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A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

Genomic sequence data may be used to test hypotheses about the process of species formation. In this paper, I implement a likelihood ratio test of variable species divergence times over the genome, which may be considered a test of the null model of allopatric speciation without gene flow against th...

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Detalles Bibliográficos
Autor principal: Yang, Ziheng
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997537/
https://www.ncbi.nlm.nih.gov/pubmed/20624726
http://dx.doi.org/10.1093/gbe/evq011
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author Yang, Ziheng
author_facet Yang, Ziheng
author_sort Yang, Ziheng
collection PubMed
description Genomic sequence data may be used to test hypotheses about the process of species formation. In this paper, I implement a likelihood ratio test of variable species divergence times over the genome, which may be considered a test of the null model of allopatric speciation without gene flow against the alternative model of parapatric speciation with gene flow. Two models are implemented in the likelihood framework, which accommodate coalescent events in the ancestral populations in a phylogeny of three species. One model assumes a constant species divergence time over the genome, whereas another allows it to vary. Computer simulation shows that the test has acceptable false positive rate but to achieve reasonable power, hundreds or even thousands of genomic loci may be necessary. The test is applied to genomic data from the human, chimpanzee, and gorilla.
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spelling pubmed-29975372010-12-06 A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data Yang, Ziheng Genome Biol Evol Research Articles Genomic sequence data may be used to test hypotheses about the process of species formation. In this paper, I implement a likelihood ratio test of variable species divergence times over the genome, which may be considered a test of the null model of allopatric speciation without gene flow against the alternative model of parapatric speciation with gene flow. Two models are implemented in the likelihood framework, which accommodate coalescent events in the ancestral populations in a phylogeny of three species. One model assumes a constant species divergence time over the genome, whereas another allows it to vary. Computer simulation shows that the test has acceptable false positive rate but to achieve reasonable power, hundreds or even thousands of genomic loci may be necessary. The test is applied to genomic data from the human, chimpanzee, and gorilla. Oxford University Press 2010 2010-03-16 /pmc/articles/PMC2997537/ /pubmed/20624726 http://dx.doi.org/10.1093/gbe/evq011 Text en © The Author(s) 2010. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Yang, Ziheng
A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title_full A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title_fullStr A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title_full_unstemmed A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title_short A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data
title_sort likelihood ratio test of speciation with gene flow using genomic sequence data
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997537/
https://www.ncbi.nlm.nih.gov/pubmed/20624726
http://dx.doi.org/10.1093/gbe/evq011
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