Pacific Salmon, Oncorhynchus spp., and the Definition of "Species" Under the Endangered Species Act

For purposes ofthe Endangered Species Act (ESA), a "species" is defined to include "any distinct population segment of any species of vertebrate fish or wildlife which interbreeds when mature. "Federal agencies charged with carrying out the provisions of the ESA have struggled for over a decade to develop a consistent approach for interpreting the term "distinct population segment." This paper outlines such an approach and explains in some detail how it can be applied to ESA evaluations of anadromous Pacific salmonids. The following definition is proposed: A population (or group of populations) will be considered "distinct" (and hence a "species ")for purposes of the ESA if it represents an evolutionarily significant unit (ESU) of the biological species. A population must satisfy two criteria to be considered an ESU: 1) It must be substantially reproductively isolated from other conspecific population units, and 2) It must represent an important component in the evolutionary legacy of the species. Isolation does not have to be absolute, but it must be strong enough to permit evolutionarily important differences to accrue in different population units. The second criterion would be met if the population contributes substantially to the ecological/genetic diversity of the species as a whole. Insights into the extent of reproductive isolation can be provided by movements of tagged fish, natural recolonization rates observed in other populations, measurements of genetic differences between populations, and evaluations of the efficacy of natural barriers. Each of these methods has its limitations. Identification of physical barriers to genetic exchange can help define the geographic extent of distinct populations, but reliance on physical features alone can be misleading in the absence of supporting biological information. Physical tags provide information about the movements of individual fish but not the genetic consequences of migration. Furthermore, measurements ofc urrent straying or recolonization rates provide no direct information about the magnitude or consistency of such rates in the past. In this respect, data from protein electrophoresis or DNA analyses can be very useful because they reflect levels of gene flow that have occurred over evolutionary time scales. The best strategy is to use all available lines of evidence for or against reproductive isolation, recognizing the limitations of each and taking advantage of the often complementary nature of the different types of information. If available evidence indicates significant reproductive isolation, the next step is to determine whether the population in question is of substantial ecological/genetic importance to the species as a whole. In other words, if the population became extinct, would this event represent a significant loss to the ecological/genetic diversity of thes pecies? In making this determination, the following questions are relevant: 1) Is the population genetically distinct from other conspecific populations? 2) Does the population occupy unusual or distinctive habitat? 3) Does the population show evidence of unusual or distinctive adaptation to its environment? Several types of information are useful in addressing these questions. Again, the strengths and limitations of each should be kept in mind in making the evaluation. Phenotypic/life-history traits such as size, fecundity, and age and time of spawning may reflect local adaptations of evolutionary importance, but interpretation of these traits is complicated by their sensitivity to environmental conditions. Data from protein electrophoresis or DNA analyses provide valuable insight into theprocessofgenetic differentiation among populations but little direct information regarding the extent of adaptive genetic differences. Habitat differences suggest the possibility for local adaptations but do not prove that such adaptations exist. The framework suggested here provides a focal point for accomplishing the majorgoal of the Act-to conserve the genetic diversity of species and the ecosystems they inhabit. At the same time, it allows discretion in the listing of populations by requiring that they represent units of real evolutionary significance to the species. Further, this framework provides a means of addressing several issues of particular concern for Pacific salmon, including anadromous/nonanadromous population segments, differences in run-timing, groups of populations, introduced populations, and the role of hatchery fish

Special Issue: Evolutionary perspectives on salmonid conservation and management

This special issue of Evolutionary Applications comprises 15 papers that illustrate how evolutionary principles can inform the conservation and management of salmonid fishes. Several papers address the past evolutionary history of salmonids to gain insights into their likely plastic and genetic responses to future environmental change. The remaining papers consider potential evolutionary responses to climate warming, biological invasions, artificial propagation, habitat alteration, and harvesting. All of these papers consider how such influences might alter selective regimes, which should then favour plastic or genetic responses. Some of the papers then go on to document such responses, at least some of which are genetically based and adaptive. Despite the different approaches and target species, all of the papers argue for the importance of evolutionary considerations in the conservation and management of salmonids

