Dr. Jennifer Lee Nielsen CURRICULUM VITAE - Contents

Dr. Jennifer Lee NielsenCURRICULUM VITAEContentsPageOne-page Résumé…………………………………………………………….....2Research – Publications…………………………………………………………3EditorshipsJournal Editor-in-ChiefAdvisory EditorBook SeriesBooksResearch – Achievements……………………………………………………….4Salmon HabitatForage BehaviorPopulation GeneticsCalifornia SteelheadMexican TroutAcoustic and Archival TagsHalibut Pop-up TagsClimate ChangeGrizzly BearsArctic CiscoResearch – Administration………………………………………………………7Research ManagementProgram ManagementGenetics LaboratoriesFisheriesConferences and Seminars………………………………………………………8OrganizationInvited SymposiaTechnical ConferencesOutreach and Public Service…………………………………………………...12Student SponsorshipProfessional MembershipTechnical ReviewsScientific AppointmentsAcademic AppointmentsPolicy AppointmentsGrants and Contracts……………………………………………………………16List of Publications……………………………………………………………..17Per Reviewed ArticlesProceedings and Technical ReportsManuscripts Submitted1

Jennifer L. Nielsen, PhDOne Page RésuméBirth Date March 21, 1946Nationality USAMarital Status Divorced, two daughtersQualifications PhD (1994), MSc (1990)University of California Berkeley; B.A.Environmental Studies (1987) TheEvergreen State CollegeWork Address USGS, Alaska ScienceCenter, 1011 East Tudor Rd., Anchorage,AK 99503Phone: 907 786-3670 Fax: 907 786-3636Email: jlnielsen@usgs.govCurrentAppointmentsResearch Scientist, USGS Alaska Science Center, FisheriesPresident American Fisheries Society (2006-2007)Council of Scientific Society Presidents Co-Chair Environment and EnergyCommittee (2005-2007)Scientific Advisor Sitka Tribe of AlaskaBering Sea Ecosystem Research Committee Inter-Agency Working GroupNSF SEARCH Climate Change Study Group Agency Advisory CommitteeEditor-in-Chief Reviews in Fish Biology and Fisheries (since 1999)Book Series Editor Reviews: Methods and Technologies in Fish Biology andFisheries (since 2000)Affiliate Professor University of Alaska, Fairbanks, School of Fisheries andMarine ScienceAffiliate Professor University of Alaska, Anchorage, Biology DepartmentNOAA Technical Recover Team Southern steelhead recovery planningBoard Membership Fisheries Conservation FoundationCareer AchievementsInterdisciplinary research in a wide range of fisheries, behavior, genetics, climate change,and fish tagging technologies producing over 120 publications (average citation ratefor last five years is 38.2 citations per year) and support for 27 graduate degrees(MSc & PhD) from 16 universities.USGS Alaska Science Center Fisheries Program Supervisor, 1999-2005.Editor-in-Chief international journal and book series with high impact factors 1999-present; edited eight international books on fish and fisheries.Served as Officer American Fisheries Society 2003-2008; President 2006-7.American Fisheries Society Award of Merit (1996), Distinguished ProfessionalAchievement (1997), Distinguished Service Award (2000).Previous Appointments2002-2006 Associate Professor, Oregon State University1998-1999 Adjunct Professor, UC Berkeley, Department Integrative Biology1995-2000 Research Associate, Moss Landing Marine Laboratory1994-1999 Visiting Scientist, Hopkins Marine Station, Stanford University1990-1999 Fisheries Research Scientist, US Forest Service1978-1989 Fisheries Scientist, Weyerhaeuser Company2

Research – PublicationsI have produced over 120 research publications sincemy first publication in 1982, including journal articles,book chapters, technical reports and internationalbooks on fisheries, conservation, genetics, taggingtechnologies and climate change. This includes over65 peer-reviewed scientific journal articles or bookchapters. Since obtaining my Ph.D. in 1994, I haveaveraged over five publications per year. My averagecitation rate for the last five years is 38.2 citations peryear; my lifetime-citation rate per paper since firstpublication is 14.9. A full list of citations follows thetext.I edited American Fisheries Society Symposium 17(1995):Evolution and the Aquatic Ecosystem:Defining Unique Units in PopulationConservation.I have recently contributed peer-reviewed bookchapters to the following volumes:Pacific Salmon Environment and LifeHistory Patterns (2007). Kudsen,American Fisheries Society;The Atlantic Salmon: Genetics,Conservation and Management (2007).Verspoor, Stradmeyer and Nielsen,Blackwell;North American Freshwater Fishes (2007)Mayden, Academic Press.EditorshipsEDITOR-IN-CHIEFIn 1999 I became Editor-in-Chief of the internationaljournal Reviews in Fish Biology and Fisheriescurrently published by Springer. The journalpublishes synthesis reviews of interdisciplinary topicson fish and fisheries. Submission and publication ofthe journal are electronic with no page charges. Thecurrent 5-year average impact factor for this journal is1.82. Since 1999 we have published Special Issues ofthis journal on:The Species Concept in Fish Biology (1999);The Role of Hybridization in theDistribution, Conservation andManagement of Aquatic Species (2000);Mexican Freshwater Fish and Fisheries(2002);Sea Ranching and Stock Enhancement(2003);Interactions of Hatchery and Wild Fishes inMarine and Estuarine Environments(2004);Rights Based Fisheries (2005);Biodiversity Crisis in Southern GalaxioidFishes (2006);Cephalopod Life-cycles (2007).ADVISORY EDITORI serve as Advisory Editor of Environmental Biologyof Fishes and co-edited a Special Issue on Genetics ofSubpolar Fish and Invertebrates (2004).BOOK SERIESIn 2000 I founded the book series Reviews: Methodsand Technologies in Fish Biology and Fisheriespublished by Springer. There have been six bookspublished in this series to date:1. Electronic Tagging and Tracking in MarineFisheries (200) Sibert & Nielsen (eds.)2. Inshore Fisheries Management (2001)Symes & Phillipson (eds.)3. Molecular Diagnosis of Salmonid Diseases(2002) Cunningham (ed.)4. Participation in Fisheries Governance(2005) Gray (ed.)5. Aspects of Illegal, Unreported andUnregulated Fishing in the Southern Ocean(2006) Baird (ed.)6. Environmental Impacts of Aquaculture(2007) Bert (ed.)BOOKSI have edited or co-edited three other book volumes:Evolution and the Aquatic Ecosystem (1995 Nielsen,American Fisheries Society). This was thefirst publication at the American FisheriesSociety to focus on an interdisciplinaryapproach to genetics and evolution in fishand fisheries.4

The Atlantic Salmon: Genetics, Conservation andManagement (2007 Verspoor, Stradmeyerand Nielsen, Blackwell). This is the firstvolume published on the managementaspects of genetics in Atlantic salmon inlanguage that is appropriate for managersnot schooled in genetics or evolution.Proceedings of the Fourth World Fisheries Congress(2007, Nielsen et al., American FisheriesSociety). This international volumecontains 211 papers from 71 differentcountries on management and conservationin fisheries around the world.Research – AchievementsDuring my research career I have followed severaldiverse paths focused on the topics of fish ecology,aquatic habitats, animal behavior, genetics, taggingtechnologies and climate change. Throughout mystudies I have sponsored 16 students through theirMasters of Science Degrees and six Doctors ofPhilosophy degrees in fisheries and oceanography at16 different universities. I have received the Award ofMerit (1996), the Distinguished Special AchievementAward (1997) and the Distinguished Service Award(2000) from the American Fisheries Society (AFS)and served as President of AFS 2006-2007.The following sections provide a brief synopsis of mypast and current research work in fisheries andgenetics. A list of grants and contracts is givenfollowing the text.SALMON HABITAT IN THE PACIFICNORTHWESTSalmonid habitat was the focus of my first researchactivity as a scientist with the WeyerhaeuserCompany in Federal Way, Washington. My workfocused on the impacts of logging on salmonid habitatand implications for the Bolt II legal decisionauthorizing Native American Tribes to specific fishingand harvest rights in the Pacific Northwest. In thiscapacity I co-authored five papers including the firstand still frequently cited paper on fish habitat infreshwater riverine systems (Bisson et al. 1982).Originally trained as an artist I illustrated the firstedition of the American Fisheries Society’s StreamHabitat Handbook. During this period I went back toschool at age 38 to The Evergreen State College toobtain a Bachelors of Science Degree inEnvironmental Studies in preparation for graduatestudies.MICROHABITAT AND FORAGEBEHAVIOR IN PACIFIC SALMONMy interest in salmonid habitat led to a critical studyof early salmonid forage behavior in diverse streamhabitats which led to my MSc at Berkeley (1990) anda highly cited paper on microhabitat specific cohoforage behavior (Nielsen 1992, TAFS). This workdemonstrated the interdisciplinary approach requiredto investigate forage behavior and early freshwatergrowth in wild coho salmon. My work at this timealso demonstrated patterns of movement and changesin population structure over time in wild coho andsteelhead populations in freshwater. Numerous grantsfunded independent research after my resignationfrom Weyerhaeuser and move to the University ofCalifornia, Berkeley for graduate studies. My grantswritten and obtained during this period exceeded anyother graduate student’s funding in natural resourcesresearch and frequently exceeded the fundingavailable to my major professor. One especiallyimportant grant obtained as a graduate student fromthe State of California in 1992, was for the educationof northern California, out-of-work salmon trollfishers in fish habitat analyses and monitoring($500,000). In 1990 I was offered a full-time researchposition with the US Forest Service SouthwestScience Center while I continued graduate school atBerkeley for my PhD.POPULATION GENETICS ANDEVOLUTIONARILY SIGNIFICANTUNITS (ESUs)My studies on forage behavior and populationstructure in juvenile salmonids in freshwater led to4

many questions about the role of genetics in salmonidbehavior and distribution. To pursue these questions Imade a sea change in direction, moved my research tothe Allen Wilson Laboratory at Berkeley in theDepartment of Molecular and Cellular Biology andtook up the study of population genetics. During thisperiod my work was highly original and producedsome of the first molecular genetic data on Pacificsalmonids using mtDNA and microsatellite loci toidentify evolutionarily significant units of populationsfor conservation and protection under the USEndangered Species Act. I was particularly focusedon applied aspects available from the new DNA toolsfound in molecular genetics. Grants and publicationsfrom my research increased significantly. I completedmy PhD on salmonid genetics and stock identificationin 1994 and was offered a Post-Doctoral appointmentat Stanford University’s Hopkins Marine Station.CALIFORNIA STEELHEAD ANDCHINOOKSoon after my introduction into molecular genetics atBerkeley I started working on DNA analyses of tissuecollections from salmonids in California. Thesecollections included samples taken from steelhead insouthern California where the state of knowledge atthat time suggested these were hatchery fish that hadlost their way in the Pacific Ocean, since there wereno significant records of natural production forsteelhead south of Monterey Bay since the 1940’s. Itwas a great surprise to me and to the rest of thefisheries research community in California when Ipublished the first reports of unique mitochondrialDNA signatures in some of these fish that were notfound in any California hatchery populations (Nielsenet al. 1994 CJFAS). Similar break-through molecularfindings were published for runs of Chinook salmon inthe Sacramento-San Joaquin River drainage andShasta rainbow trout on the McCloud River (Nielsenet al. 1994 Cons. Bio.; Nielsen et al. 1999 Mol. Ecol).More recent studies has been published on steelheadpopulations in California’s Central Valley and SnakeRiver steelhead populations throughout Idaho.My fisheries genetics findings were controversial andled to much discussion and frequent opposition to mypublished reports. The implications of documentingrare salmonid populations in extreme environments atthe southern extent of their range were unexpectedand certain to be costly for established management.However, despite significant effort and moneydirected to refuting my work by state and federalresource managers, my findings still hold today. Myserendipitous DNA results on trout and steelhead insouthern California have led to the development ofsignificant infrastructure, numerous fisheries biologycareers and many publications dedicated to salmonidsat the southern extent of their range. Many of thesepopulations are currently protected under the ESA asthreatened or endangered species.MEXICAN SALMONIDSInterest in salmonids at the southern extent of theirrange brought me to investigations of unique troutpopulations in Mexico previously studied by DavidStarr Jordan and Robert Rush Miller. FreshwaterMexican trout (Oncorhymchus mykiss nelsoni) arefound in a small number of streams in Baja California,Mexico. Rainbow trout are also common in highaltitude, spring-fed streams along the northern SierraMadre Mountains in central Mexico. Early allozymeanalyses showed that these Mexican fishes are moreclosely related to rainbow trout (Oncorhynchusmykiss) than cutthroat trout (O. clarkii).Collaborations with Mexican scientists providedcontemporary sampling opportunities on these fishes.Through grants I funded several scales of DNAanalyses on Mexican trout. I was able to show thatMexican trout in the rios Mayo, Yaqui and othernorthern Sierra Madre streams have unique molecularsignatures that place them as evolutionarily distantfrom the California rainbow trout populations asOncorhynchus chrysogaster (Mexican golden trout),and Gila and Apache trout populations found in thesouthwest US. They also do not share commonmolecular characteristics with any of these othersouthern trout species. This molecular data supportsinference on special status for these fishes. Efforts areunderway in Mexico to rename these fishes with theirown species status. It is our hope that the new focuson these rare and unique populations of trout inMexico will help conservation efforts in their nativehabitats.STEELHEAD ACOUSTIC ANDARCHIVAL TAGSAfter 18 years of studying salmon in freshwater I wasstill very curious about the two-thirds of their life theyspend at sea. In 2000 I became part of the Census ofMarine Life’s salmon project (POST) and began to5

