Genetic history and pre-Columbian Diaspora of Chibchan speaking populations: Molecular genetic evidence by Copyright 2008 Phillip Edward Melton M.A., University of Kansas, 2005 Submitted to the Department of Anthropology and the Faculty of the Graduate School of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy _________________________ Chairperson _________________________ _________________________ _________________________ _________________________ Date Defended:_________________________ The Dissertation Committee for Phillip E. Melton certifies that this is the approved version of the following dissertation: Genetic history and pre-Columbian Diaspora of Chibchan speaking populations: Molecular genetic evidence by Copyright 2008 Phillip Edward Melton M.A., University of Kansas, 2005 Submitted to the Department of Anthropology and the Faculty of the Graduate School of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy _________________________ Chairperson _________________________ _________________________ _________________________ _________________________ Date Defended:_________________________ ii Abstract This dissertation examined Y-Chromosome and mitochondrial DNA (mtDNA) genetic variation in 230 individuals from five (Rama, Chorotega, Huetar, Maléku, and Guaymi) indigenous populations inhabiting lower Central America in order to determine the evolutionary history and biological relationship among Chibchan-speakers and neighboring groups. Mitochondrial genetic diversity observed in Chibchan populations indicates a biological relationship with two Mesoamerican groups (Chorotega and K’iche Maya). However, Chibchan populations are biologically differentiated from eastern and Andean South American indigenous groups. Y-chromosome variation demonstrates a shared paternal biological relationship between Mesoamerican and northern Chibchan populations, whereas southern Chibchan and South American groups demonstrate a closer genetic association. Genetic diversity values in all five study populations were higher for Y- chromosome and lower for mtDNA haplotypes. Low mtDNA diversity and positive neutrality tests statistic values indicate that genetic drift has operated on this locus in Chibchan populations. Coalescent dates based on two haplogroup A2 (16360 and 16187) nodes indicate the divergence of Chibchan groups from earlier Paleoindian groups between 8,000 and 10,000 years ago. In addition, a genetic discontinuity was detected in Chibchan populations and is associated with the region around Lake Nicaragua. This discontinuity is connected with rising sea levels that occurred 8,000 years before present, separated lower Central from North and South America, and isolated the predecessors of modern Chibchan populations. Archaeological and linguistic evidence is used to support the endogenous development of Chibchan populations in lower Central America. Difference between low maternal and high paternal genetic diversities are interpreted as the result of two male dominated migrations. The first migration occurred with the arrival of Nahua and Oto-Manguean populations on the Pacific coast of Costa Rica and Nicaragua between 800 and 1000 A.D. The second migration occurred with European contact in the early sixteenth century. This study is concluded by supporting mtDNA evidence for the endogenous development of Chibchan-speaking populations in lower Central America. However, recent demographic events impacted the paternal genetic structure of these groups. iii This dissertation is dedicated to Jennifer, Spencer, Xavier, and Cordelia for their encouragement, understanding and patience iv Acknowledgements I would like to thank the indigenous people who participated in this study and allowed for this study to be possible. I would especially like to thank Cleveland Macrea and Jerry Macrea for their hospitality and courtesy during the fieldwork with the Rama. I would also like to thank my committee members: Dr. Michael Crawford; Dr. John Hoopes; Dr. Bart Dean; Dr. Jim Mielke; and Dr. William Woods; my fellow collaborators on this project, Dr. Ramiro Barrantes, and Norberto Baldi from the University of Costa Rica; my fellow students from the Laboratory of Biological Anthropology specifically Kristin Young; Anne Justice, Geetha Chitoor, Kritie Beaty, Chris Krawzack, Dr. Mark Zlojutro, Dr. Rohina Rubicz, and Orion Graf. The Department of Anthropology office staff: Judy Ross, Carol Archinal, and Kathleen Womack; and of course my family for providing me encouragement throughout the entire process. This research was funded by University of Kansas a General Research Fund and an International studies grants awarded to Dr. Michael Crawford plus a Carroll D. Clark award from the