PT  - JOURNAL ARTICLE
AU  - Benjamin D. Redelings
AU  - Seiji Kumagai
AU  - Liuyang Wang
AU  - Andrey Tatarenkov
AU  - Ann K. Sakai
AU  - Stephen G. Weller
AU  - Theresa M. Culley
AU  - John C. Avise
AU  - Marcy K. Uyenoyama
TI  - Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population
AID  - 10.1101/020537
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 020537
4099  - http://biorxiv.org/content/early/2015/06/07/020537.short
4100  - http://biorxiv.org/content/early/2015/06/07/020537.full
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.