The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA. Resolution of the details of their evolutionary history is complicated by their relatively recent divergence, ongoing gene flow among the subspecies, and complex demographic histories. Previous studies have been limited to some extent by the number of loci surveyed and/or by the scope of the method used. Here, we apply a method (IMa3) that provides an estimate of a population phylogeny while allowing for complex histories of gene exchange. Results strongly support a topology with M. m. domesticus as sister to M. m. castaneus and M. m. musculus. In addition, we find evidence of gene flow between all pairs of subspecies, but that gene flow is most restricted from M. m. musculus into M. m. domesticus. Estimates of other key parameters are dependent on assumptions regarding generation time and mutation rate in house mice. Nevertheless, our results support previous findings that the effective population size, Ne, of M. m. castaneus is larger than that of the other two subspecies, that the three subspecies began diverging ~ 130 - 420KYA, and that the time between divergence events was short. Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.

中文翻译：

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通过整合隔离与迁移历史进一步解析家鼠（Mus musculus）系统发育。


家鼠的三个主要亚种，即小家鼠（Mus musculus castaneus）、小家鼠（Mus musculus homeus）和小家鼠（Mus musculus musculus），估计已分化约 350-500KYA。由于它们相对较新的分歧、亚种之间持续的基因流动以及复杂的人口历史，解析它们的进化历史细节变得复杂。先前的研究在一定程度上受到调查基因座数量和/或所使用方法范围的限制。在这里，我们应用了一种方法（IMa3），该方法提供了群体系统发育的估计，同时允许复杂的基因交换历史。结果强烈支持 M. m 的拓扑。家畜作为 M. m. 的妹妹。栗和 M. m.肌肉。此外，我们还发现了所有亚种对之间基因流动的证据，但这种基因流动最受M. m.的限制。肌肉变成M.m。家畜。其他关键参数的估计取决于有关家鼠世代时间和突变率的假设。尽管如此，我们的结果支持了之前的发现，即 M. m 的有效种群规模 Ne。 castaneus 比其他两个亚种大，这三个亚种开始分化〜130 - 420KYA，并且分化事件之间的时间很短。对基因组数据进行联合人口统计和系统发育分析，可以更清晰地了解家鼠的分化历史。