Genomic insights into the peopling of the Southwest Pacific (original) (raw)

Accession codes

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

1. Ron Pinhasi and David Reich: These authors jointly supervised this work.

Authors and Affiliations

1. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, 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, 02142, Massachusetts, USA
   Pontus Skoglund, Eadaoin Harney, Swapan Mallick, Kristin Stewardson, Nick Patterson & David Reich
3. Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, 10691, 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, Jena, 07745, 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, 30322, Georgia, USA
   Kendra Sirak
8. School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, 2601, Australian Capital Territory, 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, Nanterre, 92023, France
    Frederique Valentin
11. Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, 2601, Australian Capital Territory, 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. Department of Life Sciences, CIAS, University of Coimbra, Coimbra, 3000-456, 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, Zagreb, 10000, Croatia
    Mario Novak
18. Howard Hughes Medical Institute, Harvard Medical School, Boston, 02115, Massachusetts, 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, 19122, Pennsylvania, 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, Eastern Highlands Province 441, Goroka, Papua New Guinea
    George Koki
26. Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
    Pradiptajati Kusuma
27. Department of Anthropology, Binghamton University, Binghamton, 13902, New York, 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

Authors

1. Pontus Skoglund
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2. Cosimo Posth
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3. Kendra Sirak
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4. Matthew Spriggs
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5. Frederique Valentin
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6. Stuart Bedford
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7. Geoffrey R. Clark
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8. Christian Reepmeyer
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9. Fiona Petchey
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10. Daniel Fernandes
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11. Qiaomei Fu
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12. Eadaoin Harney
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13. Mark Lipson
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14. Swapan Mallick
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15. Mario Novak
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16. Nadin Rohland
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17. Kristin Stewardson
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18. Syafiq Abdullah
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19. Murray P. Cox
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20. Françoise R. Friedlaender
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21. Jonathan S. Friedlaender
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22. Toomas Kivisild
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23. George Koki
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24. Pradiptajati Kusuma
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25. D. Andrew Merriwether
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26. Francois-X. Ricaut
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27. Joseph T. S. Wee
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28. Nick Patterson
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29. Johannes Krause
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30. Ron Pinhasi
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31. David Reich
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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.

Corresponding authors

Correspondence toPontus Skoglund, Ron Pinhasi or David Reich.

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Competing interests

The authors declare no competing financial interests.

Additional information

Reviewer Information

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

Extended data figures and tables

Extended Data Figure 1 Ancient DNA authenticity.

a, PCA performed as for Fig. 1, but with the four ancient individuals represented only by sequences that show clear evidence of post-mortem damage (PMD score of at least 3) to remove contaminating sequences that might be present17,18. The numbers of SNPs remaining after restriction to damaged sequences is 68,450 SNPs for I1368; 98,722 SNPs for I1369; 83,024 SNPs for I1370; and 117,023 SNPs for CP30. The lines indicate the projection of the samples when no damage-restriction is performed. The large number of SNPs retained, and the fact that the ancient individuals cluster tightly and have the same qualitative positioning in the plot as Fig. 1, indicates that contamination did not contribute to our findings. We also find that estimates of Papuan ancestry using PMD score restricted data are consistent with those obtained using the full data (see Methods). b, Post-mortem damage patterns for genome-wide in-solution enrichment data from four ancient individuals.

Extended Data Figure 2 _f_-statistics document the Oceanian ancestry cline.

