Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus).
General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a def...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3431316?pdf=render |
| _version_ | 1818391283523125248 |
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| author | Fabian Staubach Anna Lorenc Philipp W Messer Kun Tang Dmitri A Petrov Diethard Tautz |
| author_facet | Fabian Staubach Anna Lorenc Philipp W Messer Kun Tang Dmitri A Petrov Diethard Tautz |
| author_sort | Fabian Staubach |
| collection | DOAJ |
| description | General parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin. |
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| format | Article |
| id | doaj.art-24acb44daf514761a198b9a889e5e9ed |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-12-14T05:11:04Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Genetics |
| spelling | doaj.art-24acb44daf514761a198b9a889e5e9ed2022-12-21T23:15:58ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042012-01-0188e100289110.1371/journal.pgen.1002891Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus).Fabian StaubachAnna LorencPhilipp W MesserKun TangDmitri A PetrovDiethard TautzGeneral parameters of selection, such as the frequency and strength of positive selection in natural populations or the role of introgression, are still insufficiently understood. The house mouse (Mus musculus) is a particularly well-suited model system to approach such questions, since it has a defined history of splits into subspecies and populations and since extensive genome information is available. We have used high-density single-nucleotide polymorphism (SNP) typing arrays to assess genomic patterns of positive selection and introgression of alleles in two natural populations of each of the subspecies M. m. domesticus and M. m. musculus. Applying different statistical procedures, we find a large number of regions subject to apparent selective sweeps, indicating frequent positive selection on rare alleles or novel mutations. Genes in the regions include well-studied imprinted loci (e.g. Plagl1/Zac1), homologues of human genes involved in adaptations (e.g. alpha-amylase genes) or in genetic diseases (e.g. Huntingtin and Parkin). Haplotype matching between the two subspecies reveals a large number of haplotypes that show patterns of introgression from specific populations of the respective other subspecies, with at least 10% of the genome being affected by partial or full introgression. Using neutral simulations for comparison, we find that the size and the fraction of introgressed haplotypes are not compatible with a pure migration or incomplete lineage sorting model. Hence, it appears that introgressed haplotypes can rise in frequency due to positive selection and thus can contribute to the adaptive genomic landscape of natural populations. Our data support the notion that natural genomes are subject to complex adaptive processes, including the introgression of haplotypes from other differentiated populations or species at a larger scale than previously assumed for animals. This implies that some of the admixture found in inbred strains of mice may also have a natural origin.http://europepmc.org/articles/PMC3431316?pdf=render |
| spellingShingle | Fabian Staubach Anna Lorenc Philipp W Messer Kun Tang Dmitri A Petrov Diethard Tautz Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). PLoS Genetics |
| title | Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). |
| title_full | Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). |
| title_fullStr | Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). |
| title_full_unstemmed | Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). |
| title_short | Genome patterns of selection and introgression of haplotypes in natural populations of the house mouse (Mus musculus). |
| title_sort | genome patterns of selection and introgression of haplotypes in natural populations of the house mouse mus musculus |
| url | http://europepmc.org/articles/PMC3431316?pdf=render |
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