Subspecific origin and haplotype diversity in the laboratory mouse.

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Chromosome-Mapping, Chromosomes-Mammalian, Genetic-Speciation, Genetic-Variation, Genotype, Haplotypes, Mice-Inbred-Strains, Molecular-Sequence-Data, Phylogeny, Polymorphism-Single-Nucleotide, Species-Specificity

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Nat Genet 2011 Jul; 43(7):648-55.

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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).