Testing for Ancient Admixture between Closely Related Populations
Testing for Ancient Admixture between Closely Related Populations
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DOI：
10.1093/molbev/msr048
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发表时间：
2011-08-01
影响因子：
10.7
通讯作者：
Slatkin, Montgomery
中科院分区：
文献类型：
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作者：
Durand, Eric Y.;Patterson, Nick;Slatkin, Montgomery
进化生物学中一个经久不衰的问题是，现代人基因组中古代人的混杂程度。在本文中，我们提出了一个古老的混合测试，利用在三种群树的两个不一致的基因树的频率不对称。这个测试最初是用来检测尼安德特人和现代人之间的杂交。我们推导了一个检验统计量的分析期望，称为D统计量，它对不同人口情况下的不对称性很敏感。我们表明，D统计量对一些人口统计学假设（如祖先种群大小）不敏感，只需要假设祖先种群是随机交配的。D统计的一个重要方面是，即使没有可用的古代样本，它们也可以用于检测古代混合物。我们探讨了测序误差对混合测试假阳性率的影响，并展示了如何估计现代人群基因组中古代祖先的比例。我们还研究了祖先种群的细分模型，该模型可以导致表明最近混合的D统计。
One enduring question in evolutionary biology is the extent of archaic admixture in the genomes of present-day populations. In this paper, we present a test for ancient admixture that exploits the asymmetry in the frequencies of the two nonconcordant gene trees in a three-population tree. This test was first applied to detect interbreeding between Neandertals and modern humans. We derive the analytic expectation of a test statistic, called the D statistic, which is sensitive to asymmetry under alternative demographic scenarios. We show that the D statistic is insensitive to some demographic assumptions such as ancestral population sizes and requires only the assumption that the ancestral populations were randomly mating. An important aspect of D statistics is that they can be used to detect archaic admixture even when no archaic sample is available. We explore the effect of sequencing error on the false-positive rate of the test for admixture, and we show how to estimate the proportion of archaic ancestry in the genomes of present-day populations. We also investigate a model of subdivision in ancestral populations that can result in D statistics that indicate recent admixture.