radiation carrying the energy; itis equal to the frequency (in hertz) multiplied by Planck's constant, 6.626069 x 10-34 joule-second. A quantum of light is called a photonquasi - as if; seemingly; in a mannerQuaternary period - the second period of the Cenozoic era containingthe Pleistocene epoch and the Holocene epoch, and dating from 1.8million years to the present(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=q (2 of 2) [2/26/2008 9:15:02 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: RThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZRøst Reef - the world's largest known deep-water Lophelia coral complex.It lies in depths between 300-400m west of R+st Island in the Lofotenarchipelago, Norway. It covers an area approximately 40 km long and 3km widerace - a distinguishable group of organisms of a particular species that isgeographically, ecologically, physiologically, physically, and/or geneticallydistinct from other members of the speciesrace - a population differing from others; refers to a unit below thesubspecies level which is not given a taxonomic nameRACE (Rapid Amplification of cDNA Ends) - a technique used toobtain the 3' and 5' end of a cDNA. The technique involves threesequential enzymatic steps: reverse transcription, addition ofhomopolymeric tails, and polymerase chain reaction (PCR)radial canal - a part of the water vascular system of echinoderms.Specifically, a branch off of the ring canal that leads to an arm (ray) andgives rise to the tube feet. In hydrozoan medusae, the radial canal is partof the gastrovascular cavity. it is one of four extensions leading from themouth to the outer margin of the bellhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (1 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataradial cleavage - a type of cleavagecharacteristic of deuterostomes. Whenchanging from a four-cell stage to an eightcellstage embryo, the cells divide such thateach cell in the top four cell plane isdirectly over one other cell in the bottomplaneIllustration of radial cellcleavage. (Illustration:BIODIDAC)radial corallite - a corallite on a side of a branch as opposed to an axialcorallite on the tip of the branchradial symmetry - a basic morphologicalplan of organisms that have their bodyparts arranged around a central axis. Suchorganisms tend to be circular or cylindricalin shape, e.g., a coral polyp, or haveprojections around a central disc, e.g.,starfishRadial symmetry,illustrated by this starfish(Echinodermata).radial velocity - component of motion toward or away from a givenlocationradiant energy - energy traveling in the form of electromagnetic waves;energy emitted by the sun, typically in photons and wavesradiant flux - the rate of flow of radiant energy (electromagnetic waves)radiation - energy that comes from a source and travels through somematerial or through space. Light, heat and sound are types of radiationradii - inconspicuous septal elements which connect septa with thecolumellaradioactive decay - natural decay of the nucleus of an atom where alphaor beta and/or gamma rays are released at a fixed rateradioactive isotope - an unstable isotope of an element that decays ordisintegrates spontaneously, emitting radiationhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (2 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataradioactivity - the spontaneous decay of the nucleus of an element. Itinvolves the change in the number of protons in the nucleus and thereforecreates an atom of a new elementradiocarbon age - the age of plant or animal remains, determined bymeasuring the remaining activity of the 14C atoms in the sample: A=A0 e­t where A is the measured activity, A0 is the initial activity, e is the decayconstant, and t is the sample ageradiocarbon dating - a dating method used to determine the age ofsamples containing carbon. The method measures the disintegration ofthe 14C atom. 14C is produced in the atmosphere by cosmic raybombardment, and has a half-life of 5,570 years, making it useful fordating samples in the range of 0-40,000 yearsradiocarbon time - regular known rates of radiocarbon decay that areused to determine the exact ages of carbon-based liferadiometer - an instrument used to measure radiant energyradiometer - an instrument for measuring radiation energyradiometry - the science of the measurement of radiant energyradionuclide - any radioactive isotoperadula - a scraping organ for masticationin certain mollusks, such as snails. In manygastropods the radula consists of a variablenumber of chitinous teeth, of differentshape and size, located in the anteriorportion of the pharynx. In the cone shellfamily it has been reduced to a sharp andgrooved tooth, fit to harpoon and injectprey with a powerful venom, which is alsopotentially fatal to humansA stained section of a snailradula. The numerouschitinous teeth on thisribbon-like membrane areused to scrape, pierce,tear or cut off small piecesof food that are thendirected in a continuousstream toward thedigestive tract byconveyor belt likemovements of themembrane. (Photo: Rickhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (3 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef DataGillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)rain shadow - an area of reduced precipitation on the wind-sheltered leeside of a mountain range caused by warming of air and dissipation ofcloudiness as air descends the mountain barrierRaita Bank - one of several submerged banks in the NorthwesternHawaiian Islands. It is a raised area of the ocean floor just 60 feet belowthe surfaceramifying - branching, dividingrampart - a narrow ridge, 1-2 m high, built by waves along the seawardedge of a reef flat. It consists of boulders, shingle, gravel or reef rubble,commonly capped by dune sandramus - a branchrandom genetic drift - changes in allele frequency that result becausethe genes appearing in offspring are not a perfectly representativesampling of the parental genes, i.e., changes in allelic frequency due tosampling errorrandom sample - a sample in which each individual in a population hasthe same chance of being selected as any otherrandom sampling - a sampling technique where a group of subjects (asample) is selected for study from a larger group (a population). Eachindividual is chosen entirely by chance and each member of the populationhas a known, but possibly non-equal, chance of being included in thesample. By using random sampling, the likelihood of bias is reducedrange - the range of a set of numbers is the largest value in the setminus the smallest value in the set. It is a single numberrange - the geographical area inhabited by a species or other group; maybe continuous or discontinuousrank - in taxonomy, the level, for nomenclatural purposes, of a taxon in ataxonomic hierarchy (e.g. all families are for nomenclatural purposes atthe same rank, which lies between superfamily and subfamily)ranked data - data for which the observations have been replaced bytheir numerical ranks from lowest to highestrapacious - grasping, predatoryhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (4 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef DataRapid Ecological Assessment (REA) - a method for gathering datapertaining to ecologically significant biological components of a reefhabitat over small spatial scales. Because the method provides a quick“snapshot” of major reef biota during a single dive or snorkel survey, it isparticularly useful in assessing remote areas that are only rarely visitedand where little time can be spent. REA is usefully employed by Coral ReefEcosystem Division (CRED) at the NMFS Pacific Island Fisheries ScienceCenter. During research cruises to these remote areas, teams of CREDdivers survey the reef communities in a comprehensive manner, recordingspecies abundance, diversity, and spatial distribution simultaneously forfour key components of the ecosystem: fishes, corals, other invertebrates,and algae. Specific protocols are followed for field work and subsequentlaboratory analysesRARE - a U.S.-based conservation organization that works globally toequip people in the world’s most threatened natural areas with the toolsand motivation they need to care for their natural resourcesraster - an abstraction of the real world where spatial data is expressedas a matrix of cells or pixels, with spatial position implicit in the orderingof the pixels. With the raster data model, spatial data is not continuousbut divided into discrete units. This makes raster data particularly suitablefor certain types of spatial operation. The term may also refer to theregion of a CRT (cathode-ray tube) or LCD (liquid crystal display) monitorthat is capable of rendering imagesraster map - a map or chart encoded in the form of a regular array ofcellsrastrate - rake-likeraw sewage - untreated domestic or commercial waste waterRDBMS (Relational database management system) - a databasemanagement system with the ability to access data organized in tabularfiles that can be related to each other by a common field (item). AnRDBMS has the capability to recombine the data items from different files,providing powerful tools for data usagereach - an arm of the ocean extending into the landreaction time - the duration between the beginning of stimulation andthe initiation of a responsereagent - a compound involved in a chemical or biochemical reaction,especially one used in chemical analysis to produce a characteristicreaction in order to determine the presence of another compoundreal time - time in which reporting of events or recording of events issimultaneous with the eventhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (5 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareal-time data - data collected byautomated instrumentation andtelemetered and analyzed quickly enoughto influence a decision that affects themonitored systemSeakeys stations transmitreal-time data. (Photo:NOAA)realized niche - that portion of a fundamental niche which is actuallyoccupied by a speciesrearing habitat - an area where larval and juvenile fish find food andshelterrebar - short for reinforcing bar. A steel bar, usually with manufactureddeformations, used in concrete and masonry construction to provideadditional strength. Some in the coral trade question whether rebar maycontribute to nutrient loading and therefore promote algal growth as itrusts over a long time periodrebreather - an underwater breathing apparatus which is the source ofbreathing gas for scuba divers. A rebreather "recycles" the exhalationgasses by recovering them from the mouthpieced (and not flushing theminto the surrounding water). Since not all of the oxygen in an inhalationbreath is used, there is always some left in exhalation, and this gas goesthrough the breathing loop multiple times until it's converted into carbondioxide. This exhalation is cycled back into the unit, where the exhaledgas is run through a scrubber, removing carbon dioxide by chemicalreaction with soda lime. Oxygen is injected into the loop automatically bya computer-controlled solenoid valve in response to information receivedfrom oxygen sensors. In this way the inspiration maintains a constantpartial pressure of oxygen throughout the dive. Therefore, the diver onlyconsumes the small amount of oxygen that the body actually needs andmetabolizes.. The resulting gas is analyzed by sensors to determineoxygen content and if necessary oxygen is added to the mix for thecurrent depth from a small tank carried with the rebreather. Advantagesof a rebreather are many. It allows longer bottom times. Since no bubblesare released into the water, stealth for animal behavior studies andunderwater photography is easier to achieve. Another advantage of arebreather is the much reduced risk of decompression sicknesshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (6 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareceiving waters - water bodies that receive treated or untreated wastewatersrecent - extant; still in existencerecombinant DNA - a new DNA sequence formed by the joining, usuallyin vitro, of two non-homologous (from different sources) DNA molecules,using recombinant DNA technologiesrecombinant DNA technology - procedures used to join together DNAsegments in a cell-free system. Under appropriate conditions, arecombinant DNA molecule can enter a cell and replicate there, eitherautonomously, or after it has become integrated into a cellularchromosomerecombinant line - a new combination of DNA fragments formed bycutting DNA segments from two sources with restriction enzymefragments and then joining the fragments together with DNA ligaserecombinant organism - an organism which carries short fragments ofanother organism's genome (by means of recombinant DNA technology)recombination - in genetics, the process by which offspring derive acombination of genes different from that of either parent. In higherorganisms, this can occur by crossing overrecombinational speciation - the formation of new diploid species fromhybrids between existing speciesreconnaissance survey - a brief survey of a study area before thecollection of field datarecovery plan - a plan which lists the actions that must be taken and theobjectives that must be reached before an organism is no longerendangered or threatened and may be removed from the list ofendangered and threatened speciesrecruitment - the influx of new members into a population byreproduction or immigrationrectilinear - straight-linedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (7 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datared algae - red algae belong to theDivision Rhodophycota. Most of the over4000 species are marine. They range incomplexity from simple unicellularorganisms to unbranched and branchedfilaments to complex multiaxial uprightsand crusts. Their pigments includechlorophyll a and the phycobiliproteins, redphycoerythrin (often the dominantpigment) and blue phycocyanin, as well ascarotenes, lutein, zeaxanthin. Most redalgae have a complex life history with threephases: tetrasporophyte, gametophyte andcarposporophyteRed algae. (Photo: Dept.Natural Resources andParks, Water and LandResources Division, KingsCounty, WA; from http://dnr.metrokc.gov/wlr/waterres/marine/algae.htm)Red list species - a species identified as'Extinct', 'Extinct in the wild', 'Criticallyendangered', 'Endangered', 'Vulnerable','Lower risk', 'Data deficient' or 'Notevaluated' according to criteria laid down inthe IUCN Red List Categories (InternationalUnion for the Conservation of Nature andNatural Resources, 1994)The yellow-crownedbutterflyfish (Chaetodonflavocoronatus) is listed onthe Red list as Vulnerable.This species is known onlyfrom Guam in the westernPacific Ocean (Photo: T.Allen)red tide - discoloration of surface waters,most frequently in coastal areas, caused bylarge concentrations of microorganisms,such as algae or cyanobacteriaImage of red tide takenfrom the NOAA vessel RonBrown, April 5, 2001during the AerosolsCharacterizationExperiments (see http://www.ogp.noaa.gov/aceasia/index.htm.)(Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (8 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datared-band disease - a disease of coralsmanifested by a narrow band offilamentous cyanobacteria that advancesslowly across the surface of a coral, killingtissue as it progresses. The band is reddishto maroon in colorRed-band disease on a seafan. (Photo: Dr. A.Bruckner)redox potential (Eh) - a measure of a systems capacity to oxidizematerial; the energy gained by transferring 1 mole of electrons from anoxidant to H 2 . It is measured in volts relative to a hydrogen electrodewhich is at zeroreductionism - a hypothesis that all complex systems can be completelyunderstood in terms of their components; as opposed to holismreef - a ridge of rocks, sand, or coral that rises to or near the surface of abody of water; to partially lower a sail so that it is not as large. This helpsprevent too much sail from being in use when the wind gets strongerreef ball - an artificial reef module madefrom concrete poured into a fiberglass moldReef balls at Royal PahangReef, Malaysia (Photo:Debby Ng)reef base - the area below the consolidated slope extending up to 1 kmbut no deeper than 50 m. A synonym of talus slopehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (9 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareef block - a large, isolated rock section that has been displaced fromthe reef platform, reef margin, reef front zones or the non-calciumcarbonate bedrock, usually resulting from storm wavesReef Check - a volunteer, communitybasedmonitoring protocol designed tomeasure the health of coral reefs on aglobal scale. Reef Check is active in over 60countries and territories throughout thetropicsReef Check diverssurveying an Indonesiancoral reef. (Photo: ReefCheck)reef complex - the entire reef structure, including reef surface lagoondeposits and off-reef depositsReef Condition Monitoring Program (RECON) - the OceanConservancy’s RECON Program is a low-tech, rapid monitoring protocol forassessing the health of coral reef ecosystems at selected survey sites inthe tropical Western Atlantic (Wider Caribbean region). RECON trainsvolunteer recreational divers to observe and record valuable informationabout current conditions at selected coral reefs in Florida, the Bahamas,Colombia (San Andres & Old Province), Puerto Rico, and the US VirginIslandsreef crest - the sharp break in slope at seaward margin or edge of reefflatReef Environmental Education Foundation (REEF) - REEF is a grassroots,non-profit organization of recreational divers who regularly conductfish biodiversity and abundance surveys during their divesreef fish - a species of fish found around coral reefs and artificial reefshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (10 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareef flat - the shallow area between theshoreline intertidal zone and the reef crestof a fringing reefReef flat, PalauArchipelago, Micronesia,containing various speciesof branching coral(Acropora). (Photo: JerryWellington)reef front - a synonym of reef slopereef manager - an individual linked to the government, local community,non-government organizations, or universities who have formal, informal,traditional, or legislated responsibility to govern uses of a coral reefecosystemreef mining - the large-scale removal of living reef corals and fossilizedlimestone from shallow reef environments for domestic use as buildingmaterials, lime production and aggregatereef mound - a structure that lacks reef characteristics, such asdiversification and domination stagesreef rubble - dead, unstable coral piecesoften colonized with macroalgae. Thishabitat often occurs landward of welldevelopedreef formations in the reef crestor back reef zoneCoral reef rubble fromstorm damage. (Photo:Kip Evans)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (11 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareef slope - the portion of a reef seawardof reef crestReef slope covered withlive corals.reef system - a cluster of reefsreef top - the area comprising the reef flat and reef crestReefBase - ReefBase is a global online information system (www.reefbase.org) on coral reefs. It provides information services to coral reefprofessionals involved in management, research, monitoring, conservationand education. ReefBase's online geographic information system (GIS)allows the display of coral reef related data and information on interactivemaps. One can zoom in to a particular area of interest, switch variousdata layers on and off, and save or bookmark the map for later viewing,printing or use in presentations/documentsREEFER - an apparatus used to quantify habitat heterogeneity (habitatcomplexity). It consists of a frame of selected area, e.g. two squaremeters, containing vertical, free moving PVC-poles every X-distance (e.g.every 10 cm) over its entire width. In use, a diver lowers the REEFER untilall the poles touch the benthic substrate. Keeping the frame horizontal, asecond diver records the height that each of the poles extends above theframe. Height differences between consecutive poles are compared toestimate the surface profile in each section of sampled reef . For verticalreef walls, a variation to the REEFER, the VEEFER may be usedreferral - in taxonomy, the transfer of a subordinate taxon from onetaxon to another, e.g., species removed from one genus and referred toanotherreflexed - bent or turned backwardsrefractometer - an instrument for measuring radiation energyrefugium - an area that remains unchanged while areas surrounding itchange markedly; hence the area serves as a refuge for species requiringspecific habitatshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (12 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataregeneration - the reproduction or reconstitution of a lost or damagedorgan or part through formation of new tissuesregime - a regular pattern of occurrence or actionregional continuity - in genetics, the appearance of similar traits withina geographic region that remain over a long period of timeregression - a statistical technique used to establish the relationship of adependent variable and one or more independent variablesregression analysis - a statistical technique applied to data to determinethe degree of correlation of a dependent variable with one or moreindependent variables, in other words, to see if there is a strong or weakcause and effect relationship between things; a statistical process forfitting a line through a set of data points. It gives the intercept and slope(s) of the “best fitting” line. It tells how much one variable (the dependentvariable) will change when other variables (the independent variables)changeregression line - a line fit to a set of datapoints (scatterplot) using least-squaresregression; a graph of the mathematicalrelationship between two variablesAn example scatter plotdata set with a regressionline fit to the data.regulator - a regulator is a piece of scubaequipment that reduces the high pressureof air in a scuba air tank to a pressure levelthat is usable by the diver. It delivers air tothe diver only during inhalation. Themodern scuba regulator is a very simpleand reliable device with only a few movingparts. Regulators have two stages: a firststage that attaches to the scuba tank, anda second stage that has a mouthpiece. Airunder high-pressure from the scuba tank isreduced sequentially in each stage. Thefirst stage reduces the high tank pressureto an intermediate pressure of 100 to 150psi above the surrounding water pressure.The second stage reduces the intermediatepressure to that needed for comfortablebreathingRegulators have twostages: a first stage thatattaches to the scubatank, and a second stagethat has a mouthpiece.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (13 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataregulatory gene - a gene that acts to control the protein-synthesizingactivity of other genes; also called a 'regulator gene'rehabilitation - the recovery of specific ecosystem components in adegraded ecosystem or habitatreintroduction - introducing a native species back into its original habitatreject - in taxonomy, to set aside the name of a taxon in favor of anothernamerejected name - in taxonomy, a name which, under the provisions of theInternational Code of Zoological Nomenclature, cannot be used as a validname and which is set aside in favor of another namerelational database - a method of structuring data as collections oftables that are logically associated to each other by shared attributes. Anydata element can be found in a relation by knowing the name of the table,the attribute (column) name, and the value of the primary keyrelative frequency - the number of items of a certain type divided by thenumber of all the numbers being consideredreleaser pheromone - a chemical produced by one organism thattriggers an immediate behavior in another organismrelict - a persistent remnant of an otherwise extinct taxon; a biological orgeological feature that has survived in a considerably changedenvironmentrelief - the difference in elevation between the high and low points of aland surface; changes in terrain; elevations or depressions in the landrelief map - a contour map: a map having contour lines through points ofequal elevationremote sensing - the collection ofinformation about an object or eventwithout being in physical contact with theobject or event. Remote sensing isrestricted to methods that record theelectromagnetic radiation reflected orradiated from an object, which excludesmagnetic and gravity surveys that recordforce fieldsThis remote sensinghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (14 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Data(SeaWiFS) image showssediment stirred up alongthe North Carolina coastby Hurricane Floyd,September 1999.remote sensing tool - an instrument used in remote sensing oftencombined with a geographic information system to provide synoptic andobjective views and data of the environmentrenaturation - the conversion of denatured protein or DNA to its nativeconfiguration. This is rare for proteins. However, if DNA is denatured byheating, the two strands separate. If the heat-denatured DNA is thencooled slowly, the double stranded helix reformsrenewable resource - a resource or substance that can be replenishedthrough natural or artificial meansreniform - kidney or bean-shapedrepetitive dive - any dive within a certain time frame after a previousdive. Some dive tables consider any dive within 12 hours of a previousdive as repetitivereplacement name - in taxonomy, a new taxonomic name expresslyproposed for an already established onereplication - reproduction or duplication; in genetics, the synthesis ofduplex (double-stranded) DNA by copying from a single-strandedtemplate, i.e., the synthesis of an informationally identical macromoleculefrom a template moleculereporter gene - a gene that researchers attach to another they wish tostudyrepressor - a protein that binds to an operator adjacent to a structuralgene, inhibiting transcription of that generepressor gene - a gene that prevents a nonallele from being transcribedreproductive guild - a group of unrelated fishes with a similar form ofreproductionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (15 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datareproductive isolating mechanism - a mechanism that preventsreproduction from occurring between two populations. Pre-zygoticreproductive isolating mechanisms (which take effect before fertilization)include environmental, temporal, behavioral, mechanical, andphysiological barriers that prevent individuals of different populations fromproducing viable progeny. Post-zygotic reproductive isolating mechanisms(which take effect after fertilization) include gamete incompatibility, hybridinviability, and hybrid sterilityreproductive isolation - a species is an interbreeding natural populationthat is reproductively isolated from other such groups. Species are usuallyseparated by discontinuities, which constitute barriers that prevent, or atleast inhibit, an interspecific gene flow and gene exchange. Establishmentof reproductive isolation is essential for development of a new speciesreproductive strategy - the way in which a species allocates or budgetsenergy to produce viable offspring. Energy is diverted into actual offspringand into parental care. The energy may be invested a multitude ofoffspring that receive little or no parental care (r-strategy), or invested ina few, large offspring that require considerable parental care (K-strategy).Although some organisms are primarily r- or K-strategists, the majority oforganisms fall between these two extremes and may display traitsconsidered characteristic of both ends of the r/K spectrumresident - a permanent, non-migratory inhabitantresidual nitrogen time (RNT) - a theoretical mathematicalrepresentation of the amount of nitrogen absorbed in body tissues after ascuba dive. It is expressed on dive tables in minutes which are added tothe no-decompression limit for a repetitive dive, i.e., the time it wouldtake to off-gas any extra nitrogen remaining after a diveresilience - the ability of a community or ecosystem to recover fromdisturbances and maintain a desired condition of diversity, integrity, andecological processesresiliency - the ability of a population, community or ecosystem to returnto a healthy state after experiencing damaging events which do notexceed its recovery capabilities, e.g. recovery of a coral reef after ableaching eventresilient - resumes the original shape after deformation; elasticresolution - the ability to distinguish closely spaced objects on an imageor photograph. It is commonly expressed as the spacing, in line-pairs perunit distance, of the most closely spaced lines that can be distinguishedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (16 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataresonance - literally means “to vibrate with”. The tendency of a systemto absorb more oscillatory energy when the frequency of the oscillationsmatches the system's natural frequency of vibration (its resonantfrequency) than it does at other frequencies. In physics, resonance occurswhen two systems are vibrating within the same frequency range. Whenresonant waves meet, they create order. In contrast, when two wavesvibrating at different frequencies meet, they create chaos or dissonance;reinforcement and intensification of sound by vibrationsresonator - a structure that fills with sound and acts as a natural amplifierresource partitioning - the dividing of scarce resources in order thatspecies with similar requirements can use the resources in different ways,in different places, and at different times; the division of resources suchthat a few dominant species exploit most of the available resources whileother species divide the remainder. This helps explain why a few speciesare abundant in a community while others are represented by only a fewindividualsrespiration - a biochemical process by which living organisms take upoxygen from the environment and consume organic matter, releasing bothcarbon dioxide and heat energyrespiratory tree - a respiratory organ of sea cucumbers (Holothuroidea-Echinodermata)restoration - the return of an ecosystemor habitat to its original communitystructure, natural complement of species,and natural functionA diver prepares toreattach an elkhorn coralfragment in a Mona Island,PR, reef as part ofrestoration workperformed after the 1997grounding of the FortunaReefer. (Photo: ErikZobrist, NOAA RestorationCenter)restoration ecology - activities undertaken by humans to repairecological damage, such as establishing vegetation on degraded habitat,increasing the populations of endangered species, and decreasing thethreatened area of an ecosystemhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (17 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datarestoration monitoring - the systematic collection and analysis of datathat provides information useful for measuring restoration projectperformance at a variety of scales (locally, regionally, and nationally),determining when modification of efforts is necessary, and building longtermpublic support for habitat protection and restorationrestriction endonuclease - a class of endonucleases that cleaves DNAafter recognizing a specific sequencerestriction enzyme - an enzyme that cleaves double-stranded DNA; anendonuclease that recognizes specific nucleotide sequences and cleavesDNA at these highly specific locations. In genetic engineering, new genescan be inserted into these gapsrestriction fragment length polymorphism (RFLP) - variation in DNAsequence between individuals that is detectable by variation in the lengthof DNA fragments generated by digestion with restriction endonucleasesrestriction fragment - a fragment of DNA produced by cleaving(digesting, cutting) a DNA molecule with one or more restrictionendonucleasesrestriction map - a genetic map of a DNA sequence showing therestriction sites (where a restriction enzyme cleaves DNA) of one or morerestriction enzymesrestriction site - a sequence of DNA that is recognized by anendonuclease (a protein that cuts DNA) as a site at which the DNA is to becut; also called "restriction enzyme cutting site"reticulate - net-likereticulate - resembling or forming a networkreticulate evolution - the union of different lineages of a clade byhybridizationretractable - capable of being drawn or pulled backretractile polyp - a polyp in which the anthocodium can invert into theanthostele or into the coenenchymeretractor - a muscle that withdraws an eversible or protrusible body partretro- - backwardshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (18 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataretronym - a word or phrase created because an existing term that wasonce used alone needs to be distinguished from a term referring to a newdevelopment; a modification of an existing word occasioned by adiscovery or a new concept; as Atlantic herring in contrast to Pacificherring, acoustic guitar in contrast to electric guitar or analog watch incontrast to digital watchretrorse - bent or turned backward or downwardretrose - turned backwardsretrovirus - a virus that contains the enzyme, reverse transcriptase. Thisenzyme converts the viral RNA into double-stranded DNA copies of theirgenome, (by using reverse transcription), which can combine with theDNA of the host cell and produce more viral particles. Many naturallyoccurring cancers of vertebrates are caused by retrovirusesreverse evolution - evolution which occurs when DNA returns to anancestral form. Reverse evolution has been demonstrated in laboratoryexperiments at the University of Utah, in which a half billion year-old genewas reconstructed by combining key portions of two modern mouse genesthat descended from the archaic gene; also called "retrograde evolution"reverse transcriptase - an enzyme that is able to synthesize DNA frominformation in RNA. It requires an RNA template and a DNA or RNA primerreverse transcription - the synthesis of DNA on a template of RNA,accomplished by the enzyme, reverse transcriptaserevision - in taxonomy, a critical re-appraisal of a taxonrheokinesis - movement in relation to water currentsrheotaxis - orientation to water currents. An animal may face into thecurrent (positive rheotaxis) or face downstream of the current (negativerheotaxis)rhinophoral sheath - in sea slugs, the upstanding flange from theantero-lateral part of the mantle into which a rhinophore can be contractedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (19 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datarhinophore - paired, tentacle-like chemicalsensory apparatus found on the anteriorend or "head" of nudibranchs. They act asolfactory/taste organs. To protect themfrom damage, most are able to bewithdrawn into a pocket beneath the skin.Often there is a raised collar or sheatharound each pocket which can be clampedshut when the sea slug is disturbedThe rhinophores on thissea slug function aschemosensory organs(Photo: Bill Rudman)rhizobenthos - organisms rooted in the substratumrhizome - a horizontal stemrho - in molecular genetics, there are a number of proteins involved intermination of transcription (the process whereby RNA is synthesized froma DNA template), particularly a protein called rho, which is involved inassisting RNA polymerase to terminate transcription at certain (rhodependent)sites in the bacterium, Escherichia coli. The mechanism bywhich rho terminates transcription is not understood, and there are as yetno apparent sequence similarities in these rho-dependent terminationregionsrho-dependent terminator - a DNA sequence signaling the terminationof transcription. Termination requires the presence of the rho proteinrho-independent terminator - a DNA sequence signaling thetermination of transcription.The rho protein is not required for terminationrhomboid - diamond-shapedrhopalium - one of the sensory receptors in some jellyfish (Scyphozoa),located on the margin of the bell. Rhopalia contain statocysts forequilibrium, and ocelli, which are photosensitive cells which allow theanimal to respond to light stimulationribbed - describes a surface with a series of ridgeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (20 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataribbon reef - a large offshore linear reef, seaward of a fringing reef,which is linear but does not form a barrier to the land. A synonym of shelfedgereef and sill reefribose - a monosaccharide containing fivecarbon atoms per sugar molecule, C 5 H 10 O 5 .Ribose is a major component of ribonucleicacid (RNA)A nitrogenous base iscombined with a fivecarbonsugar, either ribose(for RNA) or deoxyribose(for DNA). The arrowspoint to the singlestructural differencebetween ribose anddeoxyribose. (Graphic:San Diego State University)ribosome - a cellular organelle composed of specific ribosomal RNA(rRNA) and proteins that are responsible for the translation of messenger(mRNA) into protein synthesisRichter scale - a logarithmic scale that measures the amount of energyreleased during an earthquake on the basis of the amplitude of thehighest peak recorded on a seismogram. Each unit increase in the Richterscale represents a 10-fold increase in the amplitude recorded on theseismogram and a 30-fold increase in energy released by the earthquakeridge - a long, narrow, continuous elevation of the sea floor covered withshallow water which may support unconsolidated sediments, rocks, orshallow reefsring canal - a part of the water vascular system of echinoderms.Specifically, a circumoral ring around the esophogus with connectingradial canals each leading to an ambulacrum .It connects to themadreporite via the stone canal; also, the part of the distributive portionof the digestive system of scyphozoan medusae that is located in themargin of the bell. The ring canal communicates with the radial andadradial canalsring species - a gene flow situation in which two reproductively isolatedpopulations occupying the same region are genetically connected by ageographic ring of populations that can interbreedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (21 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datariparian - having to do with living or beinglocated on the edges or banks of streamsor riversThis healthy riparianhabitat includes undercutbanks, woody debris in thewater, and a clean streambottom.riprap - large pieces of rock (usually 6 to 30 inches in diameter) whichhave undergone only primary crushing and sizing, or larger, uncrushedpieces. Riprap is used to stabilize slopes and shorelines and constructerosion-control structuresritualized behavior - a behavior that onceserved its own purpose but has come to actas a signal about that purpose. Forexample, agonistic behaviors thatsubstitute for physical contact and fighting,such as the erection of fins by fishes duringdisplays, the yawn of baboons, the baringof teeth in dogs and wolves, the raising offur in cats, and birds raising their feathersThe yawn of the baboon isan example of ritualizedbehavior. (Photo: GapingMaws (www.animalyawns.com))riverine - associated with a river and the area adjacent to it; includes allwetlands and deepwater habitats contained within a stream channelriverine environment - an environment created along permanent andsemi-permanent streams because of the increase in soil moisturehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (22 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datariverine habitat - a habitat occurring along a riverrivulated - marked by irregular streaksthe rivulated parrotfish,Scarus rivulatus, has apattern of irregular streakson its head (Photo: Dr.John E. Randall)RNA (Ribonucleic acid) - a single-stranded nucleic acid found in thenucleus and cytoplasm of a cell. It is a polymer of the sugar ribose,phosphate, purine and pyrimidine bases. RNA is very similar to DNA, butsubstitutes the nucleotide, uracil, for thymine. It acts as a "middle-man",converting genetic information from DNA to proteins. There are threetypes of RNA: mRNA (messenger RNA), which contains the specificsequence of nucleotides necessary to dictate amino acid sequence inproteins; tRNA (transfer RNA), which serves as the "adaptor" to positionthe appropriate amino acid next to a growing polypeptide chain duringprotein synthesis; and rRNA (ribosomal RNA), which is the RNAcomponent of ribosomes. In some viruses, RNA is the genetic materialRNA polymerase - an enzyme that catalyzes the bonding reactionbetween nucleotides of DNA and RNA. Organisms use RNA polymerase toaccelerate the process of copying DNA strands during cell reproductionRNAi (RNA-mediated interference) - a technology based on thesilencing of specific genes by double stranded RNA (dsRNA). RNAi hasgreat potential for treating many diseases, including ocular, viral diseasesand cancers by silencing RNA messages, thereby preventing theproduction of disease causing proteinsrobust - a large or heavily built body or body partrock - a naturally occurring aggregate of minerals and/or mineraloids.Rocks are classified by mineral and chemical composition; the texture ofthe constituent particles; and also by the processes that formed them.Rocks are thus separated into igneous, sedimentary, and metamorphicrockshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (23 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Dataroe - fish eggs or egg-filled ovary; the eggmass or spawn of certain crustaceans, suchas lobstersSalmon roe marked forsale at a seafood marketin Japan. (Photo: NOAA)roentgen - unit of x-radiation or gamma radiationrookery - a breeding ground for gregariousbirds or mammalsAn albatross rookery atthe Midway Atoll NationalWildlife Refuge. (Photo:USFWS/Susan Middleton)Rose Atoll National Wildlife Refuge - Rose Atoll National WildlifeRefuge is located about 2,500 miles south of Hawaii, at the east end ofthe Samoan archipelago, 180 miles east of Pago Pago, American Samoa.It is the smallest atoll in the world with about 20 acres of land and 1,600acres of lagoon. The square-shaped atoll protects two small, emergentislands. Rose Island, the larger of the two, is an important nesting areafor the threatened green sea turtle and endangered Hawksbill sea turtle.It is within the U.S. territory of American Samoarosette - rose-shaped in appearance; arranged in a fashion resembling arose flowerrostral - towards or relating to the snout or rostrumhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (24 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datarostrum - an elongate or extended snoutMost dolphins have anelongated beak called arostrum. (Photo:Copyright Corel Corp.)rotenone - a very potent general use pesticide found in the roots andstems of several tropical plants. Jewel vine (Derris spp.), Lacepod(Lonchocarpus spp.), and hoary pea (Tephrosia spp.) are the morecommon plants from which rotenone is derived. It used in some countriesto kill predatory fishes prior to introducing parent fish for naturalspawning or newly hatched fry. As an effective fish biocide, rotenone isalso used for collecting fish specimens, and in some areas for fishing,where it is added to the water and the dead and dying fishes are collectedas they float to the surface. In fishes, rotenone impedes circulation to thegills, causing asphixiationrotifer - rotifers are small invertebrates inthe Phylum Rotifera.They range in sizefrom 100 to 2500 microns, withapproximately 2000 described species.Rotifers are found in aquatic and semiaquatichabitats, but are predominantlyfreshwater inhabitants. Most species arefree-living herbivores, bacteriovores orpredators, and possess a ciliated, wheellikeorgan for feeding and locomotion.Rotifers move by swimming or crawling.Some sessile species are permanentlyattached to freshwater plantshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (25 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef DataInternal anatomy of arotifer. The major systemshave been highlighted incolor. (Graphic:Livingstone, BIODIDAC)rRNA (ribosomal RNA) - any one of several large RNA molecules thatare structural and functional components of ribosomesrubbery - a tough, resilient massrubble zone - the shallowest part of a reef crest landward of the palmatazone. It consists of broken pieces of coral washed back by stormsrudimentary - a very elementary or early stage of development; not fullydeveloped and not functional; organs in the early stage of developmentmay be rudimentaryrugose - having a rough or ridged surfacehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (26 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datarugose corals - an extinct group of non-scleractinian coralsrugosity - an important coral reefparameter that describes the amount of"wrinkling" or roughness of the reef profile.It is an index of substrate complexity.Areas of high complexity are likely toprovide more cover for reef fishes andmore places of attachment for algae, coralsand various sessile invertebratesA coral reef with a highdegree of rugosity.run aground - to take a boat into water that is too shallow for it to floatin, i.e., the bottom of the boat is resting on the groundrunoff - water that has been on land andmoves seaward as a result of rain, flooding,irrigation or flushing . Runoff is frequentlyhigh in nutrients and suspended sediments,as well as toxicantsUrban runoff or 'stormdrain pollution' is one ofthe leading causes ofwater pollution in thiscountry. (Photo: NOAA/NOS/Monterey BayNational Marine Sanctuary)rural area - an area in which most residents depend on agriculture orthe harvesting of natural resources for their livelihoodrusset - reddish brown colorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (27 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef Datarusticle - a structure consisting of up to35% iron compounds (iron oxides, ironcarbonates, and iron hydroxides) thatforms under water when wrought ironrusts. In appearance, it resembles an icicleor stalactite. The remainder of the structureis a complex community of symbiotic ormutualistic microorganisms, includingbacteria and fungi, that use the rustingmetal as a source of energy, collectivelyproducing the mineral compounds as wasteproducts and hence forming the rusticle.Structurally, the rusticle contains channelsto allow water to flow through.They arevery delicate, and easily disintegrate into afine powder if disturbed. The outer surfaceof a rusticle is red in appearance while thecore is bright orangeRusticle hanging from thestern section of the RMSTitanic showing secondarygrowths duringmaturation. (Photo: LoriJohnston)rutherford - unit of radioactive decay equal to 1 million disintegrationsper second(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=r (28 of 28) [2/26/2008 9:15:09 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: SThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZS phase - the cell cycle phase during which the DNA doubles withreplication of the chromosomesSaba Bank - the Saba Bank (17o25’ N,63o30’ W) is an undersea elevation with aflattened top, located 3–5 km southwest ofthe island of Saba. It is raised about 1000m above the surrounding sea floor. With alength of 60 to 65 km and a width of 30 to40 km, the total surface area isapproximately 2,200 km2, as measuredfrom 11-200 meter depth. ApproximatelySeventy-three percent of this area isBathygraphic map of theSaba Bank area with depthshallower than 50 m. Saba Bank is acontours down to 1000submerged, living, atoll which ranks among meters. the bank proper isthe largest in the world. The total surfacebounded by the 200 meterarea of the Bank where reef structures aredepth contour (dark blue present is estimated at approximately 150area is 200-500 meters).(Map: Saba Environmentalkm2, of which 20-40 km2 is estimated toDepartment)consist of actively growing coral reef.Because of this large expanse of reef andthe prevailing westerly ocean currents, thebank likely represents an important source of eggs and larvae of corals,fishes, crustaceans, mollusks, and other kinds of marine life for the manyislands lying to the west and north-west of the bank, including the VirginIslands and Puerto Ricohttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (1 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasabellid worm - a marine polychaeteworm in the family Sabellidae which lives inflexible tubes constructed of sand grainsembedded in mucusA sabellid worm in itsparchment tube. (NOAA/Dr J.McVey)saccate - sac-likesafety stop - on ascending from a dive, a safety stop is a specified timespent by a scuba diver at a specific depth, for nitrogen off-gassing. Whilenot mandatory during a no-decompression dive, it is a sound safetypractice. A safety stop may be 3-5 minutes at 10-15 ft below the surfacesagittal - relating to the sagittal plane, which extends through themidline of a bilateral animal, dividing it into two equal halvessagittiform - arrow-shapedSaharan dust - large quantities of dust, originating in the Sahara desertof Africa, are blown across the Atlantic Ocean each summer, and may be acontributing factor for the declining health of Caribbean coral reefs. Thedust may modify clouds and rainfall both in Africa and across the tropicalNorth Atlantic as far away as Barbados. Other studies suggest that thedust may play a role in determining the frequency and intensity ofhurricanes formed in the eastern Atlantic Oceansalinity - a measure of the salt concentration of watersalt - an ionic compound composed of a positively charged cation and anegatively charged anion, so that the product is neutral and without a netcharge. These ions can be inorganic (Cl-) as well as organic (CH3-COO-)salt marsh - a marsh periodically floodedby marine waterA salt marsh. (Photo:NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (2 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasampling - the probabilistic, systematic, or judgmental selection of a subelementfrom a larger population, with the aim of approximating arepresentative picture of the wholesampling bias - the tendency of a sample to exclude some members ofthe sampling universe and over-represent otherssampling error - the variability of a statistic from sample to sample dueto chancesampling unit - the sub-element of the total population selected forsamplingsampling universe - the largest entity to be described, of which thesample is a partsand - coarse sediment typically found inareas exposed to currents and wave energyTidal current patterns inthe sand and sea grass atlow tide.sand flat - sandy areas found indepressions and gullies in a coral reef, orbetween patch reefs, or in deeper areasbelow or beyond the reef. Seemingly nearbarren during the day, at night sand flatsteem with biological activity; also a sandytidal flat barren of vegetation. A tidal flat isan extensive, nearly horizontal, marshy orbarren tract of land that is alternatelycovered and uncovered by the tide. Itconsists of unconsolidated sediment(mostly mud and sand)A patch reef surroundedby sand flats. (Photo:http://www.biosbcc.net)sandflat - a flat expanse of sand on the coast or in an estuarysanguivore - an animal that obtains its nourishment primarily as bloodsanguivore - an organism feeding principally on bloodhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (3 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasaprophyte - any plant that lives and feeds on dead organic mattersaprotroph - an organism which feeds on dead and decaying organisms,allowing the nutrients to be recycled into the ecosystem. Fungi andbacteria are two groups with saprophytic membersSargasso Sea - the region of the North Atlantic Ocean to the east andsouth of the Gulf Stream system. This is a region of convergence of thesurface waters, and is characterized by clear, warm water, a deep bluecolor, and large quantities of a floating brown alga called sargassum orgulf weedsargassum - brown algae (Sargassum muticum) with rounded bladdersthat forms dense floating masses in tropical Atlantic waters, as in theSargasso Seasatellite - a small celestial body orbiting a larger one; a man-made objectdesigned to orbit a celestial body; a subviral particle composed of anucleic acid. For their multiplication, satellites depend on coinfection of ahost cell with a helper (master) virussatellite chromosome - a chromosome that is an addition to the normalgenomesatellite colony - a colony that develops within the tissue of a parentcolony and which has its own unattached skeletonsatellite DNA - that portion of DNA in eukaryotic cells which consists ofhighly repetitious sequences of bases (nucleotides) occurring tandemly(end-on-end), typically in the range from 5 to 500 bases. Satellite DNA islocated at very specific spots in the genome and can be isolated from therest of the DNA by density gradient centrifugation, forming a second or"satellite" bandsatellite imagery - a representation of themeasurement of energy emitted orreflected by the Earth in a variety ofwavelengths. Earth observation imagerytakes a number of forms, of which the mosttraditional are optical and near-infraredradiation, from about 0.4 (blue) to 2.0 (IR)micrometers. Apart from visual and nearinfrared,other bands of the spectrumcommonly used include thermal infrared(heat) and microwave (radar). Each ofthese has its own applicationsGOES-8 (May 1999) imageof airborne dust over theCaribbean Sea. This dustoriginated in the SaharaDesert where it wascarried off the coast bystrong winds.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (4 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasatellite mapping - digital maps derived from satellite imagessatellite virus - a satellite which encodes the coat protein in which itsnucleic acid is encapsulatedsaturation - in diving, the degree to which a gas is dissolved in the bloodor other tissues. Full saturation occurs when the pressure of gas dissolvedin the blood or tissues is the same as the ambient pressure of that gassaturation diving - the situation where a diver is at a depth or pressurefor a long enough period of time (12 hours or longer) to have the partialpressures of the dissolved gases in the body at equilibrium with the partialpressure of the gases in the surrounding environment. Scientists are ableto live in and work around underwater habitats for extended periodswithout the risk of developing decompression sickness (the bends). Diversbreathe compressed air mixed with light, inert gases, such as helium.When the diver's blood becomes saturated with helium, the time requiredfor decompression, even if the diver returns to the surface after a periodof weeks, is no greater than that required after a dive lasting just a fewhourssaxitoxin - a powerful biotoxin produced by bacteria in certain marinedinoflagellates. Saxitoxin may be concentrated in the tissues of filterfeeding shellfish, and results in shellfish poisoning when ingested byhumans; also known as mytilotoxinscaffold - the eukaryotic chromosome structure which remains when DNAand histones have been removed.The scaffold is made from nonhistoneproteinsscalaradial - an antiinflammatory drug derived from the marine spongeCacospongia scalarisscale - the degree of resolution at which ecological processes, structures,and changes across space and time are observed and measuredscale-like corallites - corallites that form a pattern which resembles fishscaleshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (5 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datascatter diagram - a two-dimensionalhistogram showing the joint probabilitydensity of two variables within a datasample; it is used to interpret data bygraphically displaying the relationshipbetween two variablesA scatter diagram.scavenger - an animal that feeds on deador decaying organic matterA scavenger feeding on adead aquatic animal.schizocoelous - the mesoderm and coelom initially develop from a solidblock of mesodermal tissue in an embryo that subsequently develops asplit down the middle.The cavity thus formed is the coelom. Schizocoelousdevelopment of the coelom occurs in protostomesschool - a social group of fishes (and someother aquatic animals), usually of the samespecies, which tends to orient and move inthe same directionA school of smallmouthgrunt with elkhorn coral inthe background. (Photo:Paige Gill, Florida KeysNMS)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (6 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataschreckreaktion - an alarm response in some fishes as a result of analarm substance (schreckstoff), or alarm pheromone being introduced intothe water via rupture of specialized dermal club cells. Presumably a fishattacked by a predator releases schreckstoff into the water, resulting inthe conspecifics making a variety of coordinated escape or fright actionsschreckstoff - a chemical alarm substance (a pheromone) produced bythe skin of some groups of fishes when injured. It stimulates conspecificsand perhaps some other fishes to exhibit fright and escape movementsscience - a method of learning about the physical universe by applyingthe principles of the scientific method, which includes making empiricalobservations, proposing hypotheses to explain those observations, andtesting those hypotheses in valid and reliable ways; also refers to theorganized body of knowledge that results from scientific studyscientific law - a statement of a scientific fact or phenomenon that isinvariable under given conditions. A law may be either quantitative(including measurement) or qualitative (general characteristics). It mustdescribe evidence that has been gathered using acceptable scientificstandards of reproducibility. Examples of scientific laws: Faraday’s Law ofelectromagnetic induction, Coulomb’s Law of electrostatic attraction,Dalton’s Law of partial pressures, and Boyle’s Gas Lawscientific name - the Linnaean binomial. A name of a species composedof two words: the genus (or generic) name and the species (or trivial)name, e.g., Acropora palmata. The scientific name is always written initalics. The first letter of the generic name is always capitalized; that ofthe species name is never capitalizedsciophilous - thriving in conditions of low light intensityScleractinia - an order of Cnidaria, usuallyproducing calcareous skeletons withhexameral symmetryA scleractinian - elkhorncoral (Acropora sp.)sclerite - a skeletal element in octocorals. Sclerites are composed ofcalcite spicules; also, a hard plate or element of the exoskeleton of somearthropodshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (7 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datascleroblast - a cell within the mesoglea of octocorals that produces ascleritesclerocyte - a cell in sponges that produces spongin or spiculessclerodermite - the basic unit of coral skeletal microstructure. A centerof calcification from which bundles of acicular aragonite crystals radiateoutward; the hard integument of Crustacea.scleroseptum - one of many radiating calcareous partitions in theskeletal cup (corallite) of stony coralsSclerospongiae - a small cass of coralline sponges (phylum Porifera)which are found inhabiting coral reefs. They possess a leuconoid grade ofconstruction and are unique in having an internal skeleton of siliceousspicules and spongin fibers like those of the Demospongiae, together witha massive calcareous basal skeleton. They are often included in the classDemospongiaescolex - the knoblike anterior end of atapeworm, having suckers and/or hookletsthat, in the adult stage, serve as organs ofattachment to the host organismThe scolex of thetapeworm, Taenia solium.(Photo: Center for DiseaseControl)scorpionfish - any of about nearly 400species of bony fishes in the familyScorpaenidae. Scorpionfishes have large,heavily ridged and spined heads.Theypossess venomous spines on their dorsalfins, each with a groove and venom sac.Scorpionfishes are well camouflaged toblend in with their environment with fleshyprojections and background coloration.Some can change their color to bettermatch their surroundings. The mostvenemous fish in the world, the reefstonefish (Synanceia verrucosa), isThe coral scorpionfish,Scorpaena albifimbria.(Illustration: NOAA)disguised to look like a encrusted rock or lump of coral. This species iswidely distributed throughout tropical, marine waters of the Indo-Pacific.