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Genetic Patterning at Austronesian Contact Zones

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Genetic Patterning at Austronesian Contact Zones Genetic Patterning at Austronesian Contact Zones Murray P. Cox A thesis submitted for the degree of Doctor of Philosophy at the University of Otago, Dunedin, New Zealand. 26 June 2003 Copyright 2003 by Murray P. Cox ABSTRACT The advance of Neolithic culture was a defining process in human history. Chronicled by the distribution of Austronesian languages, one such expansion of Neolithic peoples swept through the Indo-Pacific region just 4,000 years ago. A record of this dispersal is carried in the genes of modern people. Yet human populations have a much older history in the region, and their genetic legacies also persist to modern times. Examination of the genetic patterns that resulted from contact between these Austronesian and non-Austronesian peoples forms a central focus of this thesis. Research was directed towards three geographical regions in which Austronesian languages are still spoken today: the island nations of Indonesia, Madagascar, and Vanuatu. Inherited genetic characters were examined from nearly six hundred individuals, and analysis focused on two genetic systems. Firstly, mitochondrial DNA, which is inherited through the maternal line; and secondly, the Y chromosome, which is inherited through the paternal line. Disengaging the genetic lineages of men and women allowed exploration of possible sex-specific structuring in the contact process. An examination of spatial patterning, and the application of novel genetic techniques for dating human population expansions, gave additional facets to the study. Four thousand years of human mobility have blurred prehistoric patterns in the genetic variation displayed by modern populations. No spatial or sex-specific patterning was detected. Yet it can be inferred that less than a fifth part of the modern populace carry genetic markers once diagnostic of the dispersing Austronesian speakers. It seems that non-Austronesian populations have contributed significantly to modern populations. Genetic analysis suggests that, at least in Vanuatu, adoption of a Neolithic economy triggered a period of population growth for non-Austronesian peoples. This was contemporary with the arrival of the first Austronesians. Thus, the spread of Neolithic society seems to have been driven in part by biological dispersal, and in part by cultural diffusion. The genetic data best fit a model of leapfrogging, whereby Austronesian populations crossed the Indo-Pacific region in bounds, each of which subsequently formed a staging ground for cultural diffusion. Although not reflected so clearly in the archaeological and linguistic records, non-Austronesian peoples were active players in the emerging Neolithic world. They encountered the dispersal of the Austronesians, adapted culturally to their changing situation, and biologically, they kept on going. ACKNOWLEDGEMENTS I extend my sincerest appreciation to those individuals and institutions who contributed to the completion of this research. In particular, my thanks go to Prof. Erika Hagelberg, Mr. Ian Frame, and Ms. Melanie Pierson for their contributions to the thesis; and to the Zoology Department, University of Oslo, Norway for accommodating my research during 2002. I am especially grateful to the Indonesian, Malagasy, and ni-Vanuatu communities who participated in this study. I also extend my thanks to the following researchers who kindly provided academic guidance, dis- cussion, unpublished data, and biological samples: Ass. Prof. Karl (Sander) Adelaar (Melbourne Institute of Asian Languages and Societies, University of Melbourne, Australia); Dr. Stuart Bedford (New Zealand Historic Places Trust, Auckland, New Zealand); Prof. Peter Bellwood (School of Ar- chaeology and Anthropology, Australian National University, Canberra, Australia); Ass. Prof. Don Bowden (Department of Anatomy and Cell Biology, Monash University, Melbourne, Australia); Dr. Cristian Capelli (Department of Biology, University College London, United Kingdom); Prof. John Clegg (Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom); Dr. Mary Ganczakowski (Queen Alexandra Hospital, Portsmouth, United Kingdom); Prof. Wulf Schiefenh¨ovel (Human Ethology Group, Max-Planck Institute, Andechs, Germany); Mr. Danielle Sellitto (Department of Genetics and Molecular Biology, University of Rome “La Sapienza”, Italy); Prof. Matthew Spriggs (School of Archaeology and Anthropology, Australian National University, Canberra, Australia); Dr. John Terrell (Department of Anthropology, The Field Museum, Chicago, U.S.A.); Dr. Mark Thomas (Center for Genetic Anthropology, Department of Biology, University College London, United King- dom); Prof. Antonio Torroni (Department of Genetics and Molecular