Researchers have sequenced the second high-quality genome from a Denisovan, extracted from a 200,000-year-old tooth in Siberia's Denisova Cave. This discovery reveals at least three distinct Denisovan populations and evidence of interbreeding with unknown Neanderthals and another mysterious ancient human group. The findings expand our understanding of early human evolution in Asia.
For only the second time, scientists have obtained a complete genome from a Denisovan, an extinct group of ancient humans who inhabited Asia. The DNA comes from a single molar tooth belonging to a male Denisovan, discovered in Denisova Cave, Siberia, in 2020. Based on mutations and sediment dating, the individual lived around 205,000 years ago, with the site's layers dated to 170,000-200,000 years old. This contrasts with the previous high-quality Denisovan genome, from an individual who lived 55,000-75,000 years ago, offering a glimpse into an earlier phase of Denisovan history.
Denisovans were first identified in 2010 through DNA from a finger bone in the same Siberian cave, distinct from modern humans and Neanderthals. Their DNA persists in modern populations, particularly in South-East Asia, including the Philippines and Papua New Guinea, indicating past interbreeding with Homo sapiens. More recently, in June, a skull from Harbin, China, was identified as Denisovan based on molecular evidence, providing the first view of their facial features.
The new genome suggests at least three discrete Denisovan populations. The oldest, represented by this male, was later replaced by a second group at the cave site thousands of years afterward. A third population, not found at the cave, contributed DNA to modern humans. "Understanding how early Denisovans were replaced by later Denisovans highlights a significant human event," says Qiaomei Fu at the Institute of Vertebrate Paleontology and Paleoanthropology in China.
Further analysis shows repeated interbreeding with Neanderthals, including traces from a previously unknown Neanderthal group that lived 7,000-13,000 years before the male Denisovan. The genome also carries DNA from an unidentified ancient human lineage, evolved separately for hundreds of thousands of years, possibly Homo erectus, though no DNA from that species exists for confirmation. "This is a bombshell paper," says David Reich at Harvard University. "This study really expanded my understanding of the universe of the Denisovans," adds Samantha Brown at the National Research Center on Human Evolution in Spain. "It’s endlessly fascinating that we keep discovering these new populations," Brown notes.
The research, led by Stéphane Peyrégne at the Max Planck Institute for Evolutionary Anthropology in Germany, is detailed in a bioRxiv preprint (DOI: 10.1101/2025.10.20.683404) and awaits peer review.