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  • 1
    Online Resource
    Online Resource
    Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing
    Wiley ; 2023
    In:  North American Journal of Fisheries Management Vol. 43, No. 4 ( 2023-08), p. 1000-1016
    Details
    In: North American Journal of Fisheries Management, Wiley, Vol. 43, No. 4 ( 2023-08), p. 1000-1016
    Abstract: Impact statement Steelhead are ecologically, culturally, and economically significant and there are steelhead populations listed as threatened under the Endangered Species Act. To assist conservation efforts, we evaluated the genetic diversity of these populations as a measure of their fitness and ability to adapt to environmental changes.
    Type of Medium: Online Resource
    ISSN: 0275-5947 , 1548-8675
    URL: Issue
    URL: Article
    DOI: 10.1002/nafm.v43.4
    DOI: 10.1002/nafm.10921
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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  • 2
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    Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms
    MDPI AG ; 2022
    In:  Diversity Vol. 14, No. 12 ( 2022-11-29), p. 1045-
    Details
    In: Diversity, MDPI AG, Vol. 14, No. 12 ( 2022-11-29), p. 1045-
    Abstract: White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.
    Type of Medium: Online Resource
    ISSN: 1424-2818
    URL: Article
    DOI: 10.3390/d14121045
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2518137-3
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  • 3
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    Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009–31 July 2009
    Wiley ; 2009
    In:  Molecular Ecology Resources Vol. 9, No. 6 ( 2009-11), p. 1460-1466
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 9, No. 6 ( 2009-11), p. 1460-1466
    Abstract: This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia , Bashania fangiana, Bashania fargesii , Chaetodon vagabundus , Colletes floralis , Coluber constrictor flaviventris , Coptotermes gestroi , Crotophaga major , Cyprinella lutrensis , Danaus plexippus , Fagus grandifolia , Falco tinnunculus , Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus , Leavenworthia alabamica , Marmosops incanus , Miichthys miiuy , Nasua nasua , Noturus exilis , Odontesthes bonariensis , Quadrula fragosa, Pinctada maxima , Pseudaletia separata , Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus , Rhagoletis cerasi , Rhinella schneideri, Sarracenia alata , Skeletonema marinoi , Sminthurus viridis , Syngnathus abaster , Uroteuthis ( Photololigo ) chinensis , Verticillium dahliae , Wasmannia auropunctata , and Zygochlamys patagonica. These loci were cross‐tested on the following species: Chaetodon baronessa , Falco columbarius , Falco eleonorae , Falco naumanni , Falco peregrinus , Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi , Podocarpus lawrencei , Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle, Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo‐atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha ; these primers and assays were cross‐tested in both species.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2009.9.issue-6
    DOI: 10.1111/j.1755-0998.2009.02759.x
    Language: English
    Publisher: Wiley
    Publication Date: 2009
    detail.hit.zdb_id: 2406833-0
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  • 4
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    Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 2 ( 2022-05-16), p. 121-144
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 2 ( 2022-05-16), p. 121-144
    Abstract: The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California’s equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esab069
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
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  • 5
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    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
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
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  • 6
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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
    detail.hit.zdb_id: 2406833-0
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  • 7
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    Selection for upper thermal tolerance in rainbow trout ( Oncorhynchus mykiss Walbaum)
    The Company of Biologists ; 2015
    In:  Journal of Experimental Biology Vol. 218, No. 5 ( 2015-03-01), p. 803-812
    Details
    In: Journal of Experimental Biology, The Company of Biologists, Vol. 218, No. 5 ( 2015-03-01), p. 803-812
