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

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Date
2015-11
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
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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 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.
Type
Journal article
Subject
Animals
Fundulidae
Caryophyllaceae
Bayes Theorem
Microsatellite Repeats
Mutation
Algorithms
Models, Biological
Computer Simulation
Female
Male
Biological Evolution
Self-Fertilization
Data Accuracy
Permalink
https://hdl.handle.net/10161/21887
Published Version (Please cite this version)
10.1534/genetics.115.179093
Publication Info
Redelings, Benjamin D; Kumagai, Seiji; Tatarenkov, Andrey; Wang, Liuyang; Sakai, Ann K; Weller, Stephen G; ... Uyenoyama, Marcy K (2015). A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation. Genetics, 201(3). pp. 1171-1188. 10.1534/genetics.115.179093. Retrieved from https://hdl.handle.net/10161/21887.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Uyenoyama

Marcy K. Uyenoyama

Professor of Biology
Marcy Uyenoyama studies mechanisms of evolutionary change at the molecular and population levels. Among the questions under study include the prediction and detection of the effects of natural selection on genomic structure. A major area of research addresses the development of maximum-likelihood and Bayesian methods for inferring evolutionary processes from the pattern of molecular variation. Evolutionary processes currently under study include characterization of population structure acr
Wang

Liuyang Wang

Assistant Research Professor of Molecular Genetics and Microbiology
Alphabetical list of authors with Scholars@Duke profiles.
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