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Statistical Inference of Selection and Divergence from a Time-Dependent Poisson Random Field Model

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  • Amei Amei
  • Stanley Sawyer

Abstract

We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time (or 1.68 million years, assuming the haploid effective population size years) and a mean selection coefficient per generation . Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.

Suggested Citation

  • Amei Amei & Stanley Sawyer, 2012. "Statistical Inference of Selection and Divergence from a Time-Dependent Poisson Random Field Model," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-7, April.
    • Handle: RePEc:plo:pone00:0034413
    DOI: 10.1371/journal.pone.0034413
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    1. Carlos D. Bustamante & Rasmus Nielsen & Stanley A. Sawyer & Kenneth M. Olsen & Michael D. Purugganan & Daniel L. Hartl, 2002. "The cost of inbreeding in Arabidopsis," Nature, Nature, vol. 416(6880), pages 531-534, April.
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