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Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

Benjamin D. Redelings, Seiji Kumagai, Liuyang Wang, Andrey Tatarenkov, Ann K. Sakai, Stephen G. Weller, Theresa M. Culley, John C. Avise, Marcy K. Uyenoyama
doi: https://doi.org/10.1101/020537
Benjamin D. Redelings
*Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338
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Seiji Kumagai
*Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338
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Liuyang Wang
*Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338
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Andrey Tatarenkov
§Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525
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Ann K. Sakai
§Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525
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Stephen G. Weller
§Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525
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Theresa M. Culley
†Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45220
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John C. Avise
§Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697-2525
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Marcy K. Uyenoyama
*Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338
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Abstract

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet Process Prior model. Among the parameters jointly inferred are the population-wide rate of self-fertilization, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual.

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Posted June 07, 2015.
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Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population
Benjamin D. Redelings, Seiji Kumagai, Liuyang Wang, Andrey Tatarenkov, Ann K. Sakai, Stephen G. Weller, Theresa M. Culley, John C. Avise, Marcy K. Uyenoyama
bioRxiv 020537; doi: https://doi.org/10.1101/020537
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Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population
Benjamin D. Redelings, Seiji Kumagai, Liuyang Wang, Andrey Tatarenkov, Ann K. Sakai, Stephen G. Weller, Theresa M. Culley, John C. Avise, Marcy K. Uyenoyama
bioRxiv 020537; doi: https://doi.org/10.1101/020537

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