2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2016

Asger Hobolth, Ole F. Christensen, Thomas Mailund, Mikkel H. Schierup. Genomic relationships and speciation times of human, chimpanzee, and gorillainferred from a coalescent hidden Markov model. PLoS Genet, 3(2):e7. 2007.

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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-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.