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It has been proposed that the long\u2010standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (<jats:italic>Nm<\/jats:italic>) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels,<jats:italic><jats:styled-content style=\"fixed-case\">M<\/jats:styled-content>ytilus edulis<\/jats:italic>and<jats:italic><jats:styled-content style=\"fixed-case\">M<\/jats:styled-content>.\u00a0galloprovincialis,<\/jats:italic>across a well\u2010studied mosaic hybrid zone in<jats:styled-content style=\"fixed-case\">E<\/jats:styled-content>urope and evaluated various scenarios of speciation, with or without variation in introgression rates, using an<jats:styled-content style=\"fixed-case\">A<\/jats:styled-content>pproximate<jats:styled-content style=\"fixed-case\">B<\/jats:styled-content>ayesian<jats:styled-content style=\"fixed-case\">C<\/jats:styled-content>omputation (<jats:styled-content style=\"fixed-case\">ABC<\/jats:styled-content>) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best\u2010supported scenario was a long period of allopatric isolation during the first three\u2010quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European<jats:italic><jats:styled-content style=\"fixed-case\">M<\/jats:styled-content>ytilus<\/jats:italic>hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.<\/jats:p>","DOI":"10.1111\/jeb.12425","type":"journal-article","created":{"date-parts":[[2014,6,10]],"date-time":"2014-06-10T09:53:07Z","timestamp":1402393987000},"page":"1662-1675","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":93,"title":["Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a<i><scp>M<\/scp>ytilus<\/i>hybrid zone"],"prefix":"10.1093","volume":"27","author":[{"given":"C.","family":"Roux","sequence":"first","affiliation":[{"name":"Universit\u00e9 Montpellier 2 Montpellier France"},{"name":"CNRS\u2010UMR5554 Institut des Sciences de l'Evolution Station M\u00e9diterran\u00e9enne de l'Environnement Littoral S\u00e8te France"},{"name":"Department of Ecology and Evolution University of Lausanne Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Fra\u00efsse","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Montpellier 2 Montpellier France"},{"name":"CNRS\u2010UMR5554 Institut des Sciences de l'Evolution Station M\u00e9diterran\u00e9enne de l'Environnement Littoral S\u00e8te France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V.","family":"Castric","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Lille Nord de France USTL GEPV CNRS FRE 3268 Villeneuve d'Ascq France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"X.","family":"Vekemans","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Lille Nord de France USTL GEPV CNRS FRE 3268 Villeneuve d'Ascq France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G. 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