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Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum
Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102651/ https://www.ncbi.nlm.nih.gov/pubmed/21637331 http://dx.doi.org/10.1371/journal.pone.0018155 |
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author | Tellier, Aurélien Pfaffelhuber, Peter Haubold, Bernhard Naduvilezhath, Lisha Rose, Laura E. Städler, Thomas Stephan, Wolfgang Metzler, Dirk |
author_facet | Tellier, Aurélien Pfaffelhuber, Peter Haubold, Bernhard Naduvilezhath, Lisha Rose, Laura E. Städler, Thomas Stephan, Wolfgang Metzler, Dirk |
author_sort | Tellier, Aurélien |
collection | PubMed |
description | Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches. |
format | Text |
id | pubmed-3102651 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-31026512011-06-02 Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum Tellier, Aurélien Pfaffelhuber, Peter Haubold, Bernhard Naduvilezhath, Lisha Rose, Laura E. Städler, Thomas Stephan, Wolfgang Metzler, Dirk PLoS One Research Article Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches. Public Library of Science 2011-05-26 /pmc/articles/PMC3102651/ /pubmed/21637331 http://dx.doi.org/10.1371/journal.pone.0018155 Text en Tellier 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 Tellier, Aurélien Pfaffelhuber, Peter Haubold, Bernhard Naduvilezhath, Lisha Rose, Laura E. Städler, Thomas Stephan, Wolfgang Metzler, Dirk Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title | Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title_full | Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title_fullStr | Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title_full_unstemmed | Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title_short | Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum |
title_sort | estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102651/ https://www.ncbi.nlm.nih.gov/pubmed/21637331 http://dx.doi.org/10.1371/journal.pone.0018155 |
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