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Here, we investigated the effects of gene flow on divergence and adaptation in the <jats:italic>Mytilus<\/jats:italic> complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genomewide patterns of introgression in <jats:italic>Mytilus<\/jats:italic> and that gene flow between different species, with contiguous ranges, explained up to half of the intraspecific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, for example Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganization of genetic backgrounds, needs to be more widely considered to make better sense of genome scans.<\/jats:p>","DOI":"10.1111\/mec.13299","type":"journal-article","created":{"date-parts":[[2015,7,3]],"date-time":"2015-07-03T16:02:17Z","timestamp":1435939337000},"page":"269-286","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":118,"title":["Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels"],"prefix":"10.1111","volume":"25","author":[{"given":"Christelle","family":"Fra\u00efsse","sequence":"first","affiliation":[{"name":"Institut des Sciences de l'Evolution (UMR 5554) CNRS \u2013 Universit\u00e9 Montpellier Place Eug\u00e8ne Bataillon 34095 Montpellier France"},{"name":"Station Marine Universit\u00e9 Montpellier 2 rue des Chantiers 34200 S\u00e8te France"},{"name":"Department of Genetics University of Cambridge Downing Street CB2 3EH Cambridge UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khalid","family":"Belkhir","sequence":"additional","affiliation":[{"name":"Institut des Sciences de l'Evolution (UMR 5554) CNRS \u2013 Universit\u00e9 Montpellier Place Eug\u00e8ne Bataillon 34095 Montpellier France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John J.","family":"Welch","sequence":"additional","affiliation":[{"name":"Department of Genetics University of Cambridge Downing Street CB2 3EH Cambridge UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1856-3197","authenticated-orcid":false,"given":"Nicolas","family":"Bierne","sequence":"additional","affiliation":[{"name":"Institut des Sciences de l'Evolution (UMR 5554) CNRS \u2013 Universit\u00e9 Montpellier Place Eug\u00e8ne Bataillon 34095 Montpellier 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