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Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels.

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Fraïsse, Christelle 
Belkhir, Khalid 
Welch, John J 


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.



BAC assembly, adaptation, genome scan, outlier loci, selection, target enrichment sequencing, Alleles, Animals, Contig Mapping, Gene Flow, Genetic Speciation, Genetics, Population, Geography, Mytilus, Phylogeny, Polymorphism, Single Nucleotide, Sequence Analysis, DNA

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Mol Ecol

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This work was funded by the Agence Nationale de la Recherche (HYSEA project, ANR-12-BSV7- 0011) and the project Aquagenet (SUDOE, INTERREG IV B). This is article 2015-XXX of Institut des Sciences de l’Evolution de Montpellier.