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Reconstructing Austronesian population history in Island Southeast Asia

Mark Lipson, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger, David Reich
doi: https://doi.org/10.1101/005603
Mark Lipson
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
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Po-Ru Loh
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
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Nick Patterson
Broad Institute of MIT and Harvard, Cambridge, MA 02142
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Priya Moorjani
Broad Institute of MIT and Harvard, Cambridge, MA 02142Department of Genetics, Harvard Medical School, Boston, MA 02115
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Ying-Chin Ko
Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan 40402
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Mark Stoneking
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Bonnie Berger
Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139Broad Institute of MIT and Harvard, Cambridge, MA 02142
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  • For correspondence: reich@genetics.med.harvard.edu bab@mit.edu
David Reich
Broad Institute of MIT and Harvard, Cambridge, MA 02142Department of Genetics, Harvard Medical School, Boston, MA 02115Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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  • For correspondence: reich@genetics.med.harvard.edu bab@mit.edu
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Abstract

Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the “Austronesian expansion,” which began 4–5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow. We show that all sampled Austronesian groups harbor ancestry that is more closely related to aboriginal Taiwanese than to any present-day mainland population. Surprisingly, western Island Southeast Asian populations have also inherited ancestry from a source nested within the variation of present-day populations speaking Austro-Asiatic languages, which have historically been nearly exclusive to the mainland. Thus, either there was once a substantial Austro-Asiatic presence in Island Southeast Asia, or Austronesian speakers migrated to and through the mainland, admixing there before continuing to western Indonesia.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 27, 2014.
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Reconstructing Austronesian population history in Island Southeast Asia
Mark Lipson, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger, David Reich
bioRxiv 005603; doi: https://doi.org/10.1101/005603
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Reconstructing Austronesian population history in Island Southeast Asia
Mark Lipson, Po-Ru Loh, Nick Patterson, Priya Moorjani, Ying-Chin Ko, Mark Stoneking, Bonnie Berger, David Reich
bioRxiv 005603; doi: https://doi.org/10.1101/005603

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