Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Genomic insights into the peopling of the Southwest Pacific

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.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Data from ancient and present-day populations.
Figure 2: Genetic characteristics of the Oceanian ancestry cline.
Figure 3: A model of population history.

Similar content being viewed by others

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.

References

  1. Sheppard, P. J., Chiu, S. & Walter, R. Re-dating Lapita movement into Remote Oceania. J. Pacific Archaeol. 6, 26–36 (2015)

    Google Scholar 

  2. Kayser, M. et al. Genome-wide analysis indicates more Asian than Melanesian ancestry of Polynesians. Am. J. Hum. Genet. 82, 194–198 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Kayser, M. The human genetic history of Oceania: near and remote views of dispersal. Curr. Biol. 20, R194–R201 (2010)

    Article  CAS  PubMed  Google Scholar 

  4. Wollstein, A. et al. Demographic history of Oceania inferred from genome-wide data. Curr. Biol. 20, 1983–1992 (2010)

    Article  CAS  PubMed  Google Scholar 

  5. Matisoo-Smith, E. Ancient DNA and the human settlement of the Pacific: a review. J. Hum. Evol. 79, 93–104 (2015)

    Article  PubMed  Google Scholar 

  6. Bellwood, P. S. First Farmers: the Origins of Agricultural Societies (Blackwell Publishing, 2005)

  7. Duggan, A. T. et al. Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion. Am. J. Hum. Genet. 94, 721–733 (2014)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Kayser, M. et al. Melanesian origin of Polynesian Y chromosomes. Curr. Biol. 10, 1237–1246 (2000)

    Article  CAS  PubMed  Google Scholar 

  9. Blust, R. Remote Melanesia: one history or two? An addendum to Donohue and Denham. Oceanic Linguistics 47, 445–459 (2008)

    Article  Google Scholar 

  10. Friedlaender, J. S. et al. The genetic structure of Pacific Islanders. PLoS Genet. 4, e19 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Pinhasi, R. et al. Optimal ancient DNA yields from the inner ear part of the human petrous bone. PLoS One 10, e0129102 (2015)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  13. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015)

    Article  CAS  Google Scholar 

  14. Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  15. Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013)

    Article  CAS  Google Scholar 

  16. Melton, T. et al. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am. J. Hum. Genet. 57, 403–414 (1995)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466–469 (2012)

    Article  ADS  CAS  PubMed  Google Scholar 

  18. Skoglund, P. et al. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc. Natl Acad. Sci. USA 111, 2229–2234 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  19. Reich, D. et al. Reconstructing Native American population history. Nature 488, 370–374 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. Moorjani, P. et al. The history of African gene flow into Southern Europeans, Levantines, and Jews. PLoS Genet. 7, e1001373 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Loh, P.-R. et al.Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193, 1233–1254 (2013)

    Article  PubMed  PubMed Central  Google Scholar 

  22. Fenner, J. N. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am. J. Phys. Anthropol. 128, 415–423 (2005)

    Article  PubMed  Google Scholar 

  23. Xu, S., Pugach, I., Stoneking, M., Kayser, M. & Jin, L. Genetic dating indicates that the Asian-Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proc. Natl Acad. Sci. USA 109, 4574–4579 (2012)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  24. Pugach, I., Matveyev, R., Wollstein, A., Kayser, M. & Stoneking, M. Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol. 12, R19 (2011)

    Article  PubMed  PubMed Central  Google Scholar 

  25. Lipson, M. et al. Reconstructing Austronesian population history in Island Southeast Asia. Nat. Commun. 5, 4689 (2014)

    Article  ADS  CAS  PubMed  Google Scholar 

  26. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012)

    Article  PubMed  PubMed Central  Google Scholar 

  27. Pickrell, J. K. & Pritchard, J. K. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8, e1002967 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Bellwood, P. Holocene population history in the Pacific region as a model for worldwide food producer dispersals. Curr. Anthropol. 52, S363–S378 (2011)

    Article  Google Scholar 

  29. Jordan, F. M., Gray, R. D., Greenhill, S. J. & Mace, R. Matrilocal residence is ancestral in Austronesian societies. Proc. R. Soc. Lond. B 276, 1957–1964 (2009)

    Article  Google Scholar 

  30. Stephen Lansing, J. et al. An ongoing Austronesian expansion in Island Southeast Asia. J. Anthropol. Archaeol. 30, 262–272 (2011)