Preserving Nature

To consider the broader environmental significance of protecting species at risk of extinction, we must first consider the roles or functions that species fulfill in nature. Although nature has many definitions, here we define it to mean the end product of ecological and evolutionary processes. That is, within ahabitat, region, or biosphere, the condition of the soil, water, air, and biota reßects the outcome of physical, chemical, ecological, and evolutionary processes. We refer to this combination of abiotic and biotic conditions as nature and to the ecological and evolutionary processes that create it as natural processes. Using these definitions, we propose three approaches in which environmental actions can protect or conserve nature. The first approach is to preserve natural processes by directly managing them or providing suitable substitutions. For example, we can directly manage apolluted watershed to restore its water quality, or we can build expensive water treatment facilities to treat the water (Chichilnisky and Heal1998). The second approach is to protect nature itself, assuming that with adequate protection nature and its natural processes will persist. For example, we can designate marine protected areas that exclude human activities. The third approach is to protect the biotic components of nature that govern the environment. This approach encompasses the intent of the Endangered Species Act (ESA): to protect nature by protecting species. In this chapter, we examine the broader environmental significance of the Endangered Species Act by reviewing the roles species play in natural processes and by examining how natural processes govern our environment, how human activities modify nature, and how the Endangered Species Act can ameliorate the impacts of human activities

Preserving Nature

To consider the broader environmental significance of protecting species at risk of extinction, we must first consider the roles or functions that species fulfill in nature. Although nature has many definitions, here we define it to mean the end product of ecological and evolutionary processes. That is, within ahabitat, region, or biosphere, the condition of the soil, water, air, and biota reßects the outcome of physical, chemical, ecological, and evolutionary processes. We refer to this combination of abiotic and biotic conditions as nature and to the ecological and evolutionary processes that create it as natural processes. Using these definitions, we propose three approaches in which environmental actions can protect or conserve nature. The first approach is to preserve natural processes by directly managing them or providing suitable substitutions. For example, we can directly manage apolluted watershed to restore its water quality, or we can build expensive water treatment facilities to treat the water (Chichilnisky and Heal1998). The second approach is to protect nature itself, assuming that with adequate protection nature and its natural processes will persist. For example, we can designate marine protected areas that exclude human activities. The third approach is to protect the biotic components of nature that govern the environment. This approach encompasses the intent of the Endangered Species Act (ESA): to protect nature by protecting species. In this chapter, we examine the broader environmental significance of the Endangered Species Act by reviewing the roles species play in natural processes and by examining how natural processes govern our environment, how human activities modify nature, and how the Endangered Species Act can ameliorate the impacts of human activities

Harvest-induced evolution and effective population size

Much has been written about fishery-induced evolution (FIE) in exploited species, but relatively little attention has been paid to the consequences for one of the most important parameters in evolutionary biology-effective population size (N-e). We use a combination of simulations of Atlantic cod populations experiencing harvest, artificial manipulation of cod life tables, and analytical methods to explore how adding harvest to natural mortality affects N-e, census size (N), and the ratio N-e/N. We show that harvest-mediated reductions in N-e are due entirely to reductions in recruitment, because increasing adult mortality actually increases the N-e/N ratio. This means that proportional reductions in abundance caused by harvest represent an upper limit to the proportional reductions in N-e, and that in some cases N-e can even increase with increased harvest. This result is a quite general consequence of increased adult mortality and does not depend on harvest selectivity or FIE, although both of these influence the results in a quantitative way. In scenarios that allowed evolution, N-e recovered quickly after harvest ended and remained higher than in the preharvest population for well over a century, which indicates that evolution can help provide a long-term buffer against loss of genetic variability.Peer reviewe

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Effective population size (Ne) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of Ne is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population’s current and future viability. Nevertheless, compared with ecological and demographic parameters, Ne has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved Ne estimation; however, some obstacles remain for the practical application of Ne estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of Ne over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary Ne estimates and suggest that different sampling designs can be combined to compare largely independent measures of Ne for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary Ne and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating Ne by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating Ne estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in Ne from hatchery-based population supplementation

