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  • 11
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    Online Resource
    Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application
    Elsevier BV ; 2016
    In:  Trends in Ecology & Evolution Vol. 31, No. 2 ( 2016-02), p. 81-83
    Details
    In: Trends in Ecology & Evolution, Elsevier BV, Vol. 31, No. 2 ( 2016-02), p. 81-83
    Type of Medium: Online Resource
    ISSN: 0169-5347
    URL: Article
    DOI: 10.1016/j.tree.2015.10.009
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
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  • 12
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    Genetic Variation and Structure of Chinook Salmon Life History Types in the Snake River
    Wiley ; 2007
    In:  Transactions of the American Fisheries Society Vol. 136, No. 5 ( 2007-09), p. 1252-1262
    Details
    In: Transactions of the American Fisheries Society, Wiley, Vol. 136, No. 5 ( 2007-09), p. 1252-1262
    Abstract: We evaluated 25 inland populations of Chinook salmon Oncorhynchus tshawytscha in the Snake River with 13 microsatellite loci to test for contemporary genetic differentiation at three scales: Between life history types, among regions within life history types, and among populations within regions. The genetic distance and diversity of natural Chinook salmon populations were also contrasted with those of Chinook salmon from several hatcheries. The results provide strong evidence for reproductive isolation among ocean‐ and stream‐type life histories ( F ST range, 0.080‐0.120). Regional structuring of stream‐type Chinook salmon within subbasins was also significant, as all populations were differentiated ( F ST range, 0.017‐0.045), but populations generally clustered together by region in a neighbor‐joining dendrogram. This evidence suggests high levels of philopatry to natal areas in stream‐type Chinook salmon, but ocean‐type collections were not significantly different from one another ( F ST range, 0.001‐0.002). Higher levels of genetic diversity in ocean‐type (306 total alleles; allelic richness, 16.5) than in stream‐type collections (206 total alleles; allelic richness, 12.2) may also reflect variable levels of gene flow within each life history type and colonization history. The genetic similarity of populations within regions suggests gene flow not only from transplanted stocks but also from natural dispersal that provides metapopulation structure. None of the 25 populations in this study offered significant evidence for a genetic bottleneck ( M ratio 〈 0.68) despite apparent demographic bottlenecks in several populations throughout the Snake River drainage in the last century. The combination of dispersal through metapopulation dynamics and transfers of hatchery stocks may be responsible for reducing the genetic bottleneck signal.
    Type of Medium: Online Resource
    ISSN: 0002-8487 , 1548-8659
    URL: Article
    DOI: 10.1577/T06-240.1
    Language: English
    Publisher: Wiley
    Publication Date: 2007
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    SSG: 21,3
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  • 13
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    Relative Genetic Diversity Estimates among Four Pacific Salmonids
    Wiley ; 2011
    In:  Transactions of the American Fisheries Society Vol. 140, No. 3 ( 2011-05), p. 822-828
    Details
    In: Transactions of the American Fisheries Society, Wiley, Vol. 140, No. 3 ( 2011-05), p. 822-828
    Abstract: The genetic diversity within a species is a reflection of its evolutionary past and ongoing mutation, drift, and adaptation. Species that occupy a diverse range of habitats and that have adapted for generations under selective pressures will carry a genetic imprint of that adaptation within specific functional genes. Alternatively, genetic diversity may be reduced owing to historical bottlenecks and genetic drift. In this study, genetic diversity was estimated in four species of Pacific salmon (rainbow trout, steelhead [anadromous rainbow trout] Oncorhynchus mykiss , Chinook salmon O. tshawytscha , coho salmon O. kisutch , and sockeye salmon, kokanee [lacustrine sockeye salmon] O. nerka ) using 563–608 kilo–base pairs of DNA sequence data from 32 individuals per species. Individual samples were chosen to represent the major lineages of each species across their natural ranges. The results show the highest genetic diversity estimates for rainbow trout and the lowest for sockeye salmon. Statistically significant differences were observed between the species with the highest genetic diversity (rainbow trout) and the three remaining species. Loci with the highest genetic diversity within each species are listed as potentially being influenced by balancing selection.
