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Mitochondrial Dna Diversity and Its Determinants in the Southwest Pacific

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Mitochondrial Dna Diversity and Its Determinants in the Southwest Pacific MITOCHONDRIAL DNA DIVERSITY AND ITS DETERMINANTS IN THE SOUTHWEST PACIFIC A Dissertation Submitted to the Temple University Graduate Board In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy By Danielle Nicole James August, 2008 © Copyright 2008 by Danielle Nicole James ABSTRACT MITOCHONDRIAL DNA DIVERSITY AND ITS DETERMINANTS IN THE SOUTHWEST PACIFIC Danielle Nicole James Doctor of Philosophy Temple University, 2008 Jonathan Friedlaender, PhD The purpose of this study is to examine mitochondrial DNA variation in the Southwest Pacific and determine what factors contribute to the degree and patterning of the observed variation. Population variation is known to be influenced by factors including demographic history, natural selection, climate, isolation, island area/complexity, and population age, as older populations are generally more diverse. The groups compared are from three regions in the Southwest Pacific; (a) northeast New Guinea, (b) Manus in northern Island Melanesia and (c) Easter Island in eastern Polynesia. MtDNA surveys have revealed highly significant differences in molecular variance across these populations. According to traditional biogeographical theory, the likely determinants of these differences are (a) length of time since initial settlement, (b) the comparative isolation of particular islands or regions since settlement, and (c) the size and complexity of settlement areas. Evidence from archaeology and linguistics provides the necessary framework for the study. Detailed archaeological surveys for several of the study regions provides evidence for settlement dates as well as evidence for isolation and/or frequent contact iii with other areas, usually in the form of trade and translocation of animals and artifacts. Linguistics, though not as informative as archaeology for settlement dates, provides detailed evidence for isolation and/or contact in the form of language isolates, language families, borrowing and linguistic divergence. The mtDNA haplogroups found in this study belong to several documented haplogroups, some of Melanesian origin, and some of Southeast Asian origin. The distribution of mtDNA variants and the pattern and degree of variation was examined using Analysis of Molecular Variance, standard diversity measures and partial Mantel matrix correlations. There were strong positive correlations between insular area, isolation and degree of variation. There were also measurable differences between inland and coastal populations on the larger islands where diversity in the isolated inland populations was greater than diversity in the coastal population. While there was some confounding of the variables, the results of our analysis indicate that insular area/complexity and isolation influence the pattern of variance more than length of settlement time. iv ACKNOWLEDGEMENTS I wish to thank Jonathan and Françoise Friedlaender for their work on all facets of the project. I also wish to thank Joseph Lorenz and L. Christie Rockwell for their laboratory instruction and help with project development. I would also like to thank Charles Weitz, Leonard Greenfield and Theodore Schurr for their comments on the chapters. Thanks are also due to Krista Latham, Elizabeth Rowe and Laura Scheinfeldt. v DEDICATION Dedicated to the people who were there from beginning to end my mother – Jacqueline James, my sister - Hertasha J. James, my aunts - Bobbie J. and Carolyn Ranson and my friend - Raygan L. Harris. vi TABLE OF CONTENTS Page ABSTRACT……………………………………………………………………………...iii ACKNOWLEDGEMENTS……………………………………………………………….v DEDICATION……………………………………………………………………………vi LIST OF TABLES………………………………………………………………………...x LIST OF FIGURES………………………………………………………………………xi CHAPTER 1. FRAMEWORK…………………………………………………………………...1 Introduction….…………………………………………………………….1 Archaeology and Linguistics in Oceania………………………………….2 Human Biological Studies in Oceania…………………………………….4 Definition of Geographic Terms…………………………………………..4 2. ARCHAEOLOGY AND LINGUISTICS IN THE SOUTHWEST PACIFIC……7 Introduction………………………………………………………………..7 Archaeology in Melanesia………………………………………………...7 Initial Colonization of Sahul and the Bismarcks...……………….7 Settlement of Manus……………………………………………..11 Holocene Exchange and the Development of Agriculture………13 The Lapita Expansion……………………………………………15 Origins of Lapita and its South Asian Precursors………………..18 Settlement of Remote Oceania…………………………………...20 Conclusions………………………………………………………………22 Linguistics in Melanesia…………………………………………………23 Papuan/Non-Austronesian Languages…………………………...23 Austronesian Languages…………………………………………27 Conclusions………………………………………………………………29 vii 3. BIOLOGICAL EVIDENCE FOR THE SETTLEMENT …………………….