Time to Evolve? Potential Evolutionary Responses of Fraser River Sockeye Salmon to Climate Change and Effects on Persistence

Evolutionary adaptation affects demographic resilience to climate change but few studies have attempted to project changes in selective pressures or quantify impacts of trait responses on population dynamics and extinction risk. We used a novel individual-based model to explore potential evolutionary changes in migration timing and the consequences for population persistence in sockeye salmon Oncorhynchus nerka in the Fraser River, Canada, under scenarios of future climate warming. Adult sockeye salmon are highly sensitive to increases in water temperature during their arduous upriver migration, raising concerns about the fate of these ecologically, culturally, and commercially important fish in a warmer future. Our results suggest that evolution of upriver migration timing could allow these salmon to avoid increasingly frequent stressful temperatures, with the odds of population persistence increasing in proportion to the trait heritability and phenotypic variance. With a simulated 2°C increase in average summer river temperatures by 2100, adult migration timing from the ocean to the river advanced by ∼10 days when the heritability was 0.5, while the risk of quasi-extinction was only 17% of that faced by populations with zero evolutionary potential (i.e., heritability fixed at zero). The rates of evolution required to maintain persistence under simulated scenarios of moderate to rapid warming are plausible based on estimated heritabilities and rates of microevolution of timing traits in salmon and related species, although further empirical work is required to assess potential genetic and ecophysiological constraints on phenological adaptation. These results highlight the benefits to salmon management of maintaining evolutionary potential within populations, in addition to conserving key habitats and minimizing additional stressors where possible, as a means to build resilience to ongoing climate change. More generally, they demonstrate the importance and feasibility of considering evolutionary processes, in addition to ecology and demography, when projecting population responses to environmental change

Understanding and Estimating Effective Population Size for Practical Application in Marine Species Management

Effective population size (Ne) determines the strength of genetic drift in a population and has long been recognized as an important parameter for evaluating conservation status and threats to genetic health of populations. Specifically, an estimate of Ne is crucial to management because it integrates genetic effects with the life history of the species, allowing for predictions of a population’s current and future viability. Nevertheless, compared with ecological and demographic parameters, Ne has had limited influence on species management, beyond its application in very small populations. Recent developments have substantially improved Ne estimation; however, some obstacles remain for the practical application of Ne estimates. For example, the need to define the spatial and temporal scale of measurement makes the concept complex and sometimes difficult to interpret. We reviewed approaches to estimation of Ne over both long-term and contemporary time frames, clarifying their interpretations with respect to local populations and the global metapopulation. We describe multiple experimental factors affecting robustness of contemporary Ne estimates and suggest that different sampling designs can be combined to compare largely independent measures of Ne for improved confidence in the result. Large populations with moderate gene flow pose the greatest challenges to robust estimation of contemporary Ne and require careful consideration of sampling and analysis to minimize estimator bias. We emphasize the practical utility of estimating Ne by highlighting its relevance to the adaptive potential of a population and describing applications in management of marine populations, where the focus is not always on critically endangered populations. Two cases discussed include the mechanisms generating Ne estimates many orders of magnitude lower than census N in harvested marine fishes and the predicted reduction in Ne from hatchery-based population supplementation

Guidelines for genetic data analysis

The IWC Scientific Committee recently adopted guidelines for quality control of DNA data. Once data have been collected, the next step is to analyse the data and make inferences that are useful for addressing practical problems in conservation and management of cetaceans. This is a complex exercise, as numerous analyses are possible and users have a wide range of choices of software programs for implementing the analyses. This paper reviews the underlying issues, illustrates application of different types of genetic data analysis to two complex management problems (involving common minke whales and humpback whales), and concludes with a number of recommendations for best practices in the analysis of population genetic data. An extensive Appendix provides a detailed review and critique of most types of analyses that are used with population genetic data for cetaceans.Publisher PDFPeer reviewe