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (8 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataMost species of scorpionfishes are demersal, living on or near the bottom.They are carnivorous ambush predators feeding on crustaceans,cephalopods and fishesscotoscope - an instrument for detecting objects in darknessSCUBA (Self-Contained UnderwaterBreathing Apparatus) - a diving modeindependent of surface air supply in whichthe diver uses open circuit self-containedunderwater breathing apparatus whichsupplies air or breathing gases at ambientpressureDiver training with a fullface mask and underwatercommunications.scute - an external horny, chitinous orbony plate or scale, such as those on theshell of a turtleSea turtle with shellcomprised of hard,platelike scutes.scutiform - shield-shapedsea - a subdivision of an oceansea cow - a large, herbivorous aquaticmammal of the order Sirenia that containstwo Recent families: Dugongidae for thegenera Dugong (dugong, one species) andHydrodamalis (Steller's sea cow, onespecies hunted to extinction); andTrichechidae for the single genusTrichechus (manatees, three species). Thedugong inhabits coastal regions in thetropical parts of the Old World, and someindividuals go into estuaries and rivers.Steller's sea cow inhabited the Bering Sea,and was the only Recent member of thisorder adapted to cold waters. Manatees liveThe West Indian Manatee,Trichechus manatus, inFlorida bay. (Photo:Copyright Laurel Canty-Ehrlich, NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (9 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataalong the coast and in coastal rivers in thesoutheastern United States, Central America, the West Indies, northernSouth America, and western Africasea cucumber - an echinoderm in theclass Holothuroidea. Sea cucumberspossess a flexible, elongated body andleathery skin, and tentacles surroundingthe mouth. Although they don't superficiallyresemble other members of the phylumEchinodermata, they retain pentameral(five-rayed) symmetry, with five rows oftube feet running from the mouth downalong the sides of the body. Sea cucumbersare an abundant and diverse group that arefound in nearly every marine environment,but are most diverse on tropical, shallowwatercoral reefs.They are economicallyimportant in two main ways. They producechemical compounds that are of interest topharmaceutical firms, and as a food item inTentacles at the anteriorend of the body of this seacucumber secrete asubstance which aids inthe capture of detritus andsmall organisms on sandand rock bottom. Thediving tool (knife) is forscale (Photo:E. WilliamsNURP/NOAA)Asia, they form the basis of a multimillion-dollar industry that processesthe body wall for sale as beche-de-mer or trepangsea pansy - a soft coral in the orderPennatulacea and subclass Alcyonaria. Asea pansy is a colony of polyps havingdifferent forms and functions. A single, leaflike,giant primary polyp up to two inches indiameter forms the anchoring stem(peduncle). This peduncle can be distendedto better anchor the colony in the substrate.The primary polyp possesses secondarypolyps, autozooids (feeding polyps) andsiphonozooids (serve as intakes for water,which circulates within the colony and helpskeep it upright) on the upper surface.Thesea pansy is bioluminescent whendisturbed, due to Green Fluorescent Protein.The sea pansy, Renillareniformis, is a colonialsoft coral which anchorsitself to the substratum,but is able to crawl aboutusing its leaf-like primarypolyp (Photo: Southcarolina Department ofNatural ResourcesSoutheastern RegionalTaxonomic Center)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (10 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasea pen - a soft coral in the orderPennatulacea and subclass Alcyonaria. Seapens are colonial octocorals which exhibitspolyp dimorphism. One polyp grows verylarge, loses its tentacles and forms acentral axis. The base of this primary polypforms a bulb which may be expanded orcontracted. The bulb is used to anchor thecolony. Branching off this primary polyp arevarious secondary polyps. Some, calledautozooids, are typical feeding polyps.Others, called siphonozooids, serve asintakes for water, which circulates withinthe colony and helps keep it upright.Calcareous spicules and frequently a centralaxial rod of calcium carbonate also providesupport. One group of sea pens havesecondary polyps grouped into "polypleaves," giving these species a feather-likeappearance, from which we get thecommon name as they look something likeold-fashioned quill pens. Most species,however, do not have polyp leaves, andlook more like clubs, umbrellas, orpinwheelsOne group of sea penshave secondary polypsgrouped into "polypleaves,"giving thesespecies a feather-likeappearance, from whichwe get the common nameas they look somethinglike old-fashioned quillpens. (Photo: Kåre Telnes(www.seawater.no))sea snake - a member of the familyHydophiidae. Sea snakes are common inthe Indo-Pacific. Related to cobras, theselive-bearing reptiles are highly venomousbut not aggressive by natureThis sea snake wasphotographed andreleased during a 1998cruise of the NOAA shipMcARTHUR to SouthAmerica.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (11 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasea star - an echinoderm characterized byradial symmetry, and usually with five arms(rays) radiating from a central body. Minutepincer-like structures on the arms, calledpedicellaria, ensure that the surface of thearms stay free from algae. There are a fewsea stars that have 6 or 7 arms, and somewith even more. Injuries will also causemore arms to grow. The majority of seastars are carnivorous and feed on sponges,bryozoans, ascidians and mollusks. Otherare detritus feeders or scavengers. Somesea stars, for example the crown-of-thornsthat feeds on coral polyps, are specializedfeeders; also called "starfish"The horned sea star(Protoreaster nodosus)inhabits shallow water inthe lagoon or back reef ofIndo-Pacific coral reefs.(Photo: Teresa (Zubi)Zuberbühler) (www.starfish.ch)sea state - a description of the sea surfacewith regard to wave actionFishing vessel battlesthrough rough conditions(sea state). (Photo: NOAA/National Weather Service/Ocean Prediction Center)sea time - logged time spent at seasea urchin - sea urchins are echinodermsin the class Echinoidea, that possess a hardcalcareous shell (test) armed with spines,which may be long and pointed, or shortand pointed, or dull. The spines are usedfor locomotion (along with tube feet),protection, and for trapping drifting foodparticulates, such as algae. Most seaurchins are algal grazers but some feed onsponges, ectoprocts and ascidians, andothers on detritus. Sea urchins help to keepcorals free of overgrowing algaeThe rock boring seaurchin , Echinometramathaei, lives in holes anddepressions on rock inshallow areas. (Photo:Teresa (Zubi)Zuberbühler) (www.starfish.ch)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (12 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataSeaBat - a multibeam sonar system that provides high-resolutionbathymetry and imagery data in real time for extremely detailed 3-Drepresentation of underwater features and seabed conditionsseagrass - a flowering plant, completewith leaves, a rhizome (an underground,usually horizontally-oriented stem) and aroot system. They are found in marine orestuarine waters. Most seagrass species arelocated in soft sediments. However, somespecies are attached directly to rocks withroot hair adhesion. Seagrasses tend todevelop extensive underwater meadowsSeagrass bed.SEAKEYS - NOAA and the Florida Instituteof Oceanography (FIO) supply daily andhistorical enhanced Coastal-MarineAutomated Network (C-MAN) data via theSEAKEYS program. Since 1992, SEAKEYShas provided hourly data from up to sevenmeteorological and oceanographicmonitoring stations situated throughout theFlorida Keys National Marine Sanctuary andFlorida Bay. These stations measure theusual C-MAN meteorological parameters,such as wind speed, gusts and barometricpressure, but are enhanced withoceanographic instruments measuringsalinity, sea temperature, fluorometry andturbidity These data are collected andpresented via email and the Web daily, andare supplied through a historical databaseon the Web. Unique software developed forSEAKEYS data operates in near real-timeand provides alerts as to conditionsconducive to natural events such as coralbleaching (Coral Reef Early WarningSystem [CREWS]), larval conch survival,and in the future, harmful algal bloomsCoastal-Marine Automated Network (C-MAN) Station.seamount - a submarine mountain, usually conical in shape and volcanicin origin, that rises 1000 meters or more above the sea floor. Somedefinitions of seamounts do not include the height criterionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (13 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataSeascape - a large, multiple-use marine area, defined scientifically andstrategically, in which government authorities, private organizations, andother stakeholders cooperate to conserve the diversity and abundance ofmarine life and to promote human well-being. Seascapes typically havehigh biological diversity, ecological and economic connectivity, andaesthetic and cultural value. Seascapes may include governmentauthorizedprotected areas for addressing special management needs andprovide an opportunity for government agencies to coordinate their effortsvoluntarily to secure more effective regional management programs.Seascapes define places where conservation goals and human well-beingcan be secured through partnerships between governments, localcommunities, and non-government and private organizationsseawall - a massive structure built along the shore to prevent erosionand damage by wave actionseaward slope - the area of a barrier reef or atoll from the reef crest. Itincludes spurs, grooves, terraces, reef walls, etc.SeaWiFS - Sea-viewing Wide Field-of-view Sensor carried on the SeaStarsatelliteSecchi depth - the depth at which a Secchi disk disappears from view asit is lowered in water Secchi disk a white disk 20-30 cm in diameter, usedas a qualitative way of measuring water clarity. It is lowered from a vesseland viewed from above the surface in full solar illumination to estimatethe light attenuation in the water column. This is done empirically byrelating the depth at which the disk disappears to the attenuation of lightSecond Law of Thermodynamics - each time energy is converted fromone form to another, some of the energy is always degraded to a lowerquality,more dispersed, less useful form; no system can convert energyfrom one form to another useful form with 100 percent efficiency; energycannot be transferred spontaneously from a cold body to a hot body. As aresult of this fact, natural processes that involve energy transfer musthave one direction, and all natural processes are irreversible. This law alsopredicts that the entropy of an isolated system always increases with timesecond stage regulator - in scubabreathing equipment, the second stageregulator, which is attached to themouthpiece, reduces the intermediatepressure from the first stage regulator(attached to the air tank) to that neededfor comfortable breathing at depthThe second stageregulator is contained inthis NOAA diver'smouthpiece. (Photo:NOAA/National UnderseaResearch Program)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (14 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasecondary male or female - a male orfemale that is the result of sex change. Asecondary male would be derived from aprotogynous female, in which there is aregression of the ovaries and a proliferationof testicular tissues. A secondary femalewould be derived from a protandrous malein which the female primary sex organsreplace the testesSecondary male stoplightparrotfish. Parrotfish canundergo sex reversalsduring their life history.(Photo: GeorgeRyschkewitsch)secondary polyp - polymorphic polyps which grow as branches from thesupporting primary polyp in colonial octocorals. These secondary polypsare specialized for feeding or water circulation within the colonysecondary production - the production of living material per unit area(or volume) per unit time by herbivores. It is usually expressed as gramscarbon per meter square per yearsecretion - the passage of a molecule from the inside of a cell throughthe cell membrane into the periplasmic or interstitial space, or theextracellular medium; the organic process of synthesizing and releasingsome substance from the body of an organismsecretory product - a functionally specialized substance, not a wasteproduct, released from a gland or cell. Hormones, for example, aresecretory productssection - a thin slice of some biological material for examination under amicroscopesection, cross - sliced at right angles to the longitudinal axis of anorganism or partsection, oblique - sliced as a section that is neither parallel to thelongitudinal axis nor at right angles to this axis of an organism or partsection, saggital or longitudinal - sliced along or parallel to thelongitudinal axis of an organism or partsedentary - not moving. Many organisms, both plants and animals,spend the majority of their lives in one placehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (15 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasedimentary rock - rock formed from sediments in ancient oceans, e.g.,sandstone, limestone, and chalk. Sedimentary rocks can be changed byheat and pressure into metamorphic rocks; any rock resulting from theconsolidation of sedimentsediments - soil, sand, and minerals washed from land into water,usually after rain. They pile up in reservoirs, rivers, harbors, and coastalareas destroying habitats, and clouding the water so that sunlight cannotreach aquatic plants. Careless farming, mining, and building activitiesexpose sediment materials, allowing them to wash off the land afterrainfallseep - a small area where water that maybe of a different temperature and densityflows from below the seafloor and risesslowly into the ocean; a spot where waterthat is flowing below the earth’s surfaceslowly oozes out to form a small pool or aspring abovMethane bubbles that risethrough the seabedsediments may escapegently at the seabedthrough discrete migrationpathways and form seabedseeps (Project CRIMEA)seepage - the movement of water through a porous mediumsegmentation - in many animals, the body is divided into repeatedsubunits called segments, such as those in centipedes, insects, andannelid worms. Segmentation is the state of having or developing thistype of body planseine - a fish net that hangs vertically, with floats at the top and weightsat the bottomhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (16 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataSekisei Lagoon - the largest coral reef in Japan, located almost at thesouthernmost end of the Ryukyu archipelago and designated as a part ofIriomote National Park. The Lagoon has a rich ecosystem and is a majorsource of coral larvae for distant reefs in the Ryukyu and Honshu Islandsselective pressure - forces acting on populations that determine thatsome individuals are more reproductively successful or genetically fit thanothers, and contribute more descendants (or genes) to subsequentgenerationsself-fertilization - when a sperm cell and ovum from the same organismfuse and form a zygotesemelparity - the reproductive condition where individuals reproduceonly once during their lifetimeseminal receptacle - a sac that stores spermatozoa (sperm cells) priorto fertilization of an eggsemipermeable membrane - a thin membranous barrier that permitspassage of particles up to a certain size or of a special nature; alsoreferred to as a 'differentially permeable membrane'semispecies - populations of a species that are completely isolated fromone another but have not yet evolved into truly different speciessenescence - the aging process in mature individuals; the period nearthe end of an organism's life cyclesenior homonym - in taxonomy, the older, or earliest establishedtaxonomic namesenior synonym - in taxonomy, the older name of two synonymssens. lat. - in the broad sense (sensu lato)sensor - a device that receives electromagnetic radiation and converts itinto a signal that can be recorded and displayed as numerical data or asan imagesensory receptor - a neurological structure specialized to respond tostimuli and changes in the internal or external environment of anorganism. Sensory receptors consist of neuron endings and specializedcells in close contact with neuronsseptate shell - a shell divided into smaller chambers, as in thechambered nautilus (Cephalopoda-Mollusca)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (17 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataseptum - a thin partitionseptum (pl. septa) - the skeletal platethat projects into the calyx from the theca.Septa may be subdivided into primary,secondary, and tertiary structuresSkeleton of a coral polyp.Notice the septa radiallyarranged around a centralaxis.septum, primary - in corallites, full partitions that separate two sets ofmesenterial pairsseptum, secondary - in corallites, partial partitions that separatemesenteries within a mesenterial pairsequence - the order of neighboring amino acids in a protein or thepurine and pyrimidine bases in DNA or RNAsequencing - analytical procedures for the determination of thesequential order of amino acids in a polypeptide chain or nucleotides in aDNA or RNA moleculesequential hermaphrodite - a form of hermaphroditism whereindividuals can change sex, but the sexes are separateseratonin receptor - a receptor for the neurotransmitter seratonin (5­hydroxytryptamine or 5-HT). The receptors are located on the cellmembrane of nerve cells (neurons) and other cell types, such as smoothmuscle cellssere - the series of communities that follow one another in a naturalsuccession, as in the change from a bare field to a mature forestserehd - the serehd or Pohnpei Lory (Trichoglossus rubiginosus) is asmall, brightly colored parrot indigenous to Pohnpei Island in theFederated States of Micronesia. It is the state bird of Pohnpeiserial homology - representative or repetitive relation in the segmentsof the same organism, as in the lobster, where the parts follow each otherin a linear series; repeated structures within an organism that havesimilar developmental originshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (18 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataserial spawning - spawning more than once in a seasonseries - in taxonomy, the sample available for studyserosa - a serous membraneserotonergic - a term that means "related to the neurotransmitterserotonin". A synapse is serotonergic if it uses serotonin as itsneurotransmitter. A substance is serotonergic if it is capable of producing,altering, or releasing serotoninserotonin - a neurotransmitter (5-hydroxytryptamine, 5-HT) necessaryfor communication between nerve cellsserotonin receptor agonist - a compound that activates serotoninreceptors, mimicking the effect of the neurotransmitter serotoninserotonin receptor antagonist - a chemical that acts to inhibitserotonin receptorsserous membrane - an epithelial and connective tissue membrane thatlines body cavities and covers visceral organs within these cavities.Epithelial cells constituting this membrane secrete a fluid (serous fluid) tothe membrane's surface, which keeps the membrane moistened; alsocalled "serosa"serpulid worm - a marine polychaeteworm in the family Serpulidae whichsecretes and lives in a rigid calcareous tubeTiny tubes of a tubebuildingserpulid worm.(Photo: NOAA)serrate - saw-like; notchedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (19 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataserver - a computer which is designed to be accessed by many othercomputers. Servers can be attached to local area networks and/or behooked up to the internet. With the proper software and connections,servers can control the distribution of email, store World Wide Webdocuments, and provide access to files that are shared by many userssesquiterpene isocyanides - a class of toxic chemicals which act asdefensive chemical secretions in some sea slugssessile - describes an immobile organismbecause of its attachment to a substrate.The term has also been applied toorganisms, such as anemones, that movevery slowlyA sessile colonial anemone(Epizoanthus americanus)living in Gray's Reef offSapelo Island, GA.seston - minute particulate material moving in water that is composed ofboth living organisms, such as plankton, and non-living matter such asplant debris and suspended soil particlesset - in mathematics, a collection of things without regard to their orderseta - a cuticular hair arising from the outside of the exoskeleton of aninvertebratesetiform - bristle-like; brush-likesetose - bearing setaesewage - the total of organic waste and waste water generated byresidential and commercial establishmentssex chromosome - a heteromorphic chromosome that plays a role in sexdetermination, such as the X and Y chromosomes, whose distribution in azygote determines the sex of the organism; a chromosome whose DNAdetermines sexual characteristics in females (X)-and males (Y)sex inversion - change of sex naturally or after steroid hormoneapplication; also called "sex reversal"sex ratio - the relative number of males and females in a population.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (20 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasex-linked gene - a gene coded on a sex chromosome, such as the X­chromosome-linked genessexual dichromatism - pertaining todifferences in color and color patternbetween the sexes of a particular speciesSexual dichromatism inthe freshwater southeastAsian dwarf gourami,Colisa lalia. The male is tothe left of the female.sexual dimorphism - pertains tosystematic differences between males andfemales. The two sexes are markedlydissimilar in appearanceFemale (above) and male(below) sockeye salmon(Oncorhynchus nerka)show extreme sexualdimorphism (color, malehump).shakedown dive - a practice scuba dive to make sure that theequipment works and the divers understand proceduresshape file - a set of files that contain a set of points, arcs, or polygons(or features) that hold tabular data and a spatial location. This file formatis used in ArcView softwareshearwater - any of about 25 species ofmedium-sized, long-winged seabirds in thefamily Procellariidae. Those in the genusProcellaria are usually called 'petrel'The pink-footedshearwater (Puffinuscreatopus) occursprimarily in the easternhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (21 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataPacific (Photo: MichaelDonahue/USGS)shelf break - nearshore bathymetry characterized by rapid andsubstantial increases in depth that are continuous with the deeper parts ofthe oceanshelf escarpment - the edge of the bank/shelf where depth increasesrapidly into deep oceanic watershelf reef - a reef that forms on the continental shelf of large land massesshelf-edge reef - a synonym of ribbon reefshellfish - a term that includes bothmolluscs, such as clams and oysters, andcrustaceans, such as lobsters and shrimpEdible crabs, shrimp,lobsters, crayfish, clams,mussels, scallops, andoysters are consideredshellfish.shifting baseline - refers to the incremental lowering of environmentalstandards, in which each new generation lacks knowledge of how theenvironment used to be, redefines what is "natural," according to personalexperience, and sets the stage for the next generation's shifting baselineshoal - a submerged expanse of coral reef, surrounded by deep water,which does not form a part of a barrier or fringing reefshoal (biol.) - a social group of fishes of the same species that are notalways similar in size or equal in social status. The shoal does not usuallymove in a highly coordinated fashion, as does a school. Shoals aretypically found in shallow water or at the surface. Some consider shoals tobe schools in shallow waterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (22 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataSHOALS (Scanning HydrographicOperational Airborne Lidar Survey) -SHOALS is a laser-based scanning LIDARbathymeter which collects high-resolutionbathymetric data in shallow, offshore areas.Map products provide a view of sea-floortopography. In areas with coral reefs, thisincludes not only the top surface of the reefbut also associated channels and sand flatsSHOALS imagery of theSouth Moloka'i reef tractshows the position of adistinctive channel thatcrosses the reef and alarge hole in the reef. Thelarge hole is shown belowin oblique view. The originof features such as thisone is being investigatedby USGS scientists.(Photo: U.S. GeolgicalSurvey)shore bird - any of various species of bird,such as the sandpiper, plover, or snipe,that frequents the shores of coastal orinland watersThis sand piper is foragingfor food on a beach.(Photo: Mary Hollinger/NOAA)shore reef - a synonym of fringing reefshore species - marine fishes that are always found near the shorehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (23 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datashoreline - the line separating land andwater. It fluctuates as water rises and fallsShoreline of FanningIsland in the South Pacific.shoreline - the intersection of the land, including man-made waterfrontstructures, with the water surface. The shoreline depicted on NOS mapsand charts represents the line of contact between the land and a selectedwater elevation. In areas affected by tidal fluctuations, the shoreline is theinterpreted mean high water line. In confined coastal water of diminishedtidal influence, the mean water level line may be used. In non-tidalwaters, the line represents the land/water interface at the time of survey.In areas where the land is obscured by marsh grass, cypress or similarmarine vegetation, the actual shoreline can not be accurately represented.Instead, the outer limit line of the vegetation area is delineated (where itwould appear to the mariner as the shoreline) and is referred to as theapparent shorelineshower - precipitation that is intermittent in time, space or intensitysibling species - closely-related species that are nearly morphologicallyindistinguishablesic - thusside scan sonar - sonar designed to looksideways and at a downward angle fromboth sides of a towed unit, called atowfish. The bottom and any objects in thewater above the bottom reflect soundwaves back to the towed array. An image isproduced fom this informationDeployment of the sidescan sonar tow vehicle,http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (24 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataalso called a ‘fish’. (Photo:NOAA)sieve plate - a structure in echinoderms through which water can flow ineither direction between the water vascular system and the surroundingocean; also known as the madreporitesigma - an informal name for the standard deviation. The lower caseGreek letter sigma (s) is the usual symbol for the standard deviationsigmoid growth - a growth rate trendcharacterized by an elongated S–shaped, orsigmoid curve. It is typical of populationgrowth rate trends which begin rapidly atan exponential rate but slow as limitingfactors are encountered until a limit isapproached asymptoticallyThis sigmoid (or s-shaped)curve is characteristic ofmany growth situations.sign - evidence as is perceptible to the examiner, as opposed to thesubjective sensations of the patient (symptom). Sign, not symptomshould be used to describe lesions or conditions observed in coral, as theability to convey sensations is not a characteristic of coralsign stimulus - the effective part of anaction or object that triggers a highlystereotyped innate behavior (or fixed actionpattern) in an animal by means of ahypothetical neural pathway called theinnate releasing mechanism (IRM)The red belly of the malethree-spined stickleback(Gasterosteus aculeatus)acts as a sign stimulus to"release" aggressivebehavior in a rival male orcourtship behavior in afemale. (Photo: MidNorthants TroutAssociation/Kevin Rowley)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (25 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasignal transduction pathway - a series of sequential events by which asignal outside of a cell causes a functional change inside the cell. Signaltransduction pathways transfer the signal through a series of intermediatemolecules until final regulatory molecules are modified in response to thesignal. Signal transduction pathways are important means of regulatingnumerous cellular functions in response to changes in the cell's chemicalor physical environmentsignal-to-noise ratio - the difference between the source level of asound signal from a source and the source level of the background noisesignalment - in pathology, a detailed description of an organism whosehealth is being examined. It includes physical characteristics, taxonomicidentification, and specimen collection informationsignature sound - a unique sound that isassociated with a specific sound sourceThe signature sound of atoadfish.significance level (level of significance) - in statistics, the probabilityof a false rejection of the null hypothesis in a statistical testSikes Act - passed in 1960, and amended several times, the Sikes Actauthorizes the Secretary of Defense to develop cooperative plans forconservation and rehabilitation programs on military reservations and toestablish outdoor recreation facilities. The Act also provides for theSecretaries of Agriculture and the Interior to develop cooperative plans forconservation and rehabilitation programs on public lands under theirjurisdiction. Some coral reefs are affected by this Actsiliceous - composed of silicon or primarily of siliconsill - the lowest point on a submarine ridge or saddle at a relativelyshallow depth, separating a basin from an adjacent sea or another basinsill reef - a synonym of ribbon reefhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (26 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasilt curtain - a temporary impenetrable barrier of flexible geotextilematerial used to contain sediments within a defined zone in the aquaticenvironment. This curtain is weighted at the bottom to achieve closurewhile supported at the top through a flotation system; also called a"turbidity curtain"simple - not divided or branchedsimultaneous hermaphrodite - a form of hermaphroditism whereindividuals simultaneously possess functional testes and ovaries, and canrelease either male or female gametes during spawningsine - withoutsingle nucleotide polymorphism (SNP) - a SNP (pronounced "snip") isa small genetic change, or variation, that can occur within an organism'sDNA sequence. The genetic code is specified by the four nucleotides:adenine, cytosine, thymine, and guanine. SNP variation occurs when asingle nucleotide, such as adenine, replaces one of the other threenucleotides. SNPs found within a coding sequence are of particular interestto researchers because they are more likely to alter the biological functionof a protein. Because of the recent advances in technology, coupled withthe unique ability of these genetic variations to facilitate geneidentification, there has been a heightened activities of SNP discovery anddetectionsingle-stranded - a term used to describe nucleic acid moleculesconsisting of only one polynucleotide chain. The genomes of certainphages are single-stranded DNA molecules; rRNA, mRNA and tRNA are allsingle-stranded nucleic acidssingle-stranded DNA - a single chain of deoxyribonucleotides thatoccurs in some bacteria and viruses. It usually exists as a covalentlyclosed circlesinistral - left, as opposed to dextral, or rightsink - a process or place that acts toabsorb or remove energy or a substancefrom a system. The ocean, for example, isa sink for carbon dioxidehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (27 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataThe marine environment isa sink for many nutrients.