Estimation of population divergence times from SNP data and a test for treeness

Abstract

We present a method for estimating population divergence times from genome sequences when one individual is sampled from each population. Our method is a simplified version of one presented by Rassmussen et al. (2014) for testing for direct ancestry of an archaic genome. Our 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 denoted by F(A | B) 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. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.