The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele
The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele
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DOI：
10.1016/j.tpb.2011.04.001
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发表时间：
2011-09-01
影响因子：
1.4
通讯作者：
Song, Yun S.
中科院分区：
文献类型：
--
作者：
Jenkins, Paul A.;Song, Yun S.
分离位点的样本频谱是来自遗传基因座的等位基因样本的概率分布，条件是观察到样本是多态的。这种分布被广泛用于群体遗传推断，包括中性的统计检验，其中在独立站点上观察到的频谱中的偏斜被视为偏离中性进化的标志。频谱的理论方面已经得到了很好的研究，并有一些有趣的结果，但它们通常是在假设一个网站经历了最多一个突变事件的历史样本。在这里，我们扩展了以前的理论结果，允许最多两个突变事件每个站点，在一般的有限等位基因模型中，突变率是独立的当前等位基因状态，但过渡矩阵是完全任意的。我们的结果适用于嵌套和非嵌套突变。以前只讨论了前者，而在这里，我们表明，除了非常小的样本量外，后者更有可能被观察到。此外，对于任何突变过渡矩阵，我们获得的联合样本频谱的两个突变等位基因在一个triallelic网站，并推导出一个封闭形式的公式的预期年龄的年轻的两个突变给定的频率在人口中。目前正在对各种物种进行几个大规模的重测序项目，所得数据将包括一些三等位基因多态性。本文所描述的理论结果应证明有用的人口基因组分析等数据。(c)2011 Elsevier Inc. All rights reserved.
The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across independent sites is taken as a signature of departure from neutral evolution. Theoretical aspects of the frequency spectrum have been well studied and several interesting results are available, but they are usually under the assumption that a site has undergone at most one mutation event in the history of the sample. Here, we extend previous theoretical results by allowing for at most two mutation events per site, under a general finite allele model in which the mutation rate is independent of current allelic state but the transition matrix is otherwise completely arbitrary. Our results apply to both nested and nonnested mutations. Only the former has been addressed previously, whereas here we show it is the latter that is more likely to be observed except for very small sample sizes. Further, for any mutation transition matrix, we obtain the joint sample frequency spectrum of the two mutant alleles at a triallelic site, and derive a closed-form formula for the expected age of the younger of the two mutations given their frequencies in the population. Several large-scale resequencing projects for various species are presently under way and the resulting data will include some triallelic polymorphisms. The theoretical results described in this paper should prove useful in population genomic analyses of such data. (c) 2011 Elsevier Inc. All rights reserved.