    Abstract: Rainbow trout (Oncorhynchus mykiss Walbaum) in southern Western Australia have undergone passive selection for over 19 generations to survive high water temperatures. Based on the conceptual model of ‘oxygen- and capacity-limited thermal tolerance’, we measured critical thermal maximum (CTmax), maximum heart rate (fH,max) and aerobic scope to test the hypothesis that these rainbow trout can maintain aerobic scope at high temperatures through a robust cardiac performance supporting oxygen delivery. Across five family groups CTmax averaged 29.0±0.02°C. Aerobic scope was maximized at 15.8±0.3°C (Topt), while the upper pejus temperature (Tpej, set at 90% of maximum aerobic scope) was 19.9±0.3°C. Although aerobic scope decreased at temperatures above Topt, the value at 25°C remained well over 40% of the maximum. Furthermore, pharmacologically stimulated fH,max increased with temperature, reaching a peak value between 23.5±0.4 and 24.0±0.4°C (Tmax) for three family groups. The Arrhenius breakpoint temperature (TAB) for fH,max was 20.3±0.3 to 20.7±0.4°C, while the average Q10 breakpoint temperature (TQB, when the incremental Q10 & lt;1.6) for fH,max was 21.6±0.2 to 22.0±0.4°C. Collectively, fH,max progressively became less temperature dependent beyond 20°C (TAB and TQB), which coincides with the upper Tpej for aerobic scope. Although upper thermal performance indices for both aerobic scope and fH,max were compared among family groups in this population, appreciable differences were not evident. Compared with other populations of rainbow trout, the present assessment is consistent with the prediction that this strain has undergone selection and shows the ability to tolerate higher water temperatures.
    Type of Medium: Online Resource
    ISSN: 1477-9145 , 0022-0949
    URL: Article
    DOI: 10.1242/jeb.113993
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2015
    detail.hit.zdb_id: 1482461-9
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  • 8
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    Influence of landscape on resident and anadromous life history types of Oncorhynchus mykiss
    Canadian Science Publishing ; 2008
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 65, No. 6 ( 2008-06), p. 1013-1023
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 65, No. 6 ( 2008-06), p. 1013-1023
    Abstract: Landscape features can significantly influence genetic and life history diversity of rainbow/steelhead trout, Oncorhynchus mykiss . In this study, heterozygosity of 21 populations of O. mykiss from the Pacific Northwest, USA, was significantly negatively correlated with features such as elevation (P = 0.0023), upstream distance (P = 0.0129), and precipitation (P = 0.0331), and positively correlated with temperature (P = 0.0123). Mantel tests of isolation by distance were significant for anadromous populations (P = 0.007) but not for resident collections (P = 0.061), and suggested that fluvial distance was not the only significant physical variable that influenced genetic structure of life history types. Principal components interpolated to the drainage indicated that high-elevation sites were primarily occupied by the resident form, and high gradients and barriers act to limit anadromous distribution to lower elevation sites. These patterns of O. mykiss life history diversity provide insight regarding the interaction, distribution, and limitations of resident and anadromous forms of the species within this region.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/F08-025
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2008
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
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  • 9
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    Reproducibility in ecology and evolution: Minimum standards for data and code
    Wiley ; 2023
    In:  Ecology and Evolution Vol. 13, No. 5 ( 2023-05)
    Details
    In: Ecology and Evolution, Wiley, Vol. 13, No. 5 ( 2023-05)
    Abstract: We call for journals to commit to requiring open data be archived in a format that will be simple and clear for readers to understand and use. If applied consistently, these requirements will allow contributors to be acknowledged for their work through citation of open data, and facilitate scientific progress.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v13.5
    DOI: 10.1002/ece3.9961
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2635675-2
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  • 10
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    A centralized model for creating shared, standardized, microsatellite data that simplifies inter-laboratory collaboration
    Springer Science and Business Media LLC ; 2009
    In:  Conservation Genetics Vol. 10, No. 4 ( 2009-8), p. 1145-1149
    Details
    In: Conservation Genetics, Springer Science and Business Media LLC, Vol. 10, No. 4 ( 2009-8), p. 1145-1149
    Type of Medium: Online Resource
    ISSN: 1566-0621 , 1572-9737
    URL: Article
    DOI: 10.1007/s10592-008-9729-4
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2009
    detail.hit.zdb_id: 2015081-7
    SSG: 12
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