experiment with newly developed archival tags forPacific salmon in an attempt to study their patterns ofmovement and distribution at sea. I also used acoustictag technology to monitor the timing and pattern ofmovement of salmon at the freshwater-marineinterface. I beta-tested archival tags developed byLOTEK and off the shelf acoustic technology. Forthree years I monitored steelhead adults at a weir onthe Ninilchik River where a high proportion of repeatspawners were found in the population (20-50%).Acoustic tag technology allowed me to demonstratethat steelhead use tidal activity to accelerate theirtransition from riverine to sea habitats. Archival tagswere difficult to recover in repeat spawning fish;many of the tags were lost before recapture of the fishat the weir. However, two tagged steelhead, one maleand one female, gave us bi-minutely data fortemperature and depth for 18 months at sea. The mostprovocative finding derived from these data was thefact that both steelhead spent over 97% of their time atsea in the top six meters of the ocean. Futureengineering and better deployment protocols forsalmon archival tags will allow us to gain a betterpicture of these fish at sea.HALIBUT POP-UP TAGSThis study started when I arriver in Alaska in 1999with the live capture of seven wild Alaska halibut(>70 lbs each) and putting these fish into husbandry inlage circular tanks at the Alaska Sea Life CenterAquarium for experimental tagging with satellite popuptags. These fish adapted to captivity very easilyand they were eating from hand within three weeks.Two of my tagged halibut remained on display at theSea Life Center for 18 months. All were released astagged fish back into their original habitats. Satellitepop-up tags were tethered to the halibut with littleeffect. These tags carry an on-board computer withhigh capacity memory storage. We programmed thesetags to provide bi-minutely data on temperature, depthand light levels for up to 18 months while theseanimals were at sea.Since halibut are demersal and spend most of theirtime at depth the light sensor was developed for bluelight, the type of light that penetrates most deeplythrough seawater. We were hoping to use standardalgorithms to calculate rough estimates of geolocationusing these light sensors, apparent dawn and dusktimes and the exact clock found in the tag. Comparingthese data with depth measurements from the tagsallowed us to position tagged halibut within a radiusof about 60 nautical miles for most times of the year.Spring and fall equinox periods had high variation inthe data due to limited changes in light levels.To date we have been able to tag a total of 78 halibutfrom Alaskan waters and get information of theirpatters of movement to and from breeding grounds atgreat depths at sea, usually over 500 meters. Werecorded specific mating behaviors in these fish ontheir winter breeding grounds that was similar to otherpublished flat fish behavior. We showed geographiccontinuity in winter migrations suggesting populationstructure in Pacific halibut where none was thought toexist before. Currently genetic studies are underwayin my laboratory to confirm this structure using DNAanalyses. Support for local population structure inPacific halibut represents an important contribution tothe management of this commercial species. Thesestudies have contributed to a sea change in the wayPacific halibut are managed as a commercial speciesby the International Pacific Halibut Commission.CLIMATE CHANGE, OCEANCARRYING CAPACITY AND SALMONAT SEAI received my first climate change grant from theUSGS in 1999. I was the first biologist to get fundingfor climate change impacts on salmonids within theagency and served as the only biologist on severalearly national committees. For the last eight years Ihave addressed the issue of climate change impacts onsalmonid growth and survival at sea in the NorthPacific Ocean. Collaborators helped develop a newdigital system to record seasonal and annual scaleincrements from retrospective scale collections takenfrom salmon captured in Bristol Bay, Alaska, 1955-present. These data were used in time-series analysesto look at trends correlated to patterns of climatechange and sea condition over time. One of the mostimportant findings coming from this study is supportfor competition at sea between wild Alaska sockeyesalmon and pink salmon from Kamchatka. Theseanalyses give further support for the concept of oceancarrying capacity and the need for fisheriesmanagement to consider impacts of fish productionand harvest far from local marine habitats.BROOKS RIVER GRIZZLY BEARS6

In 2006 I received a grant from the National ParksService NRPP Program to look at brown bears in theBrooks River drainage. These grizzly bears are partof an extensive tourist bear-viewing opportunity inAlaska that is managed by NPS. Numerous bears visita low waterfall in the spring and fall to feed on salmonruns and carcasses in the Brooks River. NPS hasestablished safe and effective viewer platforms alongthe lower river for bear observations by visitors.Nothing is known about the origin of the bears visitingthis site, their genetic relationships and themechanisms that establish their spatial and temporaluse of the river. We are using mtDNA andmicrosatellite loci to develop genetic relationshipsamong the bears. We will look at temporal and spatialuse by individual bears that can be identified byknown genetic signatures using DNA from hair andtissue collections. We are also searching for circadianrhythm genes in brown bears to look for sequencevariation within those genes that may have functionalrelationships with the timing of bear use on the river.NORTH SLOPE ARCTIC CISCOUSGS collaborates with the DOI MineralsManagement Service to monitor distribution, activityand abundance of plants and animals of interest on theNorth Slope of Alaska. Before 2006, no research hadbeen done on the Arctic cisco overwinter in theColville River on the North Slope during periods ofwinter ice in the Beaufort Sea. These fish provide asubsistence harvest for the local native communitywith net harvest under the ice when the fish move intocoastal habitats in October. The local community isconcerned about increased development of the slopeand climate change effects on this importantsubsistence harvest. The putative source populationfor all the Arctic cisco in the Colville River is theMackenzie River in Canada, where three distinctspawning populations have been identified. We willuse genetic analyses to look at the relationshipsamong the Colville River harvest of Arctic cisco andputative source populations, including other potentialbreeding populations along the Beaufort and Chukchiseas. We will look at changes in recruitment fromdifferent source populations over time in relationshipto climate change and shifts in the Arctic oscillation.RESEARCH BASED AWARDS ANDHONORS1996 Special Contributions Award - California-Nevada Chapter American Fisheries Society1996 Award of Merit - Western Division of theAmerican Fisheries Society1997 Distinguished Professional AchievementAward California-Nevada ChapterAmerican Fisheries Society1997 Award of Special Recognition WesternDivision of the American Fisheries Society1998 Letter of Recognition Government ofCanada Networks of Centers of Excellence1999 Letter of Recognition & Book AwardCalifornia Coastal Commission2000 - 2003 Star Awards USGS Alaska ScienceCenter2000 On-the-Spot Award USGS BRD ICEBIRGProgram, Reston, West Virginia.2000 Distinguished Service American FisheriesSocietyResearch – AdministrationSound administration requires a team effort whereleadership primarily focuses on individual talents andskills as they relate to the common goals of thecommunity. I have administered over 40 researchprojects and several programs during my career at theuniversity, state and federal levels. I have a strongreputation for timely and rigorous research productsproduced within a cost-effective budget.RESEARCH MANAGEMENTMy research has consistently been interdisciplinaryrequiring a creative balance among multiple goals andfunding opportunities. This approach often requiredaccumulation of small grants or funding opportunitiesdedicated to various aspects of one overarchinghypothesis. At other times I have focused large sumsof money to both scientific and sociological aspects offisheries research covering multiple related projectgoals. In all cases my strategic approach to themanagement of science has been to ask the rightquestion at the right time and look for ways tointerpret that challenge to other scientists and7

managers. I have been very successful in thisendeavor.PROGRAM MANAGEMENTGENETICS LABORATORIESImmediately after my PhD in 1994, I organized andmanaged a soft-money genetics laboratory at HopkinsMarine Station, Stanford University. The laboratoryspace was offered to me by Stanford, but all researchfunding came from my own grants. This laboratorywas dedicated to the study of population genetics infish and fisheries. Special focus was placed on thegenetics of California salmonids and much of theresearch along these lines contributed to the listing ofPacific salmon in California under the ESA.In 1996 I spent three months on the South Island ofNew Zealand as a visiting scientist to assist theNational Institute for Water and Atmosphere (NIWA)in the creation of a molecular genetics laboratorydedicated to the study of plants and animals in NewZealand. The first molecular studies on Chinooksalmon and native New Zealand eels started fromwork I initiated in this laboratory during this time.FISHERIES PROGRAM ELEMENTSIn 1999 I was offered the role as supervisor of thefisheries program at the USGS Alaska Science Center.I ran their fisheries program until 1995 and supervised17 scientists and technical staff with over 23 researchprojects. During this time I successfully implementednew research at USGS for climate change, studies ofsalmon at the freshwater/marine interface, patterns ofseasonal movement in Pacific halibut and criticalmarine habitats for Pacific salmon. I implementedcutting-edge research on ocean carrying capacity andNorth Pacific salmonid fisheries. I applied newtechnologies such as satellite pop-up tags on Pacifichalibut, and archival and acoustic tagging of wildAlaska steelhead to monitor ocean migration andcritical marine habitats. See the research overviewsabove for specific projects. In 2005 I turned overleadership of the fisheries program to Dr. C.Zimmerman, whom I hired in 2001, so that I coulddedicate a large proportion of my time to theAmerican Fisheries Society for five years of service asan Officer of the Society.Conferences and SeminarsORGANIZATIONAL PARTICIPATION(1995-2008)Park City, Utah. July 16-19, 1995. Western DivisionAmerican Fisheries Society. PracticalApplications of Ecosystem ManagementGenetic Tools. Session Chair.Tucson, AZ. December 4-14, 1995. USDA EcologicalStewardship Workshop. ScientificCommittee - Genetic and Species Diversity.Santa Fe, NM. February 16-20, 1997. KeystoneSymposium on Evolution of MolecularMechanisms. Session Chair - RepetitiveDNA and the evolution of repeat units.Monterey, CA. August 24-29, 1997. AmericanFisheries Society Annual Meeting.Program Chair.Seattle, WA. June 24-27, 1998. Ecology, Ethology,and Evolution of Fishes (EEEF).Symposium Chair: "The Intersection ofMolecular and Behavioral Science."Hartford, CN. August 26, 1998. American FisheriesSociety Annual Meeting. Session Chair:Ecology, physiology, and genetics ofsalmon at the southern edge of theirdistribution: Implications for conservation.Charlotte, NC. August 14, 1999. American FisheriesSociety Annual Meeting. Organizer: Therole of hybridization in the distribution,conservation, and management of aquaticspecies.La Paz, MX. June 15, 2000. Annual MeetingAmerican Society of Ichthyologists andHerpetologists. Session Chair: Freshwaterfish and invertebrates of Mexico.8

Phoenix, AZ. August 2001. American FisheriesSociety Annual Meeting. Session Chair.Conservation, biology, genetics andmanagement of freshwater fish in theSouthwest and Mexico.Juneau, AK. July 2002. Alaska Sea GrantOrganization Committee: Genetics of subpolarfish and invertebrates.San Diego, CA. April 2003. Organization Chair andEditor: Hatchery/wild interactions inmarine and estuary habitats. WesternDivision American Fisheries Society.Vancouver, BC. May 2004. Publication CommitteeChair, 4 th World Fisheries Congress.San Francisco, CA. September 2007. AFS AnnualMeeting. President of AFS and PlenaryChair.Auckland, NZ. February 2008. OrganizingCommittee. AFS 2 nd International TaggingSymposium.INVITED PRESENTATIONS ATSYMPOSIA AND SOCIETY MEETINGS(1997-2007)Anchorage, AK. Feb. 7, 2007. AYK SSI Symposium“Retrospective analysis of Yukon and KoskokwinChinook salmon growth. G. Ruggerone, J.Nielsen and B. Agler.Anchorage, AK. Feb. 8, 2007. AYK SSI Symposium.“Growth and survival of salmon in response tocompetition and climate change.” G. Ruggeroneand J. Nielsen.Petropavlovsk-Kamchatsky, Russia. World WildlifeInternational Workshop. Nov. 30, 2006. “Growthand survival of salmon in response to competitionand climate change: Implications for interactionsof wild and hatchery salmon.” G. Ruggerone andJ. Nielsen.Fairbanks, AK. Nov. 16, 2006. American FisheriesSociety AK Chapter. “Long-term trends in annualBristol Bay and Chignik sockeye salmon scalegrowth at sea in relation to sockeye abundanceand climate change, 1955-2000.” J. L. Nielsenand G. Ruggerone.Homer, AK. Oct. 30, 2006. World Wildlife FundBering Sea Climate Camp. “Growth, abundanceand survival of salmon in response to climatechange. G. Ruggerone and J. Nielsen.Victoria, BC. June 4, 2006 ASLO 2006. “Growth andsurvival of salmon in response to climate,competition and a dynamic ocean carryingcapacity. G. Ruggerone and J. L. Nielsen.Sesimbra, Portugal. June 7, 2005. Sixth Conference onFish Telemetryl. “The potential of using pop-uparchival transmitting tags to monitor migrationand behavior of Atlantic halibut (Hippoglossushippoglossus) in Norwegian waters. K.Michalsen, A. C. Seitz and J. L. Nielsen.Victoria, BC. May 15-16, 2005. GLOBEC Symposium:Climate Variability and sub-arctic marineecosystems. “Linkages between climate, growth,competition at sea and sockeye salmon abundancein Bristol Bay, Alaska, 1955-2000” posterpresentation by G. Ruggerone, J. Nielsen and J.Meka.Honolulu, HI. October 19, 2004. PICES 13 th AnnualMeeting. “Top-down and bottom-up linkagesamong climate, growth, competition andproduction of sockeye salmon populations inBristol Bay, Alaska.” J. L. Nielsen.Sacramento, CA. October 5, 2004. California BayDelta Authority Science Conference.“Microsatellite analyses of Central Valley troutpopulations, 1999-2003.” J. L. Nielsen.Seward, AK. March 9, 2004. International ScientificSymposium for Climate Change in the Arctic:Arctic Climate Impact Assessment Meeting.“Ecosystem management: threats, vulnerabilitiesand opportunities.” J. L. Nielsen.Honolulu, HI. February 19, 2004. ASLO/TOS OceanResearch 2004 Conference. “Use of acoustic tagsand moored receivers to describe behavior andfreshwater to marine migration of post-spawnsteelhead, Ninilchik River, Alaska.” D. R. Wilson,C. E. Zimmerman, P. Richards, T. Tingy and J. L.Nielsen.Seattle, WA. October 23, 2003. October 23, 2003.SEARCH Open Science Meeting: BiologicalFeedbacks. “Linkages between climate, growth,competition at sea, and production of sockeyesalmon populations in Bristol Bay, Alaska, 1955-2000.” J. L. Nielsen and G. Ruggerone.Sacramento, CA. October 15, 2003. The WildlifeSociety Western Section Annual Meeting.“Importance of genetic verification fordetermination of Atlantic salmon in North Pacificwaters. S. L. Graziano, I. Williams, G. K. Sage, C.E. Zimmerman and J. L. Nielsen.Baltimore, MD. August 20, 2002. AFS AnnualMeeting. “Development and application ofmicrosatellites for Pacific halibut.” J. L. Nielsen,G. K. Sage, B. Pierson, I. Williams, T. Wiacek, S.Talbot, D. Wilson, and A. Seitz.Quebec City, QB. August 17, 2002. EEEF 2002.“Satellite pop-up tags and molecular geneticsdescribe unique behavior for Pacific halibut inAlaska.” J. L. Nielsen, G. K. Sage, D. Wilson, andA. Seitz.Kansas City, MO. July, 6, 2002. ASIH annualmeeting,. “Microsatellite analyses of the trout ofnorthwest Mexico” J. L. Nielsen and G. K. Sage.Spokane, WA. April 30, 2002. Toward ecosystembasedmanagement, American Fisheries SocietyWestern Division, Spokane, WA. “Hatchery andwild steelhead genetics in Idaho” J. L. Nielsen, A.Byrne, S. Pavey and G. K. Sage.Anchorage, AK. January 23, 2002. Exxon ValdesTrustee Committee Annual Meeting. “Using newTechnologies in Ecosystem Science” J. L Nielsen.9

Phoenix, AZ. August 24, 2001. American FisheriesSociety. “Molecular genetics of the trout ofnorthern Mexico” J. L. Nielsen and G. K. Sage.Santa Rosa, CA. March 30, 2001. American FisheriesSociety Cal-Neva Chapter. “Colonization by cohosalmon (Oncorhynchus kisutch) in recentlydeglaciated streams in Glacier Bay, Alaska:Inference for restoration of Pacific salmon” J. L.Nielsen, G. K. Sage, K. T. Scribner, E. Knudsen,and C. Soilseth.Boise, ID. February 22, 2001. American FisheriesSociety Idaho Chapter Meeting. PlenaryPresentation: “Genetics vs. ecomorphology in fishmanagement: Does it matter if reproductiveisolation precedes or follows divergence betweenlineages?” J. L. Nielsen.La Paz, MX. June 15, 2000. American Association ofIchthyology and Herpetology. “Molecularsystematics and evolutionary status of the trout ofthe Sierra Madre, Mexico” J. L. Nielsen.Astoria, OR. October 30, 1999. Pacific FisheriesBiologists. “Genetic analysis and management – Isnear-real-time information on the Horizon” J. L.Nielsen.Astoria, OR. October 30, 1999. Pacific FisheriesBiologists. “Advances in genetic techniques forstock discrimination: Finding the markers” J. L.Nielsen.Pennsylvania State University. June 28, 1999. JointMeeting ASIH, AES, HL, and SSAR. “Withinbasin life history divergence based on alternatereproductive strategies in steelhead: genetic andenvironmental considerations.” J. L. Nielsen.Hartford, CT. August 26, 1998. American FisheriesSociety Annual Meeting. "Molecular genetics andconservation of salmonids at the southern extent oftheir range in California and Mexico." J. L.Nielsen.Florence, Italy. July 24, 1998. VII InternationalCongress of Ecology. Special Symposium: Geneconservation: Identification and Management ofGenetic Diversity. "Incorporating molecularevolutionary hybrids into ESU criteria" J. L.Nielsen.Baltimore, MD. Sept. 25, 1997. International Congresson the Exploration of the Sea (ICES) 1997 AnnualScience Conference. "Extinction risk and geneticvariation in anadromous salmonids at the southernextent of their range." J. L. Nielsen.Seattle, WA. June 29, 1997. American Association ofIchthyology and Herpetology. Special Symposium:Nuclear DNA and the Evolutionary Genetics ofFishes, Amphibians and Reptiles. "Moleculargenetics and evolutionary status of the trout of theSonora and Chihuahua desert region of Mexico." J.L. Nielsen, M. C. Fountain, K. Cobble, J. CampoyFavela, and B. L. Jensen.PRESENTATIONS AT TECHNICALCONFERENCES, SEMINARS, ANDTECHNICAL WORKSHOPS (2000-2007)Boise, ID. May 31, 2000. Symposium on thedetection, status, and management ofintrogressed populations of cutthroat trout.“Using mitochondrial DNA and microsatelliteanalyses to determine rainbow trout introgressionin Lahontan cutthroat trout.” J. L. Nielsen(invited).Leavenworth, WA. Nov. 3, 2000. Russian-U.S.Fisheries Working Group. “Salmonid research inAlaska” J. L. Nielsen (invited).Vancouver, BC. Nov. 7, 2000. Workshop forstandardization of microsatellite alleles inChinook and sockeye salmon. “Using the internetfor standardization of microsatellite alleles.” J.L. Nielsen.Newport, OR. Nov. 16, 2000. Distinguished MarineScientist Seminar Series, Hastings MarineScience Center. “How do human impacts andgenetic lineages limit our efforts to conservesalmonids” J. L. Nielsen (invited).Vancouver, BC. Dec. 9, 2000. Census of Marine Life(CoML) Workshop on Pacific salmon tagging.“Identifying research hypotheses for the study ofwild salmon in the ocean.” J. L. Nielsen(invited).Anchorage, AK. January 24, 2001. SW AlaskaNational Parks Science and ResearchSymposium. “ Interesting salmon biology in thewake of cataclysmic geology.” T. Hamon and J.L. Nielsen.Anchorage, AK. January 24, 2001. SW AlaskaNational Parks Science and ResearchSymposium. “ Genetic population structure ofrainbow trout (Oncorhynchus mykiss) within theAlagnak River drainage.” G. K. Sage, J. Meka,J. L. Nielsen, D. Wilson, I. Williams and E.Knudsen.Anchorage, AK. January 24, 2001. SW AlaskaNational Parks Science and ResearchSymposium. “Effects of catch-and-releasefishing and hooking injury on the physiology andbehavior of Alagnak River rainbow trout.” D.Wilson, J. Meka, J. L. Nielsen and E. Knudsen.Dillingham, AK. May 3, 2001. Bering Sea SalmonScience Symposium. “Global climate changeand freshwater growth in sockeye salmon indrainages of the Bering Sea.” J. L. Nielsen(invited).Boise, ID. July 9, 2001. Special seminar IdahoDepartment of Fish and Game. “Conservationunits in resource management: Integratinggenetics and ecology.” J. L. Nielsen (invited).Amsterdam, The Netherlands. September 12, 2001.Special seminar University of Amsterdam.“Scientific publication and resource conservationin the new century.” J. L. Nielsen (invited).Bodega Bay, CA. October 26, 2001. SalmonidCoastwide genetics Meeting, Bodega Bay, CA.“Standardization of microsatellite alleles inOncorhynchus mykiss.” J. L. Nielsen (invited).Portland, OR. November 5, 2001. Pacific Rim WildSalmon and Steelhead Conference. “Testing new10

