Chapter 11 Science And Implementation

Chap. 11, Science and Implementation, (ESA Vol. 2) Ruckelshaus and Darm, 1 

Chapter 11 

Science and Implementation 

Mary Ruckelshaus and Donna Darm 

The U.S. Endangered Species Act (ESA) relies heavily on science, and thus it is not surprising 

that science has become a major battleground in the controversy surrounding its implementation 

(Doremus this volume). It seems to have been the hope of Congress that decisions could be made 

based on science alone and that giving science a key role in decision making would insulate 

decisions from politics (H.R. CONF. REP. NO. 97-835, at 19). This hope was false from the 

beginning for at least two reasons. First, scientific information is almost always incomplete and 

uncertain. Science cannot answer with certainty many of the questions that must be answered in 

ESA decision making, in the time frames allowed by the statute. Second, while scientific data, 

analysis and advice should have a central role in informing natural resource decisions, scientific 

information by itself cannot “make decisions.” The Act’s seeming denial of the policy choices 

inherent in decision making, coupled with the difficulty of making hard policy choices that have 

regulatory effect, have led to criticism of the scientific process and decisions that result (Mapes 

2001; Boyle 2002; Dalton 2002; Seattle Times 2002; Stokstad 2002; Strassel 2002; Weber 2002; 

Cart 2003; Pianin 2003; Sacramento Bee 2003a & b; Cart and Weiss 2004). 

Congressional confidence in the ability of science to inform natural resource decisions is 

clear in the history of the ESA’s predecessors (Doremus 1997, this volume). With regard to 

listing determinations, for example, the Endangered Species Preservation Act of 1966 directs the 

Secretary to seek advice and recommendations from biologists and ecologists. The Endangered


Species Conservation Act of 1969 was more forceful, directing the Secretary to make listing 

decisions on the basis of “the best scientific and commercial data available.” There is no 

definition of this term and the legislative history offers no clues. The requirement to use the best 

available science was incorporated into the 1973 Endangered Species Act, which was amended 

in 1982 (P.L. No. 97-304) to require that listing decisions under the ESA be based “solely” on 

the best scientific and commercial data available (ESA sec. 4(b)(1)(A)). 

The ESA requires agency reliance on science in other areas as well. The Secretary is to 

designate critical habitat based on the best scientific data available (ESA sec. 4(b)(2)). All 

federal agencies are to rely on the best available scientific and commercial data as they ensure 

their actions will not jeopardize the continued existence of listed species nor adversely modify 

their critical habitat (ESA sec. 7(a)(2)). Recovery plans are to adopt objective criteria for 

delisting (ESA sec. 4(f)(1)(B)(ii)). In requiring endangered species decisions to be made 

primarily on the basis of science, Congress sought to insulate the agencies from political 

pressure. Perversely, political pressure on the Services is intense, which in many cases has forced 

the policy choices inherent in science-based decisions underground (Doremus 1997). 

Some commentators have argued persuasively that “better science” will not settle the 

controversy but rather what is needed is more openness about the policy choices embedded in 

ESA decisions (Doremus 1997; Myer 2001; Yaffee 2005). The authors wholeheartedly agree, but 

we also believe better scientific information and better processes of eliciting and translating 

science can improve decision making under the ESA. The ESA has been the subject of intense 

debate in the scientific literature in terms of its effectiveness in protecting species (Schwartz 

1999; Boersma et al. 2001; Crouse et al. 2002; Scott et al. 2005). Furthermore, the question of


how much scientific information is actually used in protecting species under the ESA recently 

was thoroughly evaluated (NRC 1995). 

This chapter focuses on where the ESA calls for science and examines agency practice in 

the use of science. We ask how well science is positioned to inform implementation of the Act 

and how well decision makers are prepared to make and explain decisions based on incomplete 

science (Doremus this volume). We draw on examples to illustrate our points, and it is only 

because of our greater familiarity with the National Marine Fisheries Service (NMFS) that we 

highlight more cases involving fish and marine mammals than terrestrial organisms. We close 

with suggestions for how scientists can better serve decision making under the ESA. 

Provisions of the ESA and Expectations of Science 

The purpose of the ESA is to protect threatened and endangered species and the ecosystems on 

which they depend (ESA sec. 2(b)). To achieve that end, the Act requires the two agencies 

charged with implementation (the U.S. Fish and Wildlife Service [USFWS] and NMFS) to 

identify and list species that are threatened or endangered, and then provides substantive 

protections for listed species (table 11.1). Once species are listed, the listing agency is to 

designate critical habitat and develop recovery plans for their conservation and recovery. 

In the sections that follow, we address the following questions for each stage of the ESA 

process from listing through recovery planning: (1) What is the role of science, and what has 

agency practice revealed to be the difficulties of incorporating science? (2) How have the public 

and courts responded? and (3) How could either the science, or the process of providing science, 

be improved?


The Science Underlying Listing Determinations 

The listing process involves addressing two main biological questions: what is the species (or 

biological unit) to be listed? And what is the species’ likely risk of extinction? The USFWS and 

NMFS have developed interagency guidance on how to manage listing petitions, which primarily 

discusses how to navigate through the list of petitions for listing and for reconsideration of 

candidate species (USFWS and NMFS 1996a, 1999a), and does not offer biological criteria to 

address the issues below. 

What is a Listable Unit: Role of Science in Agency Practice 

The Act defines species to include “subspecies and any distinct population segment of any 

species of vertebrate fish or wildlife which interbreeds when mature” (ESA sec. 3(15)). 

The science job of identifying listable units involves analyses of reproductive isolation of the 

taxon in question. Taxonomic classification at the species level tends to be relatively 

straightforward, although it is rarely completed without challenges and revision. Evidence for 

reproductive isolation can come from several fronts, including molecular or allozymic genetic 

data, life history trait variation, estimates of intergroup dispersal, or geographic separation. Four 

difficult science issues have emerged in application of the ESA by USFWS and NMFS: Do all 

subspecies have equivalent “significance” taxonomically? What is a distinct population segment 

(Waples this volume)? How does hybridization between taxa affect species identification (Haig 

and Allendorf this volume)? How should artificially propagated individuals be considered? 

Species and Subspecies. The accuracy and degree of revisions of taxonomic classifications at the 

subspecies level varies greatly among species. The USFWS frequently has encountered 

situations in which it was uncertain whether a group of individuals should be classified as a


distinct population segment, a subspecies, or even a separate species (e.g., interior least tern 

(USFWS 1985), lower Keys rice rat (USFWS 1991), Mississippi gopher frog (Rana capito 

sevosa), California red-legged frog (Rana aurora draytonii) (USFWS 1996a), and tiger 

salamander (Ambystoma californiense) (USFWS 2003c)). The listing determinations for the 

California gnatcatcher (Polioptila californica californica) (USFWS 1993; Zink et al. 2000), 

Dusky seaside sparrow (Ammodramus maritimus nigrescens) (Avise and Nelson 1989) and 

Florida panther (Puma concolor coryi) (Culver et al. 2000) aroused enormous controversy after 

the listings over the issue of whether the groups to be listed were significantly divergent enough 

from more common sister taxa to be considered subspecies, and therefore listable units. The 

social and political fallout from these listing decisions continues today (e.g., Carlson 2003; 

Miami Herald 2003; Pfeifer 2003; Wilson 2003). In some respects the controversy is misplaced, 

since even if they are not subspecies many of these population groups could likely be considered 

“distinct population segments” and so eligible for listing as a “species” under the Act (Easley et 

al. 2001). In other cases, new information about the lack of reproductive isolation may lead 

USFWS and NMFS biologists to conclude a group of populations is neither a subspecies 

(contrary to a published classification) nor a DPS, as in the case of the western sage grouse 

(USFWS 2004n). 

Distinct Population Segment. The USFWS and NMFS have a joint Distinct Population Segment 

(DPS) policy (USFWS and NMFS 1996b) that provides two tests of distinctness: (1) Is the 

population or group of populations markedly separate from other populations of the same 

species? and (2) is it significant? The policy provides a noninclusive list of factors that may be 

considered to qualify a population as significant, all of them biological (or scientific) factors. 

These include persistence in an ecological setting unusual or unique for the taxon, evidence that


loss of the discrete population segment would result in a significant gap in the range of a taxon, 

evidence that the discrete population segment represents the only surviving natural occurrence of 

a taxon that may be more abundant elsewhere as an introduced population outside its historic 

range, or evidence that the discrete population segment differs markedly from other populations 

of the species in its genetic characteristics. 

Biologists may find it difficult to determine whether a population that is separate is also 

significant if they are uncertain of the taxonomic classifications above the population level. 