    Type of Medium: Online Resource
    ISSN: 0002-8487 , 1548-8659
    URL: Article
    DOI: 10.1080/00028487.2011.588129
    Language: English
    Publisher: Wiley
    Publication Date: 2011
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  • 14
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    Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout
    Wiley ; 2023
    In:  Molecular Ecology Vol. 32, No. 4 ( 2023-02), p. 800-818
    Details
    In: Molecular Ecology, Wiley, Vol. 32, No. 4 ( 2023-02), p. 800-818
    Abstract: Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout ( Oncorhynchus mykiss gairdneri ) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low‐coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids ( GREB1L , ROCK1 , SIX6 ). Genotype–environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high‐elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high‐elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v32.4
    DOI: 10.1111/mec.16810
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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    detail.hit.zdb_id: 1126687-9
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  • 15
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    Genotyping‐by‐sequencing in ecological and conservation genomics
    Wiley ; 2013
    In:  Molecular Ecology Vol. 22, No. 11 ( 2013-06), p. 2841-2847
    Details
    In: Molecular Ecology, Wiley, Vol. 22, No. 11 ( 2013-06), p. 2841-2847
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2013.22.issue-11
    DOI: 10.1111/mec.12350
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2020749-9
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  • 16
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    Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes
    Wiley ; 2014
    In:  Evolutionary Applications Vol. 7, No. 6 ( 2014-06), p. 682-701
    Details
    In: Evolutionary Applications, Wiley, Vol. 7, No. 6 ( 2014-06), p. 682-701
    Abstract: Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non‐neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the C olumbia R iver B asin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non‐neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad‐scale population structure consistent with previous studies, but fine‐scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non‐neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the C olumbia R iver region. Broad geographic patterns of neutral and non‐neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long‐term conservation of this species.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    URL: Article
    DOI: 10.1111/eva.2014.7.issue-6
    DOI: 10.1111/eva.12174
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2405496-3
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  • 17
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    Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing
    The Royal Society ; 2016
    In:  Proceedings of the Royal Society B: Biological Sciences Vol. 283, No. 1830 ( 2016-05-11), p. 20153064-
    Details
    In: Proceedings of the Royal Society B: Biological Sciences, The Royal Society, Vol. 283, No. 1830 ( 2016-05-11), p. 20153064-
    Abstract: Migration traits are presumed to be complex and to involve interaction among multiple genes. We used both univariate analyses and a multivariate random forest (RF) machine learning algorithm to conduct association mapping of 15 239 single nucleotide polymorphisms (SNPs) for adult migration-timing phenotype in steelhead ( Oncorhynchus mykiss ). Our study focused on a model natural population of steelhead that exhibits two distinct migration-timing life histories with high levels of admixture in nature. Neutral divergence was limited between fish exhibiting summer- and winter-run migration owing to high levels of interbreeding, but a univariate mixed linear model found three SNPs from a major effect gene to be significantly associated with migration timing ( p 〈 0.000005) that explained 46% of trait variation. Alignment to the annotated Salmo salar genome provided evidence that all three SNPs localize within a 46 kb region overlapping GREB1-like (an oestrogen target gene) on chromosome Ssa03. Additionally, multivariate analyses with RF identified that these three SNPs plus 15 additional SNPs explained up to 60% of trait variation. These candidate SNPs may provide the ability to predict adult migration timing of steelhead to facilitate conservation management of this species, and this study demonstrates the benefit of multivariate analyses for association studies.
    Type of Medium: Online Resource
    ISSN: 0962-8452 , 1471-2954
    URL: Article
    DOI: 10.1098/rspb.2015.3064
    Language: English
    Publisher: The Royal Society
    Publication Date: 2016
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  • 18
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    Efficient population representation with more genetic markers increases performance of a steelhead (Oncorhynchus mykiss) genetic stock identification baseline
    Wiley ; 2024
    In:  Evolutionary Applications Vol. 17, No. 2 ( 2024-02)
    Details
    In: Evolutionary Applications, Wiley, Vol. 17, No. 2 ( 2024-02)