a, Shared genetic drift with the ancient Vanuatu individuals is negatively related to shared drift with Australians. Except for the ancient Tongan individual, populations from Taiwan, the Philippines and Polynesia share the most genetic drift with the ancient Vanuatu individuals, who are not shown in the plot because they are used as reference in the computation. The trend line was fitted without the East Asian populations in the off-cline cluster. The absence of off-cline Oceanian individuals suggests the possibility that present-day Oceanians may largely be derived from a mixture of two source populations. b, The ancient Vanuatu individuals and the ancient Tongan individual maximize statistics of the form _f_4(Yoruba, Test; Australian, Oceanian), suggesting that they are the most closely related to the East Asian ancestry in Oceanians of any sampled population. The trend line was fitted using populations >0.005 on the _x_-axis, together with the two populations with the lowest values on the _x_-axis (Papuan and New_Guinea). c, Biplot of First Remote Oceanian ancestry proportions against conditional heterozygosity. Populations with intermediate admixture proportion show the greatest genetic diversity. Thick and thin error bars in all panels are 1 and 1.96 standard errors of the estimate, respectively.

Extended Data Figure 3 Admixture date estimates.

a, Histogram of the point estimate dates in Fig. 2d. b, Admixture date estimates for Tongans using different pairs of source populations (‘Lapita’ in this figure refers to the pool of ancient Vanuatu individuals). Error bars show 1 (thick whiskers) and 1.96 (thin whiskers) standard errors. WGA, whole-genome amplified DNA.

Extended Data Figure 4 Admixture graph inferred using Treemix.

a, A simple tree-like model without admixture fits the data poorly, as can be seen from the matrix of residuals between empirical and modelled allele frequency covariance on the right. b, The optimal placement of a single 25% admixture event is from the lineage related to New Guinean Highlanders into the lineage leading to Tongans. Tongans derive the other portion of their ancestry from the lineage leading to the two ancient groups of individuals. This graph has no significant deviations between empirical and modelled allele frequency covariances.

Extended Data Figure 5 Admixture graphs modelling the population history of Australians.

Outlier _f_4-statistics are shown (|Z| > 3). a, A model with a single admixture edge positing that Australians are an outgroup to the Papuan ancestry in Tongans does not fit the data (5 outlier statistics). b, An alternative model with 2 admixture edges in which the Papuan ancestry in Tongans also contributed to Australians fits the data (no outliers). c, A model with 2 admixture edges in which New Guinean Highlanders are admixed from an Australian source after the divergence of the Papuan source in Tongans does not fit the data (5 outliers). d, A model with 2 admixture edges in which the Papuan ancestry in Tongans is intermediate between the New Guinean Highlander lineage and the Australian lineage. Branch lengths are in units of _F_ST × 1,000. Lapita in this figure refers only to Vanuatu, which is the only group for which we have multiple individuals.

Extended Data Figure 6 First Remote Oceanian ancestry today comes primarily from females.

a, Illustration of the rationale for using the X chromosome to study asymmetrical admixture between males and females. The example on the left illustrates admixture with equal proportion of males and females in both the red and the yellow ancestral population. The example on the right illustrates an extreme case of asymmetrical admixture where the red ancestral population only contributes females and the yellow ancestral population only contributes males to the admixed generation, demonstrating the disproportional contribution of X chromosomes by females to the admixed population. b, Female and male ancestral contributions based on an admixture model fitted to estimated ancestry proportions on the autosomes and X chromosome. We show the 95%, 70%, and 5% highest posterior intervals for four selected populations from Polynesia (Samoans), the Solomon Islands (Kolombangara), Bougainville (Nasioi), and mainland New Guinea (Papuans).

Extended Data Table 1 In-solution DNA enrichment and sequencing of ancient individuals

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Extended Data Table 2 356 individuals newly genotyped on the Human Origins Array

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Extended Data Table 3 _f_-statistics for populations on the Oceanian cline

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Extended Data Table 4 Ancestry estimates for populations on the Oceanian cline

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Supplementary information

Supplementary Information

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Skoglund, P., Posth, C., Sirak, K. et al. Genomic insights into the peopling of the Southwest Pacific.Nature 538, 510–513 (2016). https://doi.org/10.1038/nature19844

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• Received: 20 April 2016
• Accepted: 13 September 2016
• Published: 03 October 2016
• Issue Date: 27 October 2016
• DOI: https://doi.org/10.1038/nature19844