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Eagle, ID, United States

Stark E.J.,Nampa Fisheries Research | Kozfkay C.C.,Eagle Fish Genetics Laboratory
Reviews in Fish Biology and Fisheries | Year: 2014

Captive rearing is a conservation strategy where juveniles are collected from the natural environment, reared to maturity in a hatchery environment, and then released back into the natural environment at maturity for volitional spawning. This strategy has been used to produce adult outplants for stock enhancement where natural escapement is poor or capture of adults is difficult. In both Idaho (Chinook salmon, Oncorhynchus tshawytscha) and Maine (Atlantic salmon, Salmo salar), captive rearing programs have been initiated as an experimental strategy to prevent cohort collapse and conserve genetic integrity of select depressed populations. In this paper, we provide an overview of these programs and describe some of the methods used to evaluate the effectiveness of this approach. Behaviors such as habitat selection, courting, and spawn timing were monitored. Data collected for both programs indicate that the captive fish display similar behaviors as their wild conspecifics in terms of habitat selection and spawning, although there were some differences in spawn timing. Evaluations of egg and fry production also indicate that captive-reared adults are successfully spawning and producing offspring. Each program is still waiting on final evaluations of reproductive success through genetic analyses of returning adults, but results so far indicate that this could be an additional captive propagation strategy for depressed populations. © 2014 Springer International Publishing Switzerland.

Ardren W.R.,U.S. Fish and Wildlife Service | DeHaan P.W.,U.S. Fish and Wildlife Service | Smith C.T.,U.S. Fish and Wildlife Service | Taylor E.B.,University of British Columbia | And 8 more authors.
Transactions of the American Fisheries Society | Year: 2011

The bull trout Salvelinus confluentus is a broadly distributed char in northwestern North America that has undergone significant population declines. This species is currently protected under the Endangered Species Act across its range in the coterminous United States. To clarify patterns of phylogenetic structure and to assist with identification of conservation units, we examined genetic variation within and among 75 representative bull trout populations sampled throughout the USA. Genealogies from a 520-base-pair portion of the mitochondrially encoded NADH dehydrogenase 1 gene (ND-1) revealed reciprocal monophyly between coastal and interior lineages that differed by 1.34% in DNA sequence. The geographic distribution of the two lineages was divided by the Cascade Mountains, a pattern that likely reflects postglacial dispersal from separate glacial refugia. Analysis of microsatellite variation revealed that 76% of populations had an estimated effective population size less than 50 and indicated high divergence among populations caused by genetic drift (average genetic differentiation index FST = 0.32) and mutation (average genetic differentiation index RST = 0.58). Concordant phylogeographic and phylogenetic patterns observed with microsatellite and mitochondrial DNA analyses provided evidence for two to six bull trout lineages that largely reflect historic patterns of gene flow and isolation among populations. These lineages can be further subdivided into finer-scale units due to the extremely low dispersal among populations and small effective population sizes. In fact, Bayesian analysis of population structure identified an optimal solution of 69 genetically different groups. Based on these results, we believe that conservation efforts should ideally be focused on the 118 bull trout core areas originally identified in the draft Endangered Species Act recovery plan, which are broadly defined as metapopulations.We provide examples of how other data, such as unique life history forms and ecological setting, can be used in combination with our genetic results to refine the U.S. Fish andWildlife Service's hierarchical conservation strategy for bull trout. © American Fisheries Society 2011.

Narum S.R.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Kozfkay C.C.,Eagle Fish Genetics Laboratory | Meyer K.A.,414 East Locust Lane
Molecular Ecology | Year: 2010

Natural populations that evolve under extreme climates are likely to diverge because of selection in local environments. To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss gairdneri) occupying differing climate regimes, we used a limited genome scan approach to test for candidate markers under selection in populations occurring in desert and montane streams. An environmental approach to identifying outlier loci, spatial analysis method and linear regression of minor allele frequency with environmental variables revealed six candidate markers (P < 0.01). Putatively neutral markers identified high genetic differentiation among desert populations relative to montane sites, likely due to intermittent flows in desert streams. Additionally, populations exhibited a highly significant pattern of isolation by temperature (P < 0.0001) and those adapted to the same environment had similar allele frequencies across candidate markers, indicating selection for differing climates. These results imply that many genes are involved in the adaptation of redband trout to differing environments, and selection acts to reinforce localization. The potential to predict genetic adaptability of individuals and populations to changing environmental conditions may have profound implications for species that face extensive anthropogenic disturbances. © 2010 Blackwell Publishing Ltd.

Ackerman M.W.,University of Washington | Ackerman M.W.,Eagle Fish Genetics Laboratory | Habicht C.,Alaska Department of Fish and Game | Seeb L.W.,University of Washington
Transactions of the American Fisheries Society | Year: 2011

Genetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from singlenucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single-nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south-central Alaska. We evaluated the information content of the four nonneutral loci for use in genetic stock identification and assessed their ability to improve the accuracy and precision of composition estimates. The average measure of informativeness for assignment (In) for neutral loci was 0.019, and the average In for nonneutral loci was 0.064. A simulation-based approach indicated that the addition of the nonneutral SNP loci to a neutral marker panel provided significantly higher resolution in the assignment of individuals to their populations of origin than would have been accomplished by adding an equal number of neutral loci. Nonneutral SNP loci improved the ability to identify the origin of individual fish and to estimate the composition of Pacific salmon populations in mixed fisheries. © American Fisheries Society 2011.

Haig S.M.,U.S. Geological Survey | Miller M.P.,U.S. Geological Survey | Bellinger R.,University of Hawaii at Hilo | Draheim H.M.,Eagle Fish Genetics Laboratory | And 2 more authors.
Evolutionary Applications | Year: 2016

The field of conservation genetics, when properly implemented, is a constant juggling act integrating molecular genetics, ecology, and demography with applied aspects concerning managing declining species or implementing conservation laws and policies. This young field has grown substantially since the 1980s following the development of polymerase chain reaction and now into the genomics era. Our laboratory has 'grown up' with the field, having worked on these issues for over three decades. Our multidisciplinary approach entails understanding the behavior and ecology of species as well as the underlying processes that contribute to genetic viability. Taking this holistic approach provides a comprehensive understanding of factors that influence species persistence and evolutionary potential while considering annual challenges that occur throughout their life cycle. As a federal laboratory, we are often addressing the needs of the U.S. Fish and Wildlife Service in their efforts to list, de-list, or recover species. Nevertheless, there remains an overall communication gap between research geneticists and biologists who are charged with implementing their results. Therefore, we outline the need for a National Center for Small Population Biology to ameliorate this problem and provide organizations charged with making status decisions firmer ground from which to make their critical decisions. © 2016 John Wiley & Sons Ltd.

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