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Background  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  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,  N   e,   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.    Conclusions  Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice.

Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories