title: Reconstructing Austronesian population history in Island Southeast Asia.
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 4,000-5,000 years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, we analyse genome-wide data from 56 populations using new methods for tracing ancestral gene flow, focusing primarily on Island Southeast Asia. We show that all sampled Austronesian groups harbour 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.
authors.affiliation: Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Lipson
authors.affiliation: 1] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2].
authors.forename: Po-Ru
authors.initials: PR
authors.lastname: Loh
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Nick
authors.initials: N
authors.lastname: Patterson
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3].
authors.forename: Priya
authors.initials: P
authors.lastname: Moorjani
authors.affiliation: Graduate Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan.
authors.forename: Ying-Chin
authors.initials: YC
authors.lastname: Ko
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Mark
authors.initials: M
authors.lastname: Stoneking
authors.affiliation: 1] Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Bonnie
authors.initials: B
authors.lastname: Berger
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: David
authors.initials: D
authors.lastname: Reich
mesh_terms: D001210:Asia, Southeastern; D044466:Asian People / Q000235:genetics; D004641:Emigration and Immigration; D005006:Ethnicity / Q000235:genetics; D051456:Gene Flow; D005787:Gene Frequency; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D005843:Geography; D006239:Haplotypes; D006801:Humans; D007214:Indonesia / Q000208:ethnology; D062312:Islands; D007802:Language; D015810:Linkage Disequilibrium; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software; D013624:Taiwan / Q000208:ethnology