    Article  Google Scholar 

  31. Knapp, M., Clarke, A. C., Horsburgh, K. A. & Matisoo-Smith, E. A. Setting the stage – Building and working in an ancient DNA laboratory. Ann. Anat. Anat. Anz. 194, 3–6 (2012)

    Article  CAS  Google Scholar 

  32. Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Prot. http://dx.doi.org/10.1101/pdb.prot5448 (2010)

  33. Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  34. Haak, W. et al. Massive migration from the steppe is a source for Indo-European languages in Europe. Nature 522, 207–211 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  35. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409–413 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  37. Qin, P. & Stoneking, M. Denisovan ancestry in East Eurasian and Native American populations. Mol. Biol. Evol. 32, 2665–2674 (2015)

    Article  CAS  PubMed  Google Scholar 

  38. Skoglund, P. et al. Genetic evidence for two founding populations of the Americas. Nature 525, 104–108 (2015)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  39. Moreno-Mayar, J. V. et al. Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans. Curr. Biol. 24, 2518–2525 (2014)

    Article  CAS  PubMed  Google Scholar 

  40. Reich, D. et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am. J. Hum. Genet. 89, 516–528 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Reich, D. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053–1060 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  42. Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  43. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014)

    Article  ADS  CAS  PubMed  Google Scholar 

  44. Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167–172 (2015)

    Article  ADS  CAS  PubMed  Google Scholar 

  45. Green, R. E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  46. Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014)

    Article  ADS  CAS  PubMed  Google Scholar 

  47. Raghavan, M. et al. The genetic prehistory of the New World Arctic. Science 345, 1255832 (2014)

    Article  CAS  PubMed  Google Scholar 

  48. Rasmussen, M. et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (2014)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  49. Rasmussen, M. et al. The ancestry and affiliations of Kennewick Man. Nature 523, 455–458 (2015)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  50. Skoglund, P. et al. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 344, 747–750 (2014)

    Article  ADS  CAS  PubMed  Google Scholar 

  51. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Skoglund, P. & Jakobsson, M. Archaic human ancestry in East Asia. Proc. Natl Acad. Sci. USA 45, 18301–18306 (2011)

    Article  ADS  Google Scholar 

  53. Sudmant, P. H. et al. Global diversity, population stratification, and selection of human copy-number variation. Science 349, 1174–1181 (2015)

    Article  CAS  Google Scholar 

  54. Kong, A. et al. A high-resolution recombination map of the human genome. Nat. Genet. 31, 241–247 (2002)

    Article  CAS  PubMed  Google Scholar 

  55. Moorjani, P. et al. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proc. Natl Acad. Sci. USA 113, 5652–5657 (2016)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  56. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009)

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  57. Csilléry, K., Blum, M. G. B., Gaggiotti, O. E. & François, O. Approximate Bayesian Computation (ABC) in practice. Trends Ecol. Evol. 25, 410–418 (2010)

    Article  PubMed  Google Scholar 

  58. Bronk Ramsey, C. OxCal Program v4.2.4. (Radiocarbon Accelerator Unit, Univ. Oxford, 2016)

  59. Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 Years cal BP. Radiocarbon http://dx.doi.org/10.2458/azu_js_rc.55.16947 (2013)

  60. Ambrose, S. H. Isotopic analysis of paleodiets: methodological and interpretive considerations in Food and Nutrition in History and Anthropology (USA) http://agris.fao.org/aos/records/US9514697?output=xml (1993)

  61. Petchey, F., Spriggs, M., Bedford, S., Valentin, F. & Buckley, H. Radiocarbon dating of burials from the Teouma Lapita cemetery, Efate, Vanuatu. J. Archaeol. Sci. 50, 227–242 (2014)

    Article  CAS  Google Scholar 

  62. Petchey, F., Anderson, A., Zondervan, A., Ulm, S. & Hogg, A. New marine∆ R values for the South Pacific subtropical gyre region. Radiocarbon 50, 373–397 (2008)

    Article  CAS  Google Scholar 

Download references

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

Authors and Affiliations

Authors

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 to Pontus Skoglund, Ron Pinhasi or David Reich.

Ethics declarations

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 f4(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 f4-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 FST × 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
Extended Data Table 2 356 individuals newly genotyped on the Human Origins Array
Extended Data Table 3 f-statistics for populations on the Oceanian cline
Extended Data Table 4 Ancestry estimates for populations on the Oceanian cline

Supplementary information

Supplementary Information

This file contains Supplementary Notes 1-3, Supplementary Table 1 and additional references. (PDF 420 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature19844

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing