RT Journal Article SR Electronic T1 Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population JF bioRxiv FD Cold Spring Harbor Laboratory SP 020537 DO 10.1101/020537 A1 Benjamin D. Redelings A1 Seiji Kumagai A1 Liuyang Wang A1 Andrey Tatarenkov A1 Ann K. Sakai A1 Stephen G. Weller A1 Theresa M. Culley A1 John C. Avise A1 Marcy K. Uyenoyama YR 2015 UL http://biorxiv.org/content/early/2015/06/07/020537.abstract AB 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.