{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T10:58:15Z","timestamp":1791284295497,"version":"4.1.0"},"reference-count":106,"publisher":"Wiley","issue":"10","license":[{"start":{"date-parts":[[2019,9,13]],"date-time":"2019-09-13T00:00:00Z","timestamp":1568332800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100005783","name":"New Hampshire Sea Grant, University of New Hampshire","doi-asserted-by":"publisher","award":["NA14OAR4170083"],"award-info":[{"award-number":["NA14OAR4170083"]}],"id":[{"id":"10.13039\/100005783","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Evolutionary Applications"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic\u00a0are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome\u2010wide patterns of variation, we used low\u2010coverage sequencing to perform a region\u2010wide, whole\u2010genome analysis of fine\u2010scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole\u2010genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter\u2010 and spring\u2010spawning populations revealed highly elevated relative (<jats:italic>F<jats:sub>ST<\/jats:sub><\/jats:italic>) and absolute (<jats:italic>d<jats:sub>xy<\/jats:sub><\/jats:italic>) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain\u2010pituitary\u2010gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high\u2010resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome\u2010scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.<\/jats:p>","DOI":"10.1111\/eva.12861","type":"journal-article","created":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T19:59:41Z","timestamp":1567108781000},"page":"1971-1987","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":55,"title":["Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole\u2010genome sequencing"],"prefix":"10.1111","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4305-1719","authenticated-orcid":false,"given":"Gemma V.","family":"Clucas","sequence":"first","affiliation":[{"name":"Natural Resources and the Environment University of New Hampshire Durham NH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"R. Nicolas","family":"Lou","sequence":"additional","affiliation":[{"name":"Department of Natural Resources Cornell University Ithaca NY USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina O.","family":"Therkildsen","sequence":"additional","affiliation":[{"name":"Department of Natural Resources Cornell University Ithaca NY USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrienne I.","family":"Kovach","sequence":"additional","affiliation":[{"name":"Natural Resources and the Environment University of New Hampshire Durham NH USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,9,13]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13055"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1577\/1548-8446(2004)29[10:ACSSIT]2.0.CO;2"},{"key":"e_1_2_8_4_1","unstructured":"Andrews S.(2010).FastQC: A quality control tool for high throughput sequence data."},{"key":"e_1_2_8_5_1","volume-title":"Final draft report on stock structure of Atlantic cod in the Gulf of Maine region. 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