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  • 1
    Online Resource
    Online Resource
    A validation of parentage-based tagging using hatchery steelhead in the Snake River basin
    Canadian Science Publishing ; 2013
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 70, No. 7 ( 2013-07), p. 1046-1054
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 70, No. 7 ( 2013-07), p. 1046-1054
    Abstract: Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs. We also demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of parentage-based research and management questions.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/cjfas-2012-0451
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2013
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  • 2
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    Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon ( Thaleichthys pacificus , Osmeridae), an anadromous Pacific smelt
    Wiley ; 2015
    In:  Molecular Ecology Resources Vol. 15, No. 6 ( 2015-11), p. 1421-1434
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 15, No. 6 ( 2015-11), p. 1421-1434
    Abstract: Twelve eulachon ( Thaleichthys pacificus , Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction‐site‐associated DNA ( RAD ) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single‐nucleotide polymorphisms ( SNP s) were discovered across the genome, with 193 putatively adaptive SNP s as determined by F ST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNP s were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNP s or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers ( SNP s or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size ( N e ) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNP s provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNP s that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome‐wide neutral and adaptive genetic variation for the applications of conservation and management.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2015.15.issue-6
    DOI: 10.1111/1755-0998.12400
    Language: English
    Publisher: Wiley
    Publication Date: 2015
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  • 3
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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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  • 4
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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
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  • 5
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    Discovery and characterization of novel genetic markers for use in the management of L ahontan cutthroat trout ( O ncorhynchus clarkii henshawi )
    Wiley ; 2013
    In:  Molecular Ecology Resources Vol. 13, No. 2 ( 2013-03), p. 276-288
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 13, No. 2 ( 2013-03), p. 276-288
    Abstract: The Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) is threatened by habitat destruction, over‐harvest and hybridization with nonnative trout. Currently, three Geographic Management Units ( GMU s) are recognized within the taxon. Here, we describe a suite of 68 single‐nucleotide polymorphism ( SNP ) genetic markers for use in the study and management of Lahontan cutthroat trout and a closely related subspecies, the Paiute cutthroat trout ( O. c. seleneris ). These include markers variable within the two subspecies ( n  = 35), diagnostic for the two subspecies ( n  = 23) and diagnostic for Yellowstone cutthroat trout ( O. c. bouvieri ) and other closely related subspecies ( n  = 10). Sixty‐three markers were discovered by Sanger sequencing of 171 EST loci in an ascertainment panel including Lahontan cutthroat trout from four populations representing all GMU s. Five markers were identified in a secondary sequencing effort with a single population of Lahontan cutthroat trout. TaqMan assays were validated on six Lahontan cutthroat trout populations and a diverse panel of other trout. Over 90% of the markers variable in Lahontan cutthroat trout were polymorphic in at least two populations, and 66% were variable within all three GMU s. All Lahontan diagnostic markers were also fixed for the Lahontan allele in Paiute cutthroat trout. Most of the Yellowstone diagnostic markers can also be used for this purpose in other cutthroat trout subspecies. This is the first set of SNP markers to be developed for Lahontan cutthroat trout, and will be an important tool for conservation and management.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2013.13.issue-2
    DOI: 10.1111/1755-0998.12040
    Language: English
    Publisher: Wiley
    Publication Date: 2013
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  • 6
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    Identification of Novel Single‐Nucleotide Polymorphisms in Chinook Salmon and Variation among Life History Types
    Wiley ; 2008
    In:  Transactions of the American Fisheries Society Vol. 137, No. 1 ( 2008-01), p. 96-106
    Details
    In: Transactions of the American Fisheries Society, Wiley, Vol. 137, No. 1 ( 2008-01), p. 96-106
    Abstract: Single‐nucleotide polymorphisms (SNPs) are simple base substitutions or small indels in otherwise conserved regions of nuclear or mitochondrial DNA. Assays detecting these genetic markers have been a powerful tool for conserving and managing fish populations. In nonmodel species, however, available DNA sequence data are limited and inventive techniques must be employed in screening for SNPs. In this study, we used expressed sequence tags from rainbow trout Oncorhynchus mykiss to design primers for amplification of genomic DNA fragments from Chinook salmon O. tshawytscha . The regions flanking the repeat sequence of published microsatellite loci in Chinook salmon were also chosen to examine nucleotide variation. Thirty‐two individuals representing the majority of the species' range from Russia to California were sequenced at 19 loci to identify SNPs. We discovered 58 polymorphisms during the screen and chose 13 for development into 5′ exonuclease assays (TaqMan assays). The genotypes from the TaqMan assays were compared with sequence data from individuals from the ascertainment panel to confirm proper allele designations. To evaluate the power of these markers to differentiate populations and life history types, we typed 91 individuals representing the major lineages of Chinook salmon with 11 validated assays. Significant allele frequency differences were observed among life history types of Chinook salmon at seven SNP loci, demonstrating the power of these markers to differentiate lineages.
