Subspecific origin and haplotype diversity in the laboratory mouse |
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Authors: | Yang Hyuna Wang Jeremy R Didion John P Buus Ryan J Bell Timothy A Welsh Catherine E Bonhomme François Yu Alex Hon-Tsen Nachman Michael W Pialek Jaroslav Tucker Priscilla Boursot Pierre McMillan Leonard Churchill Gary A de Villena Fernando Pardo-Manuel |
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Institution: | The Jackson Laboratory, Bar Harbor, Maine, USA. |
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Abstract: | Here we provide a genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our analysis is based on the genotypes of wild-caught mice from three subspecies of Mus musculus. We show that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly Mus musculus domesticus in origin, and the remainder is mostly of Japanese origin. We generated genome-wide haplotype maps based on identity by descent from fancy mice and show that classical inbred strains have limited and non-randomly distributed genetic diversity. In contrast, wild-derived laboratory strains represent a broad sampling of diversity within M. musculus. Intersubspecific introgression is pervasive in these strains, and contamination by laboratory stocks has played a role in this process. The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs). |
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