(Photo: copyright DigitalVision Ltd.)sink habitat - a habitat in which reproduction is insufficient to balancemortality. The population can persist in the habitat only by being a netimporter of individualssink population - a population that occupies habitat types in whichreproductive output is inadequate to maintain local population levels. Thepopulation may be replenished by emigrants from source populationssink population or species - a population or species that cannotreproduce fast enough to replace themselves. Sink populations or speciesare present only because immigrants compensate for excess deaths in thearea. Eventually, sink species will disappear from isolated areassinkhole - a depression formed in an area either by dissolving of thesurface limestone or by collapse of underlying cavitiessinus - one of several air spaces within theskull that are in contact with ambientpressure through nasal passage openings inthe posterior pharynx; a sac-like spaceThe sinuses are a group of4 pairs of air filled spacesin the head. They arecalled the ethmoid,maxillary, sphenoid, andfrontal sinuses. They warmand humidify the air asone breathes. They alsotrap and filter organic andnon-organic particles fromthe air, such as bacteria,spores, and dust.(Graphic: Cystic FibrosisCenter at StanfordUniversity)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (28 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasiphon - an opening in molluscs or inurochordates (tunicates) which draws waterinto the body cavity. In many molluscs,such as octopods and squids, the siphonmay be used to forcibly expel water,providing a means of propulsionAn octopus rapidlyswimming by forciblyexpelling water throughthe tubular siphonprojecting from the head.(Photo: Jeff Jeffords)siphonoglyph - a groove in the pharynx ofsome cnidarians that is lined with ciliawhich pump water into the animal'sgastrovascular cavity.This water currentinflates the body, circulates fluids, andprovides a volume of water to act as ahydrostatic skeletonA microscopic sectionshowing the siphonoglyphof a sea anemone fromChile, Anemoniaalicemartinae(Siphonoglyph (Si) with"reticulated pads" (Rp);Ci:cilia; M: mesoglea; Pm:pair of perfectmesenteries). (Photo:V.Häussermann & G.Försterra/U.Frankfort)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (29 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasiphonophore - siphonophores are"colonial jellyfish" which have swimmingbells at the top, and tentacles with stingingcells below that help them to catch theirprey. Each individual of the colony isspecialized for a different function, such asswimming, feeding and reproduction. Somesiphonophores can be more than 10 meterslong. They are in the phylum Cnidaria, classHydrozoa and order SiphonophoraSiphonophores areactually colonies ofindividuals, eachspecialized for differentfunctions such asswimming, feeding andreproduction. (Photocourtesy of MarshYoungbluth and NOAAOcean Explorer)siphonozooid - a specialized polyp found in colonial soft corals, such assea pens and sea pansies, which functions as as intake for water, whichcirculates within the colony and helps keep it uprightsiphosome - in hydrozoans, the region of the siphonophore colony thatbears all zooids except the nectophoressiphuncle - a tubelike structure in the body of a shelled cephalopod, suchas the chambered nautilus, extending through the partitions of eachchamber of the septate shell; the term is also used to describe tubularstructures that direct water flow, or as a feeding siphon of severaldifferent kinds of invertebratesSipuncula - an animal phylum that contains the peanut or starworms.They are small, non-segmented benthic animals (they are not worms),some of which live in coral crevices, empty mollusk shells or marine wormtubes. Several species bore into coralline rocksiRNA (short interfering RNA) - a 21-23 nucleotide-long RNA thatmediates messenger RNA (mRNA) catalysis; used in gene suppressionsister group - a taxon thought to be the closest relative of a given taxon,exclusive of the ancestral species of both taxahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (30 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasister taxa - two taxa that are more closely related to each other thaneither is to a third taxon; monophyletic taxa that are each other’s closestrelatives, i.e., they share an immediate common ancestral speciessite fidelity - the behavior of certain animals whereby they return,reproductive season after reproductive season, to the same breeding sitesixteen S RNA gene (16S rRNA gene or 16S ribosomal RNA gene) -a particular kind of RNA used as a molecular tool to extract and comparebits of a particular kind of RNA from samples in order to determine ifpreviously known or new microorganisms are present in a particularenvironment. This technique is widely used as a biomarker and formicrobial ecology studies. The 16S rRNA gene is very short, just 1,542nucleotide bases, and can be quickly and cheaply copied and sequencedskeletal density - certain massive coral species (e.g. Porites) exhibitannual variations in the density of their calcium carbonate (CaCO 3 )skeleton, similar to tree rings. The annual density bands are revealedwhen slices of coral skeleton are X-rayedskeleton - a supportive or protective structure or framework of ananimal, a plant, or part of an animal or plant. In animals it is an external(exoskeleton) or internal (endoskeleton) support structure, against whichthe force of muscles acts. Vertebrates have a skeleton of bone orcartilage; arthropods have one made of chitin; corals have one of calciumcarbonate: sponges have a mass of spicules; many other invertebratesuse a hydrostatic skeleton, which is an incompressible fluid-filled region oftheir body. In plants, the skeleton may be a rigid protective covering, asin the shell of a diatom, or the vascular system of a vascular plantskerry - a low-lying rocky island or reef, often without terrestrialvegetation, and frequently swept by wavesskewness - A measure of the degree to which a distribution isasymmetricalslug - a pulmonate or opisthobranchgastropod in which the shell is absent, orreduced and buried within the mantleLettuce sea slug (Tridachiacrispata) from the FloridaKeys National MarineSanctuary.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (31 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataslurp gun - a tube-shaped fish collecting device that operates somewhatlike a syringe by sucking up fish or other specimenssmooth - describes a surface without projections; glabroussnapper - any species of bony fishes in thefamily Lutjanidae. Snappers are found inthe tropical and subtropical regions of theAtlantic, Pacific, and Indian oceans. A feware estuarine to entirely freshwater. Manyspecies are popular food and game fishes.Some haLarge aggregations of graysnapper, Lutjanus griseus,are frequently observedamong coral reefs, rockyareas, estuaries, andmangrove habitats.(Illustration: FAO SpeciesCatalogue )sneaky male - a small, non-dominant male fish which attempts tofertilize eggs by darting suddenly onto the nest site; also called "sneaker"snorkel - a breathing device that allows aswimmer to breathe while face down in thewater. It consists of a bent plastic or rubbertube fitting into a swimmer's mouth andextending above the surfaceThis swimmer is breathingthrough a snorkle. (Photo:Courtesy of CaymanIslands Department ofTourism)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (32 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasnout - the portion of the head that is justanterior to the eyesMeasuring the snoutlength of a fish.social behavior - any kind of interaction between two or more animals,usually between animals of the same speciessocial group - a small population in which the individuals are boundtogether in relatively stable patterns of interaction and in some waysdepend upon each other for its survivalsocial rank - in animal behavior, the position an animal holds in a socialgroup of the same speciessociobiology - the systematic study of the biological basis of all socialbehavior. Sociobiology works entirely within the neo-Darwinistevolutionary paradigm in which “each phenomenon is weighed for itsadaptive significance and then related to the basic principles of populationgeneticsSocMon Guidelines - SocMon is a set of guidelines for establishing asocioeconomic monitoring program at a coastal management site. Theguidelines provide a prioritized list of socioeconomic variables useful tocoastal managers as well as the questions for data collection and thetables for data analysis. It is expected that the guidelines will be tailoredto each site’s needs. SocMon is a companion to the GCRMN SocioeconomicManual for Coral Reef Management (GCRMN Manual)soft coral - common name for species ofthe anthozoan order Alcyonacea of thesubclass Octocorallia. In contrast to thehard or stony corals, most soft corals donot possess a massive external skeletonhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (33 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataBeautiful specimen of softcoralsoft dorsal - a dorsal fin containing onlysoft rays, or the soft-rayed hind part of thedorsal fin, if both spines and soft rays arepresent (as in squirrelfish)The spiny dorsal (spd) andsoft dorsal (sod) fin of aschoolmaster snapper.(Photo: Fishing-Florida.com)sol - a liquid colloidal dispersion; a cytoplasmic phase (the other phase isa gel)solar energy - electromagnetic energy from the Sunsolar radiation - the amount of radiation or energy received from thesun at any given pointsolar year - the time it takes the Earth to make one orbit around theSun; approximately 365.2422 dayssoleiform - slipper-shapedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (34 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasolenium - in octocorals, a small gastrodermis-lined canal whichpenetrates the coenenchyme to join a network of other solenia which fusewith the larger gastrovascular canals to connect the gastrovascularcavities of the polypssolitary coral - coral polyps can be solitary or colonial. Solitary formsremain as a single individual polyp and one corallitesolstice - either of the two times of the year when the sun is the greatestdistance from the celestial equator, occurring about June 22 andDecember 22solute - the chemical substances dissolved in a solution, such as salts inseawatersolution - a liquid mixture in which the minor component, the solute, isuniformly distributed within the major component, the solventsolvent - the liquid in which a solute is dissolved to form a solutionsolvolysis - a reaction with a solvent involving the rupture of one or morebonds in the reacting solutesomatic mutation - a change in the genetic structure that can occur inany of the cells of the body except the reproductive cells, and therefore isneither inherited nor passed to offspring. Also called an 'acquired mutation'somite - a segmental mass of mesoderm in the vertebrate embryo,occurring in pairs along the notochord, and developing into skeletalmuscles and vertebrae; in some invertebrates, the term "somite" refers toa metameresonar - SONAR is an acronym for "soundnavigation and ranging." Active sonardescribes an apparatus that transmits highfrequency sound waves in water andregisters the vibrations reflected back froman object. Passive sonars listen withouttransmitting. They are usually military(although a few are scientific). Somemarine animals, such as whales anddolphins, use echolocation systems similarto active sonar to locate predators and preyMother and juvenilebottlenose dolphins(Tursiops truncatus).Dolphins and whales canuse echolocation to helpnavigate.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (35 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasonic muscle - in fishes, a muscle(s) associated with the swimbladder,which when contracted against the swimbladder wall, produces soundsassociated with territorial and reproductive behaviorsoniferous - sound producingsonograph - a hard copy display of sounddata generated either in real time or fromrecorded data. Also known as a sonogramSonograph of a crestedwarbler. Time is on the x-axis and frequency (pitch)is on the y-axis. Thesonograph shows discretepulses of sound over time.Loudness (amplitude) isindicated by the darknessof the pulse.sorus - a group or cluster of sporangiasound - a longitudinal pressure wave produced by the vibration ofmolecules in an elastic medium, which can be a liquid, solid, or gas. Asthe molecules are set in motion, they radiate outwards, colliding into othermolecules (compression), then move apart farther than their equilibriumdistance (rarefaction), travelling in this manner until they stimulate asound receptor organ, such as an ear or tactile organ.The receptortranslates the mechanical energy of the pressure wave to electrochemicalenergy of a nervous system, which stimulates a hearing or tactilesensation in the receiving organismsource DNA - the DNA from an organism that contains a target gene.This DNA is used as starting material in a cloning experimentsource habitat - a habitat that is a net exporter of individualssource population - a population that occupies a habitat suitable forreproduction, in which the quantity of offspring results in a population thatexceeds the carrying capacity of the local habitat, thereby promotingdispersalsource species - a species whose births exceed deaths in an area.Source species can provide individuals to populate other areashttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (36 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataSouthern Cross - a small conspicuous constellation in the southernhemisphere in the Milky Way near CentaurusSouthern Oscillation - a large-scale atmospheric and hydrosphericfluctuation centered in the equatorial Pacific Ocean. It exhibits a nearlyannual pressure anomaly, alternatively high over the Indian Ocean andhigh over the South Pacific. Its period is slightly variable, averaging 2.33years. The variation in pressure is accompanied by variations in windstrengths, ocean currents, sea-surface temperatures, and precipitation inthe surrounding areas. El Niño occurrences are associated with thephenomenonsovereign - an independent or non-independent jurisdiction which itselfpossesses or whose people possess in their own right the jurisdiction'ssupreme authority, regardless of the jurisdiction's or people's currentability to exercise that authoritysp(p) - abbreviation for species, singular and pluralspacer region - a sequence of nucleotides in a DNA molecule betweencoding genesspat - tiny single corallites that form immediately after themetamorphosis of planula larvaespathiform - resembling a rounded pole in formspatial data - information about the location and shape of, andrelationships among, geographic features, usually stored as coordinatesand topologyspatial index - the ratio of reef surface contour to linear distance. As partof a monitoring program employing a chain transect protocol, the spatialindex provides a way to quantify changes in the topographical complexityof the reefspatial index - as pertaining to coral reef ecosystems, the ratio of reefsurface contour distance to linear distance. A high index indicates asurface of high rugosityspatulate - spoon or broadly blade-shapedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (37 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspawn - to produce or deposit eggs; theeggs of aquatic animals; the mass of eggsdeposited by fishes, amphibians ormollusks; offspring in great numbers ormasses; to give forth young in largenumbersFish spawn (egg mass)deposited on a coral.(Photo: Kev Jacklin)spawning - in corals, the release of gametes into the waterspecialist - an organism which has adopted a lifestyle or niche specific toa particular set of conditionsspecialist species - species that have a relatively narrow ecological nichespeciation - the evolutionary process that gives rise to a new speciesspecies - in sexually reproducing organisms, a species is a group ofgenetically related organisms, usually similar in physical appearance, thatactually or potentially interbreed and are reproductively isolated fromother groupsspecies aggregate - a group of species that are morphologically similarand therefore difficult to identifyspecies at risk - an extirpated, endangered or threatened species or aspecies of special concern (formerly called "vulnerable")species diversity - the number of different species in an area and theirrelative abundancespecies group - a group of species considered together, often becausethey are difficult to differentiate without detailed examination, e.g., verysimilar species; a group of closely related species; a superspeciesspecies of concern - species about which NOAA's National MarineFisheries Service (NMFS) has some concerns regarding status and threats,but for which insufficient information is available to indicate a need to listthe species under the Endangered Species Acthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (38 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspecies of special concern - species which are particularly sensitive tohuman activities or natural events but not endangered or threatened.Special concern was formally referred to as "vulnerable"species recovery plan - a plan for restoration of an endangeredspecies through protection, habitat management, captive breeding,disease control, or other techniques that increase populations andencourage survivalspecies richness - the number of species in an area or biologicalcollectionspecific action potential - instinctive behavior, triggered by internalchemico-physiological factors that builds to a certain level, and allows thebehavior to take place. This build up is called the specific action potential.It is responsible for an animal performing one behavior in preference toother behaviorsspecific name - the second name in a binomen and in a trinomenspeciose - having many speciesspectrometer - an instrument for measuring wavelengths of light of aspectrumspectrophotometer - an instrument for measuring speed of differentparts of light spectrumspectroradiometer - a radiometer that measures radiant energy as afunction of wavelengthspermary - an organ in which male gametes (sperm cells) are produced.The term is usually used in reference to invertebrate animalsspermatangium - the male gamete-producing reproductive organ incertain algaespermatium - a non-motile male gamete produced by a spermatangiumin red algaespermatocyte - a male gametocyte, which in the meiotic process,develops into four haploid spermatids, each of which develop into aspermatozoanspermatogenesis - the process of sperm cell (spermatozoa)development in male animals, in which the diploid number ofchromosomes is reduced by half to the haploid number in the spermatozoahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (39 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspermatophore - a packet containing sperm cells which is produced bythe male genital system for transfer to the female. This method of spermtransfer is found in some vertebrates (salamanders) as well asinvertebratesspermatozoan - a sperm cell; the male reproductive cell; the malegametespicule - one of the numerous small to minute calcareous or siliceousbodies occurring in and serving to stiffen and support the tissues ofvarious invertebrates, as in the majority of sponges, alyconarians, andmany radiolarians, holothurians and compound ascidiansspicule - minute, hard, needle-like or sharp-pointed processes orprojectionsspinate - spine-like or composed of spinesspine - a sharp hard bony structure on the skeleton or skin. Body spinesserve as predator deterrents; a usually stiff, sharp, dermal rod whichsupports a fin in fishesspiniform - spine-shapedspiny lobster - a crustacean of the FamilyPalinuridae; it lacks large claws and has aflexible, leathery tail fanSpiny lobsters in aseagrass bed.spiracle - one of the external openings communicating with the air tubes(tracheae) or book lungs of certain arthropods; a tubular opening, formedfrom the modified first gill cleft, communicating with the gill cavity ofcertain ganoid (e.g., gar pike, bowfin) and all elasmobranch fishesspiral cleavage - a developing embryo has spiral cleavage if, as itundergoes cleavage and changes from a four-cell embryo to an eight-cellembryo, the cells divide at slight angles to one another, so that the noneof the four cells in one plane of the eight-cell stage is directly over a cell inthe other plane. Spiral cleavage is characteristic of protostomeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (40 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspirocyst - an anthozoan cnida structured as a thin, single walled capsulecontaining a long, sticky, spirally coiled, unarmed tubule of uniformdiameterspirocyte - a cell in anthozoans that produces a spirocystspirotele - a type of nematocystspit - a stretch of sand, attached to the land at one end, and extendingout into the seasplicing - the removal of introns and joining of exons to form acontinuous coding sequence in RNAsplit spawning - spawning occurring over consecutive nights orconsecutive lunar cycles within a reefsplitter - refers to a taxonomist who focuses more on small differencesamong taxa, emphasizing minor variation among individuals, and whotends to recognize more taxasponge - a multicellular animal (metazoa)below the tissue grade of construction.Sponges belong to the phylum Porifera.There are approximately 5,000 livingspecies classified in three distinct groups,the Hexactinellida (glass sponges), theDemospongia, and the Calcarea (calcareoussponges). They are important componentsof a coral reef ecosystemTube sponges (PhylumPorifera)with sea fans(gorgonia) in background.sponge (2) - the egg mass of a femalecrab, which she carries attached to long"hairs" on her pleopodsDepending on the size ofthe female, female bluecrabs carry and release800,000 to 8,000,000eggs (Photo: SmithsonianEnvironmental ResearchCenter)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (41 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspongidines A-D - an antiinflammatory drug derived from marinesponges in the genus Spongiaspongin - a fibrous horny protein that forms the skeletal framework ofsome spongesspongistatin - a marine pharmaceutical, extracted from the marinesponge Hyrtios erecta, which has broad-spectrum antifungal activity. Itinterferes with microtubule activity, hence the disruption of the celldivision process (mitosis)spongocoel - the central body cavity ofsponges, which opens to the outside byway of the osculum.The central cavity of thissponge is the spongocoel.Note the banded shrimp inthe spongocoel. (Photo:Dr. Anthony Picciolo)spongocyte - a cell that secretes spongin fibers in spongesspontaneous process - a process which requires no influence fromoutside the system to proceed; a process which can proceed in an isolatedsystem; in chemistry, a spontaneous process is one which occurs with thesystem releasing free energy in some form (often, but not always, heat)and moving to a lower energy (hence more thermodynamically stable)statesporangium - an organ containing or producing spores in some algae andfungispore - a small reproductive cell produced by certain bacteria, algae,fungi and nonflowering plants. Spores contain at least one genome andare highly resistant to heat excess and dehydrationsporophyll - a fertile blade in attached brown algaesporosac - a reduced gonophore of a hydromedusan that does notdevelop into free medusae, but remains attached and produces thegameteshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (42 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataspot - a circular area of pigmentThis female three-spottedgourami, Trichogastertrichopterus, gets itscommon name from theconspicuous spots on itsflank and caudal peduncle.The third "spot" is the eye.(Photo: Miguel Pais)spur and groove - a system of shallow ridges (spurs) separated by deepchannels (grooves) oriented perpendicular to the reef crest and extendingdown the upper seaward slopespyhopping - behavior of a whale when raising the head vertically out ofthe water, usually while stationary, then sinking below the surface withoutmuch splashSQL (Structured Query Language) - a specialized language for sendingqueries to databasessquall - a brief sudden and violent wind storm, often accompanied by rainor snowsquall line - any nonfrontal line or band of active thunderstormssquamous epithelium - an epitheliumconsisting of one or more cell layers, themost superficial of which is composed offlat, scalelike or platelike cellssimple squamousepithelium, only one celllayer thick, under highpower (Photo: K. Wynne/Tyler Junior College)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (43 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasqueeze - pain or discomfort in an enclosed space (sinuses, middle ears,inside a face mask) experienced by scuba divers on descent and ascent,caused by barotrauma to the affected areasquirrelfish - a bony fish in the familyHolocentridae. Squirrelfishes are small,brightly colored spiny-finned fishes,commonly found living on coral reefs. Mostsquirrelfishes are reddish in color mixedwith silver and white. All species have largeeyes. During the day they are usually foundhiding in crevices or beneath ledges. Theyare crepuscular species, most active at lowlight levels and at nightThe squirrelfish,Holocentrus adscensionis,on a reef at Little CaymanIsland (Photo:Mary LouFrost)SST (Sea Surface Temperature) - the temperature of the layer ofseawater (approximately 0.5 m deep) nearest the atmospherestability - in ecological terms, a dynamic equilibrium among the physicaland biological factors in an ecosystem or a community; relativehomeostasis; unchanging with time. This can be a static state, wherenothing changes or a steady state where resource flows occurstable isotope - an isotope of a chemical element which is notspontaneously radioactive. Elements can exist in both stable and unstable(radioactive) forms. Most elements of biological interest (including C, H,O, N, and S) have two or more stable isotopes, with the lightest of thesepresent in much greater abundance than the others. Among stableisotopes the most useful as biological tracers are the heavy isotopes ofcarbon and nitrogen. These two elements are found in the earth, theatmosphere, and all organismsstakeholder - an individual or group with an interest in the success of anorganization in delivering intended results and maintaining the viability ofthe organization's products and services. Stakeholders influenceprograms, products, and serviceshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (44 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastalked eye - an eye carried on the end ofa stalk or peduncleA red and white hermitcrab (Dardanus venosus)illustrates stalked eyes insome crustaceans (Photo:Mary Lou Frost)standard deviation - a measure of the spread or dispersion of a set ofdata. It is calculated by taking the square root of the variancestandard error of the mean - the standard deviation divided by thesquare root of the sample size. It is the standard deviation of a sample ofmeansstanding stock - the total mass of organisms comprising all or part of apopulation or other specified group or within a given area; measured asvolume, mass, or energy; biomassstarboard - the right side of a vessel to someone facing the bow or frontstart codon - the set of three nucleotides in an mRNA molecule withwhich the ribosome starts the process of translation. The start codon setsthe reading frame for translation. The most commonly used start codon isAUG, which is decoded as methionine in eukaryotes, and as N­formylmethionine in prokaryotes; also called 'initiator codon'stasipatric speciation - instantaneous speciation caused by polyploidystatistic - an estimate based on a sample or samples of a population,providing an indication of the true population parameterstatistical analysis - the application of probability theory to quantifieddescriptive datastatistical bias - in statistics, a difference between the expected value ofan estimator and the population parameter being estimatedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (45 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastatocyst - a sensory organ possessed by many invertebrates for theperception of gravity, thus body orientation and balance. Statocysts arefound in many invertebrates. Each one has a cavity lined with sensorycells and contains a statolithstatolith - a sand grain or a calcium carbonate granule or other hardsecreted substance, found in the cavity of a statocyst. Under the influenceof gravity, a statolith makes contact with the lining of the cavity, therebystimulating sensory cells that line itstatus and trends analysis - a monitoring program designed to evaluatethe current condition of physical and biological features found in anecosystem and to detect changes that may occur over time.stellate - star-shapedThe diver is holding astellate-shaped starfish.