Genomic insights into the peopling of the Southwest Pacific
Open accessAbstract
The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago marked the beginning of the last major human dispersal to unpopulated lands. However, the relationship of these pioneers to the long-established Papuan people of the New Guinea region is unclear. Here we present genome-wide ancient DNA data from three individuals from Vanuatu (about 3,100–2,700 years before present) and one from Tonga (about 2,700–2,300 years before present), and analyse them with data from 778 present-day East Asians and Oceanians. Today, indigenous people of the South Pacific harbour a mixture of ancestry from Papuans and a population of East Asian origin that no longer exists in unmixed form, but is a match to the ancient individuals. Most analyses have interpreted the minimum of twenty-five per cent Papuan ancestry in the region today as evidence that the first humans to reach Remote Oceania, including Polynesia, were derived from population mixtures near New Guinea, before their further expansion into Remote Oceania. However, our finding that the ancient individuals had little to no Papuan ancestry implies that later human population movements spread Papuan ancestry through the South Pacific after the first peopling of the islands.
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Ancient DNA studies of Polynesia have sequenced only four samples from one western Polynesian island and three near-modern samples from one eastern Polynesian island, with low genotype density and limited overlap.
“Meanwhile, ancient DNA studies have sequenced only four samples from one island in western Polynesia and three near-modern samples from one island in eastern Polynesia, all with low genotype density, still lower between-sample genotype overlap, and different time frames17,18.”
From Paths and timings of the peopling of Polynesia inferred from genomic networks (2021) · cites this paper as [17]
The paper’s ancient-DNA passage (section labeled Abstract; page unavailable) explicitly places its four sequenced individuals on two islands: three on Efate, Vanuatu, and one on Tongatapu, Tonga—not four on one western Polynesian island. It reports 139,461–231,944 covered SNPs per individual, but does not report three near-modern eastern Polynesian samples or the claimed between-sample genotype overlap. (LLM, conf=0.88)
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Experimental — accuracy not yet measuredPolynesians are predominantly descended from Austronesian-speaking voyagers.
“The Polynesians are predominantly descended from Austronesian-speaking voyagers17”
From Paths and timings of the peopling of Polynesia inferred from genomic networks (2021) · cites this paper as [17]
The paper’s ancestry-model passage (labelled Abstract in our copy; no page given) identifies a population related to the First Remote Oceanians as the primary component in present-day Polynesians, and describes seafaring settlement of Remote Oceania. It does not establish that those ancestral voyagers spoke Austronesian languages; the Extended Data table labels some present-day sampled populations Austronesian-speaking, but not the ancient voyagers. (LLM, conf=0.82)
Experimental — accuracy not yet measuredAdmixture between Papuan and Austronesian source populations occurred on Vanuatu and other Melanesian islands in the thousand years before Polynesian settlement and was carried into Polynesia during settlement.
“(Admixture between populations stemming from these two sources occurred on Vanuatu and other Melanesian islands in the thousand years before the settlement of Polynesia and was carried into Polynesia during its settlement17,79.)”
From Paths and timings of the peopling of Polynesia inferred from genomic networks (2021) · cites this paper as [17]
The paper’s Abstract (page unavailable) dates Papuan–First Remote Oceanian mixture to roughly 1,500–2,300 years before present and finds Papuan ancestry in present-day Polynesians. It does not locate that mixture on Vanuatu or other Melanesian islands, or establish that an already admixed population carried it into Polynesia during settlement. Instead, the ancient Vanuatu and Tongan individuals had little or no Papuan ancestry, and the paper infers later movements into Remote Oceania. (LLM, conf=0.86)
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Zammit, N. W., Siggs, O. M., Gray, P. E., Horikawa, K., Langley, D. B., Walters, S. N., Daley, S. R., Loetsch, C., Warren, J., Yap, J. Y., et al. (2019) · Nature Immunology · doi:10.1038/s41590-019-0492-0 · Cited by 80 · see citing works
Self-citationHudjashov, G., Endicott, P., Post, H., Nagle, N., Ho, S. Y. W., Lawson, D. J., Reidla, M., Karmin, M., Rootsi, S., Metspalu, E., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20026-8 · Cited by 72 · see citing works
Self-citationGenetic Ancestry of Rapanui before and after European Contact
Fehren-Schmitz, L., Jarman, C. L., Harkins, K. M., Kayser, M., Popp, B. N., & Skoglund, P. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.029 · Cited by 47 · see citing works
Self-citationAncient Rapanui genomes reveal resilience and pre-European contact with the Americas
Moreno-Mayar, J. V., Sousa da Mota, B., Higham, T., Klemm, S., Gorman Edmunds, M., Stenderup, J., Iraeta-Orbegozo, M., Laborde, V., Heyer, E., Torres Hochstetter, F., et al. (2024) · Nature · doi:10.1038/s41586-024-07881-4 · Cited by 20 · see citing works
- Authors
- Skoglund, P., Posth, C., Sirak, K., Spriggs, M., Valentin, F., Bedford, S., Clark, G. R., Reepmeyer, C., Petchey, F., Fernandes, D., Fu, Q., Harney, E., Lipson, M., Mallick, S., Novak, M., Rohland, N., Stewardson, K., Abdullah, S., Cox, M. P., Friedlaender, F. R., Friedlaender, J. S., Kivisild, T., Koki, G., Kusuma, P., Merriwether, D. A., Ricaut, F.-X., Wee, J. T. S., Patterson, N., Krause, J., Pinhasi, R., & Reich, D.
