A structured coalescent model reveals deep ancestral structure shared by all modern humans

Understanding the series of admixture events and population size history leading to modern humans is central to human evolutionary genetics. Using a coalescence-based hidden Markov model, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ∼1.5 million years ago came together in an admixture event ∼300 thousand years ago, in a ratio of ∼80:20 percent. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human-Neanderthal or human-Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.