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Genetic Variation in Central Asia: an Examination Of GENETIC VARIATION IN CENTRAL ASIA: AN EXAMINATION OF POPULATION HISTORY AND STRUCTURE A Dissertation by BONNY MARIE FORD Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Sheela Athreya Committee Members, David Carlson Cynthia Werner Spencer Johnston Head of Department, Cynthia Werner August 2018 Major Subject: Anthropology Copyright 2018 Bonny Ford ABSTRACT The population structure of Central Asia and the effects of population history on that structure have not been well studied. To address this gap, 4,169 mtDNA control region sequences from Central Asia and the surrounding areas (Caucasus, East Asia, East Europe, and northern and southern Asia) sourced from GenBank were analyzed. MtDNA sequences were aligned using MAFFT version 7 and haplogroups were assigned with HaploGrep 2.0. Arlequin 3.5.2 was used to calculate the haplotype diversity, nucleotide diversity, and the mean number of pairwise differences, and to perform an AMOVA. Additionally, genetic distances were calculated between all populations and used in PCA to visualize the distribution of genetic diversity. Lastly, the percentages of mtDNA haplogroups in each population were estimated and used in PCA to examine clustering patterns. The results of this study show that Central Asian populations have a high degree of genetic variation as evidenced by high haplogroup, haplotype, and nucleotide diversities. This genetic variation has been shaped by admixture with populations from East and West Eurasia, and indigenous groups from North and South Asia. Most of the haplogroups in Central Asia have an East or West Eurasian origin, with a small percentage of haplogroups from India. Two haplogroups, D4c and G2a, that may have their origins in Central Asia were also identified. A small, but significant portion of the variation in Central Asia can be accounted for by geographic region. This geographic structure is most consistent with an isolation by distance model. Finally, the history of ii population interactions within Central Asia has greatly influenced the distribution of genetic variation there. This includes not only recent interactions resulting from the policies of the Soviet Empire, but also those like the movement of Mongol groups into Central Asia beginning thousands of years ago. This study has situated Central Asia in global models of human variation and has provided a framework with which hypotheses regarding the origin and dispersal of humans, Middle and Late Pleistocene hominin interactions, and the geographic extent of Neandertals can be tested. iii DEDICATION For my husband and son, André and Sanders Ford. iv ACKNOWLEDGEMENTS Thank you to my husband André, without his support I would never have been able to complete this dissertation. He has been there for me throughout the long and arduous process of completing my PhD, whether that be providing moral support, a reality check, or taking care of our son while I spent every waking moment enmeshed in the writing process. There is no one else I would rather have by my side. I would also like to thank my committee chair, Dr. Sheela Athreya, and my committee members, Dr. Carlson, Dr. Werner, and Dr. Johnston, for their guidance and support throughout the course of this research. Sheela has been there to support me every step of the way and has provided me with invaluable feedback, support, and time. She has always believed in me and has given me the confidence to succeed. Thanks also go to my friends and the faculty and staff of the Department of Anthropology for making my time at Texas A&M University enjoyable. Lastly, I want to thank all of the researchers that uploaded their DNA sequences to GenBank and thus provided the data for this dissertation. Open access to data is absolutely essential to innovative scientific research and discovery. v CONTRIBUTORS AND FUNDING SOURCES Contributors Part 1, faculty committee recognition This work was supervised by a dissertation committee consisting of Professor Sheela Athreya and Professor(s) David Carlson and Cynthia Werner of the Department of Anthropology and Professor J. Spencer Johnston of the Department of Entomology. Part 2, student/collaborator contributions All work for the dissertation was completed independently by the student. Funding Sources Graduate study was supported by a Summertime for Advancement in Research (STAR) Award from Texas A&M University. vi TABLE OF CONTENTS Page ABSTRACT .......................................................................................................................ii DEDICATION .................................................................................................................. iv ACKNOWLEDGEMENTS ............................................................................................... v CONTRIBUTORS AND FUNDING SOURCES ............................................................. vi TABLE OF CONTENTS .................................................................................................vii LIST OF FIGURES ............................................................................................................ x LIST OF TABLES ............................................................................................................ xi CHAPTER I INTRODUCTION ....................................................................................... 1 CHAPTER II HISTORY OF CENTRAL ASIA ............................................................. 10 What is Central Asia? ................................................................................................... 10 Prehistory of Central Asia ............................................................................................ 14 Historical Background of Central Asia ........................................................................ 17 Earliest Inhabitants of Central Asia .......................................................................... 17 Ancient Era (2000 BCE to 155 CE) ......................................................................... 20 Chinese, Islamic, and Turkic Influences in Central Asia (4th – 9th centuries) .......... 23 Formation of Ethnic Identities .................................................................................. 27 Russian Conquest of Central Asia ............................................................................ 31 Central Asia under Soviet Rule ................................................................................ 33 Central Asian Autonomy .......................................................................................... 36 Application to this Study .............................................................................................. 38 CHAPTER III BACKGROUND ON ANTHROPOLOGICAL GENETICS AND GENETIC RESEARCH IN CENTRAL ASIA ................................................................ 40 Historical Background of Anthropological Genetics ................................................... 40 Current State of Genetics Research in Central Asia .................................................... 48 MtDNA Studies in Central Asia ............................................................................... 49 Y chromosome Studies in Central Asia ................................................................... 52 Multilocus Studies in Central Asia ........................................................................... 55 Application to this Study .............................................................................................. 57 vii CHAPTER IV THEORETICAL FRAMEWORK: POPULATION STRUCTURE AND HISTORY ............................................................................................................... 59 What is Population Structure? ...................................................................................... 59 What is Population History? ........................................................................................ 63 Application to this Study .............................................................................................. 65 CHAPTER V MATERIALS ........................................................................................... 68 MtDNA Sample............................................................................................................ 68 Caucasus North ......................................................................................................... 72 Caucasus South ......................................................................................................... 74 Central Asia .............................................................................................................. 76 East Asia ................................................................................................................... 79 East Europe ............................................................................................................... 81 Near East .................................................................................................................. 91 North Asia ................................................................................................................ 99 North/Central Asia ................................................................................................. 102 North/East Asia .....................................................................................................
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