From Off the Coast of Taiwan to the Japanese Archipelago: Did the Jomon People "Not Meet"? — What "Almost Zero" Denisovan DNA Reveals About the History of the Archipelago

What "Almost No 'Denisovan Shadow' in Jomon People" Means

"Jomon people have almost no DNA derived from Denisovans"—this statement is quietly redrawing the map of human history in East Asia. Reported by Live Science on November 11, 2025, the basis of this revelation is a large-scale genome study published in Current Biology by an international team including the Max Planck Institute for Evolutionary Anthropology. The study cross-compared genomes of ancient and modern humans across Eurasia, illustrating the history of interbreeding with Denisovans in East Asia in terms of "time and space." One conclusion is the surprising scarcity of Denisovan ancestry in the prehistoric Jomon people of the Japanese archipelago.Live Sciencempg.de

What Was Investigated?

The research team analyzed the genomes of 115 ancient Homo sapiens individuals and 279 modern humans from various parts of Eurasia. They tracked small DNA fragments derived from Denisovans as "fingerprints" to estimate where and how much interbreeding occurred over the past 40,000 years. The highest Denisovan ancestry was found in a Tianyuan individual from China about 40,000 years ago, with a proportion of approximately 0.25%. In contrast, the Jomon individuals showed an "extremely low" level.Live Science

Numbers Speak of "Contrast"

According to Live Science, the Denisovan ancestry shown by a Jomon individual from about 3755 years ago is "one-sixth to one-eighth" that of modern East Asians (averaged at about 0.1%). In other words, the Denisovan traces in Jomon individuals are "remarkably faint" compared to other groups in the same region. This "faintness" is likely not coincidental but reflects differences in population history.Live Science

Why is Jomon "Faint"?—Two Hypotheses

The study does not definitively determine the mechanism, but at least two explanations are offered.

1. During the early dispersal in East Asia,some lineages reached coastal Asia without contacting Denisovans.

2. Denisovans were sparsely distributed geographically,making contact opportunities rare.
   Both hypotheses suggest that the Jomon followed a path diverging from the "typical interbreeding history" of continental East Asia.mpg.de

Yet the "Denisovan Shadow" Entered the Japanese Archipelago

Interestingly, individuals from the Kofun period (around 300–710 AD) show more Denisovan ancestry than the Jomon. This can be interpreted as the result ofmigration from the continentspreading to the archipelago at the DNA level during the Yayoi to Kofun periods. This aligns with the "triple structure" model explaining ancient Japan's formation from three lineages (Jomon, Northeast Asia, East Asia) and studies indicating East Asian influx during the Kofun period.Live Science

"Reversal of Density" in East and West Eurasia

The analysis also showed a geographical gradient where ancient "continental East Asia" populations had generally higher Denisovan ancestry, whereas ancient Western Eurasia (such as Iran and Georgia) had the least. Denisovan DNA acts like a "tracking dye" for human migration, imprinting the memory of early contacts onto geography.Live Science

Where Were the "Denisovans"?

In the spring of 2025, there were reports that a jawbone found on the seabed off Taiwan was identified asDenisovan. Although DNA was not obtained, enamel protein analysis of the teeth confirmed it, reinforcing the possibility that Denisovans were distributed from Siberia to inland China, the Qinghai-Tibet Plateau, and even near Taiwan. Such a wide distribution could have led to "biased contact"—the "faintness" in Jomon might be one aspect of this bias.Reuters

The "23,000-Year Gap" Still Unfilled

The current conclusions depend on the available data. The oldest Jomon genome is about 9,000 years old, and while there is evidence of human habitation from 32,000 years ago, ancient DNA from that period remains undeciphered. Filling this gap could clarify when and where the Jomon lineage diverged from continental lineages and at what stage they did not receive the "Denisovan shadow."Live Science

Reactions on Social Media—A Glimpse from the Japanese Sphere

Since the research announcement, reactions have been observed on X (formerly Twitter), particularly among archaeology and anthropology clusters (all summaries are paraphrased).

• A thread from a research introduction account organizing the point that **"Jomon has the smallest Denisovan influence in East Asia"** and expressing anticipation for additional data.X (formerly Twitter)

• A hobby account's paper note pointing out that the results fit into the framework of **"Jomon as a deeply diverged lineage mixed with coastal East Asian ancestors."**X (formerly Twitter)

• A post discussing the comparison that **"Jomon, like Onge (Andaman), has little Denisovan,"** and debating its relation to cold adaptation and paleogeography.X (formerly Twitter)

• Academic news has spread to general magazines, withscience media like IFLScience disseminating it overseas. Numerous simplified articles for general readers have been widely shared.IFLScience

※The summaries of SNS are excerpts and summaries by the author. Refer to the original text at the linked sources.

Researchers' Comments Indicate "Interpretation"

The Max Planck side emphasizes that "Denisovan DNA is a powerful marker for reconstructing population history." Especially in East Asia, traces of "common contact events" are shared among individuals of each era, and subsequent **"dilution" mixing on the continental sidelowered the ratio over time, according to their view. Jomon stands out as a lineage that either did not undergo this "dilution" ordid not experience the primary contact in the first place.mpg.de

Implications for the History of the Japanese Archipelago

• Jomon is not an "exception" buta cross-section of diverse East Asia.

• The influx of continental elementsdue to migration during the Yayoi to Kofun periodsmay have elevated the Denisovan ancestry in the archipelago.PMC

• The triple structure model(Jomon + Northeast Asia + East Asia) being established in the 21st century and the migration image of the Kofun period are mutually reinforcing.ScienceDaily

Limitations and Next Steps

• Temporal Bias: Direct data from the older layers of Jomon (~30,000 years ago) is missing.Live Science

• Geographical Bias: Ancient genomes from the southern edge of East Asia and island regions are still scarce.

• Scarcity of Denisovan Fossils: While the range is wide, as with the jawbone off Taiwan, physical evidence is limited.Reuters

Nevertheless, this study demonstrates that "traces of human encounters" can be depicted from tiny fragments of DNA. The origin story of the Japanese archipelago also appears not as asingle line but as a collage of overlaps and gaps.