Ancient DNA from Altai Neanderthal female is first evidence of modern human contribution to Neanderthal genome
Ever since the first draft of the Neanderthal genome was published in 2010, it has been known that Neanderthals interbred with modern humans and it is now believed that around twenty percent of their genome survives in the present-day population. Subsequent work revealed the existence of a new human species in the Russian Altai, the Denisovans, and that parts of their genome also survive in the present-day population. It has also been established that the Altai Denisovans also interbred with Neanderthals in the region and with another as yet unidentified archaic species (probably Homo erectus). What has hitherto been absent up is evidence of gene flow from early modern humans into archaic genomes.
To address this issue, researchers investigated the previously-sequenced genome of a Neanderthal woman who lived in the Altai region 50,000 years ago. They found evidence of gene flow from modern humans into the ancestors of the Altai Neanderthal. The source was unclear, but was thought to be a modern population that either split from the ancestors of all present-day Africans, or was one of the early modern African lineages. It was estimated that the implied interbreeding occurred at least 100,000 years ago – well before the previously-reported gene flow from Neanderthals into modern humans outside Africa 47,000 to 65,000 years ago. However, they did not find evidence for similar gene flow from modern humans into either Denisovans or European Neanderthals.
The traditional view that modern humans did not leave Africa and the Levantine/Arabian region until around 60,000 years ago has been refuted by the discovery of teeth lying within the modern range at Fuyan Cave, China, dating to around 100,000 years ago. If modern humans were in China then it is entirely possible that they were also in the Altai at that time. Other possibilities are the Arabian Peninsula, where there is archaeological (though no fossil) evidence for a modern human presence as long ago as 127,000 years ago and Neanderthals were likely to also have been present; and the Levant where there is fossil evidence for both Neanderthals (Tabun) and modern humans (Skhul and Qafzeh) 120,000 to 110,000 years ago.
Kuhlwilm, M. et al., Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, doi:10.1038/nature16544 (2015).