Neanderthals and ancestors of anatomically modern humans did interbreed at multiple points in time, according to the large-scale genetic analyses of Neanderthal DNA fragments in contemporary East Asians and Europeans published this week in Nature Ecology & Evolution.

When anatomically modern humans dispersed from Africa, they encountered Neanderthals in western Eurasia. These encounters left a signature in the genomes of contemporary non-African populations: about 2% of their genomes include a Neanderthal component. Initially, it was assumed that only a single episode of interbreeding between modern humans and Neanderthals occurred, but the observation that the proportion of Neanderthal ancestry is 12-20% higher in East Asian individuals relative to Europeans suggested the possibility of multiple encounters.

Fernando Villanea and Joshua Schraiber analysed the asymmetry in the patterns of DNA of Neanderthal origin between individuals of East Asian and European ancestry in a large dataset of modern human genomes. The authors then simulated contributions of Neanderthal DNA to the genomes of anatomically modern humans for different numbers of interbreeding events and used a machine learning approach to explore these complex models with many parameters. They conclude that the observed patterns of DNA of Neanderthal origin in modern human genomes are best explained by not one but multiple episodes of interbreeding between Neanderthal and both East Asian and European populations.

The authors conclude that multiple episodes of modern human–Neanderthal encounters fit with the emerging view of complex and frequent interactions between different hominin groups.