Modern humans inherited part of their ancestry from multiple, genetically distinct Denisovan groups through interbreeding events. However, the history of contact with Denisovans remains unclear.

In a recent study published in the journal Current Biology, researchers conducted the first systematic paleogenetics analysis of DNA segments inherited from Denisovans, identified in ancient and present-day humans. By tracing these segments over the past 40,000 years, they reconstructed the dynamics of Denisovan ancestry over time and space across continental Eurasia.

Tracing Denisovan ancestry through time and space

By compiling published ancient genomes from across Eurasia, the team found that some of the earliest East Asians, such as the Tianyuan individual from China (dating to around 40,000 years ago), carried the highest level of Denisovan ancestry (over 0.2%) among all later ancient and present-day humans studied. Yet, patterns of shared Denisovan DNA segments between individuals indicate that this ancestry originated from common episodes of contact with Denisovans shared among East Asians across time.

"This indicates that gene flow occurred from a source with less or no Denisovan ancestry and diluted the Denisovan ancestry of early East Asians," explains population geneticist Stéphane Peyrégne who co-supervised the study. "Denisovan DNA represents a powerful marker to reconstruct population history."

As another example of how Denisovan DNA segments are informative of past population movements, this study also shows that Denisovan ancestry made its way to West Eurasia, although at a minimum level, mainly through the spread of people from Eastern Eurasia starting around 12,000 years ago.

Not all East Asians met Denisovans

Another surprising finding from this study concerns the ancient Jomon people from the Japanese archipelago and the Ryukyu/Okinawa islands who contributed to present-day Japanese. The Jomon carried the lowest Denisovan ancestry among East Asians, even though their Denisovan ancestry had the same origin as mainland populations.

This means that the Jomon descended from a lineage that did not meet Denisovans, but traced their Denisovan ancestry from later gene flow from Mainland East Asia. Alternatively, this lineage received limited gene flow from Denisovans before they diverged from other East Asians, but missed a subsequent (and major) Denisovan gene flow in the continent.

"This suggests that some groups took different routes during the early dispersals in East Asia, or Denisovans were so sparsely distributed that interactions with them were rare," says lead author Jiaqi Yang, a Ph.D. researcher at the Max Planck Institute for Evolutionary Anthropology.

Although there is still limited knowledge about the origin of the Jomon and other East Asians during the Paleolithic, these findings highlight a complex and regionally diverse history of interactions between modern humans and Denisovans. Further ancient genomic data will help clarify the timing and nature of these interactions.