electronic archival tags in Pacific salmon.”(Poster) J. L. Nielsen and D. Wilson.Portland, OR. November 6, 2001. Pacific Rim WildSalmon and Steelhead Conference. “Steelheaddistribution throughout Alaska.” (Poster) J. L.Nielsen and D. Wilson.Sitka, AK. November 13, 2001. AFS AK Chapter.“Testing satellite pop-up tags as a tool foridentifying critical habitat.” J. L. Nielsen and D.Wilson.Oakland, CA. November 14, 2001. The Status ofAnadromous Fish in Bay Area Streams. “DNAsleuthing in urban streams: using moleculargenetics to identify native California steelhead.”J. L. Nielsen (invited).Juneau, AK. November 30, 2001. DepartmentalSeminar University of Alaska. “Electronictagging and tracking of marine organisms inAlaska waters.” J. L. Nielsen (invited).Santa Cruz, CA. January 16, 2002. 4 th Annual SalmonOcean Ecology Meeting. “Testing ElectronicArchival Tags in Coho Salmon in Alaska” J. L.Nielsen (invited).Vancouver, BC. March 15, 2002. NPAFC/NASCOConference. “Long-term trends in annual BristolBay sockeye salmon scale growth at sea inrelation to sockeye abundance and environmentaltrends, 1955-2000.” (Poster) G. T. Ruggerone, J.Nielsen, E. Farley, S. Ignell, P. Hagen, B. Agler,D. Rogers, and J. Bumgarner.Anchorage, AK. June 19, 2002. Alaska’s oceans andwatersheds: sustainability in the context ofchange, EVOS Trustee Council. “Electronictagging and tracking of marine fishes?” J. L.Nielsen (invited).Amherst, MA. October 1, 2002. University ofMassachusetts, Amherst. “Electronic tagging andtracking of Pacific halibut reveals uniquespawning behavior and population substructure?”J. L. Nielsen (invited).Turners Falls, MA. October 3, 2002. USGS ConteLaboratory Seminar Series. “Competitionbetween Asian pink salmon and North Americansockeye salmon in the North Pacific Ocean.” J.L. Nielsen (invited).Shepherdstown, WV. November 1, 2002. NationalConservation Training Center, USFWS.Conservation Genetics Workshop. “ Integratingacross scales: genetics and ecology in resourcemanagement.” J. L. Nielsen (invited).Anchorage, AK. January 24, 2003. Biology SeminarSeries, University of Alaska, Anchorage.“Molecular systematics and conservation ofMexican trout (Oncorhynchus mykiss) in theSierra Madre Occidental.” J. L. Nielsen(invited).Anchorage, AK. March 12, 2003. Campbell CreekScience Center (BLM). “Women in Science:Fisheries in Alaska” J. L. Nielsen (Invited).Guelph, OT. March 27, 2003. Department of BiologySeminar Series, University of Guelph.“Implementation of new tagging technologies inAlaska’s salmon and halibut.” J. L. Nielsen(Invited).San Diego, CA. April 16, 2003. Western DivisionAFS. “Evidence for competitive dominance ofpink salmon over other salmonids in the NorthPacific Ocean.” G. Ruggerone and J. L. Nielsen(invited).San Diego, CA. April 17, 2003. Western DivisionAFS. “Genetic diversity in native and introducedMexican trout species.” A. George, K. Sage, R.Mayden, B. Kuhajda, D. Hendrickson, H.Espinosa, L. Findley, J. Tomelleri, J. Nielsen andF. Garcia de Leon.Vancouver, BC. June 12, 2003. World Summit onSalmon, Simon Fraser University. “History andEffects of Hatchery Salmon in the Pacific.” J. L.Nielsen (invited).Anchorage, AK. September 12, 2003. University ofAlaska Anchorage Biological Sciences Seminar.“The importance of genetic verification ofAtlantic salmon caught in Pacific waters. “ J. L.Nielsen (invited).Red Bluff, CA. October 8, 2003. Battle CreekWorkshop. “Molecular genetic analyses ofCentral Valley steelhead populations 2001-2002.” J. L. Nielsen (invited).Bergen, Norway. Nov. 14, 2003. Institute of MarineResources. Pop-up archival transmitting (PAT)tagging of Pacific halibut (Hippoglossusstenolepis). A. C. Seitz, B. L. Norcross, D.Wilson and J. L. Nielsen (invited).Fairbanks, AK. Nov. 18, 2003. Alaska Chapter AFS.“Identifying spawning behavior in Pacifichalibut, Hippoglossus stenolepis, using electronictags. A. C. Seitz, B. L. Norcross, D. Wilson andJ. L. Nielsen.Nuiqsut, AK. November 19, 2003. MineralsManagement Service Nuiqsut Arctic CiscoWorkshop. “Exploitation dynamics of small fishstocks like Arctic cisco.” J. L. Nielsen (invited).Fairbanks, AK. Jan. 21, 2004. University of AlaskaFairbanks Institute of Marine Science SeminarSeries. “Satellite tagging of Pacific halibut(Hippoglossus stenolepis) in the Gulf of Alaska.A. C. Seit, B. L. Norcross, D. Wilson and J. L.Nielsen (invited).Anchorage, AK. Feb. 10, 2004. Alaska Forum for theEnvironment. “Linkages between climate,growth, competition at sea and production ofsockeye salmon populations in Bristol Bay,Alaska 1955-2000. J. Meka, J. L. Nielsen, G.Ruggerone (invited).Seattle, WA. May 27, 2004. International PacificHalibut Commission; Special Projects Reports.“Satellite tagging of Pacific halibut(Hippoglossus stenolepis). A. C. Seitz, T. Loher,B. L. Norcross and J. L. Nielsen (invited).Dutch Harbor, AK. July 14, 2004. Forum of AlaskaMarine Issues, Dutch Harbor/UnalaskaCommunity Seminar Series. A. C. Seitz, T.Loher, B. L. Norcross and J. L. Nielsen(invited).11

Bergen, Norway. September 16, 2004. BiologicalSciences Seminar Series, University of Bergen.“The use of acoustic and archival tags to monitorocean migrations and critical marine habitat insalmonids.” J. L. Nielsen (invited).Sitka, AK. Nov. 17, 2004. Alaska Chapter AmericanFisheries Society. “The use of acoustic andarchival tags to monitor ocean migrations andcritical marine habitat in salmonids.” PhilRichards, C. E. Zimmerman, and J. L. Nielsen.Anchorage, AK. Sept. 12, 2005. American FisheriesSociety Annual Meeting. Growth and survival ofsalmon in response to climate change and adynamic ocean carrying capacity.” G. Ruggeroneand J. L. Nielsen.Anchorage, AK. Sept. 14, 2005. American FisheriesSociety Annual Meeting. “Hypotheticalmigration pathways of Pacific halibut in the Gulfof Alaska, based in daily maximum depth.” A. C.Seitz, D. C. Douglas, B. L. Norcross and J. L.Nielsen.Anchorage, AK. Sept. 15, 2005. American FisheriesSociety Annual Meeting. “Salmon age structureand variable resilience of Bristol Bay sockeyesalmon to climate change.” G. Ruggerone, J.Nielsen and M. Link.Kyoto, Japan. October 24, 2005. Sixth InternationalSymposium on Flatfish Ecology – Habitats inrelation to recruitment variability-generation offuture direction. “Pop-up satellite tagging ofPacific halibut in the Bering Sea and AleutianIslands” A. C. Seitz, T. Loher, B. L. Norcrossand J. L. Nielsen.Vancouver, BC. April 20, 2006. Simon FraserUniversity Department of Biology SeminarSeries. “Satellite pop-up tags and geneticsdescribe Pacific halibut population structure inAlaska” J. L. Nielsen, A. C. Seitz, I. Williamsand S. Graziano.Kamchatka, Russia. December 5, 2006. WorldWildlife Fund Workshop on Interactions of Wildand hatchery Salmon. “Growth and survival ofsalmon in response to competition and climatechange” G. Ruggerone and J. Nielsen.Outreach and Public ServiceOne of my most focused goals throughout my researchcareer has been to always provide the best possiblescience while creating and facilitating opportunitiesfor students and young professionals in my field ofinterest.STUDENT SPONSORSHIPAvelino, Olivia 2000, M. Sc. Sacramento StateUniversity. Employed in lab 1998-1999.Carpanzano, Cindy 1996, M. Sc. University ofCalifornia, Santa Barbara. Habitatrelationships in southern steelhead. JLNserved on Thesis Committee and fundedresearch.Cheney, Lisa C. 1995, M. Sc. San Jose StateUniversity, Moss Landing Marine Lab.Thesis topic: conservation genetic of thePacific sea otter. Employed in lab 1995-1996.Crewdson, Yarrow 2000, UndergraduateWhitman College, Washington. Employedin lab 2000-2002.Crow, Karen 1995, M. Sc. San Francisco StateUniversity, Moss Landing Marine Lab.Thesis topic: conservation genetics of kelpgreenling. Employed in lab 1995-1996.Ph.D. 2001 UC Santa Cruz.Fountain, Monique C. 1997, M. Sc. SanFrancisco State University. Thesis topic:Conservation genetics and the Europeangreen crab introduction into San FranciscoBay. Employed in lab 1995 – 1999.Gan, Christina A. 1997, M. Sc. Humboldt StateUniversity. Thesis topic: Golden troutgenetics of the Kern Plateau. JLN served onGraduate Committee and funded research.Employed in lab 1994-1998.George, Anna 2002-3, Ph.D. Department ofBiology, Saint Louis University. Sponsoredfor independent research on lab 2002.Collaborated on development of moleculardatabase for Mexican trout 2003.Gomez-Uchida, Daniel 2003-2006, Ph. D.Oregon State University. Thesis topic: Ademographic approach to the study of theinterplay between molecular populationgenetics and population dynamics in overfishedrockfish. JLN served on graduate andThesis Committees.Guy, Troy 2004, MSc. Oregon State University.Thesis topic: Cutthroat trout above natural12

arriers in Oregon. JLN served on Graduateand Thesis Committees.Heine, Erica 1998, M. Sc. California PolytechnicUniversity. Student technician in Nielsenlaboratory 1997- 1998.Lowery. Alex 1997, Mountain View H.S. SeniorProject - MHC polymorphisms in steelheadfrom Alaska to California. Molecularscience work done in Nielsen lab. Currentlyundergraduate at Stanford University.McClean, Scott 1999-2004. M. Sc. University ofAlaska Fairbanks. Research sponsor andsupervisor. Effects of upwelling on survivaland production of chum salmon in redds onthe Yukon River. JLN funded thesisresearch.Malone, Catherine L. 1994, B. A. University ofCalifornia Santa Cruz. Americorp volunteerin lab 1994-1995. Currently Ph. D. studentTexas A & M Univ. Employed in lab 1996.Meka, Julie 2000 – 2004. M. Sc. University ofAlaska Fairbanks. Thesis topic: stressphysiology and injury in rainbow troutsubject to catch-and-release fishing. JLNserved on Thesis Committee and fundedresearch.Neville, Helen M. 2003- 2005, Ph. D. Universityof Nevada, Reno. Thesis topic:Metapopulations structure and genetics ofLahontan Cutthroat trout. JLN served onGraduate and Thesis Committees.Pavey, Scott 2004. M. Sc. University of Alaska,Anchorage; 2004-2007 Ph. D. CandidateSimon Frasier University. Thesis topic:Rapid microevolution in sockeye salmon onthe Aniakchak River, Alaska. JLN serves onThesis Committee and funds researchcollaboratively with NPS.Pelot, Sage, 2000. Undergraduate University ofCalifornia Davis. Student appointment2000.Rasgon. Jason 1996. M. Sc. Student CaliforniaPolytechnic University. Employed in lab1996.Rathhouz. Margaret M. 1996, Ph. D. Universityof California, San Diego. Employed in lab1996-1997.Reamey, Jacklyn 2001-04, DOI SCEP NativeAmerica student appointment. PacificLutheran University, Anchorage, AK. Studytopic is Alaska blackfish genetics.Seitz, Andy 2002-6. Ph. D. University of Alaska,Fairbanks. Population substructure derivedfrom satellite pop-up tags in Pacific halibut.JLN serves on Thesis Committee andfunded research.Sundermeyer, Ruth, 1999, M. Sc. San Jose StateUniversity. Thesis topic: Molecular geneticsof steelhead in the Pajaro River basin.Employed in lab 1996 - 1999.Wiacek, Talia C. 2000, Senior University ofAlaska Anchorage, Employed in lab 2000-2003.Williams, Ian 2001-2004, M. Sc. University ofAlaska Anchorage. Thesis topic: Geneticintrogression between coastal cutthroat troutand steelhead on the Copper River, Alaska.JLN serves on Thesis Committee and fundsresearch.Wiltse, Darren S. 1998, M. Sc. San Jose StateUniversity. Employed in lab 1998 - 1999.Wise, Lawrence M. 1996, M. Sc., San FranciscoState University. Thesis: Consistency ofFocal Position by Juvenile Rainbow Troutand Brown Trout in a Central Sierra NevadaStream. JLN served on Thesis Committeeand advised funding agency (EPRI).PROFESSIONAL MEMBERSHIPAmerican Association for the Advancement ofScienceAmerican Fisheries Society (Life Member)American Society of Ichthyologists andHerpetologists (Life Member)American Society for Limnology andOceanographyCouncil of Scientific Society PresidentsDesert Fishes CouncilEcological & Evolutionary Ethology of Fishes(Life Member)Society for Conservation BiologySociety for the Study of EvolutionTECHNICAL REVIEWS REQUESTED(2005-2007)AYK SSICanadian Journal Fish and Aquatic SciencesConservation GeneticsCopeiaEnvironmental Biology of FishesEnvironmental Protection ServiceFisheriesGeneticsGeneticaMolecular Ecology13

