1. Subspecific origin and haplotype diversity in the laboratory mouse
- Author
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Pierre Boursot, Priscilla K. Tucker, John P. Didion, Alex Hon Tsen Yu, Jaroslav Piálek, Franãois Bonhomme, Ryan J. Buus, Michael W. Nachman, Leonard McMillan, Catherine E. Welsh, Jeremy Wang, Timothy A. Bell, Gary A. Churchill, Hyuna Yang, Fernando Pardo-Manuel de Villena, The Jackson Laboratory [Bar Harbor] (JAX), Department of Computer Sciences, University of North Carolina at Chapel Hill (UNC), Department of Genetics, Lineberger Comprehensive Cancer Center (UNC Lineberger), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Carolina Center for Genome Sciences, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institute of Zoology, National Taiwan University [Taiwan] (NTU), Department of Ecology and Evolutionary Biology, University of Arizona, institute of vertebrate zoology, Czech Academy of Sciences [Prague] (CAS), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of North Carolina System (UNC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Department of Ecology and Evolutionary Biology [University of Arizona]
- Subjects
Genotype ,Genetic Speciation ,Molecular Sequence Data ,Introgression ,Mice, Inbred Strains ,Subspecies ,Biology ,Polymorphism, Single Nucleotide ,Identity by descent ,Article ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Inbred strain ,Genetics ,Animals ,Phylogeny ,030304 developmental biology ,0303 health sciences ,Genetic diversity ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Phylogenetic tree ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,Haplotype ,Laboratory mouse ,Chromosome Mapping ,Genetic Variation ,Chromosomes, Mammalian ,Haplotypes ,Evolutionary biology ,030217 neurology & neurosurgery - 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).
- Published
- 2011
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