Native American gene flow into Polynesia predating Easter Island settlement (original) (raw)

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.

Author information

Author notes

1. These authors contributed equally: Alexander G. Ioannidis, Javier Blanco-Portillo

Authors and Affiliations

1. Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
   Alexander G. Ioannidis
2. National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato, Mexico
   Alexander G. Ioannidis, Javier Blanco-Portillo, Karla Sandoval, Juan Esteban Rodríguez-Rodríguez, Consuelo D. Quinto-Cortés & Andrés Moreno-Estrada
3. Department of Biosciences, University of Oslo, Blindern, Oslo, Norway
   Erika Hagelberg
4. Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
   Juan Francisco Miquel-Poblete
5. National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
   J. Víctor Moreno-Mayar
6. Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
   Kathryn Auckland, Tom Parks, Adrian V. S. Hill & Alexander J. Mentzer
7. MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
   Kathryn Robson
8. The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
   Adrian V. S. Hill
9. International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
   María C. Avila-Arcos
10. Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
    Alexandra Sockell, Julian R. Homburger, Genevieve L. Wojcik & Carlos D. Bustamante
11. Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
    Kathleen C. Barnes & Christopher R. Gignoux
12. Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
    Luisa Herrera, Soledad Berríos, Mónica Acuña, Elena Llop, Lucía Cifuentes, Ricardo A. Verdugo & Mauricio Moraga
13. Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
    Celeste Eng, Scott Huntsman & Esteban G. Burchard
14. Basic-Applied Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
    Ricardo A. Verdugo
15. Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
    Mauricio Moraga
16. Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
    Alexander J. Mentzer
17. Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
    Carlos D. Bustamante

Authors

1. Alexander G. Ioannidis
2. Javier Blanco-Portillo
3. Karla Sandoval
4. Erika Hagelberg
5. Juan Francisco Miquel-Poblete
6. J. Víctor Moreno-Mayar
7. Juan Esteban Rodríguez-Rodríguez
8. Consuelo D. Quinto-Cortés
9. Kathryn Auckland
10. Tom Parks
11. Kathryn Robson
12. Adrian V. S. Hill
13. María C. Avila-Arcos
14. Alexandra Sockell
15. Julian R. Homburger
16. Genevieve L. Wojcik
17. Kathleen C. Barnes
18. Luisa Herrera
19. Soledad Berríos
20. Mónica Acuña
21. Elena Llop
22. Celeste Eng
23. Scott Huntsman
24. Esteban G. Burchard
25. Christopher R. Gignoux
26. Lucía Cifuentes
27. Ricardo A. Verdugo
28. Mauricio Moraga
29. Alexander J. Mentzer
30. Carlos D. Bustamante
31. Andrés Moreno-Estrada

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 toAlexander 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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• Received: 27 May 2019
• Accepted: 22 May 2020
• Published: 08 July 2020
• Version of record: 08 July 2020
• Issue date: 23 July 2020
• DOI: https://doi.org/10.1038/s41586-020-2487-2