Further resolution of the house mouse ( Mus musculus) phylogeny by integration over isolation-with-migration histories
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(2020) 20:120
RESEARCH ARTICLE
Open Access
Further resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories Megan Phifer-Rixey1* , Bettina Harr2 and Jody Hey3
Abstract 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, 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. Conclusions: Joint demographic and phylogenetic analyses of genomic data provide a clearer picture of the history of divergence in house mice. Keywords: Speciation, Divergence, Population size, IMa3
Background The house mouse (Mus musculus) has long been a genetic model for human biology and disease (reviewed in [1–3]). House mice have also grown into a model system for evolutionary genetics, fueling investigations of topics ranging from meiotic drive to adaptive introgression (e.g. [4, 5]). In particular, studies in house mice have shed light on the process of speciation and the genetic basis of reproductive isolation (e.g. [6–14]). More recently, studies have leveraged the increasing geographical distribution of house mice to investigate the genetics * Correspondence: [email protected] 1 Department of Biology, Monmouth University, West Long Branch, NJ, USA Full list of author information is available at the end of the article
of phenotypic change and adaptation accompanying range expansion (e.g. [15, 16]). However, much of this work relies on an understanding of the evolutionary history of house mice that continues to be refined. 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]). While the subspecies can be crossed in the lab, in some cases, hybrid males are sterile or have reduced fertility (e.g., [7, 18, 19]). There is extensive evidence of hybridization between the subspeci
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