Biology, University of Rome “La Sapienza”, Italy); Dr. Chris Tyler-Smith (Department of Biochemistry, University of Oxford, United Kingdom); Dr. Peter Underhill (Human Population Genetics Laboratory, Stanford University, U.S.A.); Dr. Richard Walter (Department of Anthropology, University of Otago, Dunedin, New Zealand); and Prof. Henry Wright (Department of Anthropology, University of Michigan, Ann Arbor, U.S.A.). The author was supported by a New Zealand Government Doctoral Scholarship administered by the Foundation for Research, Science, and Technology (FRST); and a grant from the Kon-Tiki Museum (Oslo, Norway). Research was funded by Wellcome Trust grant 038052Z-93-Z (United Kingdom); an Otago Research Grant (University of Otago, Dunedin, New Zealand); and the University of Oslo (Norway). CONTENTS 1. Introduction .............................................. 1 2. Background .............................................. 6 2.1 Historical Groupings of Indo-Pacific Peoples . ................ 6 2.2 The Austronesian Language Family . ........... 7 2.3 Archaeology of the Indo-Pacific Region . ............. 10 2.4 Biological Variation in the Indo-Pacific Region . ................ 14 2.5 Molecular Genetic Research . .......... 19 2.6 Alternative Models of Austronesian Settlement . ................ 32 2.7 Assumptions of Biological Anthropology Research . ................ 34 3. Materials and Methods ........................................ 36 3.1 ReferenceSequences .............................. ........ 36 3.2 BiologicalSamples ............................... ........ 36 3.3 ExperimentalAnalyses. ......... 38 3.4 PhylogeneticAnalyses . ......... 48 3.5 PopulationGeneticAnalyses . .......... 52 4. Indonesia ............................................... 59 4.1 Introduction.................................... ....... 59 4.2 Results......................................... ..... 70 4.3 Discussion...................................... ...... 80 5. Madagascar .............................................. 88 Contents v 5.1 Introduction.................................... ....... 88 5.2 Results......................................... ..... 97 5.3 Discussion...................................... 106 6. Vanuatu ................................................ 114 6.1 Introduction.................................... ....... 114 6.2 Results......................................... 124 6.3 Discussion...................................... 135 7. Relatedness of Three Oceanic MtDNA Lineages .......................... 145 7.1 Introduction to the First Technical Study . .............. 145 7.2 Methodology ..................................... 145 7.3 Results......................................... 146 7.4 Discussion...................................... 153 8. Evaluation of Neutral Evolution in the MtDNA Control Region ................. 155 8.1 Introduction to the Second Technical Study . .............. 155 8.2 Methodology ..................................... 157 8.3 Results......................................... 158 8.4 Discussion...................................... 165 9. Conclusions .............................................. 168 Appendices 215 A. Reagents Used in Experiments ................................... 216 B. Y Chromosome Polymorphisms ................................... 217 C. Tables of Diversity Values ...................................... 224 D. Tables of Excoffier’s ΦST and Nei’s DA Values .......................... 227 Contents vi E. MtDNA Control Region Variation in Indonesia .......................... 229 F. MtDNA Control Region Variation in Madagascar ......................... 237 G. MtDNA Control Region Variation in Vanuatu ........................... 239 H. Summary of Genetic Data from Indonesia ............................. 245 I. Summary of Genetic Data from Madagascar ............................ 248 J. Summary of Genetic Data from Vanuatu .............................. 250 K. PERL Code for Programmes .................................... 257 K.1 Charstate ....................................... 257 K.2 Compendium ...................................... 262 K.3 Variable ........................................ 267 K.4 Poisson ......................................... 270 LIST OF FIGURES 2.1 Language groups in Island Southeast Asia. .............. 9 2.2 Indo-Pacific biological relationships according to classical genetic markers . 17 2.3 ThehumanmitochondrialDNAgenome.. .......... 20 2.4 Simplified phylogenetic tree of mtDNA lineages . ............... 22 2.5 Nine base pair deletion (∆9bp) frequencies in the western Indo-Pacific region. 25 2.6 Simplified phylogenetic tree of Y chromosome haplogroups. ................ 27 2.7 Y chromosome haplogroup frequencies in the western Indo-Pacific region. 31 3.1 Diagram of the control region amplicon . ............ 40 3.2 Placement of nine mtDNA
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