Subspecific origin and haplotype diversity in the laboratory mouse
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 la...
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| Published in | Nature genetics Vol. 43; no. 7; pp. 648 - 655 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.07.2011
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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
). |
|---|---|
| AbstractList | Here we provide the first 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 demonstrate that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly M. m. 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 demonstrate that classical inbred strains have limited and non-randomly distributed genetic diversity. In contrast, wild-derived laboratory strains represent a broad sampling of diversity Users may view, print, copy, download and text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: 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). 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 ). 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). [PUBLICATION ABSTRACT] Here we provide the first 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 demonstrate that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly M. m. 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 demonstrate 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 role in this process. The subspecific origin, haplotype diversity and identity by descent maps can be visualized and searched online. 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).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). |
| Audience | Academic |
| Author | Wang, Jeremy R Buus, Ryan J Bell, Timothy A de Villena, Fernando Pardo-Manuel Churchill, Gary A Pialek, Jaroslav Yang, Hyuna Nachman, Michael W Tucker, Priscilla Yu, Alex Hon-Tsen Welsh, Catherine E Bonhomme, François McMillan, Leonard Boursot, Pierre Didion, John P |
| AuthorAffiliation | 9 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 10 Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno and Studenec, Czech Republic 1 The Jackson Laboratory, Bar Harbor, ME 8 Department of Life Science, National Taiwan University, Taipei Taiwan ROC 10617 11 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 7 Institute of Zoology National Taiwan University, Taipei Taiwan ROC 10617 6 Université Montpellier 2, CNRS UMR5554, Institut des Sciences de l'Evolution, Montpellier, France 2 Department of Computer Science, University of North Carolina Chapel Hill, NC 3 Department of Genetics University of North Carolina Chapel Hill, NC 4 Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, NC 5 Carolina Center for Genome Science, University of North Carolina Chapel Hill, NC |
| AuthorAffiliation_xml | – name: 2 Department of Computer Science, University of North Carolina Chapel Hill, NC – name: 1 The Jackson Laboratory, Bar Harbor, ME – name: 8 Department of Life Science, National Taiwan University, Taipei Taiwan ROC 10617 – name: 11 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI – name: 5 Carolina Center for Genome Science, University of North Carolina Chapel Hill, NC – name: 10 Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno and Studenec, Czech Republic – name: 6 Université Montpellier 2, CNRS UMR5554, Institut des Sciences de l'Evolution, Montpellier, France – name: 9 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ – name: 3 Department of Genetics University of North Carolina Chapel Hill, NC – name: 4 Lineberger Comprehensive Cancer Center University of North Carolina Chapel Hill, NC – name: 7 Institute of Zoology National Taiwan University, Taipei Taiwan ROC 10617 |
| Author_xml | – sequence: 1 givenname: Hyuna surname: Yang fullname: Yang, Hyuna organization: The Jackson Laboratory – sequence: 2 givenname: Jeremy R surname: Wang fullname: Wang, Jeremy R organization: Department of Computer Science, University of North Carolina at Chapel Hill – sequence: 3 givenname: John P surname: Didion fullname: Didion, John P organization: Department of Genetics, University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Carolina Center for Genome Science, University of North Carolina at Chapel Hill – sequence: 4 givenname: Ryan J surname: Buus fullname: Buus, Ryan J organization: Department of Genetics, University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Carolina Center for Genome Science, University of North Carolina at Chapel Hill – sequence: 5 givenname: Timothy A surname: Bell fullname: Bell, Timothy A organization: Department of Genetics, University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Carolina Center for Genome Science, University of North Carolina at Chapel Hill – sequence: 6 givenname: Catherine E surname: Welsh fullname: Welsh, Catherine E organization: Department of Computer Science, University of North Carolina at Chapel Hill – sequence: 7 givenname: François surname: Bonhomme fullname: Bonhomme, François organization: Université Montpellier 2, CNRS UMR5554, Institut des Sciences de l'Evolution – sequence: 8 givenname: Alex Hon-Tsen surname: Yu fullname: Yu, Alex Hon-Tsen organization: Institute of Zoology, National Taiwan University, Department of Life Science, National Taiwan University – sequence: 9 givenname: Michael W surname: Nachman fullname: Nachman, Michael W organization: Department of Ecology and Evolutionary Biology, University of Arizona – sequence: 10 givenname: Jaroslav surname: Pialek fullname: Pialek, Jaroslav organization: Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic – sequence: 11 givenname: Priscilla surname: Tucker fullname: Tucker, Priscilla organization: Department of Ecology and Evolutionary Biology, University of Michigan – sequence: 12 givenname: Pierre surname: Boursot fullname: Boursot, Pierre organization: Université Montpellier 2, CNRS UMR5554, Institut des Sciences de l'Evolution – sequence: 13 givenname: Leonard surname: McMillan fullname: McMillan, Leonard organization: Department of Computer Science, University of North Carolina at Chapel Hill – sequence: 14 givenname: Gary A surname: Churchill fullname: Churchill, Gary A email: garyc@jax.org organization: The Jackson Laboratory – sequence: 15 givenname: Fernando Pardo-Manuel surname: de Villena fullname: de Villena, Fernando Pardo-Manuel email: fernando@med.unc.edu organization: Department of Genetics, University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Carolina Center for Genome Science, University of North Carolina at Chapel Hill |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=24333637$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/21623374$$D View this record in MEDLINE/PubMed https://hal.umontpellier.fr/hal-02347993$$DView record in HAL |
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| CODEN | NGENEC |
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| Snippet | Fernando Pardo-Manuel de Villena, Gary Churchill and colleagues provide a high-resolution phylogenetic map of mouse inbred strains based on comparisons to... 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... Here we provide the first genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our... |
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| SubjectTerms | 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 |
| Title | Subspecific origin and haplotype diversity in the laboratory mouse |
| URI | https://link.springer.com/article/10.1038/ng.847 https://www.ncbi.nlm.nih.gov/pubmed/21623374 https://www.proquest.com/docview/880396555 https://www.proquest.com/docview/874186396 https://www.proquest.com/docview/883034481 https://hal.umontpellier.fr/hal-02347993 https://pubmed.ncbi.nlm.nih.gov/PMC3125408 |
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