department of Anthropology awarded to the author. v Table of Contents CHAPTER ONE: INTRODUCTION 1 CHAPTER TWO: LITERATURE REVIEW 7 Molecular Genetic Overview 7 Mitochondrial DNA 10 Native American mtDNA 16 mtDNA and the origins of Native Americans 19 mtDNA and the peopling of South America 21 Y-Chromosome 23 Native American Y-chromosomes 26 Y-chromosomes and the peopling of the Americas 29 Y-chromosomes and peopling of South America 32 Language and the Peopling of the Americas 33 Genes and Language 37 The origins of Agriculture in the Americas 44 Summary 51 CHAPTER THREE: CHIBCHAN POPULATION BACKGROUND 53 Chibchan populations 53 Chibchan cultural history 55 Hunter/Gatherer Period 57 Specialized Domestication 57 Early Tribal Social Agriculture 58 Specialized Agriculture 59 Chiefdoms and Increased Specialization 60 Post European Contact 61 Genetic of Chibchan Populations 62 Classical Genetic Markers 63 mtDNA 70 Y-chromosome 73 Genetics summary 77 Chibchan populations Divergence 78 Mesoamerican-Chibchan Boundary 80 Rama 81 Maléku 82 Huetar 83 Guaymi 84 Chorotega 84 Summary 85 vi CHAPTER FOUR: MATERIALS AND METHODS 87 Field Methods 87 Laboratory Methods 89 DNA Extraction 89 mtDNA analysis 90 Y-chromosome analysis 95 Analytical Techniques 98 Diversity Measures 98 Measures of Selective Neutrality 99 Multidimensional Scaling Plots 101 Median-Joining Networks 103 Heterozygosity vs. rii 104 Population structure 105 Divergence times 107 Phylogeographic analysis 108 Admixture estimates 110 Summary 111 CHAPTER FIVE: RESULTS 113 MtDNA 113 Restriction Length Polymorphisms 113 HVS-I sequences 118 Diversity and Neutrality Measures 120 Median Joining Networks 122 Multidimensional Scaling Plot 127 Gene diversity versus rii 128 Phylogeographic Analysis 129 SAMOVA 130 Monmonier’s Algorithm 131 Interpolated Genetic Landscape 133 Chibchan Divergence Times 133 Y-Chromosome 134 Single Nucleotide Polymorphisms 135 Short Tandem Repeats 137 Diversity Measures 140 Y-Chromosome STR Median Joining Networks 140 Multidimensional Scaling Plot 144 Gene diversity versus rii 144 Classical Genetic Polymorphims 147 Diversity Measures 148 Multidimensional Scaling Plot 148 Heterozygosity versus rii 150 Population Structure 152 vii Wright’s F ST 152 Analysis of Molecular Variance (AMOVA) 154 Admixture Estimates 159 Summary 160 CHAPTER SIX: DISCUSSSION: 162 Genetic Diversity 162 Mesoamerican-Chibchan Population Relationships 173 Maternal vs. Paternal Genetic histories 178 Genetic drift vs. Gene Flow 184 Phylogeography, Paleoecology and Chibchan Origins 188 Summary 193 CHAPTER SEVEN: CONCULUSION 195 LITERATURE CITED 199 APPENDIX A 230 viii List of Figures Figure 1: Central America geographic areas 2 Figure 2: mtDNA genome with positions of major mtDNA haplogroups 13 Figure 3: Geographic distribution of mtDNA haplogroups 14 Figure 4: Schematic diagram of the Y-chromosome 24 Figure 5: Geographic location of Y-chromosome haplotypes 26 Figure 6: Mesoamerican linguistic area 41 Figure 7: Isthmo-Colombian area 42 Figure 8: Chibchan language family 43 Figure 9: Agricultural regions in the Americas 45 Figure 10: Central America cultural areas 53 Figure 11: Lower Central America culture area and archaeological sites 56 Figure 12: Geographic location of the five study populations 88 Figure 13: Comparative populations for mtDNA 116 Figure 14:Median Joining Network for Chibchan populations 123 Figure 15: Median Joining Network for mtDNA haplogroup A2 124 Figure 16: MDS Plot for mtDNA HVS-I sequences 128 Figure 17: Gene diversity vs. rii for mtDNA HVS-I sequences 129 Figure 18: MDS – SAMOVA plot for mtDNA HVS-I sequences 131 Figure 19: Delaunay triangulation using Monmonier’s Algorithm 132 Figure 20: Interpolated genetic landscape for mtDNA HVS-I sequences 133 Figure 21: Comparative populations for Y-chromosome 136 Figure 22: Median joining network for Y-chromosome haplogroup Q3 143 Figure 23: Median joining network for Y-chromosome haplogroup R1b 143 Figure 24: MDS plot of Y-chromosome STR haplotype data 145 Figure 25: Gene diversity vs. rii for Y-chromosome STR haplotypes 146 ix Figure 26: Comparative populations for classical genetic markers 147 Figure 27: MDS plot for classical genetic markers 150 Figure 28: Heterozygosity vs. rii for classical genetic markers 151 x List of Tables Table 1: Native American mtDNA coding region RFLP and HVS-I sites 17 Table 2: Number of participants from the five study populations 89 Table 3: Primer pairs for mtDNA haplogroups 91 Table 4: Y-chromosome STRs used in this study 95 Table 5: Primers for Y-SNP analysis 97 Table 6: Native American mtDNA haplogroups for study populations 114 Table 7: Native American mtDNA haplogroups – comparative populations 115 Table 8: mtDNA HVS-I sequences