Publications [#159869] of Marcy K Uyenoyama

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Papers Published

  1. Dutheil, J. Y., G. Ganapathy, A. Hobolth, T. Mailund, M. K. Uyenoyama, M. H. Schierup, Ancestral population genomics: The coalescent Hidden Markov Model approach, Genetics, vol. 183 (2009), pp. 259-274 (doi: 10.1534/genetics.109.103010.) .
    (last updated on 2009/12/26)

    Abstract:
    With incomplete lineage sorting (ILS), the genealogy of closely related species diers along their genomes. The amount of ILS depends on population parameters such as the ancestral eective population sizes and the recombination rate, but also on the number of generations between speciation events. We use a hidden Markov model parametrized according to coalescent theory in order to infer the genealogy along a four-species genome alignment of closely related species, and estimate population parameters. We analyze a basic, panmictic demographic model and study its properties using an extensive set of coalescent simulations. We assess the eect of the model assumptions, and demonstrate that the Markov property provides a good approximation to the ancestral recombination graph. Using a too restricted set of possible genealogies, necessary to reduce the computational load, can bias parameter estimates. We propose a simple correction for this bias, and suggest directions for future extensions of the model. We show that the patterns of ILS along a sequence alignment can be recovered eciently together with the ancestral recombination rate. Finally, we introduce an extension of the basic model that allows for mutation rate heterogeneity, and reanalyze Human-Chimpanzee-Gorilla-Orangutan alignments using the new models. We expect that this framework will prove useful for population genomics and provide exciting insights into genome evolution.

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