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Modern humans

A 2011 study found that Denisovan DNA is prevalent in Papuans, Aboriginal Australians, Near Oceanians, Polynesians, Fijians, Eastern Indonesians, and Aeta (from the Philippines); but not in East Asians, western Indonesians, Jahai people (from Malaysia), or Onge (from the Andaman Islands). This may suggest that Denisovan introgression occurred within the Pacific region rather than on the Asian mainland, and that ancestors of the latter groups were not present in Southeast Asia at the time. In the Melanesian genome, about 4–6% or 1.9–3.4% derives from Denisovan introgression. Prior to 2021, New Guineans and Australian Aborigines were reported to have the most introgressed DNA, but Australians have less than New Guineans. A 2021 study discovered 30 to 40% more Denisovan ancestry in Aeta people in the Philippines than in Papuans, estimated as about 5% of the genome. The Aeta Magbukon in Luzon have the highest known proportion of Denisovan ancestry of any population in the world. In Papuans, less Denisovan ancestry is seen in the X chromosome than autosomes, and some autosomes (such as chromosome 11) also have less Denisovan ancestry, which could indicate hybrid incompatibility. The former observation could also be explained by less female Denisovan introgression into modern humans, or more female modern human immigrants who diluted Denisovan X chromosome ancestry.

In contrast, 0.2% derives from Denisovan ancestry in mainland Asians and Native Americans. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians. The discovery of the 40,000-year-old Chinese modern human Tianyuan Man lacking Denisovan DNA significantly different from the levels in modern-day East Asians discounts the hypothesis that immigrating modern humans simply diluted Denisovan ancestry whereas Melanesians lived in reproductive isolation. A 2018 study of Han Chinese, Japanese, and Dai genomes showed that modern East Asians have DNA from two different Denisovan populations: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from Denisova Cave. This could indicate two separate introgression events involving two different Denisovan populations. In South Asian genomes, DNA only came from the same single Denisovan introgression seen in Papuans. A 2019 study found a third wave of Denisovans which introgressed into East Asians. Introgression, also, may not have immediately occurred when modern humans immigrated into the region.

The timing of introgression into Oceanian populations likely occurred after Eurasians and Oceanians split roughly 58,000 years ago, and before Papuan and Aboriginal Australians split from each other roughly 37,000 years ago. Given the present day distribution of Denisovan DNA, this may have taken place in Wallacea, though the discovery of a 7,200 year old Toalean girl (closely related to Papuans and Aboriginal Australians) from Sulawesi carrying Denisovan DNA makes Sundaland another potential candidate. Other early Sunda hunter gatherers so far sequenced carry very little Denisovan DNA, which either means the introgression event did not take place in Sundaland, or Denisovan ancestry was diluted with gene flow from the mainland Asian Hòabìnhian culture and subsequent Neolithic cultures.

In other regions of the world, archaic introgression into humans stems from a group of Neanderthals related to those which inhabited Vindija Cave, Croatia, as opposed to archaics related to Siberian Neanderthals and Denisovans. However, about 3.3% of the archaic DNA in the modern Icelandic genome descends from the Denisovans, and such a high percentage could indicate a western Eurasian population of Denisovans which introgressed into either Vindija-related Neanderthals or immigrating modern humans.

Denisovan genes may have helped early modern humans migrating out of Africa to acclimatize. Although not present in the sequenced Denisovan genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles (involved in the immune system 's natural killer cell receptors) has led to the suggestion that it introgressed from Denisovans into modern humans in West Asia. In a 2011 study, half of the HLA alleles of modern Eurasians were shown to represent archaic HLA haplotypes, and were inferred to be of Denisovan or Neanderthal origin. A haplotype of EPAS1 in modern Tibetans, which allows them to live at high elevations in a low-oxygen environment, likely came from Denisovans. Genes related to phospholipid transporters (which are involved in fat metabolism) and to trace amine-associated receptors (involved in smelling) are more active in people with more Denisovan ancestry. Denisovan genes may have conferred a degree of immunity against the G614 mutation of SARS-CoV-2. Denisovan introgressions may have influenced the immune system of present-day Papuans and potentially favoured "variants to immune-related phenotypes" and "adaptation to the local environment".

In December 2023, scientists reported that genes inherited by modern humans from Neanderthals and Denisovans may biologically influence the daily routine of modern humans.