NASANational Fish and Wildlife FoundationNational GeographicNational Science FoundationNatural Sciences and Engineering Research Councilof CanadaNorth American Journal of Fisheries ManagementNorth Pacific Research BoardNorth Pacific Research CouncilSea Grant California - Marine Ecological ReservesResearch ProgramSea Grant – University of Washington OmnibusProposalTransactions of the American Fisheries SocietyU.S. Geological SurveyU. S. Department of Agriculture, Forest ServiceU. S. Department of Agriculture, Small BusinessInnovation ResearchU. S. Department of Commerce, NOAA, NMFSU. S. Fish and Wildlife ServiceSCIENTIFIC APPOINTMENTS(1992-2007)1992-97 American Fisheries Society - NationalFisheries Action Network.1993-94 President California-Nevada ChapterAmerican Fisheries Society.1995 US Forest Service, BLM, EPA andNMFS - Scientific Advisor for geneticand species diversity.1996 Sustainable Ecosystem StewardshipCommittee.1997 Toulumne River Hatchery GeneticsReview Committee, CDFG.1997 Atlantic Salmon Conservation ReviewCommittee, DOI, Braemar Scotland1997 Ecological Stewardship Project Award,U.S. Forest Service.1997 Advisory Editor EnvironmentalBiology of Fishes, Board of Governors.1997 National Meeting Program ChairAmerican Fisheries Society.1997 Time and Place Committee AmericanFisheries Society.1998 Committee to Restore SouthernCalifornia Steelhead, U.C. ExtensionService.1997 Southern Coho Restoration Committee,California Department of Fish andGame (CDFG).1998 Advisory Editor EnvironmentalBiology of Fishes.1999 Government of Canada – Networks ofCenters of Excellence (NCE) PanelReview for Fisheries Network.1999 Committee for Integration &Collaboration for Emerging BiologicalIssues and Research Goals – ICEBIRGGenetics and Molecular Tools.1999 Editor-in-Chief Reviews in FishBiology and Fisheries.2000 Book Series Editor Reviews: Methodsand Technology in Fish Biology andFisheries.2000-03 Management Committee and GoverningBoard American Fisheries Society.2000-02 President Genetics Section AmericanFisheries Society2000 Editorial Board Guelph IchthyologyReviews.2001 Distinguished Service AwardNomination Committee AmericanFisheries Society.2001-04 Independent external expert EuropeanUnion’s SALGEN project on Atlanticsalmon genetics.2001-04 Scientific Steering Committee Censusof Marine Life – Sloan Foundation2002-05 USGS ASC SEARCH Science SteeringCommittee Representative.2002-05 Habitat Subcommittee Exxon ValdezOil Spill Trustee Council’s GEMProgram.2002-05 Publication Chair Fourth WorldFisheries Congress.2002-03 NASA Earth Science Enterprise Peer-Review Committee.2003 Elected Second Vice-PresidentAmerican Fisheries Society.2003-04 NOAA NMFS South-CentralCalifornia Coast Technical RecoveryTeam.2003-05 AFS Time and Place Committee.2003-06 AFS Hutton Sub Committee.2003-06 AFS Membership Committee, Chair.2004 AFS Carl R. Sullivan FisheryConservation Award Committee Chair.2004 AFS Meritorious Service AwardCommittee Chair.2004 AFS Certification Board of AppealsCommittee.2004 Scientific Advisory Committee Sitkatribe of Alaska.2004 First Vice-President AmericanFisheries Society.2005 Exxon Valdez Oil Spill TrusteeCouncil’s Watersheds Work Group2005 AFS Awards Committee, Chair.2005 AFS Special Committee on FisheriesConservation Foundation ProposalReview Process, Chair.2005 Vice-President American FisheriesSociety.2005 Interagency Working Group BeringSea Ecosystem Study Team.14

2006 President Elect American FisheriesSociety2006-07 Council of Scientific Society PresidentsEnvironment, Population and EnergyCommittee, Co-Chair2007 President American Fisheries Society2007-08 World Council Fisheries Society2007 Board Fisheries ConservationFoundationACADEMIC APPOINTMENTS1995 Visiting Scientists New ZealandFederal Government National Instituteof Water and Atmosphere.1995 Visiting Scientist FellowshipUniversity of Otago, NZ.1995-99 Visiting Scientist, Stanford UniversityHopkins Marine Station.1995-99 Adjunct Research Professor - MossLanding Marine Laboratory, CaliforniaState University System.1996-98 Associate Research Biologist - MarineScience Institute, University ofCalifornia, Santa Barbara.1998-99 Adjunct Professor - Department ofIntegrated Biology, University ofCalifornia, Berkeley.1999–present. Affiliate Assistant Professor ofMarine Science, School of Fisheriesand Ocean Science, Institute of MarineScience, University of Alaska,Fairbanks.1999–present. Affiliate Associate Professor,School of Fisheries and Ocean Science,University of Alaska Fairbanks.2001-05 Affiliate Associate Professor,Department of Biology, University ofAlaska, Anchorage.2002-05 Professor Graduate Faculty of OregonState University, Department ofFisheries and Wildlife.1997 Determination of Critical Habitat forSouthern Steelhead, NMFS, SierraClub, and the California CoastalCommission.2000 U.S./Russia Steelhead Life HistoryCommittee (USFWS).2000 Committee for microsatellite allelicstandardization in salmonids.2000 State of Oregon Scientific AdvisoryCommitteeIndependentMultidisciplinary Science Team –hatchery review sub-committee.2000 Scientific Steering Committee SloanFoundation’s Census of Marine Life(CoML) – electronic tags in the censusof marine salmonids.2001 Scientific Advisory Committee –LOTEK Marine Science committee forthe development of salmon archivaltags2002 Independent External Expert –SALGEN Workshop on Atlanticsalmon genetics, London, England2002 Restoration Advisory Committee –Lahontan cutthroat trout, Reno, Nevada2003 External Expert - SALGEN Workshopon Atlantic salmon genetics, Westport,Ireland2005-present. Interagency Working GroupBering Sea Ecosystem Team (BEST)2005-present. Advisory Board Alaska TribalNatural Resource Management CareerDevelopment Program - NOAAPOLICY APPOINTMENTS1997 Steelhead Restoration and ManagementPlan for California, CDFG.1997 Status Review of Coho Salmon fromWashington, Oregon, and California,NMFS.1997 Status Review for AnadromousAtlantic Salmon in the United States,NMFS.1997 Status Review of West Coast Steelheadfrom Washington, Idaho, Oregon, andCalifornia, NMFS.1997 Salmon Aquaculture Review, BritishColumbia Environmental AssessmentOffice.15

Grants & Contracts 1999 - 2007Years Sponsor Topic Funding ($)1999 CA Fish & Game Genetics of hatchery vs. wild fall-run Sacramento Chinook 25,0001999 City of Oakland Molecular genetics of urban trout in San Francisco Bay 3,0002000-05 USGS Competitive Grant Effects of climate change on sockeye growth in Alaska 444,0002000-03 State of Idaho Molecular genetics Snake R. steelhead populations 309,0002000-01 USFWS Ventura CA Genetics of rainbow trout of the Santa Ynez River basin 24,0002000-03 National Parks Service Catch-and-release fishing on trophy rainbow trout in Alaska 210,0002000-02 EVOS Satellite tagging of Pacific halibut 77,0002000-01 CA Fish & Game Sequence analyses of microsatellite loci in Chinook salmon 25,0002001-02 USGS Fisheries research on Yukon Chinook and chum salmon 410,0002001-03 EVOS Testing archival tag technology in Alaska salmon 175,0002001 USGS Fisheries research at the freshwater/marine interface 50,0002001 Great Basin Tribes Investigations of Pyramid Lake Lahontan cutthroat trout genetics 9,6002001 CA Fish & Game Genetics Central Valley steelhead 108,0002001 USFWS Genetics of steelhead in Central Valley, CA 24,0002001-02 USGS Genetics of rainbow trout after dam removal in CA 43,0002001-03 USFS White Salmon River steelhead genetics 20,0002002-04 Sloan Foundation Steelhead kelts tagging study38,0002002-03 USFWS Clear Creek rainbow trout study. 35,8002002-05 IPHC Seasonal movements of Bering Sea Pacific halibut 23,0002002-05 NSF Biodiversity of native Mexican trout 73,7352003-04 NSF EPSCoR Fellowship University of Alaska Anchorage 17,0002003-08 NPS NRPP Genetic population structure Aniakchak sockeye 128,0002003-05 USFS Natural hybridization in Copper River Delta trout 27,0002003 CA Fish & Game Genetic population structure Central Valley steelhead 35,0002004-08 USGS Competitive Grant Climate Change Initiative 720,0002004-07 NPS Katmai National Park and Preserve genetics 80,0002004-06 AYK SSI Yukon River Chinook salmon growth at sea 48,0002006-09 NPS NRPP Genetics of Brooks River brown bears 166,0002006-10 MMS OCS Genetics and otolith microchemistry Arctic cisco 800,000Total Grant & Contracts $4,148,100Previous Grants in California (1990-1999) Total – $3,578,00016

Jennifer L. Nielsen, PhDList of PublicationsPEER REVIEWED MANUSCRIPTS ANDBOOK CHAPTERS62. Nielsen, J. L. 2006. President’s Hook. Sharing theTable and the Source. Fisheries 32(1): (in press).61. Nielsen, J. L. 2006. President’s Hook. The nuancesof grey and open access publishing at AFS.Fisheries 31(12):584.60. Nielsen, J. L., C. E. Zimmerman, R. Phillips, D.Noakes, J. Holmes and S. Crawford. 2007.Biology, life history and systematics of salmonidand osmerid fishes. In R. Mayden (ed.) FreshwaterFishes of North America. Academic Press (inpress).59. Nielsen, J. L. and G. Ruggerone. 2007. Climatechange and a dynamic ocean carrying capacity:Growth and survival of Pacific salmon at sea.Proceedings Pacific Salmon Environment and LifeHistory Models: Advancing Science forSustainable Salmon. AFS Symposium Publication(in press).58. Nielsen, J. L. 2006. President’s Hook. Fair and GoodGovernance in AFS. Fisheries 31(11): 532.57. Nielsen, J. L. 2006. President’s Hook. Thoughtsfrom Kansas. Fisheries 31(10): 480-514.56. Nielsen, J. L. 2006. President’s Hook. Lookingdownstream and downcurrent: Addressingcomplexity and unintended consequences in fishand fisheries. Fisheries 31(9):428-429.55. Verspoor, E., L. Stradmeyer and J. Nielsen (Eds.)2007. The Atlantic Salmon: Genetics, Conservationand Management. Blackwell Publishing pp 514.54. Nielsen, J. L. 2007. Atlantic Salmon Genetics: Past,Present and What’s in the Future? Chapter 15. InE. Vespoor, J. Nielsen, and L. Stradmeyer (eds.)The Atlantic Salmon: Genetics, Conservation andManagement. Blackwell Scientific pp 483-494.53. Seitz, A. C., B. L. Norcross, D. Wilson and J. L.Nielsen. 2006. An evaluation of light-basedgeolocation for Pacific halibut (Hippoglossusstenolepis) in the northern Gulf of Alaska.Fisheries Research 104:571-578.52. Graziano, S. L., K. Brown and J. L. Nielsen. 2005.Comment: Nomenclature of mitochondrial DNAhaplotypes in Oncorhynchus mykiss. Transactionsof the American Fisheries Society 14:1271-1273.51. Seitz, A. C., B. L. Norcross, D. Wilson and J. L.Nielsen. 2005. Identifying spawning behavior inPacific halibut, Hippogolssus stenolepis, usingelectronic tags. Environmental Biology of Fishes73:445-451.50. Zimmerman, C. E. and J. L. Nielsen. 2005.Introduction to Special Issue: Interactions ofHatchery and Wild Salmonids in Marine andEstuarine Environments. Reviews in Fish Biologyand Fisheries 14:301-303.49. Ruggerone G. and J. L. Nielsen. 2005. Evidence forcompetitive dominance of pink salmon(Oncorhynchus gorbuscha) over other salmonids inthe North Pacific Ocean. Reviews in Fish Biologyand Fisheries 14:371-390.48. Nielsen, J. L., S. A. Pavey, T. Wiacek and I.Williams. 2005. Genetic analyses of Central ValleyO. mykiss populations: Drainage and watershedscale analyses. San Francisco Estuary &Watershed Science. Vol. 3. Issue 2 (September2005),http://repositories.cdlib.org/jmie/sfews/vol3/iss2/art347. Ruggerone, G. T., E. Farley, J. L. Nielsen and P.Hagen. 2005. Seasonal marine growth of BristolBay sockeye salmon (Oncorhynchus nerka) inrelation to competition with Asian pink salmon (O.gorbuscha) and the 1997 ocean regime shift.Fisheries Bulletin 103:355-370.46. Nielsen, J. L. and G. Ruggerone. 2005. Non-linearityin Bristol Bay sockeye salmon growth: implicationof Asian hatchery pink salmon production. InBurkett, V., D. A. Wilcox, R. Stottlemyer, W.Barrow, D. Fagre, J. Barton, J. Price, J. L. Nielsen,C. Allen, D. L. Peterson, G. Ruggerone, and T.Doyle. Nonlinear Dynamics in EcosystemResponse to Climatic Change: Case Studies andPolicy Implications. Ecological Complexity 2:357-394.45. Nielsen, J. L. and H. Regier. 2004. Sustainingsalmonid populations: a caring understanding ofthe naturalness of taxa. In D. MacDonald and E.Knudsen (eds.) Fish in Our Future? Perspectives17

