Abstract
BackgroundThe 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.ResultsResults 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.ConclusionsJoint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.
Highlights
The three main subspecies of house mice, Mus musculus castaneus, Mus musculus domesticus, and Mus musculus musculus, are estimated to have diverged ~ 350-500KYA
IMa3 analysis of 200 randomly selected autosomal loci supported a phylogeny with M. m. musculus and M. m. castaneus as sister to M. m. domesticus, with or without the inclusion of an unsampled ‘ghost’ population (Fig. 1, Table 1)
There is little evidence that an unsampled population has shaped the demographic history of these three subspecies, given that the estimates of the posterior distribution of phylogenies, as well as parameter estimates
Summary
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. House mice have grown into a model system for evolutionary genetics, fueling investigations of topics ranging from meiotic drive to adaptive introgression Studies have leveraged the increasing geographical distribution of house mice to investigate the genetics. The most numerous subspecies of house mice, Mus musculus domesticus, Mus musculus musculus, and Mus musculus castaneus, are found over different, but overlapping, geographical ranges (reviewed in [17]). The hybrid zone between M. m. domesticus and M. m. musculus has been well-studied (for review, see [20]), but M. m. domesticus in the United States harbor introgression
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