title: Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels.
abstract: Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus 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 Mytilus 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.
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS - Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.|Station Marine, Université Montpellier, 2 rue des Chantiers, 34200, Sète, France.|Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK.
authors.forename: Christelle
authors.initials: C
authors.lastname: Fraïsse
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS - Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
authors.forename: Khalid
authors.initials: K
authors.lastname: Belkhir
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, CB2 3EH, Cambridge, UK.
authors.forename: John J
authors.initials: JJ
authors.lastname: Welch
authors.affiliation: Institut des Sciences de l'Evolution (UMR 5554), CNRS - Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.|Station Marine, Université Montpellier, 2 rue des Chantiers, 34200, Sète, France.
authors.forename: Nicolas
authors.identifier: 0000-0003-1856-3197
authors.initials: N
authors.lastname: Bierne
mesh_terms: D000483:Alleles; D000818:Animals; D020451:Contig Mapping; D051456:Gene Flow; D049810:Genetic Speciation; D005828:Genetics, Population; D005843:Geography; D049878:Mytilus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: BAC assembly; adaptation; genome scan; outlier loci; selection; target enrichment sequencing