Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania
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It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
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Denisovan DNA is known to account for up to 5% of the genome of present-day Papuans.
“This has allowed us to characterise the putative contribution of Denisovan DNA, which is known to account for up to 5% of the genome of present-day Papuans [4, 63], while also comparing it to that of Neanderthal DNA and non-archaic variants that arose following the Out of Africa event.”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [4]
The Introduction (p. 1) reports a previous estimate of 4%–6% Denisovan ancestry in Near Oceanians, including New Guineans. The paper’s own estimate for New Guineans is 3.5% (p. 11). These passages support a contribution of roughly 5%, but not 5% as a firm upper limit. (LLM, conf=0.82)
Experimental — accuracy not yet measuredDenisovan ancestry is most abundant in Oceanians (up to 5%), present in South Asians and East Asians, and very low in European populations.
“Denisovan ancestry, however, shows a more varied distribution: Oceanians have by far the most Denisovan ancestry (up to 5%) (Reich et al. 2011; Vernot et al. 2016), and while South Asians and East Asians also have some Denisovan ancestry, European populations have very little (Sankararaman et al. 2016; Witt et al. 2022).”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Reich et al. 2011
The Introduction (p. 1) reports 4%–6% Denisovan ancestry in Near Oceanians, and the results (p. 5) find New Guineans among the populations with the highest proportions. The paper does not establish the cited clause’s precise upper bound of 5%; its own later estimate for New Guineans is 3.5% (p. 11). The South Asian, East Asian, and European comparisons are attached to other citations in the citing sentence. (LLM, conf=0.84)
Experimental — accuracy not yet measuredPapuans owe up to 5% of their genome to Denisovans.
“Papuans, in particular, owe up to 5% of their genome to Denisovans”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [4]
The paper identifies Papuans as having Denisovan ancestry (Near Oceanian Ancestry, p. 6). But its own estimate for New Guineans is 3.5%, while it reports an earlier sequencing estimate of 4%–6% (Denisova Gene Flow, p. 11); neither establishes 5% as an upper bound. (LLM, conf=0.85)
Experimental — accuracy not yet measuredDenisovan introgression has been observed to be more variable than Neanderthal introgression.
“Denisovan introgression has been observed to be more variable [4].”
From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [4]
Admixture with Denisovans occurred, possibly in South-East Asia, and affected the ancestors of present-day populations in Oceania, introducing 4-6 % Denisovan ancestry in today's New Guineans, Aboriginal Australians and Bougainville Islanders.
“Admixture with Denisovans also occurred, possibly in South-East Asia [21], and affected the ancestors of present-day populations in Oceania, introducing 4–6 % Denisovan ancestry (in addition to their Neanderthal ancestry) in today’s New Guineans, Aboriginal Australians and Bougainville Islanders.”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [21]
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References 34 · Cited by 656
- Authors
- Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S., & Stoneking, M.
- Affiliations
- Broad Institute (US)
- Max Planck Institute for Evolutionary Anthropology (DE)
- Kaohsiung Medical University (TW)
- National Institute of Genetics (JP)
- Monash University Malaysia (MY)
- University of Cologne (DE)
- Erasmus MC (NL)
- Corresponding author
- Reich, David
- Stoneking, Mark
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2011-10
- Volume
- 89
- Issue
- 4
- Pages
- 516-528
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC3188841
- OpenAlex
- W2113439351
- Cited by
- 656
- References
- 34
- Citations by year
- 2026: 9 · 2025: 16 · 2024: 74 · 2023: 32 · 2022: 30 · 2021: 65 · 2020: 37 · 2019: 30 · 2018: 32 · 2017: 47 · 2016: 48 · 2015: 65 · 2014: 53 · 2013: 66 · 2012: 43
- FWCI
- 236.56
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- Unimas Institutional Repository (Universiti Malaysia Sarawak) (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Japan Society for the Promotion of Science (23247040)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- Denisovans, modern human dispersal, Southeast Asia, Oceania, Aboriginal Australians, Polynesians, East Asian ancestry
- MeSH terms
- Animals, Asia, Southeastern, Pan troglodytes, DNA, Mitochondrial, Biological Evolution, Genotype, Geography, Humans, Models, Genetic, Hominidae, Models, Statistical, Polymorphism, Single Nucleotide, Oceania, Native Hawaiian or Other Pacific Islander, Gene Flow
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