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. Access through your

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BEING VIEWED BY OTHERS MEDIEVAL DNA FROM SOQOTRA POINTS TO EURASIAN ORIGINS OF AN ISOLATED POPULATION AT THE CROSSROADS OF AFRICA AND ARABIA Article 08 February 2024 PALAEOGENOMIC INSIGHTS

INTO THE ORIGINS OF EARLY SETTLERS ON THE ISLAND OF CYPRUS Article Open access 26 April 2024 THE GENOMIC LANDSCAPE OF MEXICAN INDIGENOUS POPULATIONS BRINGS INSIGHTS INTO THE PEOPLING OF THE

AMERICAS Article Open access 12 October 2021 ACCESSION CODES PRIMARY ACCESSIONS EUROPEAN NUCLEOTIDE ARCHIVE * PRJEB14728 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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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 and David Reich:

These authors jointly supervised this work. AUTHORS AND AFFILIATIONS * 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 * Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA Pontus Skoglund, Eadaoin

Harney, Swapan Mallick, Kristin Stewardson, Nick Patterson & David Reich * Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University,

Stockholm, 10691, Sweden Pontus Skoglund * Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, 72070, Germany Cosimo Posth * Max Planck

Institute for the Science of Human History, Jena, 07745, Germany Cosimo Posth & Johannes Krause * School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin

4, Dublin, Ireland Kendra Sirak, Daniel Fernandes, Mario Novak & Ron Pinhasi * Department of Anthropology, Emory University, Atlanta, 30322, Georgia, USA Kendra Sirak * School of

Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, 2601, Australian Capital Territory, Australia Matthew Spriggs * Vanuatu

National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu Matthew Spriggs & Stuart Bedford * Maison de l’Archéologie et de l’Ethnologie, CNRS, UMR 7041, Nanterre, 92023, France

Frederique Valentin * 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 * College of Arts, Society and Education, James Cook University, Queensland, 4870, Australia Christian Reepmeyer * Radiocarbon Dating

Laboratory, University of Waikato, Hamilton, 3240, New Zealand Fiona Petchey * Department of Life Sciences, CIAS, University of Coimbra, Coimbra, 3000-456, Portugal Daniel Fernandes * Key

Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing, 100044, China Qiaomei Fu * Department of Evolutionary Genetics, Max Planck Institute

for Evolutionary Anthropology, Leipzig, 04103, Germany Qiaomei Fu * Institute for Anthropological Research, Zagreb, 10000, Croatia Mario Novak * Howard Hughes Medical Institute, Harvard

Medical School, Boston, 02115, Massachusetts, USA Kristin Stewardson & David Reich * RIPAS Hospital, Bandar Seri Begawan, Brunei, Darussalam Syafiq Abdullah * Institute of Fundamental

Sciences, Massey University, Palmerston North, 4442, New Zealand Murray P. Cox * Independent Scientist, Sharon, Connecticut, 06069, USA Françoise R. Friedlaender * Department of

Anthropology, Temple University, Gladfelter Hall, Philadelphia, 19122, Pennsylvania, USA Jonathan S. Friedlaender * Estonian Biocentre, Evolutionary Biology group, Tartu, 51010, Estonia

Toomas Kivisild * Division of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, UK Toomas Kivisild * Papua New Guinea Institute of Medical Research, Eastern

Highlands Province 441, Goroka, Papua New Guinea George Koki * Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia Pradiptajati Kusuma * Department of Anthropology, Binghamton

University, Binghamton, 13902, New York, USA D. Andrew Merriwether * Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université

de Toulouse, Toulouse, 31073, France Francois-X. Ricaut * National Cancer Centre Singapore, Singapore, 169610, Singapore Joseph T. S. Wee Authors * Pontus Skoglund View author publications

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also search for this author inPubMed Google Scholar * David Reich View author publications You can also search for this author inPubMed Google Scholar 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 _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).

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

SLIDE FOR FIG. 1 POWERPOINT SLIDE FOR FIG. 2 POWERPOINT SLIDE FOR FIG. 3 RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE 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: 20 April 2016 *

Accepted: 13 September 2016 * Published: 03 October 2016 * Issue Date: 27 October 2016 * DOI: https://doi.org/10.1038/nature19844 SHARE THIS ARTICLE Anyone you share the following link with

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