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Mol Biol Evol. 2017 Oct 1;34(10):2439-2452. doi: 10.1093/molbev/msx196.

Complex Patterns of Admixture across the Indonesian Archipelago.

Author information

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
Estonian Biocentre, 51010 Tartu, Estonia.
ARL Division of Biotechnology, University of Arizona, Tucson, AZ.
School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.
Department of Anthropology, University of Maryland, College Park, MD.
Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.
Sydney Medical School, University of Sydney, Sydney, NSW, Australia.
Complexity Institute, Nanyang Technological University, Singapore.


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.


genetic admixture; genetic diversity; human migration; population structure

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