Making this determination can be very important for the degree of protection afforded a species. 

For example, in their first review of the status of southern resident killer whales (Orcinus orca), 

Federal biologists believed that the classification of orcas world-wide was probably wrong, but 

that was the taxon against which they felt they must determine “significance” (the second prong 

of the DPS test). In the absence of scientific consensus on how to group the units, the biologists 

initially concluded the southern resident group did not meet the DPS definition. Although the 

biologists making the determination did not dispute the declining trend and precarious status of 

the southern group of whales, because they could not be considered “significant” to the world- 

wide taxon, NMFS initially did not list the southern resident group of orcas under the ESA 

(NMFS 2002b). Upon reviewing new scientific information after a judge’s order to revisit the 

determination, the biologists concluded that the southern resident killer whales met both the 

discreteness and significance criteria for a DPS (Krahn et al. 2004). As a result, the southern 

resident DPS was proposed for listing as threatened under the ESA in December, 2004 (NMFS 

2004a).


NMFS adopted a policy for designating distinct population segments of Pacific salmon 

and steelhead prior to the joint DPS policy (NMFS 1991; Waples 1991, 1995). The NMFS policy 

relies on identification of evolutionarily significant units (ESUs). To be considered an ESU, a 

group of populations must be substantially reproductively isolated from other populations of the 

same species, and must represent an important component in the evolutionary legacy of the 

species. 

In delineating a DPS, one of the biggest challenges the two agencies face is how to 

address questions surrounding the significance of intraspecific variation in life histories, genetic, 

or morphological traits. It is important to determine the relationship of life history variants (e.g., 

races) to one another in order to decide into how many pieces a species could or should be 

divided for listing determinations. For example, the unique life history of sockeye salmon 

(Oncorhynchus nerka), steelhead (O. mykiss), and chinook salmon (O. tshawytscha), which have 

both anadromous and nonanadromous (or resident) forms, pose an especially thorny problem. In 

many cases where the forms occur within drainages, the anadromous forms are at risk and the 

resident forms are not (NMFS 2003). The two life history forms are usually genetically more 

similar to one another than either is to its counterpart in nearby watersheds. Should each form be 

protected separately? 

Another example of difficulty in determining the significance of within-species variation 

is the USFWS listing of the California coastal gnatcatcher as a subspecies. The birds had 

originally been identified as a subspecies based on differences in bill size and shape, tail length, 

and overall coloration--all characteristics used by ornithologists to establish taxonomic 

classifications (USFWS 1993). These characteristics had evolved since the last ice age when the


birds expanded northward from a refuge in Mexico--a very short time frame, evolutionarily 

speaking. Skeptical of the listing, private sector interests sponsored research which suggested 

that the morphological variations may not be genetically based. The USFWS revised its listing of 

the flycatcher, proposing to list it as a DPS instead (USFWS 2003). As a practical matter, in spite 

of a rash of new scientific information-gathering and analyses, the listing of the flycatcher as a 

DPS rather than a subspecies has little, if any, effect on the degree of protection it is afforded 

under the Act. 

These examples raise the problem of how to view the importance of morphological or 

behavioral variation that have evolved rapidly in response to dramatic environmental changes. 

How important is the variation to long-term persistence of the subspecies or species? Should 

these relatively newly evolved forms be protected? Some observers (and plaintiffs) argue that the 

Act is meant to protect morphologically unique forms as “distinct” population segments 

(Doremus 1997). Others suggest that the relevant inquiry should be whether, if lost, the variation 

could evolve again in a time span that would be meaningful to humans (such as a few 

generations) (Ruckelshaus et al. 2002a; Waples et al. 2004). Once a DPS is delineated, the 

relevant inquiry is whether the distinct population as a whole is at risk of extinction. This turns 

the difficult task back to the scientists of determining the importance of different morphological 

or life history forms to the continued existence of the distinct population segment (or species or 

subspecies) as a whole. 

Hybrids. Hybridization between closely related taxa can create listing challenges, especially 

when one of the hybridizing species is common and the other rare (Haig and Allendorf this 

volume) For example, the red wolf (Canis lupus rufus), which is listed as endangered under the


ESA, may interbreed with the unlisted eastern gray wolf (Canis lupus lycaon) (Wayne and Jenks 

1991; Dowling et al. 1992; Nowak 1992; Wayne et al. 1992; Brownlow 1996). A less high 

profile but equally vexing example is the Westslope cutthroat trout (Oncorhynchus clarki lewisi), 

which hybridizes with introduced rainbow trout (O. mykiss) in the western United States 

(Allendorf and Leary 1988; Behnke 1992; Rubidge et al. 2001; Rubidge 2003; Taylor et al. 

2003). Application of a proposed policy on considering hybrids (or intercrosses) under the Act 

(USFWS 1996b) did not prevent legal challenge and extensive discussion of the treatment of 

hybrids in USFWS’s ultimate decision not to list the trout (USFWS 2003a). 

Artificial propagation. Both USFWS and NMFS have had to consider species identification 

questions for taxa that include artificially propagated individuals occurring in natural habitats 

(e.g., fish produced in a hatchery, captively bred birds). Until recently, both agencies uniformly 

judged the danger of extinction and the state of recovery based on naturally reproducing 

populations. Recently, however, NMFS has proposed a policy that would consider the risk of 

extinction of species based on the likelihood of extinction of the entire species, both artificially 

propagated and naturally produced components (NMFS 2004b, 2005). The proposal raises 

interesting policy and science questions. On the policy side familiar questions include the 

acceptable degree of uncertainty and risk, both with respect to biological issues (such as 

likelihood of persistence) and management issues (such as likelihood artificial propagation 

programs will continue to be funded at a certain level or operated in a certain manner). On the 

biological side, it is very difficult for scientists to incorporate artificial propagation into 

extinction risk models because data on breeding patterns, reproductive success, and movement of 

hatchery and wild fish are so poor. And on the interface between science and policy, the NMFS’ 

proposed policy raises questions about the importance of a species’ “evolutionary trajectory.” Is


a DPS that is in danger of diverging from a natural evolutionary trajectory because of artificial 

selection “in danger of extinction”? Presumably it could be, if the artificial selection makes it 

likely the DPS will no longer be significant to the taxon (or evolutionarily significant, in the case 

of an ESU; Myers et al. 2004). 

What is a Listable Unit: Public and Court Reaction 

Courts are generally unwilling to second-guess agency biologists when it comes to taxonomic 

classification or evaluation of extinction risk. The General Accounting Office reviewed 64 listing 

decisions by the USFWS between 1999 and 2002 and found that peer reviewers 

“overwhelmingly supported” the application of science to the decisions; and found further that 

courts overturned only two listing decisions because of improper use of scientific data (GAO 

2003). However, courts will intervene where judges believe NMFS or USFWS has failed to 

follow the statute, regulations, or policies, or where the judge believes the agencies have failed to 

adequately explain the connection between the data and the conclusion. For example, a district 

court invalidated NMFS’ decision to list naturally spawned but not the hatchery spawned Oregon 

coast coho, even though NMFS found them to comprise a single ESU (Alsea Valley Alliance v. 

Evans, [161 F. Supp. 2d 1154, D. Oreg. 2001]). An appeals court threw out USFWS’s decision 

to list a population of the cactus ferruginous pygmy owl because USFWS failed to explain how 

the population was “significant” and therefore a DPS under the joint DPS policy (National 

Association of Homebuilders v. Norton, CV 00-0903 March 10, 2003). And a district court 

concluded NMFS did not use the best available science when it relied on a taxonomic 

classification for Orcinus orca that NMFS’ scientists considered out of date (Center for 

Biological Diversity v. Lohn 2003).

Chap. 11, Science and Implementation, (ESA Vol. 2) Ruckelshaus and Darm, 11 

What is a Listable Unit: Opportunities for Advancing the Role of Science 

The National Academy of Science review of use of science in the ESA was supportive of the 

Evolutionary Unit concept (NRC 1995). Much of the ongoing scientific debate over DPS/ESU 

identification is over fairly technical points, such as how best to describe evolutionarily 

significant variation for protection (summarized in Ruckelshaus et al. 2002a; Waples this 

volume). Some observers feel the USFWS and NMFS have too narrowly defined distinct 

population segments on the basis of scientific criteria (Doremus 1997), arguing that the ESA was 

intended to protect populations that have aesthetic value, that are a keystone species within their 

ecosystem, or are in some other sense unique. The concern is that the rigid “scientific” approach 

embodied in the ESU and DPS policies ignores other values that are equally valid and that 

Congress intended to protect. The two agencies, in turn, have adopted policies intended to 

implement the congressional mandate that listing decisions be based on the best “scientific” 

information available. Moreover, the ESU and DPS policies in most cases provide workable 

guidance in determining whether a species exists for purposes of the ESA. 

