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Simple method for analyzing the pattern of DNA polymorphism and its application to SNP data of human

机译：DNA多态性模式的简单分析方法及其在人SNP数据中的应用

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摘要

In order to analyze the pattern of DNA polymorphism in detail, we have developed a simple method using a new statistic theta(i) which estimates 4Nmu from the number of segregating sites whose allelic nucleotide frequency is i among n DNA sequences, where N is the effective population size and mu is the mutation rate per generation per nucleotide site. Under the assumption that mutations are selectively neutral and a population size is constant, the expectation of theta(i) is equal to that of theta, which estimates 4Nmu from the number of segregating sites, so that the distribution of theta(i) is flat. Therefore, the departure of the distribution of theta(i) from the horizontal line, which represents the value of theta, reflects change in population size and natural selection. Results of the coalescent simulation show that the distributions of theta(i) in the populations which experienced expansion and reduction are U-shaped and upside-down U-shaped, respectively. And the distributions of theta(i) in some populations that experienced bottleneck are W-shaped. Furthermore, we have applied this method to the SNP data in the International HapMap Project. Results of data analyses show that the distributions of theta(i) in the CEU (European), CHB and JPT (Asian) populations are different from that in the YRI population (African). From these results of data analyses in nuclear DNA and the pattern of polymorphism in human mitochondrial DNA already known, we infer that the CEU, CHB and JPT populationsexperienced the bottleneck.
机译：为了详细分析DNA多态性的模式，我们开发了一种使用新统计量theta（i）的简单方法，该方法可从n个DNA序列中等位核苷酸频率为i / n的分离位点的数目估计4Nmu，其中N是有效种群大小，μ是每代每个核苷酸位点的每代突变率。在突变为选择性中性且种群规模恒定的假设下，theta（i）的期望值等于theta的期望值，后者从分离位点的数量估计为4Nmu，因此theta（i）的分布是平坦的。因此，theta（i）分布与水平线的偏离（代表theta的值）反映了人口规模和自然选择的变化。合并模拟的结果表明，theta（i）在经历扩展和缩减的种群中的分布分别为U形和上下U形。并且在经历瓶颈的某些人群中theta（i）的分布呈W形。此外，我们已将此方法应用于国际HapMap项目中的SNP数据。数据分析结果表明，theta（i）在CEU（欧洲），CHB和JPT（亚洲）人口中的分布与YRI人口（非洲）中的不同。从已知的核DNA数据分析结果和人类线粒体DNA多态性模式的这些结果，我们可以推断出CEU，CHB和JPT人群遇到了瓶颈。

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