Differing Y chromosome versus mitochondrial DNA ancestry, phylogeography, and introgression in the house mouse

We used Y chromosome microsatellites to infer the phylogeography of the house mouse (Mus musculus; predominantly the domesticus subspecies) across western Europe, and compared this with mitochondrial (mt)DNA phylogeography for the same samples. Overall, the distributions of mtDNA and Y haplotype lineages within M. m. domesticus were discordant, probably as a result of behavioural differences between males and females. In island contexts, there is evidence for a greater number of Y chromosome introductions compared to mtDNA introductions, indicating that island populations are more resistant to incoming females than males. This contrasts with a subspecies hybrid zone, which acts as a nonpermeable barrier to the Y chromosome but is relatively porous to mtDNA. Interestingly, within Norway, where Mus musculus Y chromosomes are prevalent in the resident domesticus populations, the musculus Y is apparently of a single, recent origin, with a distribution that is likely the result of a positive selection allowing the subspecies barrier to be crossed. Overall, we confirm the utility of Y chromosome microsatellites for inferring global ancestry and phylogeography in the house mouse. © 2015 Crown copyright. Biological Journal of the Linnean Society © 2015 The Linnean Society of London, 2015, 115, 348–361.