Native American gene flow into Polynesia predating Easter Island settlement

Abstract

The possibility of voyaging contact between prehistoric Polynesian and Native American 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 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 individuals with Native American individuals (around ad 1200) contemporaneous 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 individuals and a Native American group most closely related to the indigenous inhabitants of present-day Colombia.

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Fig. 1: Sampled populations with unsupervised (iterative) ADMIXTURE analysis.
Fig. 2: Relationship between Polynesian, Native American and European ancestries.
Fig. 3: Analysis of European ancestry in Pacific islanders.
Fig. 4: Origin and spread of early Native American ancestry in Polynesia.

Data availability

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.

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Acknowledgements

We 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’s Genomics Core Facility at CINVESTAV, Mexico. This work was supported by the George Rosenkranz Prize for Health Care Research in Developing Countries, Mexico’s 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.

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Contributions

A.M.-E. and K.S. conceived the study. A.M.-E., A.G.I., A.J.M. and 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 authors

Correspondence to Alexander G. Ioannidis or Andrés Moreno-Estrada.

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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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Ioannidis, A.G., Blanco-Portillo, J., Sandoval, K. et al. Native American gene flow into Polynesia predating Easter Island settlement. Nature 583, 572–577 (2020). https://doi.org/10.1038/s41586-020-2487-2

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