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

被引:232
作者
Hobolth, Asger [1 ]
Christensen, Ole F.
Mailund, Thomas
Schierup, Mikkel H.
机构
[1] N Carolina State Univ, Bioinformat Res Ctr, Raleigh, NC 27695 USA
[2] Univ Aarhus, Bioinformat Res Ctr, DK-8000 Aarhus C, Denmark
[3] Univ Oxford, Dept Stat, Oxford OX1 3TG, England
关键词
D O I
10.1371/journal.pgen.0030007
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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 6 30,000 for the human-chimp ancestor and 45,000 6 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.
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页码:294 / 304
页数:11
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