(Photo: Copyright CorelCorp.)stem cell - a precursor cell whose daughter cells may differentiate intoother cell typesstenohaline - pertaining to an aquatic organism that can withstand anarrow salinity rangestenoky, stenokous - adapted for only a few specific ecological nichesstenotele - a stinging nematocyst which contains a spirally coiled threadarmed with spiral rows of projections. The triggered capsule, which isejected from the cell, discharges its tubular content (shaft, stylets andtubule) by a process of evagination. In doing so, the three joined styletspunch a hole into the prey, through which the long evaginating tubulepenetrates into the interiorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (46 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastenothermal - pertaining to an aquatic organism that can withstand anarrow temperature rangestenotopic - found in only one or a relatively small number of habitatsstereoblastula - a solid blastula, lacking a blastocoelstereocilium - a specialized microvillus that superficially resembles acilium and projects from the surface of certain cells, such as the auditoryhair cellsstereogastrula - a solid gastrula, lacking a gastrocoelstereotypical behavior - in animal behavior, any behavior that ananimal repeats in the same waystern - the rear (back) end of a vesselsternite - the ventral plate (or sclerite) of each segment of the body ofan arthropodStetson Reef - a deep water coral site along the eastern Blake Plateauoffshore South Carolina. This site is characterized by hundreds ofpinnacles, including a 152 m-tall pinnacle in 822 m of water whichsupports live bushes of Lophelia coral, sponges, gorgonians, and blackcoral bushes. This represents one of the tallest Lophelia lithoherms knownstevensine - a bioactive alkaloid isolated from a number of marinespongesstewardship - related to the environment, the concept of responsiblecaretaking, based on the premise that we do not own resources, but aremanagers and are responsible to future generations for their condition;the science, art and skill of responsible and accountable management ofresourcesstipe - stalk or erect portion, as in some brown algaestipitate - body mass supported by a long stalk or stipestochastic - random; exhibiting variability due to random eventsstolon - a type of stalk that lies in contact with the substrate; in corals, ahorizontal polyp outgrowth from which daughter polyps are buddedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (47 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastoloniferous - a type of colony formation in which the zooids areconnected by a common stolon which is in contact with the substrate, asfound in ectoproctans (moss animals)stoma - any of various small openings or pores in an animal body,especially an opening resembling a mouth in many invertebrates; also aminute pore in the epidermis of the leaf or stem of a plant; plural is'stomata'stomadaeum - the pharynx in anthozoans; foregut of higher animals;the anterior or oral portion of the alimentary canal of an embryostone canal - the section of the water vascular system in echinodermsthat connects the ring canal to the madreporitestonefish - species of carnivorous bonyfishes in the scorpionfish family,Scorpaenidae. Stonefishes are usuallyfound resting on the bottom, practicallyinvisible because of their resemblance tothe coral or rocky substrate. Its mottledcolor pattern and fleshy projections make anearly perfect camouflage. They areThis extremely venemousdistributed in the shallow tropical marinereef stonefish blends intoits environment. (Photo:waters of the Indopacific, feeding mostlyDr John E. Randall)upon small fishes and crustaceans. Itsdorsal fin possesses spines that release ahighly venomous toxin, making it the mostdangerous of known venomous fish. Onoccasion, stonefish stings have proved fatal to humansstony coral - a synonym of hard coralstop codon - a codon in mRNA for which there is no corresponding tRNAmolecule to insert an amino acid into the polypeptide chain. Proteinsynthesis is terminated and the completed polypeptide is released fromthe ribosome. Three stop codons are known: UAA, UAG, and UGA.Mutations which generate any of these three codons in a position whichnormally contains a codon specifying an amino acid are known as'nonsense mutations'; also called 'nonsense codons.' A stop codon signalsthe end of the amino acid chain in protein synthesishttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (48 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastorm surge - a rise above normal waterlevel on the open coast due to the action ofwind stress on the water surfaceStorm surge swamps ahouse. (Photo: NOAA)str (short tandem repeats) - repetitive segments of DNA of a pattern oflength from 2 to 10 bp, scattered throughout the genome in the noncodingregions between genes or within genes (introns), often used asmarkers for linkage analysis because of high variability in repeat numberbetween individuals. These regions are inherently unstable and susceptibleto mutationsstrain - a group of individuals within a species having a common origin; aspecific genetic variant of an organism; a pure-breeding lineage, usuallyof haploid organisms, bacteria or viruses; the descendants of a singleisolation in pure culturestrategic plan - a document used by an organization to align itsorganization and budget structure with organizational priorities, missions,and objectives. A strategic plan should include a mission statement, adescription of the agency's long-term goals and objectives, and strategiesor means the agency plans to use to achieve these general goals andobjectivesstratified sampling protocol - multiple transects for sampling a largesite at different depth to avoid double counting or missing organismsstratigraphy - the branch of geology that deals with the origin,composition, distribution and succession of stratastream bed - the stream bottom or surface over which a stream flowsstressor - a physical, chemical or biological factor that adversely affectsorganisms; an agent, condition or similar stimulus that causes stress to anorganismstriae - a thin, narrow groove or channel, or a thin line or band especiallyif several of them are parallel or close togetherstriated - marked with lines or groovesstridulation - the process in which a biological sound is produced whenone body part rubs against anotherhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (49 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastridulation - to produce a sound by rubbing two body parts together.Some fishes make sounds by rubbing together bodily structures,especially skeletal partsstripe - a straight line of pigment that canvary in width, and which can be orientedvertically, horizontally, or obliquely on thehead, body, or fins of an organismDistinctive striping of theMoorish Idol (Zancluscanescens). (Photo: Dr.James P. McVey, NOAA)strobe - pertaining to underwater photography, an artificial light device orflash device used to restore wavelengths of light filtered out by waterstrobila - a stage in the jellyfish life cycle.Free-swimming scyphozoan (truejellyfishes) medusae produce gameteswhich give rise to small polyps calledscyphistomae. After a period of growth, ascyphistoma divides transversely tobecome a strobila that resembles a stack ofdiscs. Each of the "discs" becomes anephyra larva, detaches from the strobilaand swims freely in the plankton. Theephyra larva will eventually grow into anadult medusaThe late strobila stage ofthe jellyfish Aurelia. Thissessile stage containsnumerous discs stacked ontop of one another.Eventually, each of thesediscs will break free fromthe stack as freeswimmingephyra larvae.(Photo: Rick Gillis, Ph.D.,Biology Dept., Universityof Wisconsin-La Crosse)stromatolite - a layered, fossilized deposit, mainly of limestone, formedby photosynthesizing colonial cyanobacteria and other microbes. They arethe oldest known fossils, dating back more than 3 billion years.Stromatolites are prokaryotes that thrived in warm aquatic environmentsand built reefs much the same way as coral does today. They werecommon in Precambrian time (i.e., more than 540 million years ago).Although stromatolites continue to form in certain areas of the worldtoday, they grow in greatest abundance in Shark Bay in western Australiahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (50 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastromatoporoid - a fossil calcareous spongestructural complexity - as pertaining to coral reef ecosystems, ameasure of the amount of coral surface area in relation to linear area. Forexample, branching coral reef habitats will have a higher structuralcomplexity than encrusting coral reef habitatsstructural gene - a DNA sequence that forms the blueprint for thesynthesis of a polypeptide, such as an enzymestructure-forming deep corals - any colonial, azooxanthellate coralsgenerally occurring at depths below 50 meters that provide verticalstructure above the seafloor that can be utilized by other species. Itincludes both branching stony corals that form a structural framework (e.g., reefs) as well as individual branching coral colonies, such asgorgonians and other octocorals, black corals, gold corals, and lace corals.These structure-forming deep corals include a number of very differentspecies that contribute to three-dimensionally complex habitats in deeperwaters. Structure-forming deep corals are defined as those coral specieswith complex branching morphology and sufficient size to providesubstrate or refuge for associated fishes and invertebratesstygobite - a species generally restricted to subterranean groundwaterstylet - a needle-like structure; incnidarians, when a cnidocyte is fired, it isinverted and a stylet pierces the skin of theprey allowing toxins to be injected; apiercing structure in in some invertebratemouthparts; also called "lancet"When a cnidocyte is fired,it is turned inside out anda stylet punctures theprey, injecting toxinswhich may causeparalysis. (Photo:DougBray, William Nalder/Univerity of Alberta)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (51 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datastyliform - having the shape of a pointed rodsubadult - an individual similar to the adult in appearance but not yetcapable of reproducingsubclass - a taxonomic group that is below a class and above an ordersubduction - the process in which one lithospheric plate collides with,and is forced down under another plateSubersic acid - an antiinflammatory agent derived from marine spongesin the genus Subereasubfamily - a taxonomic group that is below a family but above a genussubgenus - a taxonomic group that is between a genus and a speciessubgular - below the throatsubkingdom - a taxonomic group comprising a major division of akingdomsubmarine canyon - a long, narrow, steep-walled undersea valleysubmarine groove - a troughlike depression with vertical to overhangingwalls which cut across the reef front at right anglessubmerged bank - a large, relatively flat shoal or other expansivesubmerged feature that is markedly shallower than the surrounding oceanbottomsubmerged cultural resource - an historical ship, aircraft, or othercultural artifact that has come to rest on the ocean bottomsubmersible - a small underwater vessel(submarine) which requires a support shipto transport it to and from the diving area.It is used primarily for oceanographicresearch. There are also some commercialsubmersibles that carry tourists belowscuba diving depths to view coral reef wallsThe three-personsubmersible Alvin coulddive to just under 15,000feet, enabling it to reach86 percent of the world'shttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (52 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Dataocean floor. (Photo: RodCatanach, Woods HoleOceanographic Institution)suborbicular - nearly circularsuborbital - an area below the eyesuborder - a taxonomic group that is a subdivision of an ordersubordinate - in taxonomy, belonging to a lower or inferior taxonomicrank. For example, a genus is subordinate to the family to which it belongssubordinate taxon - in taxonomy, a taxon at a lower rank than thetaxon of the same coordinate group with which it is comparedsubphylum - a taxonomic group ranking that is between a phylum and aclasssubplocoid form - a coral growth form in which the corallites aresometimes separated by coenosteumsubpopulation - a well-defined set of interacting individuals thatcompose a proportion of a larger, interbreeding populationsubradular organ - a sensory organ in chitons (Polyplacophora-Mollusca) which can be protruded and pressed against the substrate in the searchfor foodsubset - in mathematics, a subset of a given set is a collection of thingsthat belong to the original setsubsidence - a gradual sinking of land with respect to its previous level;the slow sinking of air, usually associated wit high-pressure areassubspecies - a taxonomic group that is a division of a species. It usuallyevolves as a consequence of reproductive isolation of one or morepopulations within a speciessubspecific name - the third term of the trinomen, a subspeciessubstrate - the material making up the base upon which an organismlives or to which it is attachedsubterminal - located some distance away from the endhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (53 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasubtidal - permanently below the level of low tide; a continuallyunderwater environmentsubumbrella - the lower or oral surface of a medusa or jellyfishsubunit - in protein chemistry, an individual polypeptide chain in aprotein which contains more than one polypeptide chainsucker - a structure, such as those at theend of tube feet of echinoderms, or on thetentacles of octopods and squids, that canproduce a small vacuum and enable theanimal to stick to many surfacesSuckers on an octopustentacle allow the animalto adhere to almost anysurface. (Photo: J'nieWoosley/NationalZoological Park)sucker - any organ which has an adhesive actionsucking disk - a disk-like structure used by some fishes to attach itself torocks or vegetationSula Reef - a deep water Lophelia reef located on the Sula Ridge on theMid-Norwegian shelf at depths of 200 - 300 m. A very large deep watercoral reef, it is about 13 km long, 700 m wide, and up to 35 m highSulu-Sulawesi Seascape - an area of approximately 900,000 squarekilometers (about 347,492 square miles) that includes the Sulu andSulawesi Seas, in the national waters of three independent nations of theSoutheast Asian Region: Indonesia, Malaysia, and the Philippinessummit - the highest part or point; the topSundarbans - the world's largest mangrove forest located in Bangladeshat the edge of the delta where the Ganges, Brahmaputra and MeghnaRivers come togethersuperclass - a taxonomic group that is below a phylum and above a classsuperfamily - a taxonomic group that is below an order but above afamilyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (54 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasuperficial cleavage - a type of cleavage, typical of centrolecithal eggsfound in most arthropods, in which karyokinesis (nuclear division) occurswithout cytokinesis (cytoplasmic division), resulting in a syncytium.Cleavage furrows form to separate the nucleiSuperfund - money collected from a special tax on chemical feedstocksand raw petroleum. When a responsible party can not pay, Superfundmoney can be used by the US Environmental Protection Agency (USEPA)to investigate, evaluate, and clean up the hazardous waste sites identifiedon the National Priorities List (NPL); Superfund is also used to refer toUSEPA's program for investigation and cleanup of hazardous waste sitessupergene - a group of neighboring genes on a chromosome that tend tobe inherited together and sometimes are functionally relatedsuperior - the anatomical term for "above" (e.g., the head is superior tothe shoulder)supermale - a male which does not change sex and is the principalspawnersupernatant - the soluble liquid fraction of a sample after centrifugationor precipitation of insoluble solidssupernumerary - superfluous or extrasuperorder - a taxonomic group that is above an order and below a classor subclasssuperorganism - an "organism" which consists of many organisms, suchas coral or the Portuguese man-of-war (a superorganism appears to beone organism, but in fact is a number of colonial animals joined together);a social unit of animals where division of labor is highly specialized andwhere individuals are not able to survive by themselves for extendedperiods of time. An ant or bee colony is another example of asuperorganism. The concept of superorganism is controversial amongsome scientistssupporting cell - in cnidarians, a columnar cell of the epidermis orgastrodermis whose apical end may bear microvilli, cilia, or flagellasuppressor gene - a gene that can reverse the effect of a mutation inother genes, i.e., a gene that suppresses the phenotypic expression ofanother gene, especially of a mutant genesupraesophageal gangia - a nerve plexus above the esophagus in thehead of malacostracan crustaceanshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (55 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasupraesophageal ganglion - in arthropods, worms, and otherinvertebrates, the supraesophageal ganglion forms the brain, whichtypically contains integrative centers for the major sensessupraorbital - an area above the eyesuprapsammon - organisms which swim just above sand and aredependent upon it as a food sourcesupratidal - above the level of high tide; a terrestrial environment that isinfluenced by proximity to the sea. Such influences include sea spray, seabreezes and aeolian processes, and geological and biological “spillover”such as dune developmentsurf - a collective term for "breakers"; the wave activity in the areabetween the shore line and the outermost limit of breakers. In literature,surf usually refers to the breaking waves on shore and on reefssurface feeder - an organism, usually afish, that takes its food from the air/waterinterface, or feeds just below the watersurface, e.g., a needlefishNeedlefish feeding at thesurface in Oahu (Photo:Mary B. Hollinger/NOAA)surface interval - the length of time that a scuba diver spends on thesurface between two consecutive divessurface water - an open body of water, such as a stream, lake, reservoiror wetlandsurge channel - a deep channel in the windward side of a coral reefthrough which water moves in and out of the reefhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (56 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasurgeonfish - any species of brightlycolored reef-dwelling bony fishes in thefamily Acanthuridae which have laterallycompressed bodies and possess one ormore sharp erectile spines near the base ofthe tail; also called "tangs" and "doctorfish"A school of surgeonfish(blue tang) in the FloridaKeys (Photo: Florida KeysNational Marine Sanctuary)surrogate species - small number of species whose distributions andabundances are well known; used in conservation planning; assumed toreflect the distribution and abundance of the regional biota; subsumesindicators and umbrella species; also called "focal species"survey (biology) - the systematic and usually standardized collection orinventorying, processing, and analysis of representative portions of abiological community or defined site with its habitats, to determine thecommunity structure and functionsuspension feeder - an organism thatfeeds by capturing particles suspended inthe water column. A synonym of filterfeederSuspension-feedingsponge among corals.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (57 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasustainability science - a multi-disciplinary approach to science thatrecognizes the limitations of traditional scientific inquiry in dealing withthe complex reality of social institutions interacting with naturalphenomena. Sustainability science seeks to improve on the substantial butlimited understanding of nature-society interactions gained in recentdecades. This has been achieved through work in the environmentalsciences estimating and evaluating human impacts, and evidence fromsocial and development studies that takes into account environmentalinfluences on human well-being. Urgently needed is a betterunderstanding of the complex dynamic interactions between society andnature so that the trend towards increasing vulnerability is reversedsustainable development - those efforts to guide economic growth inan environmentally sound manner with an emphasis on natural resourceconservationsustainable yield - the number or weight of organisms in a populationthat can be harvested without reducing the population biomass from yearto year, assuming that environmental conditions remain the samesuture - the line of union of two bones or platesswamp - a type of wetland that is dominated by woody vegetation. Whenit does not, it is usually termed a marsh. Swamps may be fresh or saltwater and tidal or non-tidalswath - the area of Earth's surface or atmosphere measured by aninstrument during a single satellite overpass; a path or stripsweeper - any of about 25 species of bonyfishes in the family Pempheridae. Sweepersmay be found around coral reefs in theAtlantic, Pacific, and Indian Oceans. Theyhave deep, laterally compressed bodies anda single, short dorsal fin. During the day,schools of sweepers may hover in caves,and come out at night to feed on planktonA glassy sweeper(Pempheris schomburgki)photographed at Bimini(Photo: Mark Rosenstein/Active Window Productions(markrosenstein.com))sweeper polyp - a polyp that acts in an aggressive manner by stingingneighboring corals and sessile invertebrateshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (58 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasweeper tentacle - A coral polyp tentaclethat has an increased number ofnematocysts and elongates in order to'sting' neighboring corals and sessileinvertebrates. A tool in the competition forspace and resourcesA hammer coral (right)thrusts out a sweepertentacle towards amushroom anemone (left).(Photo: Scott Brooks)swell - the persistence of a wind-formedwave after the wind ceasesAn ocean swellswimmeret - one of several flat, fringed,and usually bilobed, paired appendages onthe ventral surface of the abdominalsomites of decapod crustaceans, used forswimming and reproductionThe arrow points to aswimmeret of a juvenilelobster. (Graphic: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (59 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasyconoid - a body form of mediumcomplexity in sponges where the body wallhas become folded and the choanocytes(flagellated collar cells) are not locatedalong the spongocoel, but along radialcanals. Water enters the sponge through aseries of incurrent canals and passesthrough internal pores called prosopylesinto the radial canals, which are lined withflagellated choanocytes.- It is the action ofthese choanocytes that keeps water movingthrough the sponge. From the radial canals,water then enters the central spongocoelthrough pores called apopyles, to exit tothe environment through a single opening,the osculum.Anterior end of a syconoidsponge in which the bodywall has been folded into aseries of internal andexternal canals.-1=osculum; 2= spongocoel;3= ostium; 4= radialcanal; 5= incurrent canal;6= apopyle. (Photo: RickGillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)Symbiodinium microadriaticum - a dinoflagellate symbiont(zooxanthellae) in marine cnidarianssymbiont - a symbiotic organism; either oftwo organisms participating in a symbioticrelationshipThese clownfish exist in asymbiotic relationship withthe sea anemone; theanemone providesprotection and theclownfish feed and cleanthe anemone. Differentclownfish species chooseparticular anemonespecies for their hosts.(Photo: Copyright CorelCorp.)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (60 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasymbiosis - a relationship between twospecies of organisms in which bothmembers benefit from the association(mutualism), or where only one memberbenefits but the other is not harmed(commensalism), or where one memberbenefits at the expense of the well-being ofthe other (parasitism)A clownfish has asymbiotic relationship witha sea anemone, findingprotection within theclump of stinging cellbearingtentacles.sympatric species - different species that live in the same area but areprevented from successfully reproducing by a reproductive isolatingmechanismsymplesiomorphy - in evolution, a shared primitive charactersympodial growth - growth of a coral colony in which the colony doesnot produce a trunk. New polyps offshoot along the edges of adult polyps.The youngest polyps are always on top of colonysynapomorphy - in evolution, a shared derived charactersynapse - the site where neurons communicate with each other. Asynapse is a small gap that physically separates neurons. Axon terminalsof a neuron sending a nervous impulse (the presynaptic neuron) releaseneurotransmitters into the synapse. The neurotransmitters diffuse to theother side (the postsynaptic side) where they bind to receptors on thepostsynaptic neurons, thereby relaying the nervous impulsesynapticulum - a conical or cylindrical supporting process, as thoseextending between septa in some coralssynbiotic - an appropriate synergistic combination of pre- and probioticssynchronous - occurring at the same timesynchronous breeding - a breeding system in which all members of thepopulation tend to breed at the same timesynchrony - the relation that exists when things occur at the same timehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (61 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasyncytium - a mass of cytoplasmcontaining several nuclei and enclosed in amembrane, but having no internal cellboundaries, e.g., skeletal muscle cellsSkeletal muscle cells are amultinucleate syncytium.The dark stained bodiesare nuclei. (Photo: GeneralCollege, University ofMinnesota)syndrome - a set of signs occurring together; the sum of signs of anydiseased statesynecology - the branch of ecology that deals with whole communitiesand the interactions of the organisms within themsynergism - an interaction between agents (eg, drugs) that produces aneffect greater than the combined effects of the same agents usedseparatelysyngameon - a group of discrete morphological units (semispecies) thatare interfertile; a cluster which comprises several morphospecies, i.e., "allof species or semispecies linked by frequent or occasional hybridization innaturesyngamy - the process of union of two gametes, also called fertilization.It encompasses both plasmogamy and karyogamy.synomone - a chemical substance produced by one organism that isbeneficial to both itself and a member of another speciessynonym - in taxonomy, one of two or more scientific names that arespelled differently, but refer to the same organismsynonymous substitution - in molecular biology, a nucleotidesubstitution that does not result in an amino acid replacementsynonymy - in taxonomy, the relationships between different namesapplied to the same taxon; a chronological list of taxonomic names whichhave been applied to a single taxon, including authors and dateshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (62 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef Datasynopsis - in taxonomy, a brief description of the main characters of ataxonsyntopic - relating to or displaying conditions as they existsimultaneously over a broad area; pertaining to populations or speciesthat occupy the same macrohabitatsyntype - in taxonomy, each specimen of a type series from whichneither a holotype nor a lectotype has been designated. The syntypescollectively constitute the name-bearing typesystemic - a condition or process that affects the body as a whole, notlocalized to one area or system(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=s (63 of 63) [2/26/2008 9:15:28 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: TThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZT cell - one type of white blood cell that attacks virus-infected cells,foreign cells, and cancer cells. T cells also produce a number ofsubstances that regulate the immune response; also called "Tlymphocyte." T stands for the thymus gland, where T lymphocytes matureT cell receptor - an antigen-binding protein, located on the surfaces ofCTLs (cytotoxic or killer T cells); a transmembrane protein on the surfaceof T cells that recognizes antigens associated with MHC proteins on thesurface of phagocytest-test - a statistical procedure for testing the difference between two ormore means. It is used for estimating the probability that the means havebeen drawn from the same or different populationst. - according to; on the evidence of (teste)t. c. - in the volume cited (tomus citate)table reef - an isolated flat-topped coral reef which reaches the surfacebut lacks a lagoontabula - a horizontal partition (or floor) dividing the corallite skeleton;one in a series of horizontal plates traversing a coral with a massivecalcareous skeleton. The polyps extend only down to topmost tabulahttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (1 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatabulate - having a flat surfaceCoral (Acropora) having atabulate shape.tachyauxesis - rapid growth; a part or structure that grows at a quickerrate than the organism as a wholetactile - pertaining to information, interpretations, and behavior derivedfrom the sense of touchtactile comb - a sensory projection on the umbrella margin of a medusa.It bears long, stiff hairstaeniform - ribbon-like; elongate, compressed and deep-bodiedtagging - an identification system involving various methods (fin clipping,coloring, biotelemetry, radioactive markers, tattooing, branding, tagging,etc.), used for individual identification and for studies on movement,growth and other biological activities; also called "marking"Taino - Pre-Columbian indigenous inhabitants of the Bahamas, GreaterAntilles and the northern Lesser Antillestalus slope - a synonym of reef baseTanaidacea - a minor order of small (1 mm–2 cm in length) crustaceansin the class Malacostraca. Of the approximately 1000 species, most aremarine, but some are found in coastal freshwater and estuarine habitats.They are among the most diverse and abundant animals in some marineenvironments. Most species are benthic, although some species may beplanktonic. They are found at a wide variety of depths, from the littoralzone to deep waters, in all oceans of the world, from tropical totemperate, and even in polar regionshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (2 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatank - a hollow steel or aluminum cylinder,used to contain compressed air or otherbreathing gas mixtures used by scubadivers for an air supply; also called acylinder or bottleA NOAA diver breathingcompressed air from thesteel scuba tank (orcylinder) attached to hisBCD (buoyancy controldevice). The diver isentering the water usingthe giant step technique.