on Fisheries Sustainability. American FisheriesSociety Symposium 43: 203-211.44. Nielsen, J. L., P. Richards, D. Wilson, C. E.Zimmerman and T. Tingey. 2004. Testingelectronic archival tags in Pacific salmon. ExxonValdez Oil Spill Restoration project Final Report(Restoration project 02404), U. S. GeologicalSurvey, Alaska Science Center, Anchorage,Alaska, 31 pp.43. Gharrett, A.J., S. Keller, R. G. Gustafson, P. Johnson,J. Nielsen, J. E. Seeb, L. W. Seeb, W. W. Smoker,G. A. Thorgaard and W. L. Wilmot. 2004.Introduction to genetics of subpolar fish andinvertebrates. Environmental Biology of Fishes 69:1-4.42. Thrower, F., C. Guthrie III, J. L. Nielsen, and J.Joyce. 2004. A comparison of genetic variationbetween an anadromous steelhead (Oncorhynchusmykiss) population and seven derived populationssequestered in freshwater for 70 years.Environmental Biology of Fishes 69: 111-125.41. Seitz, A., D. Wilson, B. L. Norcross and J. L.Nielsen. 2003. Pop-up archival transmitting (PAT)tags: A method to investigate the migration andbehavior of Pacific halibut Hippoglossus stenolepisin the Gulf of Alaska. Alaska Fisheries ResearchBulletin 10: 124-136.40. Nielsen, J. L., I. Williams, G. K. Sage and C. E.Zimmerman. 2003. The importance of geneticverification of identification of Atlantic salmon inPacific waters. Journal of Fish Biology 62: 871-878.39. Porath, M. T. and J. L. Nielsen. 2003 Evidence ofsexually dimorphic introgression in PinalenoMountain Apache trout. North American Journal ofFisheries Management. 23: 172-180.38. Hendrickson, D. A., H. Espanoza Perez, L. T.Findley, W. Forbes, J. R. Tomelleri, R. L. Mayden,J. L. Nielsen, B. Jensen, G. R. Campos, A. V.Romero, A. Van der Heiden, F. Camarena, F. J.Garcia de Leon. 2003. Mexican native trouts: areview of their history and current systematic andconservation status. Reviews in Fish Biology andFisheries 12(2-3): 273-316.37. Ruggerone, G. T., M. Zimmermann, K. W. Meyers,J. L. Nielsen and D. E. Rogers. 2003. Competitionbetween Asian pink salmon and North Americansockeye salmon in the North Pacific Ocean.Fisheries and Oceanography 12(3): 209-219.36. Seitz, A., D. Wilson and J. L. Nielsen. 2002. Testingpop-up satellite tags as a tool for identifyingcritical habitat for Pacific halibut (Hippoglossusstenolepis) in the Gulf of Alaska. Exxon Valdez OilSpill Restoration Project Final Report (RestorationProject 01478), U.S. Geological Survey, AlaskaScience Center, Anchorage, Alaska.35. Nielsen, J. L. and G. K. Sage. 2002. Populationgenetic structure in Lahontan cutthroat trout.Transactions American Fisheries Society. 131:376-388.34. Nielsen, J. L., J. M. Scott and J. L. Aycrigg. 2002.Endangered species and peripheral populations:Cause for conservation. Endangered SpeciesUPDATE 18:194-197.33. Nielsen, J. L. and K. Sage. 2001. Microsatelliteanalyses of the trout of Northwest Mexico.Genetica 111(No.1-3): 269-278.32. Epifanio, J. and J. L. Nielsen. 2001. SymposiumReview: The role of hybridization in thedistribution, conservation, and management ofaquatic species. Reviews in Fish Biology andFisheries 10: 245-251.31. Nielsen, J. L., E. L. Heine, C. A. Gan, and M. C.Fountain. 2000. Molecular analyses of populationgenetic structure and recolonization of rainbowtrout following a fish-kill event. California Fishand Game 86(1): 21-40.30. Nielsen, J. L., K. D. Crow, and M. C. Fountain.1999. Microsatellite diversity and conservation ofa relic trout population: the McCloud Riverredband trout. Molecular Ecology 8:129-142.29. Nielsen, J. L. and M. C. Fountain. 1999.Microsatellite diversity in sympatric reproductiveecotypes of Pacific steelhead (Oncorhynchusmykiss) from the Middle Fork Eel River,California. Ecology of Freshwater Fish 8: 159-168.28. Nielsen, J. L. 1999. The evolutionary history ofsteelhead (Oncorhynchus mykiss) along the USPacific coast: Developing a conservation strategyusing genetic diversity. ICES Journal of MarineScience 56:449-458.27. Huston, M. C., G. McVicker and J. L. Nielsen. 1999.A functional approach to ecosystem management:Implications for species diversity. Pages 45-85 inThe Ecological Stewardship Program: A commonreference for Ecosystem Management (3 Volumes).Elsevier Science Limited, Oxford, England.26. Dunham, J. B., M. M. Peacock, J. L. Nielsen, C. R.Tracy, and G. L. Vinyard. 1999. Extinction riskassessment: Integrating genetic information.Conservation Ecology [on line] 3(1): 2 Internetaccess: www.consecol.org/vol3/iss1/art2.25. Dodson, J., J. Nielsen, M. Gross, K. Friedland, R.Newberry, M. Power, C. Garcia de Leaniz, S. Roy,R. Cunjak, and J. Gibson. 1998. Development and18

implementation of a conservation plan for Atlanticsalmon. In M. Mather (ed.) Proceeding ofIntegrating Across Scales: Predicting Patterns ofChange in Atlantic Salmon. Canadian JournalFisheries Aquatic Sciences 55(Suppl. 1): 312-323.24. Nielsen, J. L. 1998. Population genetics and theconservation and management of Atlantic salmon(Salmo salar). In M. Mather (ed.) Proceeding ofIntegrating Across Scales: Predicting Patterns ofChange in Atlantic Salmon. Canadian JournalFisheries Aquatic Science 55(Suppl. 1): 145-152.23. Nielsen, J. L. 1998. Scientific sampling effects:electrofishing California's endangered fishpopulations. Fisheries 23:6-12.22. Nielsen, J. L. 1998. Threatened Fishes of the World:Oncorhynchus mykiss nelsoni Evermann 1908(Salmonidae). Environmental Biology of Fishes51:376.21. Nielsen, J. L., M. C. Fountain, J. Campoy-Favela, K.Cobble, and B. Jensen. 1998. Oncorhynchus at thesouthern extent of their range: a study based onmtDNA control-region sequence with specialreference to an undescribed subspecies of O.mykiss from Mexico. Environmental Biology ofFishes. 51: 7-23.20. Nielsen, J. L., C. A. Gan, C. Carpanzano, and M. C.Fountain. 1997. Mitochondrial DNA and nuclearmicrosatellite frequency differences in hatcheryand wild Oncorhynchus mykiss from freshwaterhabitats in southern California. Transactions of theAmerican Fisheries Society 126:397-417.19. Nielsen, J. L., M. C. Fountain, and J. M. Wright.1997. Biogeographic analysis of Pacific trout(Oncorhynchus mykiss) in California and Mexicobased on mtDNA and nuclear microsatellites.Pages 53-73 in Molecular Systematics of Fishes. T.Kocher and C. A. Stepien (eds.) Academic Press.18. Nielsen, J. L. 1996. About gender. Book review: Onthe Sex of Fish and the Gender of Scientists: acollection of essays in fisheries science. D. Pauly(1994) Environmental Biology of Fishes 47:415-416.17. Nielsen, J. L. 1996. Molecular genetics and theconservation of salmonid biodiversity:Oncorhynchus at the edge of their range. Pages383-398 in T. B. Smith and R. K. Wayne (eds.)Molecular Genetics Approaches in Conservation.Oxford University Press.16. Castleberry, D., J. Cech, D. Erman, D. Hankin, M.Healey, M. Kondolf, M. Mengel, M. Mohr, P.Moyle, J. Nielsen, T. Speed, and J. Williams.1996. Uncertainty and instream flow standards.Fisheries 21(8): 20-21.15. Quinn, T. P., J. L. Nielsen, C. A. Gan, M. J. Unwin,R. Wilmot, C. Guthrie, and F. M. Utter. 1996.Origin and genetic structure of Chinook salmon(Oncorhynchus tshawytscha) transplanted fromCalifornia to New Zealand: allozyme and mtDNAevidence. Fisheries Bulletin 94(3): 506-521.14. Nielsen, J. L. (ed.) 1995. Evolution and the AquaticEcosystem: Defining Unique Units in PopulationConservation. American Fisheries SocietyMonograph Series No. 17. 435 pp.13. Nielsen, J. L., C. A. Gan, J. M. Wright, D. B. Morris,and W. K. Thomas. 1994. Biogeographicdistributions of mitochondrial and nuclear markersfor southern steelhead. Molecular Marine Biologyand Biotechnology 3(5):281-293.12. Nielsen, J. L., D. Tupper, and W. K. Thomas. 1994.Mitochondrial DNA polymorphisms in unique runsof Chinook salmon (Oncorhynchus tshawytscha)from the Sacramento-San Joaquin River basin.Conservation Biology 8(3): 882-884.11. Nielsen, J. L., C. Gan and W. K. Thomas. 1994.Differences in genetic diversity for mitochondrialDNA between hatchery and wild populations ofOncorhynchus. Can. J. Fish Aquat. Sci.51(Suppl.1): 290-297.10. Nielsen, J. L. 1994. Invasive cohorts: Impacts ofhatchery-reared coho salmon on the trophic,developmental, and genetic ecology of wild stocks.In: D. J. Stouder, K. L. Fresh, and R. J. Feller (eds.)Theory and Application in Fish Feeding Ecology.Belle W. Baruch Library in Marine SciencesNumber 18:361-385.9. Nielsen, J. L. 1994. Molecular genetics and stockidentification in Pacific salmon (Oncorhynchusspp.). Ph. D. Dissertation, University of CA,Berkeley.8. Nielsen, J. L., T. E. Lisle and V. Ozaki. 1994.Formation of thermally stratified "cold pools" andutilization by steelhead trout, northern California.Transactions of the American Fisheries Society123:613-626.7. Goodwin, P., J. L. Nielsen and C. K. Cuffe. 1993. Thetidal Inlet characteristics of a small CaliforniaEstuary. Hydraulic Engineering 93:562-567.6. Nielsen, J. L. 1992. Microhabitat specific foragebehavior, diet and growth rates in juvenile cohosalmon. Transactions of the American FisheriesSociety. 121(4): 617:634.5. Nielsen, J. L. 1990. Environment and behavioraffecting growth and development of juvenile cohosalmon (Oncorhynchus kisutch). Masters ThesisUniversity of California, Berkeley. 148 pp.19

