Subspecific origin and haplotype diversity in the laboratory mouse

• Published in: Nature genetics Vol. 43; no. 7; pp. 648 - 655
• Main Authors: Churchill, Gary A, de Villena, Fernando Pardo-Manuel, 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
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01-07-2011; Nature Publishing Group
• Subjects: 631/1647/334/1874/345; 631/208/727/728; Agriculture; Animal Genetics and Genomics; Animals; Bacteria; Biodiversity; Bioinformatics; Biological and medical sciences; Biological diversity; Biomedical and Life Sciences; Biomedical research; Biomedicine; Cancer Research; Chromosome Mapping; Chromosomes, Mammalian - genetics; Fundamental and applied biological sciences. Psychology; Gene Function; Genetic aspects; Genetic diversity; Genetic Speciation; Genetic Variation; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genomes; Genotype; Genotype & phenotype; Genotypes; Haplotypes; Haplotypes - genetics; Human Genetics; Life Sciences; Mice; Mice, Inbred Strains - classification; Mice, Inbred Strains - genetics; Molecular Sequence Data; Mus musculus; Mus musculus domesticus; Phylogeny; Physiological aspects; Polymorphism, Single Nucleotide - genetics; Populations and Evolution; Rats as laboratory animals; Species Specificity; Studies; United States; Origin; Vertebrata; Mammalia; Mouse; Haplotype; Rodentia
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.847

Fernando Pardo-Manuel de Villena, Gary Churchill and colleagues provide a high-resolution phylogenetic map of mouse inbred strains based on comparisons to wild-caught mice. They show that the genomes of classical strains are overwhelmingly derived from
Mus musculus domesticus
whereas wild-derived laboratory strains include a broad sampling of diversity from multiple subspecies with pervasive introgression. The subspecific origin, haplotype diversity and identity-by-descent map of laboratory strains can be visualized at
http://msub.csbio.unc.edu/PhylogenyTool.html
.
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
).