Genomic insights into population history and biological adaptation in Oceania

Jeremy Choin, Javier Mendoza-Revilla, Lara R. Arauna, Sebastian Cuadros-Espinoza, Olivier Cassar, Maximilian Larena, Albert Min-Shan Ko, Christine Harmant, Romain Laurent, Paul Verdu, Guillaume Laval, Anne Boland, Robert Olaso, Jean-François Deleuze, Frédérique Valentin, Ying-Chin Ko, Mattias Jakobsson, Antoine Gessain, Laurent Excoffier, Mark Stoneking, Etienne Patin () and Lluis Quintana-Murci ()
Additional contact information
Jeremy Choin: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Javier Mendoza-Revilla: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Lara R. Arauna: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Sebastian Cuadros-Espinoza: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Olivier Cassar: Oncogenic Virus Epidemiology and Pathophysiology, Institut Pasteur, UMR 3569, CNRS
Maximilian Larena: Uppsala University
Albert Min-Shan Ko: Chinese Academy of Sciences
Christine Harmant: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Romain Laurent: Muséum National d’Histoire Naturelle, UMR7206, CNRS, Université de Paris
Paul Verdu: Muséum National d’Histoire Naturelle, UMR7206, CNRS, Université de Paris
Guillaume Laval: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Anne Boland: Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay
Robert Olaso: Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay
Jean-François Deleuze: Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay
Frédérique Valentin: Maison de l’Archéologie et de l’Ethnologie, UMR 7041, CNRS
Ying-Chin Ko: China Medical University and Hospital
Mattias Jakobsson: Uppsala University
Antoine Gessain: Oncogenic Virus Epidemiology and Pathophysiology, Institut Pasteur, UMR 3569, CNRS
Laurent Excoffier: University of Bern
Mark Stoneking: Max Planck Institute for Evolutionary Anthropology
Etienne Patin: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS
Lluis Quintana-Murci: Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS

Nature, 2021, vol. 592, issue 7855, 583-589

Abstract: Abstract The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related (‘Near Oceanian’) groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000–40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2–4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.

Date: 2021
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DOI: 10.1038/s41586-021-03236-5

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