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

In this study, phylogenetic analysis of relatively long sequences of mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus provides the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of Mus musculus musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4000 years ago and the Korean Peninsula ~2000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region with two different tract sizes, 1 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, providing 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, suggesting ancient introduction prior to the appearance of the South Chinese CAS in Japan. Our analyses also showed sporadic appearance of long fragments (2–5 Mb) from the west European subspecies Mus musculus domesticus, indicating contemporary stowaway introduction. Overall, multiple overseas introductions, and the time-lagged inter-subspecies genetic admixture, probably resulted in the heterogeneous state of Japanese wild mice.

本研究针对日本小家鼠（Mus musculus）的线粒体DNA（mitochondrial DNA）长序列（4225 bp）开展系统发育分析，首次证实小家鼠东南亚亚种（Mus musculus castaneus, CAS）与北亚亚种（Mus musculus musculus, MUS）分别通过快速种群扩张事件传入日本：其中东南亚亚种于约4000年前源自中国南方，北亚亚种则于约2000年前源自朝鲜半岛。针对两类不同片段长度（1 Mb与5 Mb）的染色体区域开展核DNA（nuclear DNA）单倍型结构分析，两类区域分别包含9个与6个串联排列的标记位点；分析结果显示，日本北部MUS背景基因组中存在平均长度约170 kb的CAS单倍型片段，在持续回交（backcrossing）的假设前提下，可粗略估算该片段的传入时长为815代。研究同时检测到一类仅在日本分布、频率更低且长度更短的类CAS单倍型，这暗示其传入时间早于中国南方CAS亚种在日本出现的时间。本分析还发现西欧亚种小家鼠（Mus musculus domesticus）来源的长片段（2–5 Mb）零星出现，表明该亚种通过当代偷渡式传入日本。总体而言，多次境外引入事件以及存在时间差的亚种间遗传混合（genetic admixture），可能共同造就了日本野生小鼠种群的异质性遗传状态。