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Atlantic salmon (<jats:italic>Salmo salar<\/jats:italic>) in the western and eastern Atlantic diverged &gt;600,000\u00a0years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans\u2010Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans\u2010Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans\u2010Atlantic differences in rearrangements: Ssa01\/Ssa23 translocation and Ssa08\/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01\/Ssa23 showing high European introgression (&gt;50%) in northern populations indicative of post\u2010glacial trans\u2010Atlantic secondary contact, contrasting with low European ancestry genome\u2010wide (3%). Ssa08\/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large\u2010scale intraspecific variation in genomic architecture of northern species.<\/jats:p>","DOI":"10.1111\/mec.15065","type":"journal-article","created":{"date-parts":[[2019,3,2]],"date-time":"2019-03-02T12:25:19Z","timestamp":1551529519000},"page":"2074-2087","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["Chromosome polymorphisms track trans\u2010Atlantic divergence and secondary contact in Atlantic salmon"],"prefix":"10.1111","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3569-8299","authenticated-orcid":false,"given":"Sarah J.","family":"Lehnert","sequence":"first","affiliation":[{"name":"Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Bentzen","sequence":"additional","affiliation":[{"name":"Biology Department Dalhousie University Halifax Nova Scotia Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony","family":"Kess","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sigbj\u00f8rn","family":"Lien","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences Norwegian University of Life Sciences \u00c5s Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John B.","family":"Horne","sequence":"additional","affiliation":[{"name":"Gulf Coast Research Laboratory University of Southern Mississippi Ocean Springs Mississippi USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Cl\u00e9ment","sequence":"additional","affiliation":[{"name":"Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's Newfoundland Canada"},{"name":"Labrador Institute Memorial University of Newfoundland Happy Valley\u2010Goose Bay Newfoundland Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian R.","family":"Bradbury","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada"},{"name":"Biology Department Dalhousie University Halifax Nova Scotia Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,4,29]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1093\/jhered\/esv015"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4684-4652-4_1"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature16062"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-294x.1998.00319.x"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0070651"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1139\/g59-023"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.fishres.2015.10.009"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/mec.13395"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1139\/cjfas-2013-0240"},{"key":"e_1_2_9_11_1","doi-asserted-by":"publisher","DOI":"10.1111\/eva.12026"},{"key":"e_1_2_9_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-432"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.3378\/027.084.0401"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2009.01.005"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv073"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-13-28"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10592-012-0400-8"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00122-008-0801-8"},{"key":"e_1_2_9_19_1","volume-title":"Genetics and the origin of species","author":"Dobzhansky T. 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