A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation

• Published in: Genetics (Austin) Vol. 201; no. 3; pp. 1171 - 1188
• Main Authors: Redelings, Benjamin D, Kumagai, Seiji, Tatarenkov, Andrey, Wang, Liuyang, Sakai, Ann K, Weller, Stephen G, Culley, Theresa M, Avise, John C, Uyenoyama, Marcy K
• Format: Journal Article
• Language: English
• Published: United States Genetics Society of America 01-11-2015
• Subjects: Algorithms; Animals; Bayes Theorem; Bayesian analysis; Biological Evolution; Caryophyllaceae; Computer Simulation; Data Accuracy; Female; Fundulidae; Gene loci; Genomics; Inbreeding; Investigations; Male; Microsatellite Repeats; Models, Biological; Mutation; Self-Fertilization; MCMC; mating system; Ewens sampling formula; selfing rate; Bayesian
• ISSN: 1943-2631; 0016-6731; 1943-2631
• DOI: 10.1534/genetics.115.179093

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 reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. 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. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers.