We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.

我们提出了一种称为G ( A | B ) 方法的方法，用于在从每个群体中抽取一个个体时，从基因组序列中估计群体谱系内的合并概率。如果对种群规模的历史做出额外假设，则可以从这些合并概率中估计种群发散时间。我们的方法基于 Rasmussen 等人提出的方法。（2014）测试一个古老的基因组是否来自一个直接祖先的种群到一个现代种群。G ( A | B _) 方法不需要区分祖先的等位基因和衍生的等位基因，也不需要在人口分化之前对人口历史的假设。我们讨论了我们的方法与两种类似方法的关系，一种由 Green 等人介绍。(2010) 并称为F ( A | B ) 方法和 Schlebusch 等人引入的另一种方法。（2017）并称为TT方法。当我们的方法应用于来自三个或更多种群的个体时，它提供了对种群历史是否是树状的测试，因为合并概率在树上是相加的。我们通过将其应用于三个高覆盖率的古老基因组、两个尼安德特人（文迪加和阿尔泰）和一个丹尼索瓦人来说明我们方法的使用。