title: Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia.
abstract: There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
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 (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal.|Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK.|ICBAS (Instituto Ciências Biomédicas Abel Salazar), Universidade do Porto, Rua de Jorge Viterbo Ferreira n.º 228, 4050-313, Porto, Portugal.
authors.forename: Andreia
authors.initials: A
authors.lastname: Brandão
authors.affiliation: Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.|Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia.
authors.forename: Ken Khong
authors.initials: KK
authors.lastname: Eng
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, 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 (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal.
authors.forename: Bruno
authors.initials: B
authors.lastname: Cavadas
authors.affiliation: Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton ACT, Canberra, 2601, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Bulbeck
authors.affiliation: Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK.
authors.forename: Francesca
authors.initials: F
authors.lastname: Gandini
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: 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: Archaeology Department, University of Sydney, New South Wales, 2006, Australia.
authors.forename: Bob
authors.initials: B
authors.lastname: Hudson
authors.affiliation: Department of Anthropology, University of Pennsylvania Museum, 3260 South St., Philadelphia, USA.
authors.forename: Joyce
authors.initials: J
authors.lastname: White
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: Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia.
authors.forename: Mokhtar
authors.initials: M
authors.lastname: Saidin
authors.affiliation: Malaysian Institute of Pharmaceuticals and Nutraceuticals Malaysia, National Institutes of Biotechnology Malaysia, Penang, Malaysia.|Human Identification Unit, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia.
authors.forename: Zainuddin
authors.initials: Z
authors.lastname: Zafarina
authors.affiliation: School of Anthropology, Institute of Human Sciences, The Pauling Centre, University of Oxford, 58a Banbury Road, Oxford, OX2 6QS, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Oppenheimer
authors.affiliation: Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK. m.b.richards@hud.ac.uk.|Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK. m.b.richards@hud.ac.uk.
authors.forename: Martin B
authors.initials: MB
authors.lastname: Richards
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 (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, 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: IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.|i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal.|Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.|Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors.forename: Pedro
authors.initials: P
authors.lastname: Soares
mesh_terms: D001210:Asia, Southeastern; D004272:DNA, Mitochondrial / Q000235:genetics; D005260:Female; D018703:Founder Effect; D018392:Genomic Imprinting; D006801:Humans; D013624:Taiwan
chemical_list: D004272:DNA, Mitochondrial