…33 OF THE PACIFIC Introduction……………………………………………………………....33 Early Genetic Studies………………………………………………….…34 Blood Group Distribution…………………………………….….34 HLA………………………………………………………….…..35 Hemoglobinopathies……………………………………….…….36 Immunoglobulins…………………………………………..…….38 Summary of Early Genetic Studies………………………………..……..39 Mitochondrial DNA……………………………………………..……….41 Evidence for the Settlement of New Guinea and……..………….45 Island Melanesia Holocene Sequences and the Settlement of ……………………..47 Remote Oceania Evidence from the Y Chromosome…………………………………...….51 Near Oceanic Y Chromosome Lineages………………………....52 Remote Oceanic Y Chromosome Lineages……………………...53 Summary of Genetic Data……………………………………………….55 Concordance of Genetic Data…………………………………....55 Discordance of Genetic Data…………………………………….55 Conclusions………………………………………………………………56 4. METHODS OF GENETIC AND STATISTICAL ANALYSIS FOR…………..57 MITOCHONDRIAL DNA RESEARCH IN THE SOUTHWEST PACIFIC Samples…………………………………………………………………..57 Laboratory Methods……………………………………………………...58 DNA Extraction………………………………………………….58 PCR Amplification…………………………….……………...…59 Sequence Analysis……………………………………………….60 Data Analysis…………………………………………………………….63 Phylogenetic Analysis……………………………………………63 viii Statistical Analysis……………………………………………….63 5. RESULTS OF MITOCHONDRIAL DNA ANALYSIS IN …………………….66 THE SOUTHWEST PACIFIC Introduction………………………………………………………………66 Haplogroup Distributions………………………………………………...68 Mitochondrial DNA Distribution in New Guinea…….…………68 Mitochondrial DNA Distribution in Manus……………………..80 Mitochondrial DNA Haplogroup Distribution in ……………….81 Easter Island Haplogroup Distribution Summary…………...………………………….83 Data Analysis…………………………………………………………….85 Network Analysis………………………………………………...85 Population Structure Analysis……………………………………89 AMOVA…………………………………………………………89 Diversity Measures………………………………………………91 Mantel Matrix Correlation……………………………………….94 Summary of Results……………………………………………………...95 6. GENETIC VARIATION AND POPULATION STRUCTIRE …………………97 IN THE SOUTHWEST PACIFIC Determinants of Genetic Variation………………………………………97 Structure of Genetic Variation in the Pacific…………………………….99 Discussion of mtDNA Variation in the Southwest Pacific……………..109 REFERENCES CITED…………………………………………………………112 ix LIST OF TABLES Table Page 4.1 List of Primers for Amplification of HVS I and HVS II……………………………60 4.2 Defining Mutations for mtDNA Haplogroups in the Southwest Pacific…………....62 5.1 mtDNA Lineage Occurrences in the Southwest Pacific…………………………….70 5.2 mtDNA Haplogroup Frequencies……………………………………………….…..71 5.3 AMOVA based on mtDNA (HVS I)………………………………………………..91 5.4 Haplotype Variation within Populations……………………………………………93 6.1 Diversity Measured for Southwest Pacific Islands………………………………...104 6.2 Island Size and Settlement Dates…………………………………………………..106 x LIST OF FIGURES Figure Page 1.1 Map of Oceania and the Geographic Boundary Between Near and Remote…………6 Oceania 2.1 Location of Pleistocene Sites in New Guinea and the Bismarck Archipelago……...10 2.2 Austronesian Language Classifications……………………………………………..30 2.3 Distribution and Sub-Grouping of Austronesian Languages………………………..31 3.1 Human mtDNA Genome……………………………………………………………44 5.1 mtDNA Schematic Tree for Eurasian Haplogroups…………………………….…..67 5.2 Haplogroup P Frequency Distribution………………………………………………73 5.3 Haplogroup Q Frequency Distribution……………………………………………...75 5.4 Frequency Distribution for Haplogroups B and R…………………………………..77 5.5 Frequency Distribution for Haplogroups M27, M28, M29 and E…………………..79 5.6 Frequency Distribution for Easter Island……………………………………………82 5.7 Median-Joining Network for New Guinea, Lineage N……………………………...86 5.8 Median-Joining Network for New Guinea, Lineage M……………………………..87 5.9 Median-Joining Network for Manus and Easter Island……………………………..88 6.1 Equilibrium Model…………………………………………………………………...98 6.2 Median-Joining Network for Haplogroup B……………………………………….107 xi CHAPTER 1 Framework Introduction As information about different genetic loci in human populations has accumulated over the past 30 years, scientists have looked for major factors that have influenced the pattern and degree of genetic variation at them. It has generally been assumed that besides selection acting on specific functioning genes, demographic factors affecting population size and historical migration events were the primary shapers of variation in human populations. This thesis explores the genetic variation in the Southwest Pacific, and links a set of populations with differing degrees of genetic variation to specific factors affecting demography. Using mitochondrial DNA, this study will analyze the genetic diversity of several islands. The study will also attempt to determine which factors contribute to the observed genetic variation on these islands. The samples used for comparison are from New Guinea, Manus Island and Easter Island. Additionally, these data will
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