MBE Advance Access published online on July 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn148
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Research Article |
Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors
1 Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
2 Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
3 Laboratory of Biometrics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
Address for correspondence: Ziheng Yang, Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK, Tel: +44 (20) 7679 4379, Fax: +44 (20) 7679 7096, Email: z.yang{at}ucl.ac.uk
Received for publication March 18, 2008. Revision received June 21, 2008. Accepted for publication June 29, 2008.
Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the two species separated, and on whether the human population experienced a severe size reduction in its early evolutionary history. In this study, the Bayesian method of ancestral inference of Rannala and Yang (2003 Genetics 164:1645-1656) was extended to accommodate variable mutation rates among loci and random species-specific sequencing errors. The model was applied to analyze a genome-wide dataset of 
15,000 neutral loci (7.4Mb) aligned for human, chimpanzee, gorilla, orangutan and macaque. We obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back 30 million years (MY) to the Cercopithecoid divergence. The results showed that ancestral populations were 5-10 times larger than modern humans along the entire hominoid lineage. The estimates were robust to the priors used and to model assumptions about recombination. The unusually low X-chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hydridization and introgression. Instead, our parameter estimates were consistent with a simple instantaneous process for human-chimpanzee speciation but showed a major reduction in X-chromosome effective population size peculiar to the human-chimpanzee common ancestor, possibly due to selective sweeps on the X prior to separation of the two species.
Key Words: Hominoid • ancestral population size • Bayesian inference • MCMC • coalescent model • sequencing errors
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