The people with the most Denisovan DNA today are the Ayta Magbukon, an indigenous group in the Philippines, who carry 30% to 40% more Denisovan ancestry than Papuans and Aboriginal Australians. Beyond this group, Denisovan DNA is found at meaningful levels across Melanesia (4 to 6 percent of total genome), at lower levels in other Southeast Asian and Pacific Islander populations, and at very low or undetectable levels in most of the rest of the world.
Populations With the Highest Levels
For years, Papuans and Aboriginal Australians were thought to carry the world’s highest proportion of Denisovan DNA. A 2021 study in Current Biology overturned that assumption. The Ayta Magbukon, a Philippine Negrito group, carry significantly more Denisovan sequence per person: roughly 52 megabases of Denisovan DNA on average, compared to about 42 megabases in Papuans. That gap holds up even though the Ayta Magbukon have 10% to 20% recent East Asian admixture that would have diluted their archaic ancestry. Researchers estimated that the ancestral Negrito population before any East Asian mixing carried about 46% more Denisovan DNA than highland Papuans, consistent with an independent admixture event between Denisovans and the ancestors of Philippine Negritos.
Melanesian populations, including Papuans, remain the most well-studied group. Their 4 to 6 percent Denisovan ancestry means that for every 100 stretches of their genome, four to six trace back to a Denisovan ancestor. Other Southeast Asian and Pacific Islander groups carry smaller but still detectable amounts.
Traces in East and South Asia
Mainland Asian populations carry Denisovan DNA too, but in much smaller quantities. A 40,000-year-old skeleton found near Beijing (known as the Tianyuan individual) carried genomic segments of Denisovan origin, and those segments match the same admixture event that contributed to present-day mainland Asians. Crucially, this is a different source of Denisovan DNA than what shows up in Papuans and Aboriginal Australians, meaning separate groups of Denisovans interbred with different waves of modern humans.
One recent finding adds nuance to the East Asian picture. The Jomon people, ancient hunter-gatherers of the Japanese archipelago who diverged early from other East Asian lineages, appear to carry little to no Denisovan ancestry. This suggests that Denisovan DNA entered East Asian populations through specific migration routes and mixing events, not as a blanket inheritance shared by everyone in the region.
At Least Three Separate Mixing Events
Denisovan ancestry in modern humans did not come from a single encounter. Genetic evidence now points to at least three distinct introgression events, each involving a different Denisovan population. These Denisovan groups varied in how closely they were related to the one individual whose genome was sequenced from a Siberian cave (the Altai Denisovan). Some were closely related to that reference genome; others were genetically distant. This means Denisovans were not a single, uniform group. They likely spanned a wide geographic range and adapted to very different environments, from high-altitude plateaus to tropical lowlands.
The physical evidence backs this up. Denisovan fossils and DNA have been recovered from Denisova Cave in Siberia and from Baishiya Karst Cave on the Tibetan Plateau, where Denisovans lived from at least 160,000 years ago until roughly 45,000 to 60,000 years ago. A tooth from Laos extends their known range into Southeast Asia. That sprawling territory helps explain how multiple, genetically distinct Denisovan populations encountered modern humans at different times and places.
Genes That Still Matter Today
Some inherited Denisovan DNA has had a measurable impact on the health and survival of modern populations. The most famous example involves Tibetans. A gene called EPAS1, which regulates the body’s response to low oxygen, carries a variant that almost certainly came from Denisovans. People with this variant produce less hemoglobin at high altitude than they otherwise would. That sounds counterintuitive, but it’s protective: excessively high hemoglobin thickens the blood, raising the risk of heart problems. The Denisovan version of EPAS1 essentially fine-tunes the body for life above 4,000 meters, and it shows the strongest signal of natural selection found anywhere in the Tibetan genome.
In Inuit and other cold-adapted populations, a stretch of Denisovan-derived DNA affects two genes involved in how the body stores and distributes fat. These variants influence the differentiation of brown and “brite” fat cells, the types of fat tissue that generate heat. Changes in gene activity show up in subcutaneous fat and the adrenal gland, both relevant to cold tolerance and energy metabolism.
Immune Function and Allergies
Denisovans also passed along variants in a cluster of three immune receptor genes that serve as a first line of defense against bacteria, fungi, and parasites. People who carry the Denisovan-like version of these genes show higher expression of all three receptors in white blood cells. The practical result is a trade-off: carriers appear to have better resistance to certain bacterial infections (including lower rates of H. pylori, the bacterium linked to stomach ulcers) but higher susceptibility to allergies. The inherited immune genes essentially crank up the sensitivity of the body’s pathogen-detection system, which helps fight infection but also means the immune system overreacts to harmless substances like pollen or dust mites.
Can You Find Out Your Denisovan Ancestry?
Major consumer DNA testing services like 23andMe report Neanderthal ancestry percentages, but Denisovan reporting is far more limited. Because Denisovan DNA is very low or undetectable in most people of European and African descent, it simply doesn’t register for the majority of customers. For people with Southeast Asian, Melanesian, or Pacific Islander heritage, some specialized research tools and academic studies can estimate Denisovan contribution, but this is not yet a standard feature of commercial ancestry reports the way Neanderthal ancestry is.
If you do have roots in Southeast Asia or Oceania, any Denisovan DNA you carry is not just a curiosity. It includes functional gene variants that may influence your immune responses, your body’s management of fat and cold, and, if you live at altitude, how efficiently your blood carries oxygen. These are not relics. They are working parts of the genome, shaped by tens of thousands of years of natural selection after the original mixing took place.