Subspecific origin and haplotype diversity in the laboratory mouse.
Chromosome-Mapping, Chromosomes-Mammalian, Genetic-Speciation, Genetic-Variation, Genotype, Haplotypes, Mice-Inbred-Strains, Molecular-Sequence-Data, Phylogeny, Polymorphism-Single-Nucleotide, Species-Specificity
Nat Genet 2011 Jul; 43(7):648-55.
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).
Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet 2011 Jul; 43(7):648-55.