(Photo: NOAA NationalUndersea ResearchProgram)taphonomy - the study of everything that happens to an organism’s bodyafter it dies; includes probable cause and manner of death, movement ofthe body, chemical and physical alteration, burial, decomposition,diagenesis and fossilizationtarget - in genomics, the DNA or RNA being hybridized to a microarray;for diagnostic tests, the molecule or nucleic acid sequence that is beingsought in a sampletau - the third charged lepton (in order of increasing mass), with electriccharge -1tautonymy - in taxonomy, the use of the same word for the name of agenus-group taxon and for one of its included species or subspeciesTautra reef - one of the world’s shallowest deep-water coral reefs,located in Norwegian waters at only 39 meters water depthtawny - brownish yellow colortaxis - an innate behavioral response to a directional stimulus (a stimulusfrom a particular direction) whereby the organism either moves toward(positive taxis) or away (negative taxis) from the stimulushttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (3 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datataxocene - a taxonomically related set of species within a communitythat have similar ecological functionstaxol - a pharmaceutical, derived from the yew tree, which is a potentanti-tumor drugtaxon - a taxonomic group or entitytaxonomic group - a taxon with all its subordinate taxa and theirindividuals; e.g. the taxonomic group Crustacea consists of all crustaceansand their taxataxonomic group - a taxon with all its subordinate taxa and theirindividuals; e.g., the taxonomic group Crustacea consists of allcrustaceans and their taxataxonomic key - a tabulation of diagnostic characters of taxa indichotomous couplets to facilitate rapid identificationtaxonomy - the science and methodology of classifying organisms basedon physical and other similarities. Taxonomists classify all organisms intoa hierarchy, and give them standardized Latin or Latinized names. Thereare seven main levels of classification in the hierarchy. They are, frommost to least inclusive: Kingdom; Phylum (or Division for algae, fungi, andplants); Class; Order; Family; Genus; and Species. Taxonomists describenew species, classify organisms, and study speciation, the evolution ofnew speciesteal - greenish blue colortechnology - the creation of products and processes for the purpose ofimproving human chances for survival, comfort level, and quality of lifetectal - pertaining to the roof of a structure, e.g. the top of the head orbrainteleost - a large group of fishes (infraclass Teleostei) which contains mostof the bony fishestelolecithal - an egg cell in which the yolk is not evenly distibutedthroughout the cytoplasm, but is concentrated in one location, andcleavage is incomplete, e.g., a bird egghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (4 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatelomere - the terminal part of a eukaryotic chromosome. Thesespecialised structures are involved in the replication and stability of linearDNA molecules. In vertebrate cells, each telomere consists of thousandsof repetitive copies of the same DNA sequence. Telomeres shorten eachtime a cell divides; when one or more telomeres reaches a minimumcritical length, cell division stops, signaling cell senescence. Thismechanism limits the number of times a cell can dividetelson - the terminal joint or movablepiece at the end of the abdomen ofcrustaceans; middle piece of the tail fanThe telson, flanked byuropods, is the centralpart of the tail fan.(Graphic: MaineDepartment of MarineResources)temperate - region in which the climate undergoes seasonal change intemperature and moisture. Temperate regions of the earth lie primarilybetween 30 and 60 degrees latitude in both hemispherestemplate - a molecule that serves as the pattern for synthesizing anothermolecule ; in the process of replication or transcription, the strand of DNAthat serves as the source of informationtemporal niche - the functional position of an organism in itsenvironment as determined by the periods of time during which it occursand is active theretemporary threshold shift - in mammals, a temporary increase in thethreshold of hearing (minimum intensity need to hear a sound) at aspecific frequency that returns to its pre-exposure level over timetendril - a slender elongated thread-like organ which may cling to objectsfor supporttendriliform - having the form or shape of a tendrilhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (5 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatentacle - a finger-like evagination of thebody wall. Tentacles surround the mouthsof coral polyps, anemones and otherinvertebrates. They are used for capturingprey, defense, reproduction, gas exchange,and light absorptionTentacles of a seaanemone. Each tentaclecontains stinging cells(nematocysts) used fordefense and food capture.(Photo: Dr. AnthonyPicciolo)tentacle-tube-foot suspension feeder - a suspension feeder that trapsparticles on distinct tentacles or tube feet (in echinoderms)tentacular bulb - the expanded base of a medusa's tentacle. It functions in digestion and nematocyst formation; also called " ocellar bulb"tentacular lobe - a lobe at the point of insertion (beginning) of a septumtentacular sheath - one of the two cavities in the sides of the body of ctenophores (comb jellies) into which the tentacles can be withdrawntentaculozooid - a dactylozooid (a colonial hydrozoan polyp that possesses a large, nematocyst-bearing fishing tentacle, and functions indefense and in food capture)tera - a metric prefix meaning 10 to the 12th power, or one trillionterabyte - a measure of data size. A terabyte of data is equivalent to1,000 gigabytes of data or 1,000,000 megabytes of data. One petabyteequals 1,000 terabytesteratogen - a chemical or other factor that specifically causesabnormalities during embryonic growth and developmentterete - round in cross-section and taperingtergite - a hard plate (sclerite) forming one of the constituents of thedorsal exoskeleton (tergum) of an animal, such as an arthropodtergum - the back of an animalterminal - at the end positionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (6 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Dataterminal male - in fishes, a supermale; the dominant maleterminal taxon - one of the units of a phylogenetic tree whose collectivephylogeny is reconstructed, i.e., the undivided tips of a tree (usuallycontemporary taxa). Terminals may be higher taxa, species, populations,individuals, fossils or even genesterminator - a sequence of DNA bases that stops RNA polymerase fromsynthesizing RNAterminus - the endternary name - in taxonomy, the trinomenterpenoid - a class of organic compound produced by soft corals fordefense and for aggressive colonization of new substratesterri - a prefix meaning "earth"territoriality - the defense of a given areaterritory - an area over which an animal establishes jurisdiction. The areais defended and no other individuals of the same species, and often ofother species, are allowed inside, except for prospective breeding partnersduring a reproductive boutTerritory (Office of Insular Affairs) - an incorporated United Statesinsular area, of which only one exists currently, Palmyra Atoll. With anarea of 1.56 square miles, Palmyra consists of about fifty small islandsand lies approximately one thousand miles south of Honolulu, HIterritory (OIA) - an unincorporated United States insular area, of whichthere are currently thirteen, three in the Caribbean (Navassa Island,Puerto Rico and the United States Virgin Islands) and ten in the Pacific(American Samoa, Baker Island, Guam, Howland Island, Jarvis Island,Johnston Atoll, Kingman Reef, Midway Atoll, the Northern Mariana Islandsand Wake Atoll)tertiary consumer - a carnivore which eats other carnivoresTESS (Threatened and Endangered Species System) - the USFWSThreatened and Endangered Species System (TESS) is a list of threatenedand endangered animals and plants native to the United States, and theoutlying Areas of the United States, the Freely Associated States, andTrust Territoryhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (7 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatessellated - a checkered appearanceA tessellated blenny.(Photo: NOAA)test - shell or hard outer covering ofechinoderms and ascidiansDorsal view of sea urchintest.test animal - an individual used for experimental research purposestetraspore - a haploid spore in the red algae life cycle which is themeiotic product of the tetrasporangium of a diploid tetrasporophyte. Thetetraspores are released, settle, and grow into gametophytestetrasporophyte - diploid phase in the life cycle of red algae whichproduces haploid tetraspores.The tetrasporophyte is the site of meiosis,more specifically, the tetrasporangia where haploid tetraspores areproduced. These tetraspores are released, settle, and grow into thegametophyte, completing the basic red algal life historytetraxon - in sponges, a spicule with four rayshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (8 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatetrodotoxin (TTX) - tetrodotoxin (TTX) isan especially potent marine neurotoxin,named after the order of fish from which itis most commonly associated, theTetraodontiformes (includes the puffers,porqupine fish, blowfish, cowfish, boxfish).The toxin appears in high concentrations inthe gonads, liver, intestines and skin ofpufferfish. The fatality rate when injestedmay be as high as 60 percent. Tetradotoxinis more than 10,000 times deadlier thancyanide. Other marine and terrestrialA specially licensedorganisms have been found to store TTX,Japanese chef preparesfor example, the Australian blue-ringedfugu, the ever-so-slightlyoctopus, parrotfish, triggerfish, gobies,tainted fillet of theextremely poisonousangelfish, ocean sunfish, globefish,blowfish, whose internalseastars, starfish, xanthid and other crabs,organs containa horseshoe crab, a number of marinetetrodotoxin.snails, flatworms, tunicates, ribbonworms,mollusks and marine algae (Jania spp.)Terrestrial organisms include the Harlequinfrogs (Atelopus spp.), three species of California newt and other easternsalamandersTexas Automated Buoy System (TABS) - Texas A & M University’sGeochemical and Environmental Research Group (GERG) operates twodata buoys near the Flower Garden Banks National Marine Sanctuary atSites N and V. The buoys measure winds, air temperature and humidity,atmospheric pressure, conductivity, and surface currents and report thedata in near real time though the Texas Automated Buoy Systemthallus - the vegetative body of a plant or alga that is not differentiatedinto organs, such as roots,stems and leavesthamnasteroid form - a coral growth form in which the septa ofadjacent corallites are confluent, often sinuous and twistedthanatocoenosis - an assemblage of organisms or their parts broughttogether after their deaths, as for example, by flowing water; 'deathassemblage'the destruction resuspension - the process in which sediment particleson the substrate are brought back into water column suspension bywaves, tides, or windtheca - the calcareous wall of the corallitethelytoky, thelytokous - parthenogenetic production of females fromunfertilized eggs; reproduction that is exclusively female with no malecontribution to the younghttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (9 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatheoretical probability - the chances of events happening asdetermined by calculating results that would occur under idealcircumstancestheory - a comprehensive explanation of a given set of data that hasbeen repeatedly confirmed by observation and experimentation and hasgained general acceptance within the scientific communitythermal stress anomaly (TSA) - an area of the ocean surface which isexperiencing warmer sea surface temperatures (SSTs) than the typicalmaximum temperature reached at that location. The typical maximumtemperature, which generally occurs in late summer, is important becausethis is the highest temperature to which corals in a particular location areaccustomed. So, when the SST exceeds this by some threshold (typicallyone degree C) corals are in danger of bleaching. Many factors such assalinity, insolation, winds, and local currents play a role in coral reefbleaching, but clearly extreme SSTs are a critical factor; also called"hotspots"thermocline - the region below the surface layer of the ocean or lake,where the temperature gradient increases abruptly (i.e. wheretemperature decreases rapidly with increasing depth). A thermocline mayreach the surface and become a front. It is usually an ecological barrierand its oscillations have significant consequences on populationdistribution and ocean productivitythermohaline circulation - the density-driven convective circulationsystem of the world's oceans. Warm Atlantic water moves northwardalong the axis of the Gulf Stream, and evaporation increases waterdensity while releasing heat to the colder atmosphere in the NorthAtlantic. Once significantly dense, the water sinks into the deep ocean,forming a downward limb of a giant conveyor-like circulation that extendsaround the world's oceansthermoreceptor - a neurological receptor that detects changes intemperaturethigmotactic - responding to touch or outer surface contactthoracic - pertaining to the chest areathorax - the central region of a crustacean bodythrombosis - the development of a blood clot in the circulatory system.Compounds derived from marine sponges are potential drugs for thetreatment of thrombosishttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (10 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datathylakoid - a phospholipid bilayer membrane within a chloroplast that isfolded repeatedly into a stack of disks called grana. The molecules thatperform the light reactions of photosynthesis are all embedded within themembranes of the thylakoidsthymine - one of the four bases in DNAthat make up the letters ATGC, thymine isthe "T". The others are adenine, guanine,and cytosine. Thymine always pairs withadenineDiagram of the chemicalstructure of thymine, oneof the four nitrogenousbases in DNA.tidal channel - a channel that dissects the tidal flat surface. It is formedand maintained by tidal currentstidal current - a horizontal movement of the water caused bygravitational interactions between the Sun, Moon, and Earthtidal delta - a delta formed at both sides of a tidal inlettidal flat - a marsh or sandy or muddy coastal flatland which is coveredand uncovered by the rise and fall of the tidetidal inlet - a waterway from the open ocean into a lagoontidal pool - an area in the littoral zone thatretains sea water at a low tide because of adepression or arrangement of rockysubstrateA tidal pool. The seawateris replemnished with eachincoming tide. Tidal poolsprovide a unique habitatfor some fishes andinvertebrates (Photo:Albert E. Theberge, NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (11 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatidal range - the difference in water level between successive high andlow tidestide - the periodic rising and falling of thewater that results from the gravitationalattraction of the moon and sun acting onthe rotating earthHigh tide combined with astorm threaten a pier.(Photo: Mary Hollinger)tide gauge - a device for measuring the height (rise and fall) of the tide;especially an instrument for automatically making a continuous graphicrecord of tide height versus timetide tables - tables which give daily predictions of the times and heightsof high and low waters. These predictions are usually supplemented bytidal differences and constants through which predictions can be obtainedfor numerous other locationstidelands - the zone between the mean high water and mean low waterlines. It is identical with intertidal zone (technical definition) when thetype of tide is semi-diurnal or diurnalTIFF (Tag Image File Format) - a common format for exchangingraster graphics (bitmap) images between application programs, includingthose used for scanner imagestime lapse photography - a photographic process in which a series ofphotographs are taken of the same basic scene at regular, timed intervalsfrom the same viewpointtime zone - a region of the Earth that has adopted the same standardtime, usually referred to as the local time. Most adjacent time zones areexactly one hour apart, and by convention compute their local time as anoffset from Greenwich Mean Time (GMT)tinctorial - relating to staining or coloringhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (12 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef DataTisler Reef - a deep water Lophelia reef located in the Skagerrak, thesubmarine border between Norway and Sweden, at depths of 74 to 155m. It has the world's only known yellow Lophelia pertusa coralstissue - a group of cells with a specific function in the body of anorganism. Tissues are composed of nearly identical cells and theirproducts, and are organized into larger units called organsTOAD (Towed Optical AssessmentDevice) - a device employing videographyused chiefly at night on the NOWRAMPcruises to the Northwestern HawaiianIslands. TOAD consists of a video cameraand lights on a frame designed to be towedjust above the substrate. The video is usedto certify or ground truth acoustic habitatsensing. Specifically, the TOAD videos showthe composition of the bottom in a fewlocations, such as sand, rubble, sea grass,coral, etc. It allows interpretation of broadarea acoustic data by comparing it to thevideo informationA towed opticalassessment (TOAD) deviceis used to record bottomcharacteristics (Photo:NOAA)tom. - volume (tomus)tombolo - a land form such as a spit or barwhich forms an isthmus between an islandand a mainland shore, or between twoislandsa tombolo connects thesmall island with themainland of a largerisland, Dominica, in theWest Indies. The Atlanticocean is to the right of thetombolo, and theCaribbean Sea is to theleft.topodeme - a deme (a local interbreeding population) occupying anyspecified geographical areatopographic map - a map containing contours indicating lines of equalsurface elevation (relief)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (13 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatopography - the set of natural or man-made physical features found ona map or chart of a region, such as mountains, valleys, bridges, and theshapes of landforms. A topographic map is a two-dimensional mapportraying three-dimensional landforms; the relief features or surfaceconfiguration of an areatopology - the branching sequence of a phylogenetic treetoponym - a place nametopotype - in taxonomy, a specimen collected at the type localitytopotypical population - in taxonomy, a population occurring at thetype localitytopsentin - a marine pharmaceutical extracted from the spongesTopsentia genitrix, Hexadella sp., and Spongosorites sp. The topsentinfamily of compounds possesses potent anti-inflammatory propertiestornaria larva - a ciliated, free-swimmingpelagic larva of a hemichordateYoung tornaria ofBalanoglossus biminiensis.(Photo: University ofSaskatchewan Archives)torpor - a dormant statetorsion - twisting of the body during development so that the posterior ofthe body takes an anterior position over the headhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (14 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatotipotent - the state of a cell that has the potential to develop into anyand all adult cell types as compared with a differentiated cell whose fate isdeterminedtowfish - an instrument, e.g., a side scan sonar, towed behind a shiptoxicant - any substance which is potentially toxictoxicity - the action of poisons, including xenobiotics, on biochemicalreactions or processes in living organisms or ecological systemstoxicology - the scientific discipline involving the study of the actual orpotential danger presented by the harmful effects of substances (poisons)on living organisms and ecosystems, of the relationship of such harmfuleffects to exposure, and of the mechanisms of action, diagnosis,prevention and treatment of intoxicationstrabeculum - in corallites, one of many rods or axial structures composedof fibrous tufts (sclerodermites), which form teeth along the upper septalmargintrace - in biology or ichnology, a visible mark (as a track, trail, burrow)left by the passage of an animal; in chemistry, an unmeasureable orinsignificant quantitytrace fossil - a sedimentary structure consisting of a fossilized track,trail, burrow, tube, or other impressions or depressions left from the lifeactivities of an animal, plant, insect, or natural force that has beenpreserved in soft sediment and lithified to solid rock; Any indication ofprehistoric organic activity, such as tracks, trails, burrows, or nests; alsocalled ichnite or ichnofossiltrace fossil classification - a classification system that parallels theLinneaean taxonomic classification of organisms. In trace fossilnomenclature, a binomial is used, with a genus and specific epithet. Withtrace fossils, the genus is called an ichnogenus, and the species is anichnospecies. The name is similarly italicized, and in full reference to theauthor plus the year of publication should be cited. "Ichnogenus" and"ichnospecies" are commonly abbreviated as "igen." and "isp.",respectivelytrade winds - a system of relatively constant low level winds that occurin the tropics. The trade winds blow from the northeast to the equator inthe Northern Hemisphere and from the southeast to the equator in theSouthern Hemispherehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (15 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatranscription - the process by which the genetic information encoded ina linear sequence of nucleotides in one strand of DNA is copied into anexactly complementary sequence of mRNA (messenger RNA). The mRNAthen carries this information to the cytoplasm of the cell, where it servesas the blueprint for the manufacture of a specific proteintransducer - the electromechanicalcomponent of a sonar system that ismounted underwater and converts electricalenergy to sound energy and vice versaSplit beam transducerreceives echoes with fourdifferent quadrants(Graphic: AmericanFisheries Society)transduction - transfer of genetic material from one cell to another bymeans of a virus or phage vectortransect - a line used to survey thedistribution of organisms or substrateacross a given area. Sample plots or pointsare established along the transect forcollecting dataNOAA divers collect dataalong a transect line.transfection - infection of a cell with nucleic acid from a virus, resultingin replication of the complete virus; gene transfer into eukaryotic cellstransforming gene - a gene that causes normal cells to change intocancerous tumor cells; also called an 'oncogene'transgenic - having genetic material (DNA) from another species. Thisterm can be applied to an organism that has genes from another organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (16 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatransient - species or population that migrates through a given area, butdoes not breed or "winter" theretransient aggregation - an aggregation characterized by individuals thatmigrate over long distances and over a short reproductive seasontransition - in molecular biology, a nucleotide substitution from onepurine to another purine, or from one pyramidine to another pyramidinetranslation - in genetics, the process whereby genetic information codedin mRNA (messenger RNA) directs the formation of a specific protein at aribosome in the cytoplasmtransmissometer - an instrument for measuring transmission of lightthrough a fluidtranspiration - the loss of water vapor from a plant to the outsideatmosphere, mainly through the stomata of leaves and the lenticels ofstemstransport - an exchange of molecules (and their kinetic energy andmomentum) across the boundary between adjacent layers of a fluid oracross cell membranestransposon - a short DNA sequence that has the ability to move fromone chromosomal position to another one in the genome, a process calledtransposition ; also known as "jumping gene"transverse - crosswisetransversion - in molecular biology, a nucleotide substitution from apurine to a pyramidine, or vice versatrap - a portable, enclosed device with one or more gates or entrancesand one or more lines attached to surface floats; also called a pottrauma - any sudden physical injury or damage to an organism caused byan external force or violence. Trauma is also used to describe severeemotional or psychological shock or distresstraumagenic device - any part of an organism which is concerned withthe causation of physical injury to another, such as teeth, spines, darts,rasping organs, beak bites, etchttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (17 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatrawler - a fishing vessel that tows anopen-mouthed fishing net drawn along thesea bottom or in the water columna double-rigged shrimptrawler with bag of onenet on board (Photo:NOAA)trench - a deep steep-sided depression in the ocean floor caused by thesubduction of oceanic crust beneath either other oceanic crust orcontinental crusttrial and error learning - a form of associative learning. Trial and errorlearning occurs when an animal connects its own behavior with aparticular environmental response. If the response has a positivereinforcement, or it is favorable to the animal, the animal will repeat thebehavior in order to receive the same response again, possibly to receivea reward. If the response is unfavorable, such as causing pain, the animalwill avoid the behaviortriaxon - in sponges, a spicule with threeraysMicroscopic triaxonspicules in a sponge.(Photo: NOAA)tribe - a taxonomic group that is between a genus and a subfamilytrichocyst - a stinging or grasping organelle in the outer cytoplasm ofprotists, especially ciliates. It consisting of a hair-like filament that can bedischarged suddenly from a minute capsulehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (18 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatrichogyne - receptive elongation of the carpogonium (femalereproductive structure) in red algae where male gametes become attachedtrifurcate - dividing into three partstriggerfish - any of several species oftropical coral reef fishes in the orderTetraodontiformes, family Balistidae, withlaterally compressed bodies, heavy scales,and tough skins. Triggerfishes are namedfor the mechanism of the three spines oftheir first dorsal fin. When the fish isalarmed the first of these spines is lockedupright by the second and drops only whenthe latter is pressed like a trigger. Thefunction of this reaction is to lock the fishfirmly in a mass of coral when attacked.The blue triggerfish(Pseudobalistes fuscus) inHurghada, Red Sea.(Photo:Thomas Jundt)Triggerfishes have powerful, chisel-liketeeth adapted for cracking the coral and mollusks upon which they feedtriglyceride - a complex molecule which is the main component ofdietary and body fat. It is made up of a combination of glycerol and threefatty acidstrihedral - with three surfaces, e.g. thebody of a trunkfishThe trihedral shape of atrunkfish as it swimsdirectly toward the viewer(Illustration: NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (19 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatrimix - a breathing gas mixture of helium,oxygen, and nitrogen. By using trimix, it ispossible for divers to descend to hundredsof feet without suffering from toxic partialpressures of oxygen (which increases withdepth), and also reduces the effect ofnitrogen narcosisMarine scientists breathingtrimix working on atransect line in order tocollect sponge and watersamples at a depth ofapproximately 60 m (200ft). (Photo: NOAA NationalUndersea ResearchProgram)trinomen - in taxonomy, the combination of a generic name, a specificname, and a subspecific name, that together constitute a scientific namesubspeciestriplet - in genetics, a sequence of three nucleotides of DNA whichspecifies an amino acid.triploid - a polyploid having three sets of homologous chromosomestripton - the nonliving particulate matter in bodies of watertritoniid - a member of a family ofnudibranchs (Tritoniidae) which feed onsoft corals, gorgonians, and otheranthozoans. A characteristic common to thetritoniids are the dorsilateral branchedcerata, used as gills and located in theedges of the dorsal surfaceThis relatively smallCaribbean tritoniid(Tritonia hamnerorum)feeds exclusively ongorgonian sea fans and issometimes found in largenumbers. (Photo: BillRudman)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (20 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatriturate - to grind or masticatetRNA (transfer RNA) - short-chain RNA molecules present in the cell, inat least 20 varieties. Each variety is capable of combining with a specificamino acid, and attaches the correct amino acid to the protein chain thatis being synthesized at the ribosome of the cell, according to instructionscoded in the mRNAtrochophore larva - the ciliatedplanktonic larva of many invertebrates,including polychaete worms, mollusks, androtifersThe trochophore larva of amarine worm. (Photo:University ofSaskatchewan Archives)troglobite - an obligate cave dwellertrolling - a fishing method where lures orbaits attached to lines are towed behind aslowly moving boatFishing vessel trolling fortuna. (Graphic: NOAA)trophic - related to or functioning in nutritiontrophic dynamics - the complex biological processes whereby energyand matter are passed up to successive levels of food webstrophic group - a group of organisms consuming resources from asimilar level in the energy cyclehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (21 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatrophic level - a classification system of organisms according to theirmeans of obtaining nutrition. A segment of the food chain in which allorganisms obtain food and energy in basically the same manner (e.g.,photosynthesis, herbivory, or carnivory) and in which all organisms arethe same number of links from the photosynthetic segmenttrophosome - a collective term for all nonreproductive structures ofcolonial hydrozoans; a structure in beard worms (Polychaeta-Siboglinidae)that harbors commensalistic chemosynthetic bacteria in cells calledbacteriocytestropical - region in which the climate undergoes little seasonal change ineither temperature or rainfall. Tropical regions of the earth lie primarilybetween 30 degrees north and south of the equatortropical depression - a mass of thunderstorms and clouds generally witha cyclonic wind circulation of between 20 and 34 knotstropical disturbance - an organized mass of thunderstorms with a slightcyclonic wind circulation of less than 20 knotsTropical Ocean Coral Bleaching Indices - indices of selected coral reefsites/regions (maintained by NOAA/NESDIS) that present satelliteobtainedmeasurements of relevance to coral reef ecosystemstropical storm - a tropical cyclone with maximum winds less than 34 m/sec (75 mile per hour)trumpetfish - any of a family of tropicalreef fishes (Aulostomidae), recognised byits long body, tubular snout with minuteteeth, its chin barbel, and a series of shortdorsal spines. A carnivore, It oftenapproaches its prey vertically, darting downfrom above and sucking the prey into itslong snoutThe trumpetfish is acommon reef fish. It feedson other reef fishes.(Photo: Keoki and YukoStender)truncate - having the end squared offhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (22 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatrunkfish - any fish species in the family Ostraciidae (order Tetraodontiformes). Trunkfishes are encased in an triangular inflexible bony carapace which protects them from predators.Only the jaw, eyes, the bases of the fins, and the caudal finprotrude from this carapace They are slowswimmers that move primarily by scullingwith their dorsal and anal fins and use theircaudal fin for sudden bursts of speed. Theyare also known as boxfishes or cowfishesThe spotted trunkfish, Lactophrys bicaudalis.(Illustration: NOAA)trust territory - a colony or territory placed under the administration ofone or more countries by commission of the United Nationstsunami - a long-period gravity wavegenerated by a submarine earthquake orvolcanic eventTsunami damage atSeward, Alaska, following1964 Good FridayEarthquake. (Photo: NOAA)tube feet - extensions of the watervascularsystem of echinoderms, protrudingfrom the body and often ending in suckers.They may be used for locomotion and/orfor maintaining a tight grip on prey or onthe substrateThe ventral side of aPacific starfish shows itstube feet.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (23 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatube worm - a marine worm in the phylumAnnelida, class Polychaeta, that lives withintubular cases made of mineral or chitinoussecretions or of aggregated grit. Otherworm-like invertebrates in the phylaPogonophora and Phoronida have also beenreferred to as tubewormsThe Christmas tree worm,S pirobranchus giganteus,is a tube worm thatinhabits coral reefs(Photo: Keoki and YukoStender)tubercle - any small, usually hard, knobby excrescence or lump. Inpycnogonids and some cheliceramorph arthropods, the central eyes arecarried on a tubercletubicolous - inhabiting a tube or tubularstructure; tube dwelling, such as somemarine polychaete wormsa sabellid tube worm livesit life in a parchment tube(Photo:Dr James McVey/NOAA)tubiform - a shape resembling a tubeThe trumpetfish has asnout which is tubiform ortubular in shape. (Photo:Copyright Digital StockCorp.)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (24 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Datatubules of Cuvier - eversible toxic or sticky tubules associated with thebases of the respiratory trees of some sea cucumbers (Holothuroidea-Echinodermata)tumid - swollen, inflated.tumor - a mass of new tissue, with nouseful physiological function, growingindependently of its surroundingsA coral (Porites lutea) witha tumor (Photo: CNMI/Coastal Resourcesmanagement)tumorigenesis - the production or formation of tumorstunic - the outer covering of a tunicate(Urochordata). The tunic is mostlycomposed of a protein and carbohydratesOrange colonial tunicate atGray's Reef NationalMarine Sanctuary. Each ofthe individual tunicate'sbody is covered by thetunic. (Photo: NOAA)Turbellaria - a class of generally small and free-living members of theflatworm phylum Platyhelminthes. Classification within the Turbellaria is ina state of flux as it is unclear whether the class is truly monophyletic.Most are marine and benthic, but some also inhabit fresh water and moisttemperate and tropical terrestrial habitats. Most members of class arepredatory on small invertebrates; the rest are herbivores, ectoparasites,or scavengers. Many coral reef-inhabiting turbellarians in the orderPolycladida are very colorfulhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (25 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef Dataturbidimeter - an instrument for measuring turbidity of liquidsturbidity - cloudy water, usually caused by the suspension of fineparticles in the water column. The particles may be inorganic, such as silt,or organic, such as high densities of single-celled organismsturbidity current - a current of of rapidly moving, sediment-laden watermoving down a slope through air, water, or another fluid. The currentmoves because it has a higher density and turbidity than the fluid throughwhich it flowsturbidity flow - a flow of dense, muddy water moving down a slope dueto a turbidity currentturbinate - resembling an inverted coneturquoise - blue green colorturriform - tower-shapedtusk - an enlarged toothtwilight - the time immediately before sunrise and after sunset when thesky remains illuminatedtwilight zone - the term, "twilight zone" represents a transition from aregion that receives sunlight during the daylight hours, to a region thatremains in perpetual darkness. The coral-reef twilight zone is roughlydefined as coral-reef habitat at depths between about 200 feet (60meters) and 500 feet (150 meters). The upper limit represents theapproximate maximum depth to which stony corals tend to dominate thereef structure, and the lower limit represents the maximum depth atwhich significant photosynthesis occurs (the maximum depth to which theliving coral reef extends)tympaniform - drum-shapedtype - in taxonomy, the standard of reference for determining the preciseapplication of a name. Each taxon has, actually or potentially, a type: typeof a nominal species is a specimen (type specimen or holotype); type of anominal genus is the nominal species (type species); type of a nominalfamily is the nominal genus (type genus)type collection - in taxonomy, a collection of type specimensType I error - the error of rejecting the null hypothesis when it is truehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (26 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef DataType II error - the error of not rejecting the null hypothesis when it isfalsetype locality - in taxonomy, the geographical (and, where relevant,stratigraphical) location of the occurrence of the population from whichthe type specimen (i.e. holotype, lectotype or neotype) was takentype material - in taxonomy, a collective term for all type specimenstype series - in taxonomy, the series of specimens which eitherconstitutes the name-bearing type (syntypes) of a nominal species orsubspecies or from which the name-bearing type has been or may bedesignatedtype species - in taxonomy, the nominal species that is the namebearingtype of a nominal genus or subgenustype specimen - in taxonomy, any specimen of the type seriestyphoon - a hurricane that forms in thewestern Pacific OceanA satellite view of atyphoon in the westernPacific ocean (Image:NOAA)typological species - a species defined on the characters of the typespecimen; a group of organisms in which individuals are members of thespecies if they conform to certain fixed properties(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=t (27 of 27) [2/26/2008 9:15:35 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: UThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zu - a common replacement for the Greek letter µ as a symbol for themicron or micrometer. The correct symbol for this unit is µmU.S. Coral Reef Task Force (USCRTF) - established by PresidentClinton in June, 1998, through Executive Order 13089 on Coral ReefProtection, to lead the U.S. response to this growing global environmentalcrisis. Chaired by the Secretary of the Interior and the Secretary ofCommerce, the USCRTF is composed of the heads of 11 federal agenciesand the Governors of 7 states, territories or commonwealths withresponsibilities for coral reefs. The USCRTF is responsible for overseeingimplementation of the Executive Order, and developing and implementingcoordinated efforts to: map and monitor U.S. coral reefs; research thecauses and solutions to coral reef degradation; reduce and mitigate coralreef degradation from pollution, overfishing and other causes; andimplement strategies to promote conservation and sustainable use of coralreefs internationallyU.S. Pacific Remote Insular Area (PRIAs) - PRIAs consist of thefollowing islands and coral reefs appurtenant to such island, reef or atoll,as applicable: Baker Island, Howland Island, Jarvis Island, Johnston Atoll,Kingman Reef, Wake Island, and Palmyra Atollubiquitous - having a worldwide distribution; common to abundant in agiven areaultimate - last or farthestultramarine - deep blue colorhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (1 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef Dataultrasonic - sound waves that have frequencies higher than whathumans can hear, usually greater than 20,000 Hz. Some animals such asbats, a species of cave bird, and cetaceans use these high frequencyultrasonic sounds for communication and navigationUltraviolet-A (UV-A) - UV with wavelengths 315 - 400 nmUltraviolet-B (UV-B) - UV with wavelengths 280 - 315 nmUltraviolet-C (UV-C) - UV with wavelengths less than 280 nmumbo - the earliest part of a bivalve orbrachiopod shell; in bivalves, it is the mostdorsal section of the shell, while inbrachyopods, it is the most posteriorA bivalve shell: 1 = umbo;2 = periostracum (thepigmented outermostlayer of the shell). (Photo:Rick Gillis, Ph.D., BiologyDept., University ofWisconsin-La Crosse)umbraculiform - umbrella-shapedumbrella - describes the body of a jellyfishor medusaThe transparent umbrellaof this jellyfish makes itless obvious to predators.umbrella species - in conservation biology, species with large arearequirements. Conservation of these species should automaticallyconserve a host of other speciesunaltered fossil - a fossil which retains much or all of its originalchemical and structural compositionhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (2 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef Dataunavailable name - in taxonomy, a name which does not meet allmandatory provisions of the International Code of ZoologicalNomenclature and thus has no status in nomenclature. Unavailable namesinclude: nomen oblitum, nomen negatum, nomen nudum, nomen nullum,nomen vetitumuncinate - hooked at the tipundercurrent - a current below another current, or beneath the surfaceunderwater dB - the unit used to measure the intensity of anunderwater sound. Underwater dB refers to "decibels referenced to 1microPascal," which is abbreviated as "dB re 1 µPa." Sound intensity givenin underwater dB is not directly comparable to sound intensity giveundulating - moving in wavesunincorporated territory - a United States insular area in which theUnited States Congress has determined that only selected parts of theUnited States Constitution applyuniplanar - occurring in one planeuniramous appendage - a type of appendage that is characteristic ofinsects and other members of the arthropod subphylum Uniramia. Itconsists of an unbranched series of segmentsunite - in taxonomy, to combine or join two or more taxaUnited States Insular Area - United States territory that is neither apart of one of the fifty states or the District of Columbia. Insular area isthe current generic term used by the U.S. State department to refer toany commonwealth, freely associated state, possession or territorycontrolled by the US government. Several islands in the Pacific Ocean andCaribbean Sea are considered insular areas of the United States. PalmyraAtoll is an incorporated, uninhabited island, owned by the NatureConservancy but administered by the Office of Insular Affairs.Unincorporated and inhabited U.S. possessions are Puerto Rico, U.S.Virgin Islands, American Samoa, Guam, and the Commonwealth of theNorthern Mariana Islands. Uninhabited areas are the United States MinorOutlying Islands, which are: Baker Island, Howland Island, Jarvis Island,Johnston Atoll, Kingman Reef, Midway Islands, Wake Island, PalmyraAtoll, and Navassa Island (disputed with Haiti)United States territory - any extent of region under the jurisdiction ofthe federal government of the United States, including all waters (aroundislands or continental tracts). The United States has traditionallyproclaimed the sovereign rights for exploring, exploiting, conserving, andmanaging its territoryhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (3 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef DataUniversal Time (UT or Z) - the correct name for the time systempreviously called Greenwich Mean Time (GMT). The symbol Z is oftenpronounced "Zulu," the name of the letter Z in the international radioalphabetunorganized territory - an unincorporated United States insular area forwhich the United States Congress has not enacted an organic actunpublished name - in taxonomy, any name which has not been printedand circulated to meet the criteria of publication as stated by theInternational Code of Zoological Nomenclatureunused name - in taxonomy, an available senior synonym that is notknown to have been used as a valid name in the past 50 yearsunzip - a method for uncompressing files on a PC after downloading themfrom the Internet. Many files are stored on servers in a compressedformat, making them take up less disk space, and reducing the time ittakes to download them. These files must be decompressed to make themusable by your computer. WinZip and pkunzip are popular free softwareprograms that will uncompress filesupload - transferring data (usually a file) from the computer you areusing to another computer. The opposite of "download"upstream - toward the source or upper part of a stream or current;against the currentuptake - the entry of a substance into the body, into an organ, into atissue, into a cell, or an organism's body fluids by passage through amembrane or by other meansupwelling - the process by which warm, less-dense surface water isdrawn away from a shore by offshore currents and replaced by cold,denser water brought up from the subsurfaceuracil - one of the four bases in RNA. Theothers are adenine, guanine, and cytosine.Uracil replaces thymine, which is the fourthbase in DNA. Like thymine, uracil alwayspairs with adenineDiagram of the chemicalstructure of uracil, one ofthe four nitrogenous basesin RNA.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (4 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef Dataurban area - an area in which a majority of the people are not directlydependent on natural resource-based occupationsurea - a waste product of metabolism eliminated via the kidneys. Inelasmobranchs (sharks, rays, skates), urea is found in the blood where ithelps to maintain osmotic balanceuridine - the nucleoside having uracil as its base. Uracil is attached to aribose ringURL (Universal Resource Locator) - a website address, such as: www.coris.noaa.govUrochordata (Tunicata) - a subphylum ofthe animal phylum Chordata that containsthe ascideans (sea squirts). Most adults aresessile and bear little resemblance to theother chordates. They are commoninhabitants of coral reefs and mangroverootsOrange colonial tunicates(Urochordata) at Gray'sReef National MarineSanctuary.uropod - fan-shaped, paired posteriorabdominal appendage in certaincrustaceans, e.g., lobsters or shrimp, thatare used for swimmingVentral view of crayfish.(Photo: Copyright LTTM2003)UV (ultraviolet) radiation - the region of the electromagnetic spectrumconsisting of wavelengths from 1 to 400 nmuvelloid - resembling a small cluster of grapeshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (5 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef Data(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=u (6 of 6) [2/26/2008 9:15:36 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: VThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zv. et. - see also (vide etiam)vaccine - a preparation that contains an antigen, consisting of dead orweakened whole or parts of disease-causing organisms, that is used toconfer immunity against the disease that the organisms cause. Vaccinepreparations can be natural, synthetic or derived by recombinant DNAtechnologyvacuolated - possessing vacuolesvacuole - a membrane-bounded vesicle ineukaryotic cells that has a secretory,endocytotic, phagocytotic or storagefunctionA water vacuole in anameba. (Graphic:Wappingers Schools)vacuolization - the formation or multiplication of vacuolesvagile - freely motile; wandering; mobilehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (1 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavagility - the capacity of an organism or population to change its locationor distribution with time; ability to migratevaginate - enclosed by a sheathvagrant - a species that has strayed beyond its natural range but has notestablished reproducing populationsvalence - the chemical combining capacity of an element or ion; thenumber of electrons that are used by an atom to form a compound. Avalence electron is in the outer or next outer shell of an atomvalid name - in taxonomy, the correct name for a given taxon, whichmay have several available names, one of which (usually the oldest) ischosen as the valid name. The valid name is always an available name,but an available name is not always a valid namevalidated name - in taxonomy, a formerly invalid or unavailable namethat has been made valid or available by the International Code ofZoological Nomenclature, e.g. by annulment or suppression of seniorhomonyms or synonymsvalve - the shell or shells of certainorganisms, such as clams, oysters, andsnailsA giant Tridacna clam withits two valves open.variance - the population variance of a random variable is a non-negativenumber which gives an idea of how widely spread the values of therandom variable are likely to be; the larger the variance, the morescattered the observations on average. It is a measure of the 'spread' of adistribution about its average valuevariant - any individual or group that deviates form the typical anatomyor behavior; in genetics, an organism that is genetically different from thewild type organismhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (2 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavariegated color pattern - an irregular pattern of small, dark and lightmarkings, with many of the dark marks connectedvas deferens - a duct that carries spermatozoa away from a testisvascular plant - any plant containing a system of vessels which transportwater and nutrients between different parts of the plant (e.g., from theroots to the leaves)vasculature - the network of blood vessels in an organ or body part;tissue consisting of cells joined to form tubes for transporting fluidsthrough a bodyvasiform - vessel-shapedvector - an abstraction of the real world where positional data isrepresented in the form of coordinates. In vector data, the basic units ofspatial information are points, lines and polygons. Each of these units iscomposed simply as a series of one or more coordinate points. Forexample, a line is a collection of related points, and a polygon is acollection of related lines. Vector images are defined mathematically as aseries of points joined by lines. Vector-based drawings are resolutionindependent. This means that they appear at the maximum resolution ofthe output device, such as a printer or monitor. Each object is selfcontained,with properties such as color, shape, outline, size, and positionon the screenvector - an organism which carries or transmits a pathogen; a vehiclethat transfers genetic material into a host cell or organism. Typically,vectors are of two types: viral- or DNA-based. DNA vectors areautomously replicating, circular macromolecules that can be easilymanipulated to carry genetic information and are transferred into cells bystandard laboratory techniques. These vectors include plasmids, cosmids,and yeast artificial chromosomes (YACs). Recombinant viruses that havebeen bioengineered to be harmless can also carry new genetic informationfor transfer into cells, or into an entire host organism (an example of genetherapy)VEEFER - see "REEFER"vegetal coloration - a resemblance to vegetation which allowsorganisms to conceal themselves from predators or preyvegetal hemisphere - the half of an oocyte or egg with more yolk, orthe corresponding half of an early embryo with the slower dividing yolkladencellsvegetal pole - the portion of an oocyte or egg that is opposite the animalpole and contains most of the yolk granules. See "animal pole"http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (3 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavegetative reproduction - a reproductive process that is asexual and sodoes not involve a recombination of genetic material. It involvesunspecialized plant parts which may become reproductive structures (suchas roots, stems, or leaves); also called "vegetative propagation"velarium - a structure that resembles a hydrozoan velum In scyphozoanmedusae, but has a different embryonic originveliger - a molluskan larva in which the foot, mantle and shell first maketheir appearancevelocity - the rate of change of position over time, calculated by dividingdistance by timevelum - a circular shelf of tissue attached to the underside of theumbrella in a hydrozoan mesusa. It functions in locomotionveneer reef - a reef with very little calcium carbonate accretion. A nonreefcoral communityvenomous - pertaining to an organismthat has a venom, usually secreted by agland, that is injected through hollowspines or teethA venomous cone shell.When close to its prey,usually another gastropodmollusk, it expands itslong proboscis exploringfor soft parts. A radulardart, bearing venom, isinjected into the prey;death quickly results.(Photo: Dr. James P.McVey, NOAA Sea GrantProgram)vent - the posterior opening of the intestine, gonads, and kidney ducts.The vent is located just anterior to the anal fin in fishesventral - pertaining to, or situated near, the belly, or underside, of ananimalhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (4 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Dataventral disk - a "sucking disc " formed bythe uniting of the pelvic fins in some fishes;for example, clingfishesA clingfish's ventral discallows it to hold onto rocksin strong currents or whenwaves crash over tidepools.ventral fin - a synonym for pelvic finVerhulst's Law - although individuals may benefit from the presence ofconspecifics, population growth cannot go on forever without negativeconsequences. Eventually, an upper boundary is reached beyond whichpopulation density cannot increasevermetid reef - a reef composed of vermetid gastropods (a family ofmarine snails) built on some substrate such as coralline algae or bivalveshells. These filter-feeding shelled snails, called worm-shells, aregregarious colonial animals which develop massive structures. A vermetidreef may be seen in southwestern Florida, south of Fort Meyers in the TenThousand Islands areavermetid tube - the "tube" of the wormshellsnailA vermetid tube amongcoral branches. The snail'soperculum covering theshell's opening is visible.(Photo: Ron Shimek)vermiculation - a worm-like markingvermiform - worm-shapedhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (5 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavermilion - bright red colorvermivore - an animal which feeds upon worms and worm-like animalsvernacular name - the colloquial or common name of a taxon, i.e., inany language or form other than that of biological nomenclature.Vernacular names have no status in nomenclatureverruca - a wart-like projection; a small cylindrical projection arising fromthe corallum that contain calicesverrucose - having a warty appearanceversus - against; in contrast tovertebra - one of the bony segments of the vertebral column ofvertebrate animals; in brittlestars (Echinodermata-Ophiuroidea), avertebra is one of the many articulated ossicles that join together alongthe length of the arms. They occupy most of the interior of each arm, andhave sockets by which they connect to each othervertebrate - an animal that possesses avertebral column (back bone), such asfishes, amphibians, reptiles, birds andmammalsVertebrate animals of thefish class Osteichthyes.