AbstractThe possibility of voyaging contact between prehistoric Polynesian and Native American聽populations has long intrigued researchers. Proponents have pointed to the existence of New World crops, such as the sweet potato and bottle gourd, in the Polynesian archaeological record, but nowhere else outside the pre-Columbian Americas1,2,3,4,5,6, while critics have argued that these botanical dispersals need not have been human mediated7. The Norwegian explorer Thor Heyerdahl controversially sugGEsted that prehistoric South American聽populations had an important role in the settlement of east Polynesia and particularly of Easter Island (Rapa Nui)2. Several limited molecular genetic studies have reached opposing conclusions, and the possibility continues to be as hotly contested today as it was when first suggested8,9,10,11,12. Here we analyse genome-wide variation in individuals from islands across Polynesia for signs of Native American admixture, analysing 807 individuals from 17 island populations and 15 Pacific coast Native American groups. We find conclusive evidence for prehistoric contact of Polynesian聽individuals with Native American聽individuals (around ad 1200) contemporaneous聽with the settlement of remote Oceania13,14,15. Our analyses suggest strongly that a single contact event occurred in eastern Polynesia, before the settlement of Rapa Nui, between Polynesian聽individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia. Subscription info for Chinese customersWe have a dedicated website for our Chinese customers. Please go to naturechina.com to subscribe to this journal.Go to naturechina.comRent or Buy articleGet time limited or full article access on ReadCube.from$8.99Rent or BuyAll prices are NET prices. Individual-level genotypes for new data presented here are available through a data-access agreement to respect the privacy of the participants for the transfer of genetic data from the European Genome Archive (EGA; https://www.ebi.ac.uk/ega/home), under accession number EGAS00001004209. Code availability Details regarding the packages and versions used are included in the Methods. Codes for the matrix completions described in the paper are available at https://github.com/AlexIoannidis/completion. References1.Brown, J. M. The Riddle of the Pacific (T. F. Unwin, 1924).2.Heyerdahl, T. American Indians in the Pacific (Allen Unwin, 1952).3.Yen, D. E. The Sweet Potato and Oceania (Bishop Museum Press, 1974).4.Montenegro, A., Avis, C. Weaver, A. Modeling the prehistoric arrival of the sweet potato in Polynesia. J. Archaeol. Sci. 35, 355鈥?67 (2008). Google Scholar聽 5.Roullier, C., Benoit, L., McKey, D. B. Lebot, V. 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USA 111, 2632鈥?637 (2014).CAS聽 PubMed聽 ADS聽Google Scholar聽 Download referencesAcknowledgementsWe thank the participants and volunteers who donated DNA samples for this study and the many researchers who contributed to collecting samples, in particular J. Martinson, D. Weatherall and J. Clegg, as well as H.-W. Peng (Taiwan), T. Teariki (Cook Islands) and J. Roux (French Polynesia). We thank P. P. Edmunds Paoa, mayor of the Municipality of Easter Island, the Rapahango family, H. Huke, T. Hotu, O. Hey Riroroko, J. Emilio Estay and S. Fareea for providing local support during fieldwork and community engagement on Rapa Nui. We also thank the Rapa Nui Museum and the Office of Rapa Nui Patrimony for outreach support, and the people of Rapa Nui for making this study possible. We thank M. Stoneking for facilitating access to published data that enabled early stages of the analyses, as well as the ChileGenomico project consortium for providing access to reference genotype data from 16 Aymara individuals and 32 of Mapuche ancestry. We acknowledge the National Institutes of Health (NIH) genome-wide association study (GWAS) Data Repository for granting access to the POPRES data set. We also thank the support from the Core Staff at the UCSF Institute for Human Genetics for contributing with genotyping capacity, and the Stanford Center for Computational, Evolutionary and Human Genomics (CEHG) for supporting the initial stages of this project. We are grateful for genotyping and IT support from J. Cervantes, M. Torres and technicians from LANGEBIO鈥檚 Genomics Core Facility at CINVESTAV, Mexico. This work was supported by the George Rosenkranz Prize for Health Care Research in Developing Countries, Mexico鈥檚 CONACYT Basic Research Program (grant number CB-2015-01-251380), and the International Center for Genetic Engineering and Biotechnology (ICGEB, Italy) grant CRP/MEX15-04_EC (each awarded to A.M.-E.); the American Society of Engineering Education NDSEG Fellowship and the National Library of Medicine (NLM) training grant T15LM007033 (awarded to A.G.I.); the Chilean funding programs FONDEF, FONDECYT and CONICYT (grants D10I1007, 1130303 and USA2013-0015, respectively); and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) and the Wellcome Trust Fellowship with reference 106289/Z/14/Z (to A.J.M.). Views expressed are those of the author(s) and not necessarily those of the NIHR, the NHS or the UK Department of Health.Author informationAuthor notesThese authors contributed equally: Alexander G. Ioannidis, Javier Blanco-PortilloAffiliationsInstitute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USAAlexander G. IoannidisNational Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, MexicoAlexander G. Ioannidis,聽Javier Blanco-Portillo,聽Karla Sandoval,聽Juan Esteban Rodr铆guez-Rodr铆guez,聽Consuelo D. Quinto-Cort茅s聽 聽Andr茅s Moreno-EstradaDepartment of Biosciences, University of Oslo, Blindern, Oslo, NorwayErika HagelbergDepartamento de Gastroenterolog铆a, Facultad de Medicina, Pontificia Universidad Cat贸lica de Chile, Santiago, ChileJuan Francisco Miquel-PobleteNational Institute of Genomic Medicine (INMEGEN), Mexico City, MexicoJ. V铆ctor Moreno-MayarWellcome Centre for Human Genetics, University of Oxford, Oxford, UKKathryn Auckland,聽Tom Parks,聽Adrian V. S. Hill聽 聽Alexander J. MentzerMRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UKKathryn RobsonThe Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UKAdrian V. S. HillInternational Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, MexicoMar铆a C. Avila-ArcosCenter for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USAAlexandra Sockell,聽Julian R. Homburger,聽Genevieve L. Wojcik聽 聽Carlos D. BustamanteDivision of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USAKathleen C. Barnes聽 聽Christopher R. GignouxHuman Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, ChileLuisa Herrera,聽Soledad Berr铆os,聽M贸nica Acu帽a,聽Elena Llop,聽Luc铆a Cifuentes,聽Ricardo A. Verdugo聽 聽Mauricio MoragaProgram in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USACeleste Eng,聽Scott Huntsman聽 聽Esteban G. BurchardBasic-Applied Oncology Department, Faculty of Medicine, University of Chile, Santiago, ChileRicardo A. VerdugoDepartment of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, ChileMauricio MoragaBig Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UKAlexander J. MentzerDepartment of Biomedical Data Science, Stanford University, Stanford, CA, USACarlos D. BustamanteAuthorsAlexander G. IoannidisView author publicationsYou can also search for this author in PubMed聽Google ScholarJavier Blanco-PortilloView author publicationsYou can also search for this author in PubMed聽Google ScholarKarla SandovalView author publicationsYou can also search for this author in PubMed聽Google ScholarErika HagelbergView author publicationsYou can also search for this author in PubMed聽Google ScholarJuan Francisco Miquel-PobleteView author publicationsYou can also search for this author in PubMed聽Google ScholarJ. V铆ctor Moreno-MayarView author publicationsYou can also search for this author in PubMed聽Google ScholarJuan Esteban Rodr铆guez-Rodr铆guezView author publicationsYou can also search for this author in PubMed聽Google ScholarConsuelo D. Quinto-Cort茅sView author publicationsYou can also search for this author in PubMed聽Google ScholarKathryn AucklandView author publicationsYou can also search for this author in PubMed聽Google ScholarTom ParksView author publicationsYou can also search for this author in PubMed聽Google ScholarKathryn RobsonView author publicationsYou can also search for this author in PubMed聽Google ScholarAdrian V. S. HillView author publicationsYou can also search for this author in PubMed聽Google ScholarMar铆a C. Avila-ArcosView author publicationsYou can also search for this author in PubMed聽Google ScholarAlexandra SockellView author publicationsYou can also search for this author in PubMed聽Google ScholarJulian R. HomburgerView author publicationsYou can also search for this author in PubMed聽Google ScholarGenevieve L. WojcikView author publicationsYou can also search for this author in PubMed聽Google ScholarKathleen C. BarnesView author publicationsYou can also search for this author in PubMed聽Google ScholarLuisa HerreraView author publicationsYou can also search for this author in PubMed聽Google ScholarSoledad Berr铆osView author publicationsYou can also search for this author in PubMed聽Google ScholarM贸nica Acu帽aView author publicationsYou can also search for this author in PubMed聽Google ScholarElena LlopView author publicationsYou can also search for this author in PubMed聽Google ScholarCeleste EngView author publicationsYou can also search for this author in PubMed聽Google ScholarScott HuntsmanView author publicationsYou can also search for this author in PubMed聽Google ScholarEsteban G. BurchardView author publicationsYou can also search for this author in PubMed聽Google ScholarChristopher R. GignouxView author publicationsYou can also search for this author in PubMed聽Google ScholarLuc铆a CifuentesView author publicationsYou can also search for this author in PubMed聽Google ScholarRicardo A. VerdugoView author publicationsYou can also search for this author in PubMed聽Google ScholarMauricio MoragaView author publicationsYou can also search for this author in PubMed聽Google ScholarAlexander J. MentzerView author publicationsYou can also search for this author in PubMed聽Google ScholarCarlos D. BustamanteView author publicationsYou can also search for this author in PubMed聽Google ScholarAndr茅s Moreno-EstradaView author publicationsYou can also search for this author in PubMed聽Google ScholarContributionsA.M.-E. and K.S. conceived the study. A.M.-E.,聽A.G.I., A.J.M. and聽C.D.B. provided overall project supervision and management. A.M.-E., E.H., R.A.V., M.M., A.J.M., C.D.B. and C.R.G. contributed to study design. A.S., G.L.W., K.C.B., C.E., S.H., E.G.B., C.D.B. and A.M.-E. carried out genotyping experiments and quality control. A.G.I., J.B.-P., J.V.M.-M., J.E.R.-R., C.D.Q.-C., J.R.H. and A.M.-E. analysed the data. A.G.I. developed the analytical methods. A.M.-E., A.G.I. and J.B.-P. interpreted the results. A.M.-E., K.S., E.H., J.F.M.-P., K.A., T.P., K.R., A.V.S.H., M.C.A.-A., A.S., G.L.W., K.C.B., L.H., S.B., M.A., E.L., C.E., S.H., E.G.B., L.C., R.A.V., M.M., A.J.M. and C.D.B. contributed to acquisition of the data. A.G.I. wrote the manuscript, and A.G.I., A.M.-E., E.H., J.B.-P., J.V.M.-M. and M.M. edited the manuscript.Corresponding authorsCorrespondence to Alexander G. Ioannidis or Andr茅s Moreno-Estrada.Ethics declarations Competing interests C.D.B. is a member of the scientific advisory boards for Liberty Biosecurity, Personalis, 23andMe Roots into the Future, Ancestry.com, IdentifyGenomics, Genomelink and Etalon and is a founder of CDB Consulting. C.R.G. owns stock in 23andMe and is a member of the scientific advisory board for Encompass Bioscience. 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