Local inter-species introgression is the main cause of extreme levels of intra-specific differentiation in mussels

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 genome-wide patterns of introgression in Mytilus, and that gene flow between different species, with contiguous ranges, explained up to half of the intra-specific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than ...