Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model.

ABSTRACT: The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 +/- 0.4 million years), and fairly large ancestral effective population sizes (65,000 +/- 30,000 for the human-chimp ancestor and 45,000 +/- 10,000 for the human-c

SUBMITTER: Hobolth A 

PROVIDER: S-EPMC1802818 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature