Jomon people show minimal Denisovan ancestry, new genetic study finds
A new genetic analysis published Oct. 20 in Current Biology reports that prehistoric Jomon people from the Japanese archipelago carried "little to no" DNA from Denisovans, the enigmatic archaic humans related to Neanderthals. The study examined hundreds of ancient and modern genomes to better pinpoint when and where Homo sapiens interbred with Denisovan populations.
The authors analyzed genomes from 115 ancient Homo sapiens remains recovered across the Americas, West Eurasia, Siberia and East Asia, supplemented by 279 present-day genomes from the Simons Genome Diversity Project. Ancient samples ranged from about 45,000 years ago in present-day Bulgaria to roughly 766 years ago in Siberia.
"Surprisingly, individuals from Japan's Jomon period (roughly 16,000–3,000 years ago) carried the least Denisovan ancestry among ancient and present-day East Asians," the researchers wrote.
The strongest Denisovan signal in the ancient dataset came from the roughly 40,000-year-old Tianyuan individual from China, whose genome contained about 0.25% Denisovan ancestry. Analyses indicate Tianyuan's Denisovan input likely came from multiple distinct Denisovan groups encountered before the Last Glacial Maximum (approximately 26,500–19,000 years ago).
By contrast, one Jomon genome dated to 3,755 years ago carried only about one-sixth to one-eighth of the Denisovan DNA typically observed in modern East Asians (modern East Asians average roughly 0.1% Denisovan ancestry). This suggests that the earliest Jomon populations either did not intermix with Denisovans or inherited far less Denisovan ancestry than neighboring mainland populations.
Denisovan-derived genes later appear in Japanese populations: individuals from the Kofun period (approximately A.D. 300–710) show higher Denisovan ancestry than the Jomon samples. The authors link this increase to large-scale migrations of East Asian groups into the archipelago during and after that era.
Possible explanations and limitations
The study's authors propose several explanations for the low Denisovan signal in Jomon genomes. Early human groups may have taken different migration routes through East Asia, avoiding contact with Denisovan populations, or Denisovans may have been sparsely distributed so that encounters were rare and regionally uneven.
However, the researchers emphasize limitations in the current dataset. The oldest available Jomon genome is only about 9,000 years old, while archaeological evidence indicates modern humans were present in the Japanese archipelago as early as 32,000 years ago. Genetic data covering that ~23,000-year gap could clarify when and how different ancestries entered Japan and help resolve the early population history of the region.
Why this matters
Tracing Denisovan ancestry provides a useful marker for reconstructing ancient population movements across Eurasia. These results refine our understanding of how Denisovan genes were distributed and mixed into modern human populations—revealing that interaction with Denisovans was complex, regionally varied, and shaped by migration events long before recorded history.
Reference: Jiaqi Yang et al., Current Biology, Oct. 20 (study on Denisovan ancestry in ancient and modern genomes).
