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Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (\n                    <jats:italic>Mallotus villosus<\/jats:italic>\n                    ). We first assembled a 490\u2010Mbp draft genome of\n                    <jats:italic>M.\u00a0villosus<\/jats:italic>\n                    to map our RAD sequence reads. Then, we used a large data set of genome\u2010wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8\u00a0million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large\n                    <jats:italic>\n                      N\n                      <jats:sub>e<\/jats:sub>\n                    <\/jats:italic>\n                    and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype\u2013environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.\n                  <\/jats:p>","DOI":"10.1111\/mec.15499","type":"journal-article","created":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T14:29:07Z","timestamp":1591280947000},"page":"2379-2398","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish"],"prefix":"10.1111","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3250-6295","authenticated-orcid":false,"given":"Hugo","family":"Cayuela","sequence":"first","affiliation":[{"name":"Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS) Universit\u00e9 Laval Quebec City QC 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