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Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

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  • Thomas Mailund
  • Julien Y Dutheil
  • Asger Hobolth
  • Gerton Lunter
  • Mikkel H Schierup

Abstract

Due to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report a negative correlation between chromosome size and ancestral effective population size, which we interpret as a signature of recombination increasing the efficacy of selection.Author Summary: We present a hidden Markov model that uses variation in coalescence times between two distantly related populations, or closely related species, to infer population genetics parameters in ancestral population or species. The model infers the divergence times in segments along the alignment. Using coalescent simulations, we show that the model accurately estimates the divergence time between the two populations and the effective population size of the ancestral population. We apply the model to the recently sequenced orangutan sub-species and estimate their divergence time and the effective population size of their ancestor population.

Suggested Citation

  • Thomas Mailund & Julien Y Dutheil & Asger Hobolth & Gerton Lunter & Mikkel H Schierup, 2011. "Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model," PLOS Genetics, Public Library of Science, vol. 7(3), pages 1-15, March.
  • Handle: RePEc:plo:pgen00:1001319
    DOI: 10.1371/journal.pgen.1001319
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    References listed on IDEAS

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    1. Nick Patterson & Daniel J. Richter & Sante Gnerre & Eric S. Lander & David Reich, 2006. "Genetic evidence for complex speciation of humans and chimpanzees," Nature, Nature, vol. 441(7097), pages 1103-1108, June.
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    Cited by:

    1. Hobolth, Asger & Jensen, Jens Ledet, 2014. "Markovian approximation to the finite loci coalescent with recombination along multiple sequences," Theoretical Population Biology, Elsevier, vol. 98(C), pages 48-58.
    2. Kevin J Liu & Jingxuan Dai & Kathy Truong & Ying Song & Michael H Kohn & Luay Nakhleh, 2014. "An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes," PLOS Computational Biology, Public Library of Science, vol. 10(6), pages 1-13, June.
    3. Kumagai, Seiji & Uyenoyama, Marcy K., 2015. "Genealogical histories in structured populations," Theoretical Population Biology, Elsevier, vol. 102(C), pages 3-15.
    4. Steinrücken, Matthias & Paul, Joshua S. & Song, Yun S., 2013. "A sequentially Markov conditional sampling distribution for structured populations with migration and recombination," Theoretical Population Biology, Elsevier, vol. 87(C), pages 51-61.

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