title: Resolving the ancestry of Austronesian-speaking populations.
abstract: There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
authors.affiliation: Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.|IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Soares
authors.affiliation: Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City, 10449, Taiwan.
authors.forename: Jean A
authors.initials: JA
authors.lastname: Trejaut
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.|ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal.
authors.forename: Teresa
authors.initials: T
authors.lastname: Rito
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|I3S - Institute for Research Innovation in Health, University of Porto, 4200-135, Porto, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Cavadas
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
authors.forename: Catherine
authors.initials: C
authors.lastname: Hill
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.|Centre for Global Archaeological Research, Universiti Sains Malaysia (USM), 11800, Penang, Malaysia.
authors.forename: Ken Khong
authors.initials: KK
authors.lastname: Eng
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.|Department of Applied Social Studies, University of Winchester, Sparkford Road, Winchester, SO22 4NR, UK.
authors.forename: Maru
authors.initials: M
authors.lastname: Mormina
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|I3S - Institute for Research Innovation in Health, University of Porto, 4200-135, Porto, Portugal.|Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.|ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313, Porto, Portugal.
authors.forename: Andreia
authors.initials: A
authors.lastname: Brandão
authors.affiliation: Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.|Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh, EH16 4UX, UK.
authors.forename: Ross M
authors.initials: RM
authors.lastname: Fraser
authors.affiliation: Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City, 10449, Taiwan.
authors.forename: Tse-Yi
authors.initials: TY
authors.lastname: Wang
authors.affiliation: Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City, 10449, Taiwan.
authors.forename: Jun-Hun
authors.initials: JH
authors.lastname: Loo
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
authors.forename: Christopher
authors.initials: C
authors.lastname: Snell
authors.affiliation: Department of Obstetrics and Gynecology, National Taiwan University, Roosevelt Rd., Taipei, 10617, Taiwan.
authors.forename: Tsang-Ming
authors.initials: TM
authors.lastname: Ko
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|I3S - Institute for Research Innovation in Health, University of Porto, 4200-135, Porto, Portugal.|Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
authors.forename: António
authors.initials: A
authors.lastname: Amorim
authors.affiliation: Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
authors.forename: Maria
authors.initials: M
authors.lastname: Pala
authors.affiliation: Department of Statistics, University of Glasgow, 15 University Gardens, Glasgow, G12 8QQ, UK.
authors.forename: Vincent
authors.initials: V
authors.lastname: Macaulay
authors.affiliation: Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton, Canberra, ACT, 2601, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Bulbeck
authors.affiliation: Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.|MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland.
authors.forename: James F
authors.initials: JF
authors.lastname: Wilson
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rua São Francisco Xavier, Rio de Janeiro, 20550-900, Brazil.
authors.forename: Leonor
authors.initials: L
authors.lastname: Gusmão
authors.affiliation: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|I3S - Institute for Research Innovation in Health, University of Porto, 4200-135, Porto, Portugal.|Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319, Porto, Portugal.
authors.forename: Luísa
authors.initials: L
authors.lastname: Pereira
authors.affiliation: Institute of Human Sciences, School of Anthropology, University of Oxford, The Pauling Centre, 58a Banbury Road, Oxford, OX2 6QS, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Oppenheimer
authors.affiliation: Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei City, 10449, Taiwan.
authors.forename: Marie
authors.initials: M
authors.lastname: Lin
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. m.b.richards@hud.ac.uk.|Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK. m.b.richards@hud.ac.uk.
authors.forename: Martin B
authors.initials: MB
authors.lastname: Richards
mesh_terms: D001210:Asia, Southeastern; D044466:Asian People / Q000235:genetics*; D041322:Chromosomes, Human, Y / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D030541:Databases, Genetic; D005260:Female; D056726:Genetic Association Studies; D056426:Genetic Loci; D015894:Genome, Human; D006801:Humans; D008297:Male; D008957:Models, Genetic; D010802:Phylogeny; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D004272:DNA, Mitochondrial