A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation
A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation
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DOI：
10.1534/genetics.115.179093
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发表时间：
2015-09
期刊：
影响因子：
3.3
通讯作者：
B. Redelings;S. Kumagai;A. Tatarenkov;Liuyang Wang;A. Sakai;S. Weller;T. Culley;J. Avise;M. Uyenoyama
中科院分区：
文献类型：
--
作者：
B. Redelings;S. Kumagai;A. Tatarenkov;Liuyang Wang;A. Sakai;S. Weller;T. Culley;J. Avise;M. Uyenoyama
我们提出了一个贝叶斯方法来描述通过自花受精和随机异交的混合繁殖的种群的交配系统。我们的方法使用模式的遗传变异的基因组作为推断纯两性畸形，gynodiopathy下的繁殖的基础，和一个模型开发来描述自我的kryptolebias marmoratus。我们扩展了标准的聚结模型，以适应这些交配系统，明确占多位点的身份不平衡，近交衰退，交配类型之间的生育能力的变化。我们将Ewens抽样公式（ESF）下的无限等位基因突变模型，以获得一个新的表达交配系统参数的可能性。我们的马尔可夫链蒙特卡罗（MCMC）算法分配位点特定的突变率，从一个共同的突变率分布，这本身是估计从数据使用狄利克雷过程先验模型。我们的采样器旨在容纳额外的信息，包括有关性比，近亲繁殖衰退的强度和繁殖的其他方面的意见。它可以提供联合后验分布的人口范围内的单亲个体的比例，基因座特异性突变率，以及世代的数量，因为最近的异交事件为每个采样的个人。此外，估计一个给定的模型的所有基本参数允许估计这些参数的功能，包括每个性别和相对有效数量的基因库的比例。
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.