Ancient Jomon Lacked Denisovan DNA — A Rare Exception That Rewrites Part of East Asian Prehistory

07:29 PM, 12/05/2025

The Current Biology study finds that prehistoric Jomon people from the Japanese archipelago (≈16,000–3,000 years ago) carried almost no Denisovan ancestry, unlike most East Asian groups. Researchers analyzed ancient genomes across Eurasia and found Denisovan DNA common in many East Asian lineages but absent in Jomon samples. The team offers two main explanations: the Jomon derive from a separate, less-admixed branch, or Denisovan admixture arrived after the Jomon became isolated. The result refines models of human dispersal and shows Denisovan DNA is a powerful tracer of population history.

Ancient Jomon Lineage Missing Denisovan Ancestry

Researchers report a surprising genetic anomaly: prehistoric Jomon people of the Japanese archipelago carried almost no Denisovan ancestry, a pattern that runs counter to most other East Asian lineages. The finding appears in a study published in Current Biology and sheds new light on complex human dispersals and archaic contact across Eurasia.

What the Study Found

By compiling and analyzing ancient genomes from across Eurasia, the team mapped the distribution and timing of Denisovan admixture in modern humans. While many East Asian populations display detectable Denisovan-derived DNA—often at higher levels than Western Eurasians—the Jomon (who lived on the Japanese archipelago roughly 16,000–3,000 years ago) showed the lowest Denisovan ancestry among both ancient and present-day East Asians.

How Researchers Interpreted the Result

The authors propose two main, non-mutually exclusive explanations for this absence:

Separate Early Branch: The Jomon may descend partly from a distinct branch of modern humans that initially did not interbreed with Denisovans and later remained relatively isolated.
Later Denisovan Admixture Into Mainland Populations: Denisovan genetic contributions may have entered broader East Asian populations after Jomon ancestors became isolated on the archipelago, so the Jomon missed that admixture episode.

Evidence and Broader Implications

Genome comparisons indicate that many East Asian groups share Denisovan-derived segments consistent with a common admixture event, but those segments are absent in Jomon genomes. As the study notes, this pattern "implies different dispersals for modern humans into East Asia and suggests that Denisovans were sparsely distributed in the region."

"Denisovan DNA represents a powerful marker to reconstruct population history," said Stéphane Peyrégne, co-supervisor of the study, noting that gene flow from sources with little or no Denisovan ancestry could dilute Denisovan signals in some early East Asian groups.

Why This Matters

The Jomon exception complicates simple narratives of archaic-human interaction across Eurasia and highlights uneven geographic distribution of Denisovans and their genetic legacy. Using Denisovan markers as a tracer helps researchers refine models of migration, isolation, and population contact in prehistoric East Asia.

Further Reading: The full analysis and datasets are detailed in the paper published in Current Biology.

Ancient Jomon Lacked Denisovan DNA — A Rare Exception That Rewrites Part of East Asian Prehistory

Ancient Jomon Lineage Missing Denisovan Ancestry

What the Study Found

How Researchers Interpreted the Result

Evidence and Broader Implications

Why This Matters

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