- Affiliations
- Broad Institute (US)
- Max Planck Institute of Geoanthropology (DE)
- University College Dublin (IE)
- Australian National University (AU)
- James Cook University (AU)
- University of Waikato (NZ)
- Harvard University (US)
- Raja Isteri Pengiran Anak Saleha Hospital (BN)
- Massey University (NZ)
- Temple University (US)
- University of Cambridge (GB)
- Papua New Guinea Institute of Medical Research (PG)
- Eijkman Institute for Molecular Biology (ID)
- Binghamton University (US)
- National Cancer Centre Singapore (SG)
- Corresponding author
- Skoglund, Pontus
- Pinhasi, Ron
- Reich, David
- ORCID
- Skoglund, Pontus
- Posth, Cosimo
- Sirak, Kendra
- Spriggs, Matthew
- Bedford, Stuart
- Clark, Geoffrey R.
- Reepmeyer, Christian
- Petchey, Fiona
- Fernandes, Daniel
- Fu, Qiaomei
- Lipson, Mark
- Mallick, Swapan
- Novak, Mario
- Rohland, Nadin
- Cox, Murray P.
- Kivisild, Toomas
- Kusuma, Pradiptajati
- Merriwether, D. Andrew
- Wee, Joseph T. S.
- Patterson, Nick
- Krause, Johannes
- Pinhasi, Ron
- Reich, David
- Venue
- Nature
- Published
- 2016-10-03
- Volume
- 538
- Issue
- 7626
- Pages
- 510-513
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5515717
- OpenAlex
- W2524596543
- Semantic Scholar
- c1958cda26f2fe0c480bca42ba9cce5d643a4c8e
- Cited by
- 414
- References
- 61
- Citations by year
- 2026: 22 · 2025: 56 · 2024: 84 · 2023: 24 · 2022: 30 · 2021: 36 · 2020: 32 · 2019: 37 · 2018: 56 · 2017: 33 · 2016: 3
- FWCI
- 34.70
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion, public-domain)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- ResearchOnline at James Cook University (James Cook University) (submittedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, public-domain)
- HAL (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Science Foundation (1032255)
- Howard Hughes Medical Institute
- National Geographic Society
- Deutsche Forschungsgemeinschaft (KR 4015/1-1)
- Agence Nationale de la Recherche (ANR-14-CE31-0013)
- National Natural Science Foundation of China
- Irish Research Council (GOIPG/2013/36, GOIPD/2013/1)
- Chinese Academy of Sciences
- Max-Planck-Gesellschaft
- Vetenskapsrådet
- Centre National de la Recherche Scientifique (UMR 7041)
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM100233)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Geography, Planning and Development › Pacific and Southeast Asian Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- ancient DNA, Vanuatu, Tonga, Lapita culture, human dispersal, population admixture, East Asian ancestry, Polynesia, South Pacific islands
- MeSH terms
- Pacific Island People, Female, Genetics, Population, Humans, Male, New Guinea, Vanuatu, Phylogeny, Polynesia, Tonga, Genome, Human, Genomics, Asian People, History, Ancient, Human Migration
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