Data from: Inference of selective force on house mice genomes during secondary contact in East Asia

The house mouse (Mus musculus), commensal to humans, has spread globally
via human activities, leading to secondary contact between genetically
divergent subspecies. This pattern of genetic admixture can provide
insights into the selective forces at play in this well-studied model
organism. Our analysis of 163 house mouse genomes, mainly from East Asia,
revealed substantial admixture between the subspecies castaneus and
musculus, particularly in Japan and southern China. We revealed, despite
the admixture, that all Y chromosomes in the East Asian samples belonged
to the musculus-type haplogroup, potentially explained by genomic
conflict under sex ratio distortion due to varying copy numbers of
ampliconic genes on sex chromosomes. We also investigated the influence of
natural selection on the post-hybridization of the subspecies castaneus
and musculus in Japan. Even though the genetic background of most Japanese
samples closely resembles the subspecies musculus, certain genomic regions
overrepresented the castaneus-like genetic components, particularly in
immune-related genes. Furthermore, a large genomic block containing a
vomeronasal/olfactory receptor gene cluster predominantly harbored
castaneus-type haplotypes in the Japanese samples, highlighting the
possible role of olfaction-based recognition in shaping hybrid genomes.