title: Subspecific origin and haplotype diversity in the laboratory mouse.
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).
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine, USA.
authors.forename: Hyuna
authors.initials: H
authors.lastname: Yang
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Wang
authors.forename: John P
authors.initials: JP
authors.lastname: Didion
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Buus
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Bell
authors.forename: Catherine E
authors.initials: CE
authors.lastname: Welsh
authors.forename: François
authors.initials: F
authors.lastname: Bonhomme
authors.forename: Alex Hon-Tsen
authors.initials: AH
authors.lastname: Yu
authors.forename: Michael W
authors.initials: MW
authors.lastname: Nachman
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Pialek
authors.forename: Priscilla
authors.initials: P
authors.lastname: Tucker
authors.forename: Pierre
authors.initials: P
authors.lastname: Boursot
authors.forename: Leonard
authors.initials: L
authors.lastname: McMillan
authors.forename: Gary A
authors.initials: GA
authors.lastname: Churchill
authors.forename: Fernando Pardo-Manuel
authors.initials: FP
authors.lastname: de Villena
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D033481:Chromosomes, Mammalian / Q000235:genetics*; D049810:Genetic Speciation; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D051379:Mice; D008815:Mice, Inbred Strains / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013045:Species Specificity