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Fine-Scale Phylogenetic Discordance across the House Mouse Genome
Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a m...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770633/ https://www.ncbi.nlm.nih.gov/pubmed/19936022 http://dx.doi.org/10.1371/journal.pgen.1000729 |
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author | White, Michael A. Ané, Cécile Dewey, Colin N. Larget, Bret R. Payseur, Bret A. |
author_facet | White, Michael A. Ané, Cécile Dewey, Colin N. Larget, Bret R. Payseur, Bret A. |
author_sort | White, Michael A. |
collection | PubMed |
description | Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose. |
format | Text |
id | pubmed-2770633 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-27706332009-11-21 Fine-Scale Phylogenetic Discordance across the House Mouse Genome White, Michael A. Ané, Cécile Dewey, Colin N. Larget, Bret R. Payseur, Bret A. PLoS Genet Research Article Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose. Public Library of Science 2009-11-20 /pmc/articles/PMC2770633/ /pubmed/19936022 http://dx.doi.org/10.1371/journal.pgen.1000729 Text en White et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article White, Michael A. Ané, Cécile Dewey, Colin N. Larget, Bret R. Payseur, Bret A. Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title | Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title_full | Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title_fullStr | Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title_full_unstemmed | Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title_short | Fine-Scale Phylogenetic Discordance across the House Mouse Genome |
title_sort | fine-scale phylogenetic discordance across the house mouse genome |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770633/ https://www.ncbi.nlm.nih.gov/pubmed/19936022 http://dx.doi.org/10.1371/journal.pgen.1000729 |
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