Cited by 191Forensic and Genetic ResearchGenetic diversity and population structurePacific and Southeast Asian Studies

Complex Patterns of Admixture across the Indonesian Archipelago

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Hudjashov, Georgi, Karafet, Tatiana M., Lawson, Daniel J., Downey, Sean, Savina, Olga, Sudoyo, Herawati, Lansing, J. Stephen, Hammer, Michael F. +1 more·2017·Molecular Biology and Evolution

Abstract

Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.

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  • Recent studies have shown the existence of genetic structure characterising the Indonesian archipelago, with Papuan-and thus, Denisovan-ancestry showing a marked west to east cline.

    “Recent studies have shown the existence of genetic structure characterising the Indonesian archipelago, with Papuan—and thus, Denisovan—ancestry showing a marked west to east cline [6, 53].”

    From Denisovan introgression has shaped the immune system of present-day Papuans (2022) · cites this paper as [53]

    The Discussion reports a west-to-east cline in Papuan ancestry, and the Introduction notes substantial Denisovan introgression in eastern Indonesian populations. The paper does not establish that Denisovan ancestry itself follows the same cline. (LLM, conf=0.86)

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Research works printed but not linked: 2

  1. Blench RM. 2012 Almost everything you believed about the Austronesians isn’t true In: Tjoa-Bonatz ML, Reinecke A, Bonatz D, editors. Selected papers from the 13th international conference of the European Association of Southeast Asian archaeologists. Singapore: NUS Press.
  2. Kennerknecht I, Hämmerle JM, Blench RM. 2012 The peopling of Nias, from the perspective of oral literature and molecular genetic data In: Tjoa-Bonatz ML, Reinecke A, Bonatz D, editors. Selected papers from the 13th international conference of the European Association of Southeast Asian archaeologists. Singapore: NUS Press.

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Authors
Hudjashov, G., Karafet, T. M., Lawson, D. J., Downey, S., Savina, O., Sudoyo, H., Lansing, J. S., Hammer, M. F., & Cox, M. P.
Affiliations
  • Estonian Biocentre (EE)
  • University of Arizona (US)
  • University of Bristol (GB)
  • University of Maryland, College Park (US)
  • The University of Sydney (AU)
  • Nanyang Technological University (SG)
  • Massey University (NZ)
Corresponding author
  • Hudjashov, Georgi
  • Cox, Murray P.
Venue
Molecular Biology and Evolution
Published
2017-07-11
Volume
34
Issue
10
Pages
2439-2452
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
OpenAlex
W2734900454
Cited by
191
References
61
Citations by year
2026: 7 · 2025: 50 · 2024: 60 · 2023: 3 · 2022: 14 · 2021: 8 · 2020: 12 · 2019: 28 · 2018: 6 · 2017: 2
FWCI
8.71
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Explore Bristol Research (submittedVersion, cc-by-nc)
Funders
  • Wellcome Trust (104125/Z/14/Z)
  • University of Oxford
  • Nanyang Technological University
  • Royal Society Te Apārangi (RDF-10-MAU-001)
  • Massey University
  • Tartu Ülikool
  • Institute of Genetics
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Social Sciences › Geography, Planning and Development › Pacific and Southeast Asian Studies
Keywords
genetic admixture, Indonesian archipelago, Austronesian expansion, demographic history, haplotype diversity, Holocene, Philippines, Oceania, New Guinea, Island Southeast Asia, Neolithic expansion
MeSH terms
Asia, Asia, Southeastern, DNA, Mitochondrial, Asia, Eastern, Genetics, Population, Haplotypes, Humans, Indonesia, Genetic Variation, Genome, Human, Evolution, Molecular, Oceania, Asian People, Islands, Human Migration

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