Extinction Risk: Role of Science in Agency Practice 

Once the listable unit (i.e., species, subspecies, or DPS) is identified, its risk of extinction must 

be estimated under section 4(a) of the ESA (table 11.1). The Act defines an “endangered 

species” as one that is “in danger of extinction throughout all or a significant portion of its 

range” (ESA sec. 3(6)) and a “threatened species” as one that is “likely to become an endangered 

species within the foreseeable future” (ESA sec. 3(19)). Risk evaluations are necessarily a 

combination of scientific analyses and policy judgments about the degree of “acceptable” risk


and the time frames over which risk should be evaluated (Burgman 2005). Decision makers must 

then interject a judgment about whether a species’ risk of extinction triggers the statutory 

definitions of “endangered” or “threatened.” 

Qualitative approaches to estimating species risk, if transparent and systematic, can be just as 

reliable as quantitative approaches (e.g., Keith et al. 2004, McCarthy et al. 2004). Nevertheless, 

neither the USFWS nor NMFS regularly use widely accepted qualitative approaches to 

estimating extinction risk for listing decisions, such as the IUCN red-list criteria (IUCN 1994) or 

NatureServe’s heritage ranking system, originally developed by states’ heritage programs in 

collaboration with The Nature Conservancy (NatureServe 2003). NMFS implemented its own 

risk evaluation matrix to assess the status of over 50 ESUs of Pacific salmonids (Wainwright and 

Kope 1999), accounting for diversity and spatial distribution concerns, in addition to the more 

familiar abundance and population growth trend criteria present in other approaches (e.g., 

Allendorf et al. 1997, Shelden et al. 2001). In the more recent listing determinations, NMFS 

incorporated a method of indicating the certainty of risk evaluations for each ESU, borrowing 

from a method of generating distributions of “certainty scores” used for the Forest Ecosystem 

Management Team (FEMAT 1993). 

Quantitative extinction risk models (known collectively as Population Viability Analyses, or 

PVA) require at a minimum information on population size, population growth rate, and 

variability in population growth rate over time (Dennis et al. 1991; Boyce 1992; Morris et al. 

1999). The critical first step of identifying demographically independent populations is almost 

never done in PVA analyses, in spite of evidence that ignoring population structure can cause 

grave errors in estimates of extinction risk (Morris et al. 1999). In a recent counter-example,


NMFS identified independent populations before conducting viability modeling for Pacific 

salmonids (McElhany et al. 2000; Ruckelshaus et al. 2002b). 

The data needed to parameterize even the simplest PVA models are almost always incomplete 

(Reed et al. this volume). Furthermore, simple extensions of past trends are not always accurate. 

Additional uncertainties in using PVA to model extinction risk occur in decisions about model 

structure--for example, how to depict population responses at small sizes, the effects of density- 

dependent population regulation, and choice of a quasi-extinction threshold have huge effects on 

model results (Morris et al. 1999). Because of uncertain data inputs, it is important to explore the 

sensitivity of PVA results to alternative assumptions (e.g., Dennis et al. 1991; Holmes 2001; 

Holmes and Fagan 2002), as NMFS has done for estimating the status of Pacific salmon and 

Steller sea lions (Eunetopias jubatus) in listing and recovery decisions (Gerber and VanBlaricom 

2001; NMFS 2003; PSTRT 2002; WLCTRT 2003). 

Applications of PVA generally assume that the trends and variability in input parameters 

observed in the past are representative of those to be observed in the future period over which the 

population dynamics are projected. This is almost certainly an incorrect assumption--climate 

change, changes in human management of the landscape, introduction and spread of 

nonindigenous species, and changing rates and intensity of human-influenced catastrophes (e.g., 

fire, toxic, or oil spills) are likely to result in novel future conditions. A relatively new and 

promising approach is to use scenario planning, whereby scientists ask whether an estimated risk 

of extinction (or any population outcome) changes under alternative views of future conditions 

(see “Recovery Planning” in this chapter; Clark et al. 2001; Carpenter 2002; Peterson et al. 

2003).


An emerging issue for the USFWS and NMFS is interpretation of the statutory definition of an 

endangered species as one that is in danger of extinction “throughout all or a significant portion 

of its range.” As mentioned previously, while early USFWS listings were often ambiguous about 

the basis for listing less than a full subspecies, recent practice has rested on the identification of a 

DPS. Dissatisfied with some determinations not to list, plaintiffs have begun to challenge the 

agencies for failure to separately examine whether a species, subspecies or DPS is in danger of 

extinction in only a portion of its range (flat-tailed horned lizard: Defenders of Wildlife v. Norton 

2001; Canada lynx (Lynx canadensis): Defenders of Wildlife v. Norton 2002; green sturgeon: 

Environmental Protection Information Center (EPIC) v. NMFS 2004.) The two agencies have so 

far not articulated an interpretation of this statutory phrase, but some implied interpretations 

could have important consequences for future listings. Recent decisions by the USFWS have 

applied a biological test that is similar to the significance test of the DPS policy--that is, 

examining whether a population group is biologically significant even though it is not discrete 

(e.g., Florida black bear: USFWS 1998; Canada lynx: USFWS 2000). It is unclear whether the 

USFWS and NMFS believe that a species in danger of extinction in only a portion of its range 

must be listed throughout its entire range (see Marbled Murrelet v. Lujan, No. C91-522WDR, 

1992 U.S. Dist. LEXIS 14645 (Sept. 16, 2992). If the test of significance is a biological one (for 

example, a species overall is neither threatened nor endangered, but is in danger of extirpation in 

a biologically important part of its range), the incongruous result from existing court decisions 

would be that a population group that is not a DPS but is in danger of extirpation could lead to 

the listing of an entire species that is neither threatened nor endangered.


Extinction Risk: Public and Court Reaction 

Doremus (1997) suggested that negative public reaction to listing decisions is a reaction to 

unbridled agency discretion in identifying species and determining risk of extinction. In general, 

however, it seems the public reaction to listing tends to be less about whether the USFWS and 

NMFS have misapplied science and more amazement that federal laws will protect such 

creatures as rats and bugs, often against private interests. Courts tend to be deferential to agency 

listing determinations (GAO 2003), except when they conclude that the agencies failed to follow 

the statute or agency regulations. Although public comment on listing proposals often contests 

the agencies’ analysis of extinction risk (e.g., recent northern spotted owl [Strix occidentalis 

caurina] and marbled murrelet [Brachyranphus marmoratus marmoratus] status reviews by a 

consulting firm contracted by USFWS; Daly 2003), the authors are unaware of any successful 

court challenges in that area. 

Extinction Risk: Opportunities for Advancing the Role of Science 

The USFWS and NMFS recently completed an interagency policy outlining the criteria by which 

the they will evaluate the effects of federal, state, and local conservation efforts when making 

listing decisions (“Policy for Evaluating Conservation Efforts” USFWS and NMFS 2003). These 

so-called “conservation measures” are those that recently have been, or soon will be 

implemented, and whose effects on the risk status of the species under review have not yet been 

realized. The criteria include addressing how likely it is that specific conservation measures will 

be implemented, and if implemented, how likely they are to be effective. The latter question is a 

scientific one that in some cases is exceedingly challenging to address (see discussion in 

“Recovery Planning” below).


The USFWS and NMFS would be well served by adopting guidance for making endangered and 

threatened species determinations. The guidance should acknowledge that making listing 

determinations is not just a science exercise but has three important policy components: (1) the 

time period over which persistence should be measured, (2) the level of risk that results in a 

threatened or an endangered finding, and (3) the burden of proof for demonstrating the effects of 

conservation measures. Guidance needs to be flexible enough to account for the inaccuracy of 

extinction risk estimates and for the biological differences among different species. For example, 

the time period over which extinction is considered may depend upon the inherent variability in 

demographic characteristics of a species or the ability of scientists to forecast long-term trends. 

What level of risk results in an endangered or a threatened finding might also vary depending 

upon the uncertainties involved. The guidance would need to leave room for decision makers and 

scientists to work together to understand the biological implications of alternative risk levels 

(e.g., modelers can illuminate for decision makers what a 0.99, 0.95, or 0.80 probability of 

extinction looks like) so that the population status estimated is appropriate for the policy 

determination that must be made (Doremus this volume). 