(Photo: Dr. AnthonyPicciolo)vertical classification - classification which stresses common descentand tends to unite ancestral and descendant groups of a phyletic line in asingle higher taxon, separating them from contemporaneous taxa havingreached a similar grade of evolutionary changevertical fin - the unpaired dorsal, caudal and anal fins. Vertical fins arealso called median finsvertical migration - the diel behavior of zooplankton and some nekton todescend from surface waters during the daytime and ascend to thesurface during nighttime hoursvertical zonation - horizontal banding of communities of organisms inresponse to a vertical environment gradienthttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (6 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavesiculate - thin and bladder-likevestigial structure - an incompletely or ineffectively developed structurewhich is greatly reduced from the original ancestral form and is no longerfunctionalVestimentifera - a former phylum of benthic marine tube worms, nowconsidered by many to belong to the family Siboglinidae of the phylumPolychaeta. Vestimentiferans live close to hydrothermal vents on midoceanridges and around cold sulphidic or hydrocarbon seeps oncontinental slopes. They feed primarily on symbiotic (mutualistic)hydrogen sulfide- or methane-oxidizing bacteria living in an internalorgan, the trophosomevestimentum - a short region immediately behind the head of avestimentiferan tube worm.The front part of the vestimentum forms acollar. This region may secrete the tubeviable - having the capacity to live, grow, germinate or develop; capableof life or normal growth and developmentvibraculum - a bryozoan heterozooid that possesses long setae, orbristles, and may function in cleaning the colonyVibrio - a genus of motile, gram-negative,rod-shaped bacteria characterized by short,slightly sinuous filaments and anundulatory motion. Some species in thisgenus cause cholera in humans and otherdiseases in other animals, including coralsVibrio vulnificus pili, abacterium normally foundin temperate estuarinewaters, and as a colonizerof molluscan shellfish,such as oysters. (Photo:NOAA Northwest FisheriesScience Center)vibrotaxis - an organism's response to mechanical vibrationshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (7 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavicariant event - an unexpected or abnormal eventvicariant speciation - speciation when a single, widespread population isdivided by (1) the emergence of an extrinsic barrier, (2) extinction ofintervening populations, or (3) migration of some individuals into aseparate regionvice - in place of; rather thanvideo transect - a nondestructive, repeatable procedure for assessingand monitoring diurnally active fishes and other macroscopic marineorganisms. Videotaping along a linear transect reduces the variance inerror inherent with visual observations made by a diver or snorkeler, andallows virtually unlimited time for study of the images by many individualsvilliform - taking the form of villi (finger-like projections); in fishes,pertains to teeth which are slender and crowded closely together in bandsvillus - a small, fingerlike or hairlike projection of the small intestinal wallthat contains connective tissue, blood vessels, and a lymphatic vessel, andwhich functions in the absorption of nutrientsviolaceous - violet colorviolet - bluish purple colorviral DNA - DNA (deoxyribonucleic acid) that makes up the geneticmaterial of virusesvirion - a complete infectious viral particle, existing outside of a host cell,with nucleic acid and capsid, and in some types, an outer lipid envelopeviroid - an infectious particle similar to a virus, but smaller. It consistsonly of a strand of nucleic acid without the protein coat (capsid)characteristic of a virusvirology - the study of virusesvirtual library - virtual libraries provide online access to specializedcollections of information resources. Normally they include bibliographiccitations with links to full text documents and other online resources suchas video or photos. Virtual Libraries can also serve as gateways toinformation and resources on science, management, and policy forresearchers, scientists, resource managers, policymakers, stakeholders,and the general public. Restoration, Marine Protected Areas, and CoralReefs are examples of three NOAA virtual libraries in such areasvirulence - the ability to infect or cause diseasehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (8 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavirulence - the disease-producing ability of a microorganismvirus - a sub-microscopic, obligate intracellular parasite that replicatesitself only within cells of living hosts; many are pathogenic; the structureof a virus is basically a strand of nucleic acid (DNA or RNA) wrapped in athin protein shell. A virus is not a cell, and is "lifelike" only whenreplicating itself at the expense of the host cellviscera - the internal organs, collectively, of an coelomate organism,especially those located within the abdominal cavity, but also to theorgans within the thoracic and mediastinal cavitiesvisceral hump - the main body of a mollusk, which contains most of theorgans, including a complete digestive and excretory tract as well as thereproductive organs. The visceral hump also includes the mantle, whichconsists of two external flaps of tissue that secretes the material thatforms the shell on some species, and it protects the mantle cavity. Themantle cavity contains the gills, which excrete waste and circulate oxygen.Most mollusks have a shell, which sits on the visceral hump and a protectsthe main body from predatorsviscid egg - an adhesive egg that is deposited on sand, gravel, plants,etc. to which it sticks by means of the egg's sticky surfaceviscosity - a measure of resistance to flow in a liquidvisible radiation - energy at wavelengths from 400 - 700 nm that isdetectable by the human eyevisible wavelengths - wavelengths approximately 400 to 700 nmvisualization tool - a method of visually displaying data, such as avisualization theater, computer display, and map and chartvitamin - a chemical substance, required in trace concentrations, whichacts as a cofactor with an enzyme in catalyzing a biochemical reactionvitamin B complex - a large group of water soluble vitamins thatfunction as co-enzymesVitareef program - a program that was established in order to provide astandardized method of characterizing the conditions of reef corals. It canand has been used by both researchers and non-scientists to documentobservations of reefs at specific points in time, which can be followed upin subsequent observations to assess changes in the state of individualcoral colonies, selected coral species, or a reef as a wholehttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (9 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef Datavitellaria larva - a ciliated larva of echinoderms, such as sea lillies(Crinoidea), some sea cucumbers (Holothuroidea), and brittle stars(Ophiuroidea)viviparity - a form of reproduction where the offspring are nourished inthe reproductive tract of the female (other than by a yolk sac) and thenexpelled from the mother as free-swimming young. Mangrovereproduction by means of propagules is also a form of viviparity in plantsvocalization - a sound intentionally produced by an animalvolant - flying or capable of flyingvolcanism - the set of geological processes that result in the expulsion oflava, pyroclastics, and gases at the Earth's surfacevoucher specimen - any specimen that serves as a basis of study and isretained as a reference. It should be in a publicly accessible scientificreference collection. A type specimen is a particular voucher specimenwhich serves as a basis for the taxonomic description of a speciesvulnerable species - a species that is particularly at risk because of lowor declining numbers, a small range, or for some other reason, but is notthreatened or endangered(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=v (10 of 10) [2/26/2008 9:15:39 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: WThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZWahlund effect - a subdivided population contains fewer heterozygotesthan predicted despite the fact that all subdivisions are in Hardy-Weinbergequilibrium, i.e., internally subdivided species have more homozygositythan an equivalent fused population would, creating more phenotypicallyexpressed variationwake - waves generated in the water by a moving vesselwalking shark - a small, slender-bodied, bottom-dwelling epauletteshark (Hemiscyllium sp), one of the carpet sharks, that uses its pectoralfins to "walk" across the seafloorwall - the reef slope, which may suddenly drop off into deeper water,forming a nearly vertical wallWallace's Line - a hypothetical line which separates the zoogeographicalregions of Asia and Australasia. It is named after Alfred Russel Wallacewho noticed the apparent boundary during his travels through the EastIndies in the 19th Century. The line runs through the Malay Archipelago,between Borneo and the Celebes and Bali and Lombok. West of the lineare found mostly species that are related to Asiatic species, to the eastmostly species that are related to Australian specieswarning signal - in animal behavior, any visual, acoustic, or chemicalsignal (stimulus) broadcast by an organism to warn others of its presence;also includes threat signals directed toward an opponent of the same ordifferent specieshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (1 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Datawash zone - the depth zone in which sediments are disturbed by waveaction near the shorelinewastewater - water that is a mixture of water and dissolved orsuspended solids carrying wastes from homes, businesses and industrieswastewater treatment plant - a facility containing a series of tanks,screens, filters and other processes by which pollutants are removed fromwaterwater - pure water consists of hydrogenand oxygen, H 2 O. It is a binary compoundthat occurs at room temperature as acolorless, odorless, tasteless, transparentliquid which is very slightly compressible. Itfreezes at 0 degrees C and boils at 100degrees C. It is the most important naturalsolvent, and frequently contains impurities,which are mostly removed by distillationWave sweeps toward acoastline. (Photo:Copyright Digital VisionLtd.)water column - the water mass between the surface and the bottomwater mass - a large body of water whose density characteristics aredistinct from the surrounding aquatic environment because of inherenttemperature or salinity differenceswater pik method - a laboratory technique which uses a water pik toseparate tissues from the skeletons of hard corals or removezooxanthellae from coral polyp tissueswater pressure - the force per unit area exerted by the weight of water.Each 33 feet of sea water exerts a pressure equivalent to one atmosphere,or 14.7 psiwater strider - an insect (a bug) in the order Hemiptera. Some species,mostly in the genera Hermatobates and Halobates, are marine inhabitantsof mangroves, intertidal coral reef flats, and the water surface near coraland rocky reefs in the Indo-Pacific region; marine species also called "seaskaters"water table - the level or depth below the ground that is saturated withwaterhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (2 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Datawater table - the level below the earth's surface at which the groundbecomes saturated with water. The water table is set where hydrostaticpressure equals atmospheric pressure; the surface between phreaticwater which completely fills voids in the rock and ground air whichpartially fills higher voidswater vascular system - in echinoderms, a system of internal canalsand appendages that are water-filled and functions as a means oflocomotionwatercourse - a natural channel for waterwatershed - an area of land that drainsdownslope to the lowest point. The watermoves through a network of subterraneanand surface drainage pathways whichconverge into streams and rivers,eventually reaching an estuary and finallythe ocean. Because water movesdownstream, any activity that affects thewater quality, quanity, or rate of movementat one location can affect locationsdownstream to the ocean and out to coralreefsAngel Falls, Venezuela.This great waterfallcontributes to the OronocoRiver watershed. Nutrientsand minerals from therainforests and savannasof the Oronoco River basinare transported with theOronoco current and mayeffect coral reefs in thesoutheastern Caribbean.(Photo: Copyright Dr.Anthony R. Picciolo, NOAA)wave crest - the top of a wavewave height - the vertical distance between the crest and adjacenttrough of a wavewave length - the distance between two successive wave crests ortroughshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (3 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Datawave trough - the low spot between two successive wavesWCMC Global Coral Disease Database - the World ConservationMonitoring Centre (WCMC) and NOAA maintain the Global Coral DiseaseDatabase which is populated with over 2000 records of coral diseasesfrom approximately 155 sources. The occurrence of a disease on a coralspecies (or genus) was recorded for each location and date on which itwas observed. A unique combination of coral species, disease, date, andlocation therefore constitutes a single recordweather - temperature, precipitation, and wind speed and direction thatoccur on a daily basisWeb Reef Advisory System (WRAS) - the Web Reef Advisory System(WRAS) was developed by ReefBase and Reef Check, in collaboration withthe Coastal Resources Center at the University of Rhode Island and theDepartment of Biological Sciences at the University of Southern California,as "an online application to input, view, and analyze Reef Check surveydata. It calculates indicators of how good or bad a shape a particular reefis in, and what the underlying causes may be, based on Reef Checksurveys." WRAS allows users to view, analyze, and add data. The filelocation is: www.reefcheck.org/datamanagement/Weberian apparatus - the four anterior vertebrae and associated tissuesin some fishes (catfishes, loaches, minnows, suckers) that connect the gasbladder to the inner ear, conveying pressure changes and soundwedge shaped - a form that is thick at one edge and tapered to a thinedge at the otherweight belt - a belt worn during scuba diving that contains lead weights,either solid masses or as shot in pouches. The weight belt allows a diverto descend in the water column against the forces buoying the diverupwardswet collection - a museum collection of specimens that are stored inethanol, isopropanol, formalin or other liquid preservativeswetland - an area that, at leastperiodically, has waterlogged soils or iscovered with a relatively shallow layer ofwater. Bogs, freshwater and saltwatermarshes, and freshwater and saltwaterswamps are examples of wetlandsWetlands provide forvaluable nursery areas formany organisms.http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (4 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Datawhite hole - an area along the spur andgroove system (zone) where the sandchannel widens considerablyA scientist stands in asand channel within a reefspur-and-groove zone.white pox disease - a coral diseasecharacterized by circular lesions with coraltisue degradation on the Caribbean elkhorncoral, Acropora palmata. The pathogen is abacterium, Serratia marcescen.White pox disease ischaracterized by whitecircular lesions on thesurface of infectedcolonies (Photo: Dr. A.Bruckner, NOAA)white skeleton - the exposed white calcium carbonate skeleton of a coralcolonywhite-band disease - a coral diseasecharacterized by complete coral tissuedegradation of Caribbean acroporid corals.­Two species of Acroporidae are affected,the elkhorn coral, Acropora palmata, andthe staghorn coral, A. cervicornis. Thedisease exhibits a sharp demarcationbetween apparently healthy coral tissueand exposed coral skeleton.- These signsare identical to plague, except that whiteband is acroporid specific (and plague hasnot been found on acroporids).- Tissue lossusually proceeds- from the base of thecolony branch to the tip, although it canElkhorn coral populationshave suffered widespreaddeclines from white-banddisease (Photo: Dr. A.Bruckner, NOAA)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (5 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Databegin in the middle of a branch in A.cervicornis. White band disease affectsacroporid corals throughout the Caribbean and has decimated populationsat a regional scale.The infective agent has not yet been isolated. For moreinformation and illustrations, see: http://www.coral.noaa.gov/coral_disease/white_band.shtmlwhorl - a ring; one turn of a spiralwild - living in a natural state; living in naturewild type - the form of an organism that occurs most frequently in naturewildlife refuge - an area designated for the protection or replenishmentof wild animals, within which hunting and fishing are either prohibited orstrictly controlledwind vane - an instrument used to determine wind directionwindlass - a winch used to raise a ship's anchorwindward - refers to the side of an island or reef that faces the prevailingwindWindward Passage - a channel between eastern Cuba and western Haitithat connects the Atlantic Ocean with the Caribbean SeaWinogradsky column - a glass column with an anaerobic lower zone andan aerobic upper zone, which allows growth of microorgansims underconditions similar to those found in a nutrient-rich body of water.It is asimple device for culturing a large diversity of microorganismswork - in physics, the transfer of energy from one object or system toanother by applying a force over a distance. The formula for work is(force) x (distance)work (taxonomy) - in the International Code of ZoologicalNomenclature, any text whether published, unpublished, or carrying adisclaimer containing a name or other information bearing onnomenclaturework of an animal - results of the activity but not part of the animalitself, e.g., tracks, trails, worm-tubes, borings (but excludes some fossilevidence such as internal molds, external impressions and replacements)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (6 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef DataWorld Commission on Protected areas (WCPA) - the world's leadingglobal network of protected area specialists.The mission of the WCPA is"to promote the establishment and effective management of a world-widerepresentative network of terrestrial and marine protected areas, as anintegral contribution to the IUCN mission"World Conservation Union - the name of the IUCN used since 1990.See IUCNWorld Register of Marine Species (WoRMS) - an authoritative andcomprehensive list of names of marine organisms, including informationon synonymy. While highest priority goes to valid names, other names inuse are included so that this register can serve as a guide to interprettaxonomic literature (www.MarineSpecies.org)WorldFish Center - an autonomous, nonprofit organization which wasestablished as an international center in 1977. Its mission is to reducepoverty and hunger by improving fisheries and aquaculture. The Center isan operational entity with programs funded by grants from privatefoundations and governments. It is governed by an international Board ofTrustees; its policies are implemented by the Director General. In 1992,the WorldFish Center became a research center of the CGIAR(Consultative Group on International Agricultural Research). The CGIAR isan informal association of more than 60 public and private sectormembers; formerly known as "ICLARM"worm reef - a massive structure composed of clusters of oval, table-likemounds constructed by marine polychaete worms in the familySabellariide. They consist of all sorts of sediments consolidated by amucoprotein cement produced by the worm. This reef may start in theintertidal zone and extend into the subtidal zone. Some are in deeperwater. Unlike the colorful and ornate coral reefs, worm reefs are drab,monotonous and rounded clusters, mounds and platforms that growupward and outward from the durable substrate from which their coloniesdevelop. Worm reefs offer several ecological benefits. They providefeeding and browsing grounds for a diverse community of marineorganisms and an ideal home for attaching plants, sponges and shelterseekinganimals. Also, unlike coral reefs, worm reefs are not restricted tothe tropicsworm shell - a snail in the gastropodfamily Vermetidae. Worm shells aregregarious species forming an intertwiningmass of long, white, worm-like tubes, oftensunken into a reef substrate. They get theircommon name of "worm shell" becausetheir shells superficially resemble the shellsof some tube-building marine polychaeteworms. After a short motile existance, theycement their shell to a hard substrate, andas they grow, the shells may coil ormeander over the substrate producing atube that looks quite like a tube worm.Worm shells are filter-feeders which spin aA crab at the opening of avermetid worm shell,http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (7 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef Datamucus net to trap floating food particles,such as planktonDendropoma maxima(Photo: Teresa Zubi)wrack - organic material, usually from dead seagrass or algae that washup on shorelineswrasse - a large family (Labridae) ofbrightly-colored bony fishes which arecommon inhabitants of coral reefs. Manyhave spiny fins, thick lips, and strong teeth.They range in size from about three inchesto three meters. Some species of smallwrasses are "cleaners," which regularyremove ectoparasites from the skin andgills of larger fishesThe wrasse, Corisdorsomacula (Photo: JohnE. Randall)WW2BW (White Water to Blue WaterInitiative) - the White Water to BlueWater (WW2BW) Initiative was formulatedin 2002 during the World Summit onSustainable Development. WW2BWresponds to the World Summit’s “Oceans”agenda with an integrated approach tosustainable use of water resources. In aneffort to address water pollution andscarcity, United States governmentThis photograph, used in aagencies, including the State Department,poster for WW2BW,suggests the relationshipsNOAA, USAID, as well as the Unitedbetween the forested land,Nations, governments of the Widerfresh water, the humanCaribbean Region, and a number of non-community, and the sea.governmental organizations have comeThe photograph highlightstogether to plan and implement programsthe pitons of St. Lucia inthe Caribbean Sea.which will lead to the conservation and(Photo: Dr. Anthony R.sustainable management of bothPicciolo, NOAA)freshwater and coastal marine resources inthe Caribbean. WW2BW stimulatespartnerships to promote integratedwatershed and marine-based ecosystems management in support ofsustainable development. Four thematic areas are supported: integratedwatershed management, marine ecosystem-based management,sustainable tourism, and environmentally sound marine transportation.The outcome of the WW2BW partnership in the Wider Caribbean mayserve as the blueprint for future programs on watershed and marineecosystem-based management in Africa and the South Pacific(Top)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (8 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef DataRevised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=w (9 of 9) [2/26/2008 9:15:41 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: XThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZX linkage - in genetics, the inheritance pattern of genes found on the Xchromosome but not on the YX-organ - groups of neurosecretory cells in the eyestalks of crustaceansthat secrete a molt-inhibiting hormonexantho- - a prefix meaning yellowxanthochromic - yellow or golden colorA yellow tang, Zebrasomaflavescens. (Photo: JimMcVey, NOAA)xanthophore - a chromatophore which produces yellow pigments in theform of carotenoidshttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=x (1 of 3) [2/26/2008 9:15:42 AM]

Discover NOAA's Coral Reef Dataxenobiotic - a chemical which is not a natural component of theorganism exposed to it; a chemical or other stressor that does not occurnaturally in the environment. Xenobiotics occur as a result ofanthropogenic activities such as the application of pesticides and thedischarge of industrial chemicals to the environment; a synthetic chemicalbelieved to be resistant to environmental degradation. A branch ofbiotechnology called 'bioremediation' seeks to develop biological methodsto degrade such compoundsxenoecic - pertains to an organism thatinhabits the empty living space or shell ofanother organismA xenoecic cichlid fishoccupying the shell of amollusk. (Photo: M.K.Oliver, Ph.D./ Cichlidfishes of lake Malawi,Africa)xenology - homology that arises via lateral gene transfer betweenunrelated species (e.g., by retroviruses)xenoparasite - an organism not usually parasitic on the host but thatbecomes so because of a weakened condition of the hostxenophyophore - a giant protozoanprotist (Syringammina fragilissima), up to25 cm in diameter, that inhabits deep-seahabitats. Large aggregations ofxenophyophores appear on the DarwinMoundsA xenophyophorephotographed on the BlakeRidge. They constructcomplex, golf-ball-sizedtests from sand andsediment grains. (NOAAphoto)http://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=x (2 of 3) [2/26/2008 9:15:42 AM]

Discover NOAA's Coral Reef Dataxenotransplantation - transplantation of tissue from one species toanother speciesxeric - arid; characterized by dry conditions; requiring only a smallamount of moisturexiphoid - sword-shaped; also called "xiphiform"xylem - tissue in vascular plants that carries water and nutrients from theroots to the shoot and leaves. The xylem contains tracheids, vessels, fibercells and parenchyma. It also provides structural support(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=x (3 of 3) [2/26/2008 9:15:42 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: YThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | ZY junction - in genetics, the point of active DNA replication where thedouble helix opens up so that each strand can serve as a templateY linkage - in genetics, the rare inheritance pattern of genes found onthe Y chromosome but not on the XY-organ - a gland situated near the external adductor muscles of themandibleof some crustaceans that secretes the molting hormoneYAC (yeast artificial chromosome) - a vector used to clone DNAfragments from 300 kb to one megabase (unit of length for DNAfragments equal to one million nucleotides) in length. These clones canspan large portions of the genome rapidly, but can be highly unstableyear class - fish of a given species spawned or hatched in a given yearyearling - a one-year-old individual in its second year of lifeyeast - a single-celled fungus that reproduces by buddingyellow-band disease - a coral disease characterized large rings orpatches of bleached, yellow tissue on Caribbean stony corals, althoughtissue loss is minimal (cm/yr). It affects the star corals, Montastraeaannularis and M. faveolata and is widespread throughout the Caribbeanregion. No pathogen has been isolated. For more information andillustrations, see: http://www.coral.noaa.gov/coral_disease/yellow_band.shtmlhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=y (1 of 2) [2/26/2008 9:15:43 AM]

Discover NOAA's Coral Reef Datayolk - nutritive material of an ovum, consisting of protein and fat, storedfor the nutrition of an embryo or early larvayolk cell - in a telolecithal egg (an egg in which the yolk is not distributedevenly, but concentrated in one region), the yolk cells are the cells formedwhen cleavage reaches the yolk regionyolk sac - a vascularized extra-embryonic membrane of amniote embryosthat forms around the yolk of the egg cell in birds and reptiles. Inmammals, the yolk sac membrane grows out around the empty blastocoel(blastula cavity) formed within the inner cell mass in the cleaving embryo.The blastocoel is renamed the yolk sac. In birds and reptiles, the bloodvessels in its walls transport yolk nutrients to the embryo. In mammals,these vessels still form even though they don't supply nutrients to theembryo. They remain to form blood vessels in the digestive tractyolk-sac larva - a fish larva which has already hatched from the egg buthas not yet started feeding and still absorbs the yolk in the ventrallyattachedyolk sacyoung-of-the-year (YOY) - fish that are less than one year old; hatchedduring the spawning season(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=y (2 of 2) [2/26/2008 9:15:43 AM]

Discover NOAA's Coral Reef DataMain PageReferencesGlossary of Terminology: ZThe glossary is organized alphabetically by page -- A through Z. Literaturesources are listed on the References Page.The entire glossary is also provided as a PDF document (7.2 MB). Thedocument includes all terms, photographs, images, and literature sources.This SiteAll of NOAAGlossary PagesA | B | C | D | E | F | G | H | I | J | K | L | MN | O | P | Q | R | S | T | U | V | W | X | Y | Zzeitgeber - a periodic environmental signal that entrains a biologicalrhythm. For example, a cycle for a circadian rhythm, but may also be atemperature or even social cyclezenith - the point of the celestial sphere which is directly overheadzip - a compressed file format (.zip); to compress a file using a zip utility.Compression is generally used to speed up the transport of large ormultiple files. After the file has been downloaded, a decompressionapplication is needed to "unzip" itzoanthella - an elongate larval form of Zoanthidea with a ventral band ofvery long ciliazoanthid - an anemone of the family Zoanthidae, usually found inintertidal areas and coral reefs . In some species the polyps separate fromeach other almost completely after budding, while in other species, thepolyps are all interconnected by a common mat of tissuezoanthina - an oval larval form of Zoanthidea with a girdle of long cilianear the oral polezoarium - the form of a bryozoan colonyhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=z (1 of 4) [2/26/2008 9:15:44 AM]

Discover NOAA's Coral Reef Datazoea - a free-swimming larval stage ofvarious crustaceansA zoea larva. (Photo:Marine EcologyLaboratory, ShimodaMarine Research Center,University of Tsukuba)zonate - divided by parallel planes, e.g., zonate tetraspores, found incertain species of red algaezonation - the occurrence of single species or groups of species inrecognizable bands that might delineate a range of water depth or a rangeof height in the intertidal zonezone - a large-scale physical feature within the ecosystem. Reef zones aredetermined by currents, wave surge, exposure to sunlight and waterdepth, and may be comprised of a number of habitatszoning - a process in which a marine protected area is divided intodiscrete zones and particular human uses of each zone are permitted,often with conditions such as gear limitations in fishing and wastedischarge prohibitions in tourism. In the U.S., marine sanctuaries, nationalparks, national wildlife refuges, and state MPAs are some examples ofareas that may be zonedzoochory - the dispersal of plant seeds or spores by animals.Endozoochory is zoochory within the animal's body. Exozoochory iszoochory where the seeds are attached to the outside of the animal's bodyzooecium - the skeleton of a bryozoan zooidzoogenic - pertaining to changes caused by animals or their activitieszooid - of the distinct individuals forming a colonial invertebrate animal,such as a hydrozoanzooidal - pertaining to a zooid, as for example, a zooidal formhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=z (2 of 4) [2/26/2008 9:15:44 AM]

Discover NOAA's Coral Reef Datazoology - the scientific study of animal life. Zoological sciences includethe studies of evolution, systematics, cell biology, biochemistry, micro andmacro anatomy, development, genetics, physiology, ecology,biogeography, biodiversity, behavior and sociobiologyzoonose - a disease of non-human animals that may be transmitted tohumans, or may be transmitted from humans to non-human animalszoophyte - an invertebrate which resembles a plant in appearance ormode of growth, as for example, hard corals, sea fans, and other softcorals, sea anemones, hydroids, bryozoans, sponges, etc., especially anyof those that form compound colonies having a tree-like formzooplankton - animal component of the plankton communityzoosemiotics - the study or analysis of animal communicationzoospore - a motile, flagellated sporezootoxin - any poisonous or venemous substance produced by an animalzooxanthellae - a group of dinoflagellatesliving endosymbiotically in association withone of a variety of invertebrate groups (e.g., corals). In corals, they providecarbohydrates through photosynthesis,which are used as one source of energy forthe coral polyps. They also providecoloration for the coralsZooxanthellae. (Photo:Scott Santos)zooxanthellate coral - a coral that has zooxanthellae in its tissuesZulu time (Z) - one of several names for the 24-hour time period. Othernames for this time measurement are Universal Time Coordinate (UTC) orGreenwich Mean Time (GMT)zygocardiac ossicles - triangular plates, usually bearing denticles, whichproject into the cavity of the cardiac stomach in decapod crustaceans,such as shrimps,crabs and lobsters; part of the gastric millhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=z (3 of 4) [2/26/2008 9:15:44 AM]

Discover NOAA's Coral Reef Datazygote - a fertilized egg with the diploid number of chromosomes formedby the union of the nuclei of male and female gameteszymogen - an inactive enzyme precursor that requires a biochemicalchange, such as a hydrolysis reaction revealing the active site, for it tobecome an active enzyme(Top)Revised by CoRIS WebmasterSite hosted by National Oceanic and Atmospheric Administration , U.S. Department of Commercehttp://coris.noaa.govhttp://www8.nos.noaa.gov/coris_glossary/index.aspx?letter=z (4 of 4) [2/26/2008 9:15:44 AM]