Yang, Z;
(2010)
A likelihood ratio test of speciation with gene flow using genomic sequence data.
Genome Biology and Evolution
, 2
, Article evq011v1. 10.1093/gbe/evq011.
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Abstract
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.
| Type: | Article |
|---|---|
| Title: | A likelihood ratio test of speciation with gene flow using genomic sequence data |
| Location: | England |
| Identifier: | PMCID: PMC2997537 |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/gbe/evq011 |
| Publisher version: | http://dx.doi.org/10.1093/gbe/evq011 |
| Language: | English |
| Additional information: | © 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 |
| Keywords: | Animals, Gene flow, Genetic speciation, Genome, Human, Genomics, Gorilla gorilla, Humans, Likelihood Functions, Models, Genetic, Mutation, Pan troglodytes, Time Factors |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/106212 |
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