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MBE Advance Access published online on February 22, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj109
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted February 13, 2006

Research Article

The Effect of Gene Flow on the Coalescent Time in the Human-Chimpanzee Ancestral Population

Hideki Innan 1 * and Hidemi Watanabe 2

1 Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, TX 77030
2 Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan

* To whom correspondence should be addressed.
Hideki Innan, E-mail: hideki.innan{at}uth.tmc.edu


  Abstract

The coalescent process in the human-chimpanzee ancestral population is investigated using a model which incorporates a certain time period of gene flow during the speciation process. a is a parameter to represent the degree and time of gene flow, and the model is identical to the null model with an instantaneous species split when a = {infty}. A maximum likelihood (ML) method is developed to estimate a, and its power and reliability is investigated by coalescent simulations. The ML method is applied to nucleotide divergence data between human and chimpanzee. It was found the null model with an instantaneous species split explains the data best, and no strong evidence for gene flow is detected. The result is discussed in the view of the mode of speciation. An ML method is also developed to estimate the male-female ratio ({alpha}) of mutation rate, in which the coalescent process in the ancestral population is taken into account.

Keywords: gene flow; coalescent; speciation; human.
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