Genomic insights into population history and biological adaptation in Oceania
Open accessAbstract
The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes 1. 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 ago 2-4. 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.
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Pugach, I., Duggan, A. T., Merriwether, D. A., Friedlaender, F. R., Friedlaender, J. S., & Stoneking, M. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx333 · Cited by 85 · see citing works
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A General Mechanistic Model for Admixture Histories of Hybrid Populations
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Perttilä, J., Merikanto, K., Naukkarinen, J., Surakka, I. L., Martín, N. W., Tanhuanpää, K., Grimard, V., Taskinen, M., Thiele, C., Salomaa, V. V., et al. (2009) · Journal of Molecular Medicine · doi:10.1007/s00109-009-0490-z · Cited by 65 · see citing works
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Foragers, fishers and farmers: origins of the Taiwanese Neolithic
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Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu
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Self-citationParanoid psychosis in the elderly
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The evolutionary history and human settlement of Australia and the Pacific
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Human immune diversity: from evolution to modernity
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Philippine Ayta possess the highest level of Denisovan ancestry in the world
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Self-citationDenisovan introgression has shaped the immune system of present-day Papuans
Vespasiani, D. M., Jacobs, G. S., Cook, L. E., Brucato, N., Leavesley, M., Kinipi, C., Ricaut, F.-X., Cox, M. P., & Gallego Romero, I. (2022) · PLOS Genetics · doi:10.1371/journal.pgen.1010470 · Cited by 46 · see citing works
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Koller, D., Wendt, F. R., Pathak, G. A., De Lillo, A., De Angelis, F., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2022) · BMC Biology · doi:10.1186/s12915-022-01449-2 · Cited by 27 · see citing works
“Although few studies investigated archaic introgression in non-EURdescent groups such as Pacific [25], East Asian [26], Tibetan [27], and Island South East [28] populations, to our knowledge no investigation systematically explored the impact of archaic introgression across human traits and diseases across multiple an…”
Background
- Authors
- Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A. M.-S., Harmant, C., Laurent, R., Verdu, P., Laval, G., Boland, A., Olaso, R., Deleuze, J.-F., Valentin, F., Ko, Y.-C., Jakobsson, M., Gessain, A., Excoffier, L., Stoneking, M., Patin, E., & Quintana-Murci, L.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Uppsala University (SE)
- Chinese Academy of Sciences (CN)
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (FR)
- China Medical University (TW)
- University of Bern (CH)
- Max Planck Institute for Evolutionary Anthropology (DE)
- ORCID
- Choin, Jeremy
- Mendoza-Revilla, Javier
- Arauna, Lara R.
- Cassar, Olivier
- Larena, Maximilian
- Ko, Albert Min-Shan
- Harmant, Christine
- Laurent, Romain
- Verdu, Paul
- Laval, Guillaume
- Boland, Anne
- Olaso, Robert
- Deleuze, Jean-François
- Valentin, Frédérique
- Ko, Ying-Chin
- Jakobsson, Mattias
- Excoffier, Laurent
- Stoneking, Mark
- Patin, Etienne
- Quintana-Murci, Lluis
- Venue
- Nature
- Published
- 2021-04-14
- Volume
- 592
- Issue
- 7855
- Pages
- 583-589
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3152915323
- Cited by
- 208
- References
- 103
- Citations by year
- 2026: 20 · 2025: 65 · 2024: 35 · 2023: 34 · 2022: 31 · 2021: 22 · 2020: 1
- FWCI
- 19.49
- Type
- journal article
- Language
- en
- Open access
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- Bern Open Repository and Information System (University of Bern) (submittedVersion)
- Funders
- Agence Nationale de la Recherche (ANR-10-INBS-0009, ANR-10-LABX-0069, ANR-16-CONV-0005, ANR-10-LABX-0062)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Social Sciences › Geography, Planning and Development › Pacific and Southeast Asian Studies
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- Papuan populations, population bottleneck, East Asian ancestry, Taiwan indigenous peoples, Neolithic dispersal, admixture, Denisovan introgression, Neanderthal introgression, lipid metabolism, pathogen exposure, polygenic adaptation, selective sweeps, island adaptation, human dispersal
- MeSH terms
- Genetic Introgression, Adaptation, Biological, Animals, Australia, Biological Evolution, Asia, Eastern, Genetics, Population, Humans, Pacific Ocean, Taiwan, Genome, Human, Genomics, Oceania, History, Ancient, Neanderthals, Islands, Human Migration, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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