Introgression patterns between house mouse subspecies and species reveal genomic windows of frequent exchange

Based on whole genome sequencing data, we have studied the patterns of introgression in a phylogenetically well defined set of populations, sub-species and species of mice (Mus m. domesticus, Mus m. musculus, Mus m. castaneus and Mus spretus). We find that many discrete genomic regions are subject to repeated and mutual introgression and exchange. The majority of these regions code for genes that are involved in parasite defense or genomic conflict. They include genes involved in adaptive immunity, such as the MHC region or antibody coding regions, but also genes involved in innate immune reactions of the epidermis. We find also clusters of KRAB zinc finger proteins that control the spread of transposable elements and genes that are involved in meiotic drive. These findings suggest that even well separated populations and species maintain the capacity to exchange genetic material in a special set of evolutionary active genes.