    Type of Medium: Online Resource
    ISSN: 0002-8487 , 1548-8659
    URL: Article
    DOI: 10.1577/T07-011.1
    Language: English
    Publisher: Wiley
    Publication Date: 2008
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  • 7
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    Genome‐wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout
    Wiley ; 2013
    In:  Molecular Ecology Vol. 22, No. 11 ( 2013-06), p. 3061-3076
    Details
    In: Molecular Ecology, Wiley, Vol. 22, No. 11 ( 2013-06), p. 3061-3076
    Abstract: Little is known of the genetic basis of migration despite the ecological benefits migratory species provide to their communities and their rapid global decline due to anthropogenic disturbances in recent years. Using next‐generation sequencing of restriction‐site‐associated DNA ( RAD ) tags, we genotyped thousands of single nucleotide polymorphisms ( SNP s) in two wild populations of migratory steelhead and resident rainbow trout ( O ncorhynchus mykiss ) from the P acific N orthwest of the U nited S tates. One population maintains a connection to the sea, whereas the other population has been sequestered from its access to the ocean for more than 50 years by a hydropower dam. Here we performed a genome‐wide association study to identify 504 RAD SNP markers from several genetic regions that were associated with the propensity to migrate both within and between the populations. Our results corroborate those in previous quantitative trait loci studies and provide evidence for additional loci associated with this complex migratory life history. Our results suggest a complex multi‐genic basis with several loci of small effect distributed throughout the genome contributing to migration in this species. We also determined that despite being sequestered for decades, the landlocked population continues to harbour genetic variation associated with a migratory life history and ATP ase activity. Furthermore, we demonstrate the utility of genotyping‐by‐sequencing and how RAD ‐tag SNP data can be readily compared between studies to investigate migration within this species.
    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.12082
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
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  • 8
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    Population genomics of P acific lamprey: adaptive variation in a highly dispersive species
    Wiley ; 2013
    In:  Molecular Ecology Vol. 22, No. 11 ( 2013-06), p. 2898-2916
    Details
    In: Molecular Ecology, Wiley, Vol. 22, No. 11 ( 2013-06), p. 2898-2916
    Abstract: Unlike most anadromous fishes that have evolved strict homing behaviour, P acific lamprey ( E ntosphenus tridentatus ) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within‐region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site–associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism ( SNP ) loci for 518 individuals collected across a broad geographical area including B ritish C olumbia, W ashington, O regon and C alifornia. A subset of putatively neutral markers ( N =  4068) identified a significant amount of variation among three broad populations: northern B ritish C olumbia, C olumbia R iver/southern coast and ‘dwarf’ adults ( F CT  = 0.02, P  ≪ 0.001). Additionally, 162 SNP s were identified as adaptive through outlier tests, and inclusion of these markers revealed a signal of adaptive variation related to geography and life history. The majority of the 162 adaptive SNP s were not independent and formed four groups of linked loci. Analyses with matsam software found that 42 of these outlier SNP s were significantly associated with geography, run timing and dwarf life history, and 27 of these 42 SNP s aligned with known genes or highly conserved genomic regions using the genome browser available for sea lamprey. This study provides both neutral and adaptive context for observed genetic divergence among collections and thus reconciles previous findings of population genetic heterogeneity within a species that displays extensive gene flow.
    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.12150
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 2020749-9
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  • 9
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    Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing
    Wiley ; 2015
    In:  Molecular Ecology Resources Vol. 15, No. 4 ( 2015-07), p. 855-867
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 15, No. 4 ( 2015-07), p. 855-867
    Abstract: Genotyping‐in‐Thousands by sequencing ( GT ‐seq) is a method that uses next‐generation sequencing of multiplexed PCR products to generate genotypes from relatively small panels (50–500) of targeted single‐nucleotide polymorphisms ( SNP s) for thousands of individuals in a single Illumina HiSeq lane. This method uses only unlabelled oligos and PCR master mix in two thermal cycling steps for amplification of targeted SNP loci. During this process, sequencing adapters and dual barcode sequence tags are incorporated into the amplicons enabling thousands of individuals to be pooled into a single sequencing library. Post sequencing, reads from individual samples are split into individual files using their unique combination of barcode sequences. Genotyping is performed with a simple perl script which counts amplicon‐specific sequences for each allele, and allele ratios are used to determine the genotypes. We demonstrate this technique by genotyping 2068 individual steelhead trout ( Oncorhynchus mykiss ) samples with a set of 192 SNP markers in a single library sequenced in a single Illumina HiSeq lane. Genotype data were 99.9% concordant to previously collected TaqMan ™ genotypes at the same 192 loci, but call rates were slightly lower with GT ‐seq (96.4%) relative to Taqman (99.0%). Of the 192 SNP s, 187 were genotyped in ≥90% of the individual samples and only 3 SNP s were genotyped in 〈 70% of samples. This study demonstrates amplicon sequencing with GT ‐seq greatly reduces the cost of genotyping hundreds of targeted SNP s relative to existing methods by utilizing a simple library preparation method and massive efficiency of scale.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2015.15.issue-4
    DOI: 10.1111/1755-0998.12357
    Language: English
    Publisher: Wiley
    Publication Date: 2015
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  • 10
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    Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River
    Wiley ; 2017
    In:  Ecology and Evolution Vol. 7, No. 23 ( 2017-12), p. 10350-10360
    Details
    In: Ecology and Evolution, Wiley, Vol. 7, No. 23 ( 2017-12), p. 10350-10360
    Abstract: Coho salmon were extirpated in the mid‐20th century from the interior reaches of the Columbia River but were reintroduced with relatively abundant source stocks from the lower Columbia River near the Pacific coast. Reintroduction of Coho salmon to the interior Columbia River (Wenatchee River) using lower river stocks placed selective pressures on the new colonizers due to substantial differences with their original habitat such as migration distance and navigation of six additional hydropower dams. We used restriction site‐associated DNA sequencing ( RAD ‐seq) to genotype 5,392 SNP s in reintroduced Coho salmon in the Wenatchee River over four generations to test for signals of temporal structure and adaptive variation. Temporal genetic structure among the three broodlines of reintroduced fish was evident among the initial return years (2000, 2001, and 2002) and their descendants, which indicated levels of reproductive isolation among broodlines. Signals of adaptive variation were detected from multiple outlier tests and identified candidate genes for further study. This study illustrated that genetic variation and structure of reintroduced populations are likely to reflect source stocks for multiple generations but may shift over time once established in nature.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.2017.7.issue-23
    DOI: 10.1002/ece3.3492
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2635675-2
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