Research is needed on how best to make population or species demographic parameter estimates 

from spotty census information (Reed et al. this volume). Abundance information for many 

species of conservation concern consists of presence/absence data, index counts, or censuses 

during a specific life stage that is easy to count, such as breeding aggregations. Making a 

determination about the viability status of a species requires that these population or species 

subsamples be translated into whole population or species counts--what are the best methods for 

making that translation? What are the advantages and pitfalls associated with different 

approaches to estimating species numbers from population subsamples?


Additional important features that if incorporated could greatly improve quantitative extinction 

risk models for ESA are how factors in the environment might act together to accelerate or 

mitigate downward population trends, and how ecological interactions affect single-species 

dynamics (see also “Recovery Planning” below; rev. NRC 1995). 

The Science Underlying Critical Habitat Designations 

At the time of listing, the USFWS and NMFS are to designate critical habitat to the maximum 

extent prudent and determinable (see ‘4(b) Critical habitat designation’ in table 11.1). If critical 

habitat is not determinable at the time of listing, they have one year to complete the designation. 

The Act defines critical habitat as “the specific areas within the geographical area occupied by 

the species . . . on which are found those physical or biological features . . . essential to the 

conservation of the species,” and specific areas outside the geographical area occupied by the 

species . . . upon a determination by the Secretary that such areas are essential for the 

conservation of the species.” From this construction, the statute seems to contemplate an 

approach to critical habitat designation that favors occupied areas: the agencies are first to 

identify habitat elements essential to species conservation (for example, a particular type of tree 

for nesting, vegetation for forage or cover, gravel streambeds for spawning, etc.) and then 

include in the designation any areas within the species’ present range where those elements are 

present. Only for areas outside the species’ present range must there be a determination that the 

area itself is “essential for conservation.” In practice, the agencies, plaintiffs and some courts 

have blurred the two standards and required that all areas, occupied or unoccupied, meet the test 

for unoccupied habitat: the area itself must be essential for conservation. For example, in a case 

involving the silvery minnow, the court stated that critical habitat “must be limited


geographically to what is essential to the conservation of the threatened or endangered species.” 

(Middle Rio Grande Conservancy District v. Babbitt, 206 F.Supp.2d 1156 (D.N.M. 2000)). And 

in a case involving the Alameda whipsnake the court stated: “critical habitat for occupied land is 

defined in part . . . as specific areas ‘essential to the conservation of the species.’” 

(Homebuilders Association of Northern California v. USFWS, 268 F.Supp.2d 1197 (E.D. Cal. 

2003)). . 

The USFWS and NMFS have long maintained that critical habitat designation adds little 

to species protection (Clark 1999; but see Taylor et al. 2005). Section 7 of the ESA requires 

federal agencies to ensure that their actions do not jeopardize species’ continued existence and 

do not destroy or adversely modify their critical habitat. The two agencies have for the most part 

treated an action that adversely modifies critical habitat as also jeopardizing the species’ 

continued existence, making the prohibition against adverse modification redundant. Agency 

regulations defining both jeopardy and adverse modification in similar terms (actions affecting 

“both the survival and recovery” of the species) have reinforced this approach. Critics point out 

that critical habitat designation is especially important for species protection in unoccupied 

habitat, where the USFWS and NMFS may be less likely to reach a jeopardy finding (Taylor et 

al. 2003, 2005). Two separate reviews indirectly looked at the effects of critical habitat 

designations on reported trends in species abundance and content of recovery plans, and the 

results were mixed (Clark et al. 2002; Hoekstra et al. 2002; Taylor et al. 2003, 2005). The 

authors believe the current landscape is too unsettled to draw a reliable conclusion from past 

practice. Recent court decisions have invalidated the agencies’ regulatory definition of adverse 

modification as not being sufficiently tied to conservation (Gifford Pinchot Task Force v. U.S. 

Fish and Wildlife Service, No. 03-35279 (9th Cir. Aug. 6, 2004); Sierra Club v. U.S. Fish and


Wildlife Service, 245 F.3d 434 (5th Cir. 2001). As future section 7 practice adjusts to the new 

legal rulings, the two tests may prove not to be redundant and the designation of critical habitat 

may indeed provide increased protection for listed species. 

An extension of the view that the designation of critical habitat has little or no impact 

argues that there are no economic consequences of designation to consider. The result is a history 

of critical habitat designations, where they have been made, lacking a meaningful analysis of the 

economic impact (See New Mexico Cattle Growers Association v. U.S. Fish and Wildlife 

Service, 248 F.3d 1277 (10th Cir. 2001). Successful court challenges to designations (or the lack 

of designations) have led to multiple requirements for the USFWS to designate habitat in very 

short time frames. Moreover, courts have ordered the agencies to consider economic impacts of 

designation, even if they are “coextensive” with the impacts of applying the section 7 jeopardy 

requirement (New Mexico Cattle Growers Association v. U.S. Fish and Wildlife Service, 248 

F.3d 1277 (10th Cir. 2001). This requirement is contrary to the best available science regarding 

economic analysis, which would require an estimate of the costs of designation based on a 

comparison of the world with and without the designation (OMB 2003), and the requirement to 

do a full economic analysis for a burgeoning number of court-ordered designations has severely 

strained USFWS’s resources. 

In response, the USFWS has vigorously objected to the requirement (e.g., testimony of 

Assistant Secretary Craig Manson 2003; 69 FR 3064, January 22, 2004). Past congressional 

efforts have failed to amend the ESA to change the timing of critical habitat designation to 

coincide with recovery planning instead of listing (See Chafee-Kempthorne bill, S. 105-1180, SS 

2(b) [1997]), but it remains a topic of congressional interest (see H.R. 2933 [2004]). For the


moment, it appears unlikely there will be relief for the USFWS from the critical habitat 

requirement (Washington Post 2004). 

Role of Science in Agency Practice 

Section 4(b)(2) requires critical habitat designation to be based on the best scientific data 

available, although the USFWS and NMFS may exclude areas from designation if economic or 

other relevant impacts outweigh the benefits of designation. Under the straightforward 

interpretation of the language in the Act, the science task would also be fairly straightforward, at 

least with respect to occupied habitat. For many species there is a body of knowledge about the 

elements in their habitat that are essential for their persistence--what they eat, where they mate 

and nest, and so forth. Under the approach that requires a determination of essentiality for both 

occupied and unoccupied habitat, the task becomes much more difficult. Usually at the time of 

listing (and often many years after listing), the agencies know very little about species’ habitat 

needs and thus identification of critical habitat is highly uncertain. For scientists, the question is 

often not just how much occupied and unoccupied habitat the species needs, but how many 

populations must exist for the species, subspecies, or distinct population segment to be viable. 

Also, at the time of listing, there usually are limited data on land use patterns and economic 

activities and there is no experience to suggest how these activities would be modified as a result 

of section 7 consultations. This is information that is necessary for a scientifically meaningful 

economic analysis. 

The agencies’ joint designation of critical habitat for the Gulf sturgeon illustrates some of the 

issues surrounding such a designation. The two agencies examined the population structure and 

concluded that the seven extant populations were largely reproductively isolated, that


maintaining genetic diversity was important, that therefore the populations at the extremes of the 

range are important to conserve (containing the extremes of diversity), that the intermediate 

populations are important for connectivity, and that therefore all habitat currently occupied by 

those seven populations is essential for conservation (USFWS 2003d). Like the judgments made 

in analyzing extinction risk, these are clearly not judgments made in a policy vacuum. The 

question of how many populations are needed for conservation and how much habitat each needs 

for conservation are not just scientific questions. The answers depend upon tolerance to risk and 

time scales over which the risk is considered. 

One of the more contentious debates surrounding critical habitat designation concerns the 

consideration by the USFWS and NMFS of economic costs of designation and their discretion 

under section 4(b)(2) to exclude areas from designation if the benefit of exclusion outweighs the 

benefit of designation. The two agencies have only recently begun to apply economic analysis in 

their designations, and their use of the science of economics is not well-developed. Their past 

practice of collapsing the jeopardy and adverse modification requirements into a single test has 

complicated the economic analysis. 

Public and Court Reaction 

The provisions for critical habitat designation have proven a major flash point for advocates and 

critics of species protection (e.g., Sacramento Bee 2003b; Wilson 2003; Cart and Weiss 2004). It 

is the most prominent place in the statute where habitat plays a role, consistent with the fact that 

Congress recognized in adopting the Act that habitat destruction was one of the leading causes of 

extinctions. It is also one of the few places in the statute where economics comes into play, 

making it a rallying point for the development-regulated community. Added to that is the


perception of landowners that when private land is designated as critical habitat the federal 

government is “taking” their property and will restrict use of their land. Finally, the USFWS and 

NMFS have long maintained that critical habitat designation adds nothing to species protection 

and have resisted designating habitat altogether or have simply designated habitat without much 

analysis (Patlis 2001). Given these views and perceptions, it is not surprising that the agencies 

fail to make critical habitat designations, and critical habitat designations made frequently end up 

in court (GAO 2003). 

