Marshall John M, Weiss Robert E
Department of Biomathematics, UCLA School of Medicine, Los Angeles, CA 90095-1766, USA.
Genetics. 2006 Aug;173(4):2357-70. doi: 10.1534/genetics.105.053314. Epub 2006 Jun 4.
The distribution of microsatellite allele sizes in populations aids in understanding the genetic diversity of species and the evolutionary history of recent selective sweeps. We propose a heterogeneous Bayesian analysis of variance model for inferring loci involved in recent selective sweeps by analyzing the distribution of allele sizes at multiple loci in multiple populations. Our model is shown to be consistent with a multilocus test statistic, ln RV, proposed for identifying microsatellite loci involved in recent selective sweeps. Our methodology differs in that it accepts original allele size data rather than summary statistics and allows the incorporation of prior knowledge about allele frequencies using a hierarchical prior distribution consisting of log normal and gamma probability distributions. Interesting features of the model are its ability to simultaneously analyze allele size data for any number of populations and to cope with the presence of any number of selected loci. The utility of the method is illustrated by application to two sets of microsatellite allele size data for a group of West African Anopheles gambiae populations. The results are consistent with the suppressed-recombination model of speciation, and additional candidate loci on chromosomes 2 (079 and 175) and 3 (088) are discovered that escaped former analysis.
微卫星等位基因大小在种群中的分布有助于理解物种的遗传多样性和近期选择性清除的进化历史。我们提出了一种异质性贝叶斯方差分析模型，通过分析多个种群中多个位点的等位基因大小分布来推断参与近期选择性清除的位点。我们的模型与为识别参与近期选择性清除的微卫星位点而提出的多基因座检验统计量ln RV一致。我们的方法不同之处在于它接受原始等位基因大小数据而非汇总统计量，并允许使用由对数正态和伽马概率分布组成的分层先验分布纳入关于等位基因频率的先验知识。该模型的有趣之处在于它能够同时分析任意数量种群的等位基因大小数据，并应对任意数量选择位点的存在。通过将该方法应用于一组西非冈比亚按蚊种群的两组微卫星等位基因大小数据，说明了该方法的实用性。结果与物种形成的抑制重组模型一致，并且发现了2号染色体（079和175）和3号染色体（088）上逃脱先前分析的额外候选位点。
