Data from: Heterogeneous genetic makeup of the Japanese house mouse (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

Current phylogenetic analyses of relatively long sequences of mitochondrial DNA (4,225 bp) in the Japanese house mouse Mus musculus provided the first evidence that both south Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of M. m. musculus (MUS) came to Japan through rapid population expansion events, from Southern China around 4,000 years ago and the Korean Peninsula around 2,000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region with two different tract sizes, of 1 Mb and 5 Mb, consisting of nine and six tandemly arranged markers, respectively yielded a possible average fragment length of 170 kb of CAS haplotypes in the MUS background genome in northern Japan, It provided a rough estimate of its elapsed time of 815 generations under an assumption of continued backcrossing. Less frequent and shortened CAS-like haplotypes specific to Japan were detected, suggestive of ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed the sporadic appearance of long DOM fragments (2–5 Mb), indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, are likely to have resulted in the heterogeneous state of Japanese wild mice.