Courts have responded to the agencies’ treatment of critical habitat designation with impatience, 

chastising their reluctance to designate and ordering critical habitat designations to be completed 

expeditiously. That reluctance and impatience of the courts has created a cycle in which the two 

agencies lack adequate time to conduct a thorough analysis, and courts grant less deference than 

they might to a more thorough analysis. Further complicating implementation of this provision 

are court decisions finding the agencies’ regulatory definition of adverse modification invalid, 

cited above. The lack of guidance by the two agencies and a growing number of court opinions 

serve to make the situation more uncertain. 

Opportunities for Advancing the Role of Science 

There are promising biological approaches that could be used to at least partially address the 

question of how much occupied and unoccupied habitat is needed for species persistence (Hanski 

1999), but the logistics of parameterizing analyses or models are daunting. For example, 

population matrix models can be used to address the question of how changes in survival at 

particular life stages affect overall population dynamics or persistence (rev. Caswell 2001). If the 

data are available, scientists could use such models to ask whether the quality or quantity of


specific habitats affecting a species (at a particular life stage) significantly affects the overall 

population demography--in other words, the species’ likelihood of recovering. An example of 

such an application with a listed species is the endangered Kemp’s Ridley sea turtle 

(Lepidochelys kempii) , in which matrix models suggested that the survival of subadults and 

adults in the ocean was most critical to overall population status (Heppell et al. 1996; Heppell 

and Crowder 1998). Such a result could be used to help target critical life stages and the habitats 

upon which they depend. Another approach is to empirically relate (or predict with models) 

changes in habitat to changes in species status (e.g., Jenkins et al. 2003). Unfortunately, the 

answer to the last part of the question posed under section 4(b)(2)--what habitat conditions or 

amounts significantly affect life-stage-specific survivals?--usually is not known (see “Recovery 

Planning” below). 

The science of economics also could contribute to improving the designation process. Section 

4(b)(2) requires the USFWS and NMFS to consider the impacts of designation and balance the 

benefits of exclusion against the benefits of designation. Federal guidelines recommend putting 

the two types of benefits into the same metric in a cost-benefit framework (OMB 2003). 

Although information may be readily available that allows economic impacts to be quantified 

and monetized, quantifying the benefits to species from critical habitat designation is more 

difficult. 

Thus, best economics practice would have the agencies measure the incremental impact and 

benefit of designation, yet the courts have ruled otherwise (New Mexico Cattle Growers, supra.). 

How should the agencies proceed in this situation? Best economic practice would have them 

conduct a formal cost-benefit analysis, yet the short statutory time frames, limited information


and resources, and considerable latitude for discretion suggest formal cost-benefit analysis may 

be neither possible nor necessary. One observer has suggested that approaches other than cost- 

benefit analysis, such as a cost-effectiveness framework, may be more appropriate (Sinden 

2004). This recommendation is consistent with OMB guidance in cases where benefits are 

difficult to monetize (such as benefits to health or the environment). 

The National Academy of Sciences suggests changes to the critical habitat designation process 

that might require legislation, including the identification of habitat critical to survival at time of 

listing with the designation of the rest of critical habitat at the time of recovery planning (NRC 

1995). Tying critical habitat designation to recovery planning has many proponents. A bill 

introduced in the 103rd Congress would have amended the ESA to call for critical habitat 

designation at the time of recovery planning and mandated recovery plans within two years (S. 

105-1180 [1997]). The Department of the Interior has gone on record supporting such a 

connection (Manson 2004). The General Accounting Office recommends that the USFWS and 

NMFS adopt guidance on critical habitat designation (which probably would require a regulatory 

change [GAO 2003]). 

The authors agree with the General Accounting Office that it is within the agencies’ power to 

make some improvements in the process through strategic guidance. Clearer guidance would 

help scientists focus on the scope of their task. Until the agencies amend the regulatory definition 

of adverse modification, it will be unclear what standard the they are applying in their section 7 

consultations and whether they continue to view the prohibitions against jeopardy and adverse 

modification of critical habitat as providing redundant protection. Guidance on the economic 

analysis called for in the Act would also help the USFWS and NMFS expedite designations. In


particular, criteria for determining whether consideration of economic or other relevant impacts 

outweigh the benefits of designation would be helpful. 

The Science Underlying Limitations on Federal Actions: Section 7 Consultation 

Federal agencies must ensure any action they fund, permit, or carry out does not jeopardize the 

continued existence of listed species or result in the destruction or adverse modification of their 

critical habitat (table 11.1; section 7(a)(2)). When a federal agency intends an action that may 

affect a listed species, it must consult with the listing agency. For actions that adversely affect 

the species, the agency provides its biological opinion as to whether the action as proposed is 

likely to jeopardize the continued existence of a listed species or adversely modify its critical 

habitat. If the agency’s opinion is that the action is likely to cause jeopardy or adverse 

modification, it must offer a reasonable and prudent alternative. The consultation provisions of 

the statute require that all agencies “shall use the best scientific and commercial data available” 

in fulfilling the consultation requirement. 

Conducting an analysis of jeopardy and adverse modification is one of the most common tasks 

required of the USFWS and NMFS and at the same time one in which the standards are most 

obscure (Rohlf 1989, 2001). The statute does not define jeopardy or adverse modification. The 

two agencies have adopted regulatory definitions of these terms (USFWS and NMFS 1999b), but 

their consultation handbook lays out an analytical approach that does not track the regulatory 

definitions. The regulations define “jeopardize the continued existence of” to mean “to engage in 

an action that reasonably would be expected, directly or indirectly, to reduce appreciably the 

likelihood of both the survival and recovery of a listed species in the wild by reducing the 

reproduction, numbers, or distribution of that species.” Adverse modification is defined as an


alteration that “appreciably diminishes the value of critical habitat for both the survival and 

recovery of a listed species.” This fairly straightforward test would seem to require the agencies 

to compare the likelihood of a species survival and recovery with and without the proposed 

action, or the value of critical habitat with and without the proposed action. If the likelihood of 

survival and recovery “with” the action represents a reduction that is “appreciable,” the action 

jeopardizes. If it appreciably diminishes the value of critical habitat for survival and recovery, it 

is an adverse modification. 

In practice, however, the agencies seldom take that approach, and the their consultation 

handbook lays out a different chain of logic. The handbook does not provide further guidance on 

what it means to appreciably reduce the likelihood of survival and recovery (USFWS and NMFS 

1999b). Instead, it directs the agencies to consider the status of the species, the environmental 

baseline, the effects of the action, and cumulative effects to determine whether the species is 

likely to survive and recover. The handbook does not say what the agencies should do after 

summing up those factors. If the species is not expected to survive and recover, how much must 

the action under consultation contribute to that failure before it is considered jeopardy? Or, less 

likely, if the species is expected to survive and recover, does it matter how much modification 

occurs to the species’ remaining habitat? Analysis of adverse modification of critical habitat is 

further complicated by two circuit courts invalidating the regulatory definition, as discussed 

previously. 

In addition to offering an opinion on whether an action is likely to jeopardize a species’ 

continued existence or adversely modify its critical habitat, the USFWS and NMFS must issue 

an incidental take statement authorizing a given level of take associated with the proposed


action. Where the action involves habitat modification (for example, a grazing allotment), the 

agencies must determine what level of take will be associated with the habitat modification. 

Although such a determination must be made based on scientific analyses, it is very difficult for 

scientists to quantify a species’ response to habitat alterations, especially smaller-scale changes 

in habitat. 

Although the statute and agency regulations require the use of the best available science by the 

federal agencies, this is an area in particular where the tools of science are inadequate, by 

themselves, to answer the questions asked. The agencies often lack information to determine in 

advance what effect an action is likely to have on the listed species. Another complication is that 

for many species, risks are cumulative, and assessing the effect of each individual action on 

species status is exceedingly difficult. A final confounding factor is the frequent reality that 

threats come from many different actions in different sectors, forcing the agencies to make a 

choice about how much of the conservation burden should fall on a given sector (Box 11.1). 


The variety of agency action considered in section 7 consultations is extremely diverse, as are the 

species affected. This variety makes it challenging to draw useful lessons from agency practice. 

In Box 11.1, we offer a few examples to help draw out some lessons for scientists and policy 

makers. 


The main opportunity for advancing the role of science in implementing section 7 is for the 

agencies to provide clear guidance about the general standards for jeopardy and adverse


modification. Action agencies frequently complain that “jeopardy” is ill-defined and 

implementation is not uniform. It has also been suggested that the USFWS and NMFS could 

provide clearer guidance for individual species, for example on identifying critically low 

population levels, viable population levels, and allowable levels of take. 

Any standards the USFWS and NMFS provide should allow for scientific information to be 

fully taken into account, along with the policy considerations. For example, how important a 

particular factor is in limiting species recovery should be relevant to any determination, 

especially when it is considered in the context of other factors limiting recovery. As with all of 

sections of the Act, a life-cycle framework for estimating the potential effects of an action on 

species status would appear to be the best way to adequately address the question posed in 

section 7. Whether that life-cycle framework takes the form of a quantitative, formal life cycle 

model or a qualitative framework within which the cumulative effects of actions throughout the 

life history are considered does not matter nearly as much as adopting that perspective. In 

general, because of the inherent scientific uncertainty in estimating the biological consequences 

of numerous, small-scale actions, section 7 consultations should be treated as experiments that 

are monitored and adjusted as needed over time (see Box 11.1.) 

The Science Underlying Limitations on Private Actions 

Once species are listed as endangered, the Act prohibits any person from taking a member of that 

species (table 11.1). Take is defined broadly to include harm, and harm can include destruction 

of habitat to the extent it actually injures or kills individual animals. Science comes into play 

when those whose actions may take a listed species seek an exception from the take prohibition. 

Exceptions can be granted under section 10 (habitat conservation plans or HCPs) or section 4(d).


Regardless of the legal avenue, the standard is similar--the proposed take cannot result in 

jeopardy to the species continued existence or the destruction of adverse modification of its 

habitat. 


The USFWS and NMFS face the same challenges in permitting take that they face in 

consultations with federal agencies. As in the case of consultations, they must consider the effect 

of a single action for which they may or may not have a larger context. Furthermore, the 

difference in time frames between consultations with federal actors and take permits for private 

actors is an added complication. Between federal agencies, the situation is often more fluid. 

Consultation can be readily reinitiated when there are changed circumstances or new 

information. Private parties, on the other hand, often make significant investments on the basis of 

the take permits they receive and accordingly seek a longer-term commitment from the federal 

agencies. In an effort to encourage more landowners to protect endangered species, the agencies 

adopted a series of policies to offer greater assurances that agreements with the federal 

government would be lasting, for example through the “No Surprises” (USFWS and NMFS 

1998) and “Safe Harbor” (USFWS 1999, 2001a & 2003b, Bean et al. 2001) rules. 


The opportunities for improvement in the use of science under sections 10 or 4(d) are similar to 

those under section 7--if the USFWS and NMFS encourage transparent evaluation of the 

cumulative effects of actions, in light of the overall effect of other actions throughout a species’ 

life cycle, the decisions under these sections of the Act will be much improved.


The Act poses a challenging but important question under sections 7 and 10 (as well as section 

4(f), recovery planning, discussed below) that requires description of at least three key biological 

linkages: (1) identification of landscape-level processes that drive environmental factors 

imperiling a species, (2) relationships between critical environmental factors and species status, 

and (3) effects of actions that can directly or indirectly affect species status through changes to 

environmental factors or the processes that control them. To really answer those questions 

requires years of data collection, observations, modeling, and then analysis for each species of 

concern. Undertaking such work is important so that a basic understanding of the causes of 

species declines can be developed. 

In the meantime, while we await more relevant results, decisions under the ESA must be 

made in the face of imperfect biological understanding. Biologically robust shortcuts (e.g., 

identifying data or information critical to making such estimates and where the biggest errors in 

making such judgments are likely) are sorely needed to help inform decisions being made right 

now (e.g., Burgman 2005). Furthermore, a broad review of science underpinning HCPs found 

that scientific guidance underlying a monitoring plan and clearly stated monitoring requirements 

were lacking in most HCPs (Kareiva et al. 1998). Given the inability of science to assess the 

efficacy of actions described in HCPs, such agreements (and others made under section 7) would 

most wisely be treated truly as experiments and include clear provisions for monitoring. 

The Science Underlying Recovery Planning 

The Act requires the USFWS and NMFS to adopt recovery plans for listed species but does not 

specify a time within which plans must be completed (table 11.1). The recovery plan is expected 

to describe the biological conditions that are necessary for recovery of the species, or the state


under which the species can be delisted. Recovery plans do not have any regulatory effect, but 

they can be used to coordinate and guide the agencies’ decision making in section 7 

consultations or in issuing take permits across a species’ range. The Act has minimal 

requirements for recovery plans--they must specify objective measurable criteria for delisting, 

specific actions that will achieve those objectives, and an estimate of the time and cost involved 

in completing the actions. 


Science has a clear role to play in determining the objective, measurable criteria that will lead to 

delisting. The considerations are similar to those involved in the population viability analysis that 

starts the ESA process (although in practice once a species is listed there may be a higher 

threshold for determining it is recovered than for making a determination of “not warranted” in a 

listing context). Aside from describing the conditions that would give a high level of confidence 

in species viability, there also is a role for science in identifying factors limiting recovery and in 

determining the biological consequences of site-specific management actions aimed at 

recovering the species. 

The NMFS has a recovery planning guidance document, which is general and provides 

broad latitude in how plans are developed and in their content (NMFS 1992). In response to the 

need for more technical recovery planning guidance for the many listed ESUs of Pacific salmon, 

NMFS has written a conceptual document that describes what a viable, or delistable, salmon 

ESU looks like (McElhany et al. 2000). NMFS defines a viable salmonid population (i.e., a VSP) 

as one that has sufficient abundance, productivity or population growth rate, spatial structure, 

and diversity so that it has a negligible risk of extinction in 100 years. This construct has proven


to be very useful in keeping the scientific basis for recovery plans consistent among the 26 listed 

ESUs of salmon for which recovery-planning analyses are underway (Ruckelshaus et al. 2002a). 

The fundamental technical questions that are addressed for salmon recovery planning are: (1) 

What was the historical population structure of the ESU? (2) What are the characteristics of a 

viable population for each of the historically independent populations in the ESU? (3) What are 

possible configurations (which might differ from historical conditions) of the distribution, risk 

status, and diversity characteristics of populations across a viable ESU? and (4) What suites of 

actions are needed for recovery of the ESU? Answers to questions 2 and 3 provide viability 

criteria for populations and ESUs, and analyses underlying question 4 allow for evaluation of 

alternative actions and their predicted effects on population and ESU status. 

As described previously in “Listing Determinations”, the NMFS uses a mix of 

quantitative extinction risk models and qualitative risk evaluations in setting viability criteria 

under recovery planning for Pacific salmon and many of its listed marine mammals and turtles. 

The USFWS approaches recovery planning differently than NMFS. Instead of establishing 

species-based viability criteria and then identifying which actions can achieve those criteria, 

USFWS focuses technical analyses in recovery planning on threats to species viability and 

actions to abate those threats. In a recent review of USFWS recovery plans, most reviewed plans 

described recovery criteria in qualitative, rather than quantitative, terms (Gerber and Hatch 

2002). The same review found that for those species whose status was improving since listing, 

more of their recovery plans contained quantitative criteria than for those listed species whose 

status was declining (Gerber and Hatch 2002).


The science questions in this implementation stage of the Act are very broad, so there 

isn’t likely to be a single answer that emerges from scientific analyses aimed at describing a 

recovered species or the actions that are sufficient to allow recovery. For example, for some 

species, there may be more than one way to achieve viability criteria, and if a species is 

comprised of a number of extant populations, there may be multiple configurations of population 

distribution and risk status that can constitute a recovered species or ESU (Ruckelshaus et al. 

2002b). 

NMFS is incorporating scenario planning into its estimates of the likely effects of habitat, 

hatchery, and harvest management actions on the population status of listed salmon 

(Ruckelshaus et al. 2002a). Alternative future conditions to be included in population risk 

models are being elicited from watershed councils so that they can have greater confidence that 

the set of actions they plan to implement will achieve the desired population status for the 

salmon returning to their streams. 


An in-depth review of the science in recovery planning concluded that both the science 

underpinning recovery plans and how science is used in their implementation need improvement 

(Clark et al. 2002). The role of science at this stage is most appropriately to use analyses that 

illuminate consequences of alternative actions, rather than attempting to provide “the answer.” In 

such cases where alternative suites of actions to achieve recovery are possible, collaboration with 

policy and planning staff who will influence implementation of actions is important (Rinkevich 

and Leon 2000; Wollondeck and Yaffee 2000; Brick et al. 2001; Yaffee 2005). Furthermore, as 

with section 7 consultations and section 10 conservation plans, because of the uncertainty


associated with predicting the effects of most actions on species status, implementation of 

actions should be treated as experiments that are monitored with vigilance (Boersma et al. 2001; 

Crouse et al. 2002). 

