Complex Patterns of Admixture across the Indonesian Archipelago
Open accessAbstract
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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Self-citation
- 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.
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07-11
- Volume
- 34
- Issue
- 10
- Pages
- 2439-2452
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC5850824
- 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
- hybrid
- doi.org
- 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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