Abstract

The appearance of people associated with the Lapita culture in the South Pacific around 3,000 years ago1 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 Oceania2,3,4,5. 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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Accessions

Primary accessions

European Nucleotide Archive

Data deposits

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB14728. The newly reported SNP genotyping data for the subset of individuals who provided informed consent consistent with fully public distribution are available at http://genetics.med.harvard.edu/reichlab/Reich_Lab/Datasets.html. To access data for the remaining samples, researchers should send a signed letter to D.R. containing the following text: “(a) I will not distribute the data outside my collaboration; (b) I will not post the data publicly; (c) I will make no attempt to connect the genetic data to personal identifiers for the samples; (d) I will use the data only for studies of population history; (e) I will not use the data for any selection studies; (f) I will not use the data for medical or disease-related analyses; (g) I will not use the data for commercial purposes.” Extended Data Table 2 specifies which samples are consistent with which type of data distribution.

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Acknowledgements

We thank the 356 volunteers who donated samples for genome-wide analysis; M. Stoneking for co-funding genotyping of the Bismarck samples; M. Brilliant, H. Norton, and L. Scheinfeldt, for help in the preparation of the Bismarck samples and establishment of a repository for them at the Marshfield Foundation; A. Wissgott for help in data generation from the ancient Tongan individual; A. Kim, I. Pugach, and M. Stoneking for comments, and I. Mathieson for critiques and advice on estimating sex-specific ancestral contributions. The maps in Figs 1a and 3b–e maps were plotted in R using the world() map of the ‘fields’ and ‘maps’ packages (using public domain data from the CIA World Data Bank II). P.S. was supported by the Wenner-Gren foundation, SciLifeLab, and the Swedish Research Council (VR grant 2014-453). The Teouma research by M.S. and S.B. was supported by the Australian Research Council (Discovery Grants DP0880789 and DP110101415), the National Geographic Society, and the Australia-Pacific Science Foundation. F.V. was supported by CNRS-UMR 7041. M.N. was supported by an Irish Research Council grant (GOIPD/2013/1). D.F. was supported by an Irish Research Council grant (GOIPG/2013/36). Q.F. was funded by the Key Research Program of Frontier Sciences of CAS (QYZDB-SS W-DQC003), the National Natural Science Foundation of China (L1524016) and the Chinese Academy of Sciences Discipline Development Strategy Project (2015-DX-C-03). T.K. was supported by ERC starting grant FP7-261213. C.P. and J.K. were supported by the Baden Wuerttemberg Foundation. J.K was supported by the DFG grant KR 4015/1-1 and the Max Planck Society. R.P. was supported by ERC starting grant ADNABIOARC (263441). D.R. was supported by NIH grant GM100233, by NSF HOMINID BCS-1032255, and is a Howard Hughes Medical Institute investigator.

Author information

Author notes

    • Ron Pinhasi
    •  & David Reich

    These authors jointly supervised this work.

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Pontus Skoglund
    • , Qiaomei Fu
    • , Eadaoin Harney
    • , Mark Lipson
    • , Swapan Mallick
    • , Nadin Rohland
    • , Kristin Stewardson
    •  & David Reich
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Pontus Skoglund
    • , Eadaoin Harney
    • , Swapan Mallick
    • , Kristin Stewardson
    • , Nick Patterson
    •  & David Reich
  3. Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden

    • Pontus Skoglund
  4. Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany

    • Cosimo Posth
  5. Max Planck Institute for the Science of Human History, 07745 Jena, Germany

    • Cosimo Posth
    •  & Johannes Krause
  6. School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Dublin, Ireland

    • Kendra Sirak
    • , Daniel Fernandes
    • , Mario Novak
    •  & Ron Pinhasi
  7. Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA

    • Kendra Sirak
  8. School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, Australian Capital Territory 2601, Australia

    • Matthew Spriggs
  9. Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu

    • Matthew Spriggs
    •  & Stuart Bedford
  10. Maison de l’Archéologie et de l’Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France

    • Frederique Valentin
  11. Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, Australian Capital Territory 2601, Australia

    • Stuart Bedford
    •  & Geoffrey R. Clark
  12. College of Arts, Society and Education, James Cook University, Queensland 4870, Australia

    • Christian Reepmeyer
  13. Radiocarbon Dating Laboratory, University of Waikato, Hamilton 3240, New Zealand

    • Fiona Petchey
  14. CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal

    • Daniel Fernandes
  15. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  16. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Qiaomei Fu
  17. Institute for Anthropological Research, 10000 Zagreb, Croatia

    • Mario Novak
  18. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Kristin Stewardson
    •  & David Reich
  19. RIPAS Hospital, Bandar Seri Begawan, Brunei Darussalam

    • Syafiq Abdullah
  20. Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

    • Murray P. Cox
  21. Independent Scientist, Sharon, Connecticut 06069, USA

    • Françoise R. Friedlaender
  22. Department of Anthropology, Temple University, Gladfelter Hall, Philadelphia, Pennsylvania 19122, USA

    • Jonathan S. Friedlaender
  23. Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia

    • Toomas Kivisild
  24. Division of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK

    • Toomas Kivisild
  25. Papua New Guinea Institute of Medical Research, Goroka, Eastern Highlands Province 441, Papua New Guinea

    • George Koki
  26. Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia

    • Pradiptajati Kusuma
  27. Department of Anthropology, Binghamton University, Binghamton, New York 13902, USA

    • D. Andrew Merriwether
  28. Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université de Toulouse, Toulouse 31073, France

    • Francois-X. Ricaut
  29. National Cancer Centre Singapore, Singapore 169610, Singapore

    • Joseph T. S. Wee

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Contributions

N.P., J.K., R.P. and D.R. supervised the study. M.S., F.V., S.B., G.R.C., and C.R. assembled archaeological material and information. P.S., C.P., Q.F., M.L., S.M., N.R. and D.R. analysed genetic data. C.P., K.Si., F.P., D.F., E.H., M.N., N.R, and K.St. performed laboratory work. S.A., M.P.C., F.R.F., J.S.F., T.K., G.K., P.K., D.A.M., F-X.R., and J.T.S.W. assembled the sample collection from present-day populations. P.S. and D.R. wrote the manuscript with major input from C.P., M.S., F.V., G.R.C., M.P.C., J.S.F, J.K. and R.P. and additional input from all other co-authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Pontus Skoglund or Ron Pinhasi or David Reich.

Reviewer Information

Nature thanks P. Bellwood, C. Capelli and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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    Supplementary Information

    This file contains Supplementary Notes 1-3, Supplementary Table 1 and additional references.

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https://doi.org/10.1038/nature19844

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