Scientists learn not all early East Asians mixed with Denisovans, upending common beliefs

Modern humans carry traces of Denisovan DNA inherited from multiple genetically distinct groups. A new paleogenomic study pulls those threads together and shows when, where, and how that ancestry ebbed and flowed across Eurasia over the last 40,000 years.

Experts at Max Planck Society assembled published ancient genomes from across the continent and systematically scanned for DNA segments inherited from Denisovans in both ancient and present-day people.

By following these fragments through space and time, they were able to chart waves of contact, later dilution by newcomers, and the long-distance movements that carried Denisovan ancestry far from its original sources.

The result is the first continent-wide, time-layered picture of how Denisovan DNA moved through human populations after the initial interbreeding events.

Fossil reveals Denisovan peak

One of the clearest anchors in the timeline is the Tianyuan individual from northern China, dated to roughly 40,000 years ago.

Among all later ancient and living humans examined, this person carried the highest measured proportion of Denisovan ancestry – just over 0.2 percent.

That figure is modest in absolute terms but striking in context, because it outpaces levels seen in later East Asians and reveals that the earliest populations in the region once carried a stronger Denisovan imprint.

Crucially, the shared patterns of Denisovan segments among different East Asian individuals point to common episodes of contact, not a jumble of unrelated encounters.

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

Denisovan DNA thins, drifts west

If early East Asians started out with more Denisovan ancestry, what happened next? The segment patterns suggest that later population movements from groups with little or no Denisovan DNA spread into East Asia and thinned that signal over time.

At the same time, a trickle of Denisovan ancestry flowed in the opposite direction: the study detected a minimal but real presence in West Eurasia, carried by people moving out of Eastern Eurasia beginning around 12,000 years ago.

That “leakage” doesn’t imply direct West Eurasian–Denisovan contact. Instead, it traces later human migrations that transported the genetic legacy westward.

Denisovan DNA gap in Japan

Not every lineage in East Asia met Denisovans directly. Ancient genomes from the Jomon of the Japanese archipelago and the Ryukyu/Okinawa Islands – who contributed to today’s Japanese – show the lowest Denisovan ancestry among East Asians.

The most parsimonious explanation is that Jomon ancestors branched from a lineage that did not encounter Denisovans, and only later received limited Denisovan DNA via gene flow from continental populations.

A second possibility is an early, weak Denisovan contact before they split from other East Asians, followed by missing a later, larger pulse on the mainland.

“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,” said lead author Jiaqi Yang, a Ph.D. researcher at the Max Planck Institute for Evolutionary Anthropology.

The Jomon case underscores how regional dispersal paths could have funneled some groups toward Denisovan contact zones while routing others around them entirely.

Multiple Denisovans, multiple histories

The big picture that emerges is not a single “Denisovan event,” but repeated episodes of interbreeding with genetically distinct Denisovan groups. Such episodes were then followed by layers of human migration that reweighted that ancestry.

Some early East Asians carried more Denisovan DNA, later diluted by incoming populations. Small amounts rode east-to-west movements into Europe and the Near East.

In island Japan, a lineage largely sidestepped direct contact and only later picked up the signal from the mainland.

The mosaic fits with what we know from fossils and genomes: Denisovans were not a single, uniform population, and their range and density likely varied dramatically across Pleistocene Asia.

Ancient DNA maps human history

Because Denisovan segments are distinctive and relatively rare, they act like dye in water, allowing researchers to trace past population mixing that would otherwise be invisible.

In this study, those fragments reveal both the timing of dilution in East Asia and the later spread into West Eurasia, while also highlighting outliers like the Jomon that chart different paths.

As Peyrégne notes, the fragments are “a powerful marker to reconstruct population history,” turning archaic DNA into a map of human movement.

Lessons from Denisovan DNA

The researchers emphasize that gaps remain. Much of Paleolithic East Asia is still a genomic blank spot, and Denisovan remains are scarce.

More ancient genomes – especially from understudied regions and time windows – will clarify when the major pulses of Denisovan admixture occurred.

In addition, they will shed new light on how many Denisovan populations were involved and how later migrations reshaped the landscape of ancestry.

The study is published in the journal Current Biology.

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