Science obviously can play a critical role in providing more relevant biological data 

pertaining to imperiled species. The importance of basic natural history information for 

informing decisions under the ESA cannot be overstated (e.g., What constitutes a reproductively 

isolated group of individuals for a given species? In which habitats does a species occur 

throughout its life cycle? What are survival rates for the species in alternative habitat types? 

What is the relative reproductive success of pairings between alternative life history types?) 

Scientists within and outside the USFWS and NMFS have called for greater attention to 

multispecies and ecosystem effects in recovery plans (USFWS and NMFS 1994; Miller 1996). 

Indeed, the agencies developed a joint policy on a desired “ecosystem approach” to the ESA 

(USFWS and NMFS 1994). The potential importance of such community and ecosystem-level 

effects to prospects for species recovery is large. Recent examples in the literature illustrating the 

potential importance of community-level effects to the status of listed species include north 

Pacific whaling effects on sea otters in Alaska (Springer et al. 2003), ecological functions 

provided by grizzly bears (Pyare and Berger 2003), and predation by Caspian terns (Sterna 

caspia) on juvenile salmon in the Columbia River (Roby et al. 2003). Nevertheless, how best to 

include such community- or ecosystem-level effects in a recovery plan is not clear. Some have 

cautioned that satisfying the desire for multispecies protection by including more species in a 

single recovery plan may not be the answer. Clark et al. (2002) conclude that multispecies plans 

may in fact reduce the focus on individual species to the detriment of their conservation status.


Finally, science-policy issues that could benefit from greater guidance from the USFWS 

and NMFS mentioned in previous sections of the Act also pertain to recovery planning. These 

include a clear discussion of what an “acceptable” risk might be under recovery planning for 

different species, transparent discussion of how uncertainty in biological conclusions was 

accounted for in decisions, and whether there are clear differences between jeopardy and 

recovery standards applied by the agencies. 

What Can Scientists Do to Improve ESA implementation? 

Originally, the ESA was formulated to address a significant biological fact--species extinctions 

were occurring at an alarming rate--thus biological information and analyses should be at the 

core of decisions pertaining to species protection and recovery. What have scientists contributed 

to these pressing biological questions? What can we do now to help redress the problems with 

how science is used in ESA decisions? 

The contributions of academic and agency science to addressing biological questions 

asked of ESA implementation have been unevenly distributed among topical areas. In particular, 

quantitative approaches and analyses designed to identify units for conservation and those used 

in estimating species viability (or conversely, risk of extinction) have received the lion’s share of 

attention in the scientific literature (fig. 11.1). These methods are not without controversy, but 

they are relatively well tested and examined, and many of their limitations have been discussed 

(Waples this volume; Boyce 1992; Akçakaya et al. 1999; Morris et al. 1999; Coulson et al. 2001; 

Brook et al. 2000, 2002; Ruckelshaus et al. 2002a; Ellner and Fieburg 2003). Unfortunately, the 

quantitative approaches that are plentiful in the literature are useful for only a small fraction of


the species considered under the auspices of the ESA, because of the dearth of data to 

parameterize even the simplest quantitative approaches, as mentioned above. 

The science of characterizing degrees of imperilment using qualitative approaches also 

has improved greatly in the 30 years since inception of the Act (e.g., IUCN 1994; Akçakaya et 

al. 2000; NatureServe 2003), and greater attention to these methods would be helpful in ESA 

decisions for a majority of the species considered (Keith et al. 2004; McCarthy et al. 2004). 

Analytical methods to address the remaining questions asked in the ESA implementation 

process have barely emerged in the scientific literature (fig. 1). In particular, the science 

underlying identification of the effects of actions on species status lags far behind. Such analyses 

are needed to address questions under sections 7 and 10 (i.e., do these actions significantly 

reduce the species’ likelihood of survival and recovery?), Section 4(b) (i.e., what habitat 

quantities and qualities are necessary for the survival and recovery of the species?), and Section 

4(f) (i.e., what actions are sufficient to achieve species viability criteria?). It is no wonder that 

analyses addressing these questions in the ESA are not prevalent in the literature--the work is 

challenging, time-consuming, and difficult to generalize across species and locations. Especially 

lacking are empirical studies or analytical approaches to addressing the effects of specific actions 

on particular life stages, and how those are manifest at the overall population-dynamic or species 

level. 

Communication between scientists and decision makers is critical so that scientific results 

are relevant and decision makers are ready to incorporate results in their deliberations. Simple in 

concept, this interaction is complicated in practice by the different worlds in which the two live-- 

scientists can say “I don’t know” and can readily accept that it may take years to answer some


scientific questions, while decision makers must make decisions in the limited time frames 

afforded by the Act. Those differences can lead to frustration on both sides. The authors believe 

from our own experiences that the effort is well worth the trials involved (Ruckelshaus et al. 

2002a). Previous studies have highlighted the need for help from conservation scientists in more 

effectively linking basic biology or ecology to management decisions (Floyd 2001; Clark et al. 

2002). A good example of this is the American Fisheries Society’s recent appointment of a 

special committee to explore the concept of “best available science” and what it might mean in 

practice for fisheries management (Harris 2003). Approaches such as those developed under 

decision theory (Clemen 1996; Burgman 2005) and multicriteria mapping (Arrow and Raynaud 

1986; Bana e Costa 1990) are potentially useful, but we could find no examples of how these 

tools have been applied for decision making under the ESA. 

As others have emphasized, science can have a significant impact on decisions under the 

ESA, as long as it isn’t relied upon to be the sole arbiter in decisions (Doremus 1997; see Yaffee 

2005). Scientists, for their part, need to clearly explain to policy and decision makers how their 

choices may be informed by science, and where those limits occur (e.g., how certain are 

predictions of a species persistence probability over the next 50 years? 100 years?) Furthermore, 

scientists and decision makers truly interested in clarifying the role that science plays in 

implementation of the ESA should be willing to participate in public forums, where the same 

transparency of data/inputs and assumptions in analyses can be openly discussed to illustrate 

how science is used in decisions under the Act. It is a rare manager of endangered species who 

will communicate through forums to which scientists are accustomed, such as the published 

literature (e.g., Rosenberg 2002). If scientists are free to interact with policy- and decision 

makers in other processes designed to encourage open exchange, a clearer understanding can be


had of what questions are being asked, and which require science input or policy guidance, or 

both. 

It is critical that discussions between scientists and policy makers, and those involving 

the public, emphasize clearly what is the scientific basis for a result, and what additional policy 

determinations were brought to bear in making a decision under the Act. For example, all of the 

scientific results described above that are relevant to different questions under the Act 

incorporated one or more points of policy guidance, such as the acceptable risk of extinction, the 

time frame for evaluating risk or likelihood of recovery, or the acceptable uncertainty in the 

effects of actions on species status. To improve scientific credibility and agency decision- 

making, both scientists and decision makers need to be clear about where data end and analysis 

begins. Quantitative models often use a mix of actual data and assumptions to produce fairly 

precise results. The precision of the results often causes laypersons and decision makers alike to 

ascribe too much accuracy to model results. If scientists and decision makers do not clearly 

distinguish between facts and assumptions, and how each drives the results, laypersons will 

challenge the facts, rather than question the assumptions. 

A recent example of problems with data underlying ESA decisions involved the method 

of collecting samples of hair for DNA testing to detect the occurrence of the listed Canada lynx 

on U.S. national forests. The federal and state biologists charged with providing the hair samples 

for DNA testing were accused of tampering with the data, because they included hair samples of 

taxidermy and other lynx from outside the prescribed geographic sampling area in the mix with 

bobcat and hair samples of unknown origins. The biologists stated they included such lynx 

samples to verify the accuracy of the genetics laboratory conducting the testing; forestry industry


representatives accused the biologists of trying to rig the results to reduce logging pressure on 

federal lands; and the genetics laboratory got caught in the cross fire (Dalton 2002; Mills 2002). 

A congressional investigation concluded that unauthorized samples were submitted in violation 

of the interagency sampling protocol (GAO 2002). The damage to the credibility of government 

science from this incident was discussed in papers throughout the country (e.g., Mapes 2001; 

Boyle 2002; Strassel 2002). Much of this controversy could have been avoided if the process of 

gathering and analyzing data and its interpretation was transparent. 

