基于全基因组SNP数据的人口统计学调整的中性检验
Demography-adjusted tests of neutrality based on genome-wide SNP data
摘要：
中性进化假设的检验通常建立在标准的零模型上，该模型假设突变是中性的，种群规模随时间保持不变。然而，目前还不清楚如果放弃最后一个假设，这些测试会受到什么影响。在这里，我们扩展了统一的框架测试的基础上的网站频谱，介绍了Achaz和Ferretti，不同规模的人口。一个关键因素是指定频谱的前两个时刻。我们表明，这些时刻可以确定分析，如果人口经历了两个瞬时大小的变化在过去。我们将我们的方法应用于1000个基因组计划中收集的10个人群的数据，估计他们的人口统计学，并定义人口统计学调整版本的Tajima的$D$，Fay & Wu的$H$和Zeng的$E$。调整后的检验统计量便于人口之间的直接比较，它们表明，在原始检验中看到的人口之间的差异大多可以用人口统计学来解释。我们进行了全基因组筛选偏离中性，并确定了最近的积极选择的候选区域。我们提供跟踪文件，其中包含调整后的和原始测试的值，以上传到UCSC基因组浏览器。
英文摘要：
Tests of the neutral evolution hypothesis are usually built on the standard null model which assumes that mutations are neutral and population size remains constant over time. However, it is unclear how such tests are affected if the last assumption is dropped. Here, we extend the unifying framework for tests based on the site frequency spectrum, introduced by Achaz and Ferretti, to populations of varying size. A key ingredient is to specify the first two moments of the frequency spectrum. We show that these moments can be determined analytically if a population has experienced two instantaneous size changes in the past. We apply our method to data from ten human populations gathered in the 1000 genomes project, estimate their demographies and define demography-adjusted versions of Tajima's $D$, Fay & Wu's $H$, and Zeng's $E$. The adjusted test statistics facilitate the direct comparison between populations and they show that most of the differences among populations seen in the original tests can be explained by demography. We carried out whole genome screens for deviation from neutrality and identified candidate regions of recent positive selection. We provide track files with values of the adjusted and original tests for upload to the UCSC genome browser.
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