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Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate
It is known that the effective population size (N(e)) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size a...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409433/ https://www.ncbi.nlm.nih.gov/pubmed/30428070 http://dx.doi.org/10.1093/molbev/msy212 |
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author | Zeng, Kai Jackson, Benjamin C Barton, Henry J |
author_facet | Zeng, Kai Jackson, Benjamin C Barton, Henry J |
author_sort | Zeng, Kai |
collection | PubMed |
description | It is known that the effective population size (N(e)) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variation in N(e) and u between loci. These methods rely on either polymorphism data alone or both polymorphism and divergence data. In addition to inferring demography, we can use the methods to study a variety of questions: 1) comparing sex chromosomes with autosomes (for finding evidence for male-driven evolution, an unequal sex ratio, or sex-biased demographic changes) and 2) analyzing multilocus data from within autosomes or sex chromosomes (for studying determinants of variability in N(e) and u). Simulations suggest that the methods can provide accurate parameter estimates and have substantial statistical power for detecting difference in N(e) and u. As an example, we use the methods to analyze a polymorphism data set from Drosophila simulans. We find clear evidence for rapid population expansion. The results also indicate that the autosomes have a higher mutation rate than the X chromosome and that the sex ratio is probably female-biased. The new methods have been implemented in a user-friendly package. |
format | Online Article Text |
id | pubmed-6409433 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-64094332019-03-15 Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate Zeng, Kai Jackson, Benjamin C Barton, Henry J Mol Biol Evol Methods It is known that the effective population size (N(e)) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variation in N(e) and u between loci. These methods rely on either polymorphism data alone or both polymorphism and divergence data. In addition to inferring demography, we can use the methods to study a variety of questions: 1) comparing sex chromosomes with autosomes (for finding evidence for male-driven evolution, an unequal sex ratio, or sex-biased demographic changes) and 2) analyzing multilocus data from within autosomes or sex chromosomes (for studying determinants of variability in N(e) and u). Simulations suggest that the methods can provide accurate parameter estimates and have substantial statistical power for detecting difference in N(e) and u. As an example, we use the methods to analyze a polymorphism data set from Drosophila simulans. We find clear evidence for rapid population expansion. The results also indicate that the autosomes have a higher mutation rate than the X chromosome and that the sex ratio is probably female-biased. The new methods have been implemented in a user-friendly package. Oxford University Press 2019-02 2018-11-14 /pmc/articles/PMC6409433/ /pubmed/30428070 http://dx.doi.org/10.1093/molbev/msy212 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methods Zeng, Kai Jackson, Benjamin C Barton, Henry J Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title | Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title_full | Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title_fullStr | Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title_full_unstemmed | Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title_short | Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate |
title_sort | methods for estimating demography and detecting between-locus differences in the effective population size and mutation rate |
topic | Methods |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409433/ https://www.ncbi.nlm.nih.gov/pubmed/30428070 http://dx.doi.org/10.1093/molbev/msy212 |
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