Finally, one of the most positive and lasting impacts scientists can have on improving the 

degree to which science informs implementation of the ESA is to push management experiments. 

Because the Act poses biological questions that almost always will have to be answered with 

imperfect information, the only way to encourage action in the face of uncertainty (and feel okay 

about it) is to encourage implementation of alternative actions as experiments. Furthermore, 

carefully estimating what we can learn from experiments before launching into controversial sets 

of actions is well worth the effort (e.g., Paulsen and Hinrichsen 2002), as is carefully monitoring 

the results. In the end, to enhance protection of species under the ESA, biologists must get 

involved. Such involvement is not without potential costs (e.g., Halpern and Wilson 2003), but 

conducting sound research is not enough to protect a species if the results from a beautiful 

biological study sit in a journal, unread. 

Acknowledgments 

We thank Krista Bartz for conducting the analyses for and producing Figure 11.1. Michael 

Bean, Frank Davis, Mike Ford, Dale Goble, Jeff Hard, Linda Jones, Jim Lecky, Marta


Nammack, Mark Plummer, Mike Sissenwine, Russ Strach, John Stein, and Usha Varanasi 

provided helpful comments on this chapter and greatly improved its message. 

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Number of pertinent articles 

Search terms 

400 

300 

200 

100 

0 


Figure 11.1 The number of articles published since 1980 that address science questions posed in 

the Endangered Species Act. The published articles are those that occur in the ISI Web of 

Science Science Citation Index Expanded database between 1980 and September, 2003 

(Thompson ISI, 2003). Search terms pertaining to each science question are listed below each 

panel; articles that emerged for more than one search term within a question category were only 

counted once. 

1980-1983 

1984-1987 

1988-1991 

1. 

What is a 

“listable” species? 

1992-1995 

1996-1999 

2000-2003 

Distinct population segment* 

Endangered Species Act 

Evolutionarily significant unit 

ESUs 

1980-1983 

1984-1987 

1988-1991 

2. 

What is its 

risk of extinction? 

1992-1995 

1996-1999 

2000-2003 

Population viability analysis 

Population viability analyses 

Viability analys* 

Risk of extinction 

Extinction risk 

1980-1983 

1984-1987 

1988-1991 

3. 

What is critical habitat 

for the listed species? 

1992-1995 

Critical habitat* 

Essential habitat* 

1996-1999 

2000-2003 

1980-1983 

1984-1987 

1988-1991 

4. 

Does the action “jeopardize” 

the species’ existence? 

1992-1995 

1996-1999 

2000-2003 

Jeopard* AND endangered species 

Section 7 AND endangered


Table 11.1. Key science-related provisions within the Endangered Species Act that would benefit 

from amplification 

ESA provision Science-related 

question addressed by 

provision 

Further work needed on 

analyses pertaining to 

provision 

4(a) Listing Is there a “species”? Improved definition of 

4(a) Listing What is the species’ 

4(b) Critical habitat 

designation 

risk of extinction? 

What habitat features 

are essential to species’ 

conservation and how 

much habitat is needed 

the “distinct population 

segment/evolutionarily 

significant unit” concept 

Improved definition of 

time scales, attention to 

multiple indicators of 

risk, methods of 

estimating rates of 

reproduction of at-risk 

species 

Relationship between 

habitat quality/quantity 

and species extinction 

risk 

Further work needed 

on application of 

provision 

Agency guidance on 

how to address 

hybridization, definition 

of taxonomic 

“significance,” and 

artificially propagated 

individuals 


consideration of 

extinction risk and 

“significant portion” of 

range 


designating critical 

habitat, how to weigh 

benefits/costs; consider


7(a)(2) Federal 

consultation 

10(a)(1)(B) Habitat 

Conservation Plans 

for conservation? sequence of application 

What effect will a 

particular action have 

on species’ survival or 

recovery? 

Does an action result in 

take, and if so, how 

much?* 

4(f) Recovery planning What are the 

characteristics of a 

recovered species? 

What factors are 

limiting recovery? 

What habitat is 

essential to recovery? 

Relative importance of 

different limiting factors 

in extinction risk; how 

effects of individual 

actions relate to whole 

population/species 

impacts 

All of the above 

More-open science 

process in section 7 

consultations; guidance 

on considering 

piecemeal vs. whole life- 

cycle approach 

More public 

participation in policy 

oversight of the planning 

process 

* This question also arises in section 9 enforcement actions, which are not addressed in this chapter.


Box 11.1. Examples of the role of science in implementation of section 7 limitations on federal 

actions under the Endangered Species Act 

Dealing with scientific uncertainty. The manner in which inevitable scientific uncertainty 

is incorporated into section 7 consultations is key to using science to inform sound 

decisions. In the high-profile case of Bureau of Reclamation operations of the Klamath 

River Basin water management project, the National Research Council was brought in to 

help resolve what many characterized as a scientific dispute (Cooperman and Markle 

2003). The Council reviewed 3 analyses: (1) the Bureau’s proposed action for operating 

the project and its predicted effects on listed sucker fish and coho salmon, (2) NMFS’ and 

USFWS’ 2001 biological opinions that found that the proposal would jeopardize the 

species and offered reasonable and prudent alternatives that would avoid jeopardy (NMFS 

2001, USFWS 2001b), and (3) the Bureau’s and the Services’ 2002 revisions to their 

assessments and biological opinions on a new set of proposed actions revised based on a 

court order (NMFS 2002d, USFWS 2002). The NRC’s final report (NRC 2004) highlights 

several recommendations aimed at reducing the uncertainty in the biological conclusions 

by the Services that the Bureau’s proposed actions will not jeopardize the listed species. 

Such recommendations include (1) the USFWS and NMFS are urged to complete recovery 

plans for the 2 species that should identify how research and monitoring will support 

species recovery and facilitate identification of what actions are allowed under section 7 

and 10 consultations, (2) scientists should be allowed sufficient time to publish key 

research findings in peer-reviewed scientific journals, (3) a diverse team of “cooperators” 

should be convened for designing ecosystem-based management actions that have local


support for implementation, and (4) experiments should be conducted to test the 

effectiveness and feasibility of specific remediation strategies (NRC 2002 and 2004). 

In another example, NMFS was thwarted in an attempt to deal with uncertainties 

associated with future allocation of necessary conservation actions among sectors in the 

Columbia River Basin. The Federal Columbia River Power System is a system of 13 dams 

and reservoirs on the Columbia and Snake Rivers in Oregon, Washington, and Idaho. The 

basin is home to 12 species of endangered salmon and steelhead whose migrations are 

affected by operation of the power system. In 2000, NMFS issued a biological opinion on 

operation of the power system, recognizing that a recovery plan was not yet in place and 

that any recovery of Columbia River salmon and steelhead would require contributions 

from many sectors (NMFS 2000a). In an effort to be clear about how it was allocating the 

conservation burden, NMFS and the other federal agencies involved presented a 

conceptual recovery plan (NMFS 2000b). That plan described, for example, the 

assumptions that would have to be made about continued harvest restrictions into the 

future if the sum of impacts on listed fish was to avoid jeopardy. This opinion was 

invalidated by a district court finding that the agency improperly relied on assumed future 

actions that were not “reasonably certain to occur” (National Wildlife Federation v. NMFS, 

CR 01-640-RE [OR 2003]), leaving in question the ability of the Services to consider the 

“big picture” when section 7 biological opinions have implications for allocation of take. 

Considering actions in isolation. For many species it is the cumulative effect of many 

actions that have led to their imperilment and it is difficult for the Services in a section 7 

consultation to make the case that a single small action, when added to the many other


small actions, jeopardizes the species’ continued existence. In the case of water 

withdrawals from the Columbia River, NMFS did issue a jeopardy opinion to the Corps of 

Engineers on the basis that Columbia River flows were already below species’ needs in 

many years, the cumulative impact of withdrawals contributed to those low flows, and 

there was no mechanism in place to limit future withdrawals. Even though the withdrawal 

under consideration was very small compared to overall flows in the Columbia, NMFS 

concluded the proposed action would jeopardize Columbia River salmon and steelhead 

because of the cumulative effect of past and future withdrawals (NMFS 1998). This 

decision stirred considerable controversy in the Basin, leading Washington’s Department 

of Ecology to appeal to the NRC, asking the NRC to review the science supporting flow 

levels in the Columbia. Although the question put to the panel was framed in terms of the 

incremental risk posed by a very small incremental degradation in flows, the panel resisted 

being drawn into answering the narrow question. In its preliminary findings, the panel 

appears to support the analysis that because flows currently are inadequate, even small 

increases in water withdrawals will increase risk (NRC 2004).

Chapter 11 Science And Implementation

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