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We used pooled whole genome sequencing, gene annotation, and environmental covariates to evaluate patterns of genomic differentiation and to investigate mechanisms responsible for divergence among proximate Pacific cod (<jats:italic>Gadus macrocephalus<\/jats:italic>) populations from the Bering Sea and Aleutian Islands and more distant Washington Coast cod. Samples were taken from eight spawning locations, three of which were replicated to estimate consistency in allele frequency estimation. A kernel smoothing moving weighted average of relative divergence (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>) identified 11 genomic islands of differentiation between the Aleutian Islands and Bering Sea samples. In some islands of differentiation, there was also elevated absolute divergence (<jats:italic>d<\/jats:italic><jats:sub>XY<\/jats:sub>) and evidence for selection, despite proximity and potential for gene flow. Similar levels of absolute divergence (<jats:italic>d<\/jats:italic><jats:sub>XY<\/jats:sub>) but roughly double the relative divergence (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>) were observed between the distant Bering Sea and Washington Coast samples. Islands of differentiation were much smaller than the four large inversions among Atlantic cod ecotypes. Islands of differentiation between the Bering Sea and Aleutian Island were associated with SNPs from five vision system genes, which can be associated with feeding, predator avoidance, orientation, and socialization. We hypothesize that islands of differentiation between Pacific cod from the Bering Sea and Aleutian Islands provide evidence for adaptive differentiation despite gene flow in this commercially important marine species.<\/jats:p>","DOI":"10.1111\/eva.13488","type":"journal-article","created":{"date-parts":[[2022,10,13]],"date-time":"2022-10-13T17:09:45Z","timestamp":1665680985000},"page":"1907-1924","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genomic differentiation in Pacific cod using<scp>P<\/scp>ool\u2010<scp>S<\/scp>eq"],"prefix":"10.1111","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5177-276X","authenticated-orcid":false,"given":"Ingrid","family":"Spies","sequence":"first","affiliation":[{"name":"Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center Seattle Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn","family":"Tarpey","sequence":"additional","affiliation":[{"name":"School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trond","family":"Kristiansen","sequence":"additional","affiliation":[{"name":"Farallon Institute, Inc. 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