{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T03:08:12Z","timestamp":1792292892326,"version":"4.4.0"},"reference-count":115,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T00:00:00Z","timestamp":1707868800000},"content-version":"vor","delay-in-days":13,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Evolutionary Applications"],"published-print":{"date-parts":[[2024,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Fish hatcheries are widely used to enhance fisheries and supplement declining wild populations. However, substantial evidence suggests that hatchery fish are subject to differential selection pressures compared to their wild counterparts. Domestication selection, or adaptation to the hatchery environment, poses a risk to wild populations if traits specific to success in the hatchery environment have a genetic component and there is subsequent introgression between hatchery and wild fish. Few studies have investigated domestication selection in hatcheries on a genomic level, and even fewer have done so in parallel across multiple hatchery\u2013wild population pairs. In this study, we used low\u2010coverage whole\u2010genome sequencing to investigate signals of domestication selection in three separate hatchery populations of Chinook salmon,\n                    <jats:italic>Oncorhynchus tshawytscha<\/jats:italic>\n                    , after approximately seven generations of divergence from their corresponding wild progenitor populations. We sequenced 192 individuals from populations across Southeast Alaska and estimated genotype likelihoods at over six million loci. We discovered a total of 14 outlier peaks displaying high genetic differentiation (\n                    <jats:italic>F<\/jats:italic>\n                    <jats:sub>ST<\/jats:sub>\n                    ) between hatchery\u2013wild pairs, although no peaks were shared across the three comparisons. Peaks were small (53\u2009kb on average) and often displayed elevated absolute genetic divergence (\n                    <jats:italic>D<\/jats:italic>\n                    <jats:sub>\n                      <jats:italic>xy<\/jats:italic>\n                    <\/jats:sub>\n                    ) and linkage disequilibrium, suggesting some level of domestication selection has occurred. Our study provides evidence that domestication selection can lead to genetic differences between hatchery and wild populations in only a few generations. Additionally, our data suggest that population\u2010specific adaptation to hatchery environments likely occurs through different genetic pathways, even for populations with similar standing genetic variation. These results highlight the need to collect paired genotype\u2013phenotype data to understand how domestication may be affecting fitness and to identify potential management practices that may mitigate genetic risks despite multiple pathways of domestication.\n                  <\/jats:p>","DOI":"10.1111\/eva.13656","type":"journal-article","created":{"date-parts":[[2024,2,14]],"date-time":"2024-02-14T09:54:31Z","timestamp":1707904471000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["Genomic evidence for domestication selection in three hatchery populations of Chinook salmon,\n                    <i>Oncorhynchus tshawytscha<\/i>"],"prefix":"10.1111","volume":"17","author":[{"given":"Natasha S.","family":"Howe","sequence":"first","affiliation":[{"name":"Department of Biology Texas Christian University  Fort Worth Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7391-2727","authenticated-orcid":false,"given":"Matthew C.","family":"Hale","sequence":"additional","affiliation":[{"name":"Department of Biology Texas Christian University  Fort Worth Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles D.","family":"Waters","sequence":"additional","affiliation":[{"name":"National Oceanographic and Atmospheric Administration, National Marine Fisheries Service Alaska Fisheries Science Center, Auke Bay Laboratories  Juneau Alaska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sara M.","family":"Schaal","sequence":"additional","affiliation":[{"name":"National Oceanographic and Atmospheric Administration, National Marine Fisheries Service Alaska Fisheries Science Center, Auke Bay Laboratories  Juneau Alaska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0148-4241","authenticated-orcid":false,"given":"Kyle R.","family":"Shedd","sequence":"additional","affiliation":[{"name":"Alaska Department of Fish and Game, Division of Commercial Fisheries Gene Conservation Laboratory  Anchorage Alaska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wesley A.","family":"Larson","sequence":"additional","affiliation":[{"name":"National Oceanographic and Atmospheric Administration, National Marine Fisheries Service Alaska Fisheries Science Center, Auke Bay Laboratories  Juneau Alaska USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,2,14]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/zoo.1430050212"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1095\u20108649.2003.00267.x"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msac242"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1139\/cjfas\u20102016\u20100334"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.0022\u20101112.2004.00563.x"},{"key":"e_1_2_8_7_1","volume-title":"New genetic baseline for Upper Cook Inlet Chinook salmon allows for the identification of more stocks in mixed stock fisheries: 413 loci and 67 populations","author":"Barclay A. 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Larson W. A. Shi Y. Gruenthal K. Christensen K. Dann T. Seeb J. &Seeb L.(2023).Is structural variation necessary to create islands of divergence in high gene flow species? 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D.","year":"1990"},{"key":"e_1_2_8_71_1","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.118.301336"},{"key":"e_1_2_8_72_1","volume-title":"Unuk and Chickamin Chinook Salmon Stock Status and Action Plan","author":"Meredith B. L.","year":"2022"},{"key":"e_1_2_8_73_1","doi-asserted-by":"publisher","DOI":"10.3389\/fnbeh.2018.00210"},{"key":"e_1_2_8_74_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365\u20102664.2003.00815.x"},{"key":"e_1_2_8_75_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.livprodsci.2004.11.001"},{"key":"e_1_2_8_76_1","unstructured":"Moberly S. A. &Kaill W. M.(1977).Development of a Chinook salmon enhancement program. Alaska Department of Fish and Game Sport Fish Division Federal Aid in Sport Fish Restoration Annual Performance Report 1976\u20131977 Project F\u20109\u20109(18)AFS41\u20104. Juneau AK.https:\/\/www.adfg.alaska.gov\/fedaidpdfs\/FREDF\u20109\u20109(18)AFS41\u20104.pdf"},{"key":"e_1_2_8_77_1","doi-asserted-by":"publisher","DOI":"10.1139\/cjfas\u20102012\u20100135"},{"key":"e_1_2_8_78_1","first-page":"61","volume-title":"Advances in Marine Biology","author":"Naish K. A.","year":"2007"},{"key":"e_1_2_8_79_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2020.1671"},{"key":"e_1_2_8_80_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.293.5536.1786"},{"key":"e_1_2_8_81_1","doi-asserted-by":"publisher","DOI":"10.1080\/03632415.2011.626661"},{"key":"e_1_2_8_82_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts460"},{"key":"e_1_2_8_83_1","volume-title":"The behavior and ecology of Pacific salmon and trout","author":"Quinn T. 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