4. Bisson, P. A., J. L. Nielsen, J. W. Ward. 1988.Summer production of coho salmon stocked inMount St. Helens streams 3-6 years after the 1980eruption. Transactions of the American FisheriesSociety 117:322-335.3. Bisson, P. A., K. Sullivan and J. L. Nielsen. 1988.Channel hydraulics, habitat use, and body form ofjuvenile coho salmon, steelhead, and cutthroat troutin streams. Transactions of the American FisheriesSociety 117:262-273.2. Bisson, P. A., J. L. Nielsen, M. W. Chilcote, B. A.Crawford & S. A. Leider. 1986. Occurrence ofanadromous brown trout in two lower ColumbiaRiver tributaries. North American Journal ofFisheries Management 6:290-292.1. Bisson, P. A., J. L. Nielsen, R. A. Palmason, L. E.Grove. 1982. A system of naming habitat types insmall streams with examples of habitat utilizationby salmonids during low stream flow. Pages 62-73,in N.B. Armantrout, editor, Acquisition andutilization of aquatic habitat inventory information.Proceedings of a symposium held 28-30 October1981, Portland, Ore. Western Division, AmericanFisheries Society.PROCEEDINGS AND TECHNICALREPORTS65. Garziano, S. L. and J. L. Nielsen. 2006. ProgressReport 2006: Brooks River Brown Bear Project.Technical Report submitted to NPS, KatmaiNational Park October, 2006.64. Seitz, A. C., T. Loher, and J. L. Nielsen. 2006.Seasonal movements and environmentalconditions experienced by Pacific halibut alongthe Aleutian Islands, examined by pop-upsatellite tags. International Pacific HalibutCommission Technical Report (in press).63. Boughton, D. A., P. Adama, E. Anderson, C.Fusaro, E. Keller, E. Kelly, L. Lentsch, J. L.Nielsen, K. Perry, H. Regan, J. Smith, C. Swift,L. Thompson and F. Watson. 2006. Steelhead inthe southern domain: Population characterizationfor purposes of recovery. NOAA TechnicalMemorandum NOAA-TM-NMFS-SWFSC-394.62. Nielsen, J. L., T. Wiacek and S. L. Graziano. 2005.Population genetic structure of rainbow trout inthe upper Ventura River watershed based onmicrosatellite and mtDNA analyses. FinalTechnical report submitted to USGS WesternFisheries Research Center, Seattle, WA, Aug. 19,2005.61. Seitz, A. C., T. Loher and J. L. Nielsen. 2005.Seasonal movements and environmentalconditions experienced by Pacific halibut in theBering Sea, examined by pop-up satellite tags.Technical Report submitted to InternationalPacific Halibut Commission, March 2005.60. Farley, E. V., Jr., J. M. Murphy, L. Eisner, J. H.Helle, J, H. Moss, M. D. Adkinson and J. L.Nielsen. 2005. Critical-size, critical-periodhypothesis: An example of the relationshipbetween early marine growth of juvenile BristolBay sockeye salmon, ocean conditions, andsubsequent marine survival. North PacificAnadromous Fish Commission Technical Report5. Proceedings of the BASIS Workshop,Sapporo, Japan, October 2004.59. Hamon, T., S. A. Pavey, J. L. Miller and J. L.Nielsen. 2005. Aniakchak sockeye salmoninvestigations. Alaska Parks Science 3(2): 35-39.58. Nielsen, J. L. 2004. Exploitation dynamics of smallfish stocks like Arctic cisco. Pages 45-47 inProceedings of a workshop on the variability ofArctic cisco (Qaaktaq) in the Colville River.November 18-20, 2003, Kisik CommunityCenter, Nuiqsut, Alaska.57. Graziano, S. L. and J. L. Nielsen. 2004. Geneticpopulation structure of rainbow trout from theWhite Salmon River subdrainage: Includinginference on hybridization with coastal cutthroattrout. Technical Report submitted to US ForestService Gifford Pinchot National Forest. WindRiver, WA. June 27, 2004.56. Nielsen, J. L. 2004. Investigations of the linkagesbetween climate, growth and production ofsockeye salmon populations in Bristol Bay,Alaska. Final technical Report submitted toUSGS Global Change Initiative, June 10, 2004.55. Graziano, S. L. and J. L. Nielsen. 2004. Geneticpopulation structure of rainbow trout in theWhite Salmon River subbasin includinginference on hybridization with coastal cutthroattrout. Final Technical Report submitted June2004, to Pat Fuller, USFS Gifford PinchotNational Forest, Wind River Work Center,Carson WA.54. Nielsen, J. L., R. Valenzuela, T. Wiacek and S.Graziano. 2004. Genetic population structure ofSnake River steelhead in Idaho. Technical20

Report submitted to Idaho Department of Fishand Game. Jan 11, 2004.53. Nielsen, J. L. 2003. History and effects of hatcherysalmon in the Pacific. Pages 153-168 in P.Gallaugher and L. Wood (editors) Proceedings ofthe World Summit on Salmon, Simon FraserUniversity, June 10-13, 2003. Simon FraserUniversity Continuing Studies in Science,Burnaby,BC.http://www.sfu.ca/cstudies/science/summit/nielsen.htm52. Nielsen, J. L., S. Pavey, T. Wiacek, G. K. Sage andI. Williams. 2003. Genetic analyses of CentralValley trout populations, 1999-2003. FinalTechnical Report submitted to CaliforniaDepartment of Fish and Game and US Fish andWildlife Service Region 1. December 8, 2003.51. Nielsen, J. L., J. Olsen, T. Wiacek, E. Kretschmer,G. Greenwald and J. Wenburg. 2003. Populationgenetic structure of Santa Ynez rainbow trout –2001, based on microsatellite and mtDNAanalyses. Final Technical Report submitted to USFish and Wildlife Service Region 1, Redding,California June 2003.50. Nielsen, J. L., G. K. Sage, S. Pavey, R. Valenzuelaand T. Wiacek. 2003. Hatchery and wildsteelhead in Idaho: Report #1 DworshakHatchery stocks in the Clearwater drainage.Report submitted to Idaho Department of Fishand Game 10 February 2003. 16 pp.49. Nielsen, J. L. and T. Wiacek 2003. Populationgenetic structure of Alameda Creekrainbow/steelhead trout – 2002. TechnicalReport submitted to Hagar EnvironmentalScience. 3 January 2003. 18 pp.48. Hagen, P., B. Agler, D. Oxman, B. Smoker, G.Ruggerone and J. Nielsen. 2002. Salmon scalesas dataloggers: an image analysis approach fordata extraction. Proceedings of the 2002 ExxonValdez conference, Anchorage, Alaska.47. Nielsen, J. L. and G. K. Sage. 2002. Microsatellitesequence reveals significant haplotype diversityin Central Valley chinook stocks. Final TechnicalReport Submitted to California Department ofFish and Game June 2002.46. Nielsen, J. L. and G. K. Sage. 2002. Geneticanalysis of temporal spawning populations ofLahontan cutthroat trout (Oncorhynchus clarkihenshawi) from Pyramid Lake. Technical reportsubmitted to Bailey Environmental, June 2002.45. Ruggerone, G., J. Nielsen, E. Farley, S. Ignell, P.Hagen, B. Agler, D. Rogers and J. Bumgarner.2002. Long-term trends in annual Bristol Baysockeye salmon scale growth at sea in relation tosockeye abundance and environmental trends,1955-2000. Proceedings of the Joint Meeting onCauses of Marine Mortality of Salmon in theNorth Pacific and North Atlantic Oceans and inthe Baltic Sea. North Pacific FisheriesCommission Annual Meeting, March 2002,Vancouver, B.C. NPAFC Technical Report No.4: 56-58.44. Nielsen, J. L. and G. K. Sage. 2002. Microsatelliteanalyses of San Mateo Creek trout, 2001.Technical Report submitted to US Department ofDefense, Camp Pendleton, CA. January 14, 2002.43. Finn, J. E., S. H. Maclean, J. L. Nielsen and E. E.Knudsen. 2001. Spawning ecology of summerand fall run chum salmon in two systems of theYukon River Delta. Page 38 in Proceedings ofthe 20 th Northeast Pacific Pink and Chum SalmonWorkshop, March 21-23, 2001, Seattle, WA.42. Nielsen, J. L. 2001. Report on mitochondrial DNAhaplotypes and microsatellite loci for San Mateosteelhead/rainbow trout. Final technical reportsubmitted 9/30/01 Department of Defense, CampPendleton, CA.41. Camarena, F., G. R. Campos, A. Daxa, H.Espinoza, L. Findley, W. Forbes, F. Garcia deLeon, A. Van der Heiden, D. A. Hendrickson, B.Jensen, R. Mayden, J. Nielsen, J. Ruiz, J.Tomelleri and A. Varela 2001. Truchasmexicanas: an international partnership for thestudy of native trout of southern North America.American Fisheries Society Annual Meeting,Vol. 131, p. 97. AFS Annual Meeting, Phoenix,Arizona, 19-23 August 2001.40. Avelino, O. and J. L. Nielsen. 2000. Geneticanalysis of hatchery and wild fall-run Chinooksalmon (Oncorhynchus tshawytscha) in theCentral Valley, California. Grant FG 8002 IFTechnical Report submitted to CaliforniaDepartment of Fish and Game, Inland FisheriesDivision, Sacramento, CA 76 pp.39. Nielsen, J. L. 2000. Variation in mtDNA andnuclear microsatellite DNA markers from SanGabriel Creek rainbow trout. Report submittedto Federation of Fly Fishers, Southwest Council,September 19, 2000.38. Nielsen, J. L. 2000. Population genetic structurein Lahontan cutthroat trout (Oncorhynchus clarkihenshawi). USFWS Reno NV Grant#142408H057 Final report.37. Burnham-Curtis, M., S. Haig, T. King, G. Kurath,J. Nielsen, and G. Smith 2000. Genetics andmolecular tools: Setting the standard forbiological science in USGS. Summary ofdiscussions and dialogue from the workshop:Integration and Collaboration on Emerging21

