Estimation of ancestral population divergence times and effective population sizes from complete human genome sequences

Adam Siepel (February 25, 2010)

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Complete genome sequences are now available for individuals representing several distinct human populations. The primary motivation for collecting these sequences has been to characterize human diversity, facilitate disease association studies, and pave the way for an era of "personalized medicine". However, these data also contain valuable information about human evolution. Here I will describe an effort currently in progress to estimate evolutionary parameters such as the times at which major population groups diverged and the effective sizes of ancestral human populations, based on sequence data for two West Africans, two East Asians, two individuals of European descent, and a Khoisan hunter gatherer from the Kalahari Desert in Southern Africa. This work involves an interesting mixture of traditional phylogenetics and population genetics, and also requires a number of challenging technical issues -- concerning alignment and sequencing error, and genotype estimation -- to be addressed. I will describe our statistical model, which is derived from the MCMCCOAL model by Rannala and Yang, and our Markov chain Monte Carlo methods for inference. I will also present preliminary results from our analysis and discuss their relationship with what is currently known about early human evolution.