100,000 years of gene flow between Neandertals and Denisovans in the Altai mountains

Summary paragraphThe Siberian Altai mountains have been intermittently occupied by both Neandertals and Denisovans, two extinct hominin groups1,2. While they diverged at least 390,000 years ago3,4, later contacts lead to gene flow from Neandertals into Denisovans5,6. Using a new population genetic method that is capable of inferring signatures of admixture from highly degraded genetic data, I show that this gene flow was much more widespread than previously thought. While the two earliest Denisovans both have substantial and recent Neandertal ancestry, I find signatures of admixture in all archaic genomes from the Altai, demonstrating that gene flow also occurred from Denisovans into Neandertals. This suggests that a contact zone between Neandertals and Denisovan populations persisted in the Altai region throughout much of the Middle Paleolithic. In contrast, Western Eurasian Neandertals have little to no Denisovan ancestry. As I find no evidence of natural selection against gene flow, this suggests that neutral demographic processes and geographic isolation were likely major drivers of human differentiation.