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，首次证实小家鼠南亚亚种（Mus musculus castaneus, CAS）与小家鼠北亚亚种（Mus musculus musculus, MUS）均通过快速种群扩张事件迁入日本：二者分别于约4000年前从中国南方、约2000年前从朝鲜半岛抵达日本。针对两段长度分别为1 Mb与5 Mb的染色体区域（分别包含9个和6个串联排列的分子标记），本研究开展了核DNA单倍型（haplotype）结构分析。结果显示，日本北部MUS背景基因组中CAS单倍型的平均片段长度约为170 kb；若假设持续回交（backcrossing），可粗略估算该片段的传入时长约为815代。研究还检测到一类日本特有的、频率更低且长度更短的类CAS单倍型，这提示在中国南方CAS亚种迁入日本之前，已有古老的外来引入事件。此外，本研究观察到西欧亚种小家鼠家鼠亚种（Mus musculus domesticus）的长片段（2–5 Mb）零星出现，表明存在当代偷渡式引入事件。综上，多次海外迁入事件与亚种间遗传混合的时间滞后效应，共同造就了日本野生小家鼠的异质性遗传状态。