Biological Issues and Research Goals(ICEBIRG) I: Genetics and Molecular Tools.USGS – BRD Ruston, VA.36. Nielsen, J. L. 2000. Report on mitochondrial DNAhaplotypes for San Mateo steelhead. Appendix Bin Steelhead Rainbow Trout in San Mateo Creek,San Diego County, California. Report for theNational Marine Fisheries Service by theCalifornia Department of Fish and Game, NativeAnadromous Fish and Watershed Branch, SouthCoast Region, February, 2000. Sacramento,California. 3 pp.35. Nielsen, J. L. 2000. Microsatellite analyses of SanFrancisquito Creek rainbow trout. Reportsubmitted to Center for Conservation, StanfordUniversity, Stanford, CA. Jan. 12, 2000. 19 pp.34. Nielsen, J. L. and M. C. Fountain 1999.Microsatellite analyses of Alameda Creekrainbow/steelhead trout. Technical Reportsubmitted October 7, 1999 to Applied MarineSciences, Inc. Livermore, CA. 17 pp.33. Nielsen, J. L., M. C. Fountain, D. R. Sundermeyer,E. L. Heine, C. L. Malone and O. L. Avelino.1999. Microsatellite variation in chinook salmonspawning runs from Central Valley, California1992-1997. Technical Report submitted toCalifornia Department of Fish and Game,Sacramento, CA. 37pp.32. Nielsen, J. L., D. S. Wiltse and M. C. Fountain1999. Testing for rainbow trout introgression inArizona Apache trout populations usingmicrosatellites. Technical report submitted Aug.11, 1999 to Arizona Game and Fish. 24 pp.31. Nielsen, J. L., O. L. Avelino and M. C. Fountain.1999. Tests of genetic population structure inStanislaus River trout using microsatellites.Technical report submitted Aug. 24, 1999 to S. P.Cramer and Associates. 22 pp.30. Nielsen, J. L. 1999. Variation in mtDNA andnuclear microsatellite DNA markers in PinoleCreek trout. Technical Report submitted March19, 1999 to East Bay Municipal Utilities District.28 pp.29. Nielsen, J. L. 1998. Molecular genetics and theconservation of salmonids biodiversity:Oncorhynchus at the edge of their range. Pages234 – 279 in Proceedings of the SymposiumRestoring the Southern California Steelhead. M.H. Capelli (ed.) University of CaliforniaExtension, Santa Barbara, CA.28. Dunham, J. B., G. L. Vinyard, and J. L. Nielsen.1998. Evaluating the genetic identity of PilotPeak cutthroat in relation to hatchery broodstockdevelopment at the Lahontan National FishHatchery and recovery of Lahontan cutthroattrout in the Truckee River subbasin. FinalTechnical Report to U. S. Fish and WildlifeService Region 1, Reno, Nevada. 17pp.27. Nielsen, J. L. 1998. Molecular genetic populationstructure in steelhead/rainbow trout(Oncorhynchus mykiss) from the Santa YnezRiver, 1994-1997. Technical Report submitted tothe Santa Ynez River Technical AdvisoryCommittee 8/5/98. 31 pp.26. Nielsen, J. L. 1998. Genetic issues concerningsouthern coho restoration in California.Technical Report CDFG & Southern CohoRestoration Team submitted 11/13/97 9 pp.25. Nielsen, J. L., M. C. Fountain, D. R. Sundermeyer,E. L. Heine, C. L. Malone and O. L. Avelino.1998. Microsatellite variation in Chinook salmonspawning runs from the Central Valley,California, 1992-1997. Final Technical Reportsubmitted to California Department of Fish andGame, Sacramento CA, July 16, 1998. 42 pp.24. Nielsen, J. L. 1997. Genetic variation inMokelumne River trout (Oncorhynchus mykiss)using mitochondrial DNA and ten microsatelliteloci. Revised technical report submitted 7October 1997 to East Bay Municipal UtilityDistrict, Oakland, California. 38 pp.23. Nielsen, J. L. 1997. Molecular genetics andevolutionary status of the trout of the SierraMadre. Proceedings of Wild Trout VI: Puttingthe Native Back in Wild Trout, Aug. 17-20,1997, Montana State University, Bozeman MT.pp 103-109.22. Nielsen, J. L. 1997. Mitochondrial DNA and tennuclear microsatellite loci depict populationstructure in rainbow trout (Oncorhynchus mykiss)from southeast Alaska. Technical Reportsubmitted 7/97 to National Marine FisheriesService, Auke Bay Laboratory, Juneau AK. 32pp.21. Nielsen, J. L. 1997. Molecular genetic diversityand stock structure in rainbow trout from theClavey River. Technical Report submitted6/5/97 to CA Department of Fish and Game,Wild Trout Committee Sacramento, CA andUSDA FS Region 5, San Francisco, CA.20. Nielsen, J. L. 1997. Mitochondrial DNA andnuclear microsatellite polymorphisms in Chinooksalmon from the Sacramento-San Joaquin basin,1991-1995. Technical report FG6038IFsubmitted to CA Department of Fish and Game,Inland Fisheries Division, Sacramento CA.19. Nielsen, J. L. 1996. Using mitochondrial andnuclear DNA to separate hatchery and wild22

stocks of rainbow trout in California and Mexico.Pages 139-147 in E. M. Donaldson and D. D.MacKinlay (eds.) Aquaculture BiotechnologySymposium Proceedings International Congresson the Biology of Fishes, July 14-18, 1996, SanFrancisco, CA.18. Nielsen, J. L. 1996. Anadromous Fishes of theMonterey Bay National Marine Sanctuary.NOAA Monterey Bay National MarineSanctuary web site17. Nielsen, J. L. and M. C. Fountain. 1996. KernRiver basin trout stock structure: evidence usingmtDNA and nuclear microsatellites. USDAForest Service Region 5 Technical Report. 21 pp.16. Nielsen, J. L., M. C. Fountain, and K. Crow. 1996.Molecular systematics of a relic trout population:the McCloud River redband trout. CDFG ReportFG5004-IF, California Department of Fish andGame, Inland Fisheries Division, Sacramento,CA. 61 pp.15. Nielsen, J. L. 1995. Variation in individual lifehistory strategies in coho salmon from northernCalifornia. Pages 40-41 in Janis Duncan-Vaughn(ed) Proceedings of the Thirteenth AnnualSalmonid Restoration Federation Conference,Feb. 23-26, 1995, Santa Rosa and Rohnert ParkCA.14. Nielsen, J. L. 1995. Mitochondrial DNA frequencydistributions in Chinook salmon from theSacramento-San Joaquin Basin and GuadalupeCreek, 1992-1994. CDFG Report No. IFGAD95-22, CA Department of Fish and Game, InlandFisheries Division, Redding, CA. 17 pp.13. Nielsen, J. L. 1995. Upper Sacramento Riverrainbow trout: genetics and stock identificationusing mtDNA and microsatellites. CDFG Region1 Cantara Technical Report FG3772-CA, 2440Athens Ave. Redding, California. 61 pp.12. Nielsen, J. L. 1995. Upper Sacramento RiverRainbow trout: molecular genetics and stockidentification. CDFG Report No. IFG95-03, CADepartment of Fish and Game, Inland FisheriesDivision, Redding, CA. 37 pp.11. Nielsen, J. L., C. A. Gan, and Kelly Cuffe. 1994.Effects of habitat and population manipulation onunique genotypes of chinook and steelhead inurbanized watersheds in California. Pages 77-83in M. L. Keefe (ed.) Salmon EcosystemRestoration: Myth and Reality. Proceedings ofthe 1994 Northeast Pacific Chinook and CohoWorkshop, Eugene OR, Nov. 7-10, 1994.10. Monroe, J. and J. L. Nielsen. 1994. Evolution andthe aquatic ecosystem: Defining unique units inpopulation conservation: Executive Summary.American Fisheries Society, Bethesda, MD. 19pp.9. Nielsen, J. L., C. Gan, J. M. Wright, and W. K.Thomas. 1994. Phylogeographic patterns inCalifornia steelhead using mtDNA andmicrosatellites. Proceedings of the 1993CALCOFI Conference: Genetics of Organisms ofthe California Current. Lake ArrowheadConference Center 2-4 Nov. 1993. CaliforniaCooperative Oceanic Fisheries InvestigativeReports Vol. 35:90-92.8. Cuffe, C. K., P. Goodwin, and J. L. Nielsen. 1994.Physical and biological effects of inlet closureand breaching - Russian River estuary,California. Proceeding of the Western DivisionAmerican Fisheries Society and WesternAssociation of Fish and Wildlife Associations,July 26-30, 1993. Sacramento, CA.7. Nielsen, J. L., W. K. Thomas, C. A. Gan, and D.Tupper. 1994. Intrapopulation differences foundin California steelhead trout using directsequence of mtDNA. Pages 63-65 in Proceedingsof Application of DNA Technology to theManagement of Pacific Salmon. NOAA NMFSworkshop, March 22-23, 1993. National MarineFisheries Service, 2725 Montlake Blvd., Seattle,WA 98112. pages 63-65.6. Nielsen, J. L., P. Goodwin, C. K. Cuffe and T.Light. 1994. Russian River Estuary Study, 1992-1993: Hydrologic, Limnological, and BiologicalAspects of an Estuary Management Plan.Technical report published by the PlanningDepartment of Sonoma County, Santa Rosa, CA.186 pages plus IX appendices.5. Nielsen, J. L. 1992. The role of cold-pool refugia inthe freshwater fish assemblage in northernCalifornia rivers. Pages 79-88 in: Proceedings ofa symposium on biodiversity in northwesternCalifornia, Santa Rosa, CA, October 28-30,1991. Published by the Wildland ResourcesCenter Division of Agriculture and NaturalResources, University of California, Berkeley,CA. Report 29, December 1992.4. Nielsen, J. L., M. Maahs & G. Baldwin. 1991.Anadromous Salmonid Resources of MendocinoCoastal and Inland Rivers, 1989-1991: AnEvaluation of Rehabilitation Efforts Based onCarcass Recovery and Spawning Activity. ReportNo. FG9364 California Department of Fish andGame, Inland Fisheries Division, Sacramento CA98 p.3. Bisson, P. A., B. R. Fransen and J. L. Nielsen 1990.Habitat mediated response on stream-dwellingcoho salmon to experimentally elevated foodavailability. American Fisheries Society OregonChapter Annual Meeting Symposium.23

2. Bisson, P. A., J. T. Heffner, J. W. Ward, R. E. Bilbyand J. L. Nielsen. 1987. A summary report of theDeschutes River Basin sediment, flow,temperature and fish habitat. WeyerhaeuserTechnical Report Paper No. 044-5002.by Mount Saint Helens volcano. Pages 422-435,in Proceedings of the Annual Meeting of theWestern Division, American Fisheries Societyand the Western Association of Fish and WildlifeAgencies, held July 16-19, Victoria, BritishColumbia.1. Bisson, P. A., J. L. Nielsen and J. W. Ward. 1985.Experimental release of coho salmon(Oncorhynchus kisutch) into a stream impactedMANUSCRIPTS SUBMITTED FOR PUBLICATION 2006-07Nielsen, J. L., C. Zimmerman, S. Graziano. Geneticsand otolith microchemistry investigations ofArctic cisco overwintering in the Colville River.Technical Report to MMS OCS Program. (inprocess).Boughton, D. A., P. Adama, E. Anderson, C. Fusaro, E.Keller, E. Kelly, L. Lentsch, J. L. Nielsen, K.Perry, H. Regan, J. Smith, C. Swift, L.Thompson and F. Watson. Viability criteria forsteelhead populations and metaopulations of thesouthern and south-central California coast.Bulletin Southern California Science.Pavey, S. A., T. R. Hamon and J. L. Nielsen. Revisitingthe “evolutionary dead-end” hypothesis insockeye salmon life history. CJFAS.Ruggerone, G. T., J. L. Nielsen and J. Bumgarner.Linkages between climate, growth at sea, andsockeye abundance in Bristol Bay, Alaska 1955-2002. Deep Sea ResearchSeitz, A. C., T. Loher, B. L. Norcross and J. L. Nielsen.Seasonal movements and behavior of Pacifichalibut (Hippoglossus stenolepis) in the BeringSea and Aleutian Islands. FisheriesOcenaography.Seitz, A. C., D. C. Douglas, B. L. Norcross and J. L.Nielsen. Minimum-distance dispersal model ofdemersal fish in the Gulf of Alaska. MarineProgress Oceanography.Seitz, A. C., T. Loher, B. L. Norcross and J. L. Nielsen.Conceptual model for the population structure ofPacific halibut (Hippoglossus stenolepis) usinginsights from satellite tagging. FisheriesOceanography.Williams, I., G. H. Reeves, S. Graziano and J. L.Nielsen. Natural hybridization between two troutspecies, Copper River Delta, Alaska.Transactions AFS.Nielsen, J. L., R. Valenzuela, T. Wiacek, S. Grazianoand Alan Byrne. Population genetic structure inSnake River steelhead. Environmental Biology ofFishes.Zimmerman, C. E. and J. L. Nielsen. Freshwater tomarine migration of post-spawn steelhead(Oncorhynchus mykiss) in the Ninilchik River,Alaska. Alaska Fisheries Research Bulletin.Nielsen., J. L., S. Graziano, A. Seitz. Moleculargenetics of Alaska’s Pacific halibut populations.Alaska Fisheries Research Bulletin.24