    Abstract: Genetic stock identification (GSI) is an important fisheries management tool to identify the origin of fish harvested in mixed stock fisheries. Periodic updates of genetic baselines can improve performance via the addition of unsampled or under‐sampled populations and the inclusion of more informative markers. We used a combination of baselines to evaluate how population representation, marker number, and marker type affected the performance and accuracy of genetic stock assignments (self‐assignment, bias, and holdout group tests) for steelhead ( Oncorhynchus mykiss ) in the Snake River basin. First, we compared the performance of an existing genetic baseline with a newly developed one which had a reduced number of individuals from more populations using the same set of markers. Self‐assignment rates were significantly higher ( p 〈 0.001; +5.4%) for the older, larger baseline, bias did not differ significantly between the two, but there was a significant improvement in performance for the new baseline in holdout results ( p 〈 0.001; mean increase of 25.0%). Second, we compared the performance of the new baseline with increased numbers of genetic markers (~2x increase of single‐nucleotide polymorphisms; SNPs) for the same set of baseline individuals. In this comparison, results produced significantly higher rates of self‐assignment ( p 〈 0.001; +9.7%) but neither bias nor leave‐one‐out were significantly affected. Third, we compared 334 SNPs versus opportunistically discovered microhaplotypes from the same amplicons for the new baseline, and showed the latter produced significantly higher rates of self‐assignment ( p 〈 0.01; +2.6%), similar bias, but slightly lower holdout performance (−0.1%). Combined, we show the performance of genetic baselines can be improved via representative and efficient sampling, that increased marker number consistently improved performance over the original baseline, and that opportunistic discovery of microhaplotypes can lead to small improvements in GSI performance.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    URL: Article
    DOI: 10.1111/eva.v17.2
    DOI: 10.1111/eva.13610
    Language: English
    Publisher: Wiley
    Publication Date: 2024
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  • 19
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    Effects of Supplementation in Upper Yakima River Chinook Salmon
    Wiley ; 2022
    In:  Transactions of the American Fisheries Society Vol. 151, No. 3 ( 2022-05), p. 373-388
    Details
    In: Transactions of the American Fisheries Society, Wiley, Vol. 151, No. 3 ( 2022-05), p. 373-388
    Abstract: To promote recovery of natural salmonid populations, managers are utilizing hatchery supplementation programs to increase abundance of spawners on the spawning grounds. However, studies have provided evidence that captive breeding can result in domestication, demonstrated by lower fitness of hatchery‐origin compared with natural‐origin fish. Supplementation programs, therefore, typically use natural‐origin broodstock in an effort to minimize long‐term negative fitness impacts. Here we evaluated the upper Yakima River spring supplementation program for Chinook Salmon Oncorhynchus tshawytscha , which has broodstock comprised exclusively of unmarked fish presumed to be of natural‐origin. Using 5 years of spawner data, we tested for effects of hatchery breeding and rearing on total adult returns and their individual reproductive success when spawning naturally. Our study revealed that supplementation increased overall abundance of fish spawning naturally on the spawning grounds. However, on average, compared with natural‐origin spawners, hatchery‐origin fish had reduced reproductive success, which also translated to reduced reproductive success in three out of five return years for natural‐origin fish that spawned with hatchery‐origin fish. As expected, body length and return timing were also significant predictors of reproductive success. However, more generations of data are needed to establish the extent to which reduced reproductive success is passed on to naturally produced progeny.
    Type of Medium: Online Resource
    ISSN: 0002-8487 , 1548-8659
    URL: Issue
    URL: Article
    DOI: 10.1002/tafs.v151.3
    DOI: 10.1002/tafs.10354
    Language: English
    Publisher: Wiley
    Publication Date: 2022
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  • 20
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    Thermal adaptation and acclimation of ectotherms from differing aquatic climates
    Wiley ; 2013
    In:  Molecular Ecology Vol. 22, No. 11 ( 2013-06), p. 3090-3097
    Details
    In: Molecular Ecology, Wiley, Vol. 22, No. 11 ( 2013-06), p. 3090-3097
    Abstract: To elucidate the mechanisms of thermal adaptation and acclimation in ectothermic aquatic organisms from differing climates, we used a common‐garden experiment for thermal stress to investigate the heat shock response of redband trout ( O ncorhynchus mykiss gairdneri ) from desert and montane populations. Evidence for adaptation was observed as expression of heat shock genes in fish from the desert population was more similar to control (unstressed) fish and significantly different ( P  ≤   0.05) from those from the montane population, while F1 crosses were intermediate. High induction of heat shock proteins (Hsps) in the montane strain appeared to improve short‐term survival during first exposure to high water temperatures, but high physiological costs of Hsp production may have led to lower long‐term survival. In contrast, the desert strain had significantly lower heat shock response than the montane fish and F1 crosses, suggesting that these desert fish have evolved alternative mechanisms to deal with thermal stress that provide better balance of physiological costs. Genomewide tests of greater than 10 000 SNPs found multiple SNP s that were significantly associated with survival under thermal stress, including Hsp47 which consistently appeared as a strong candidate gene for adaption to desert climates. Candidate SNP s identified in this study are prime targets to screen more broadly across this species' range to predict the potential for adaptation under scenarios of climate change. These results demonstrate that aquatic species can evolve adaptive responses to thermal stress and provide insight for understanding how climate change may impact ectotherms.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2013.22.issue-11
    DOI: 10.1111/mec.12240
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
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