University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Spring 2011 A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography Matthew Dulik University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Archaeological Anthropology Commons, Biological and Physical Anthropology Commons, Genetics Commons, and the Molecular Genetics Commons Recommended Citation Dulik, Matthew, "A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography" (2011). Publicly Accessible Penn Dissertations. 1545. https://repository.upenn.edu/edissertations/1545 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1545 For more information, please contact [email protected]. A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography Abstract This dissertation explores the genetic histories of several populations living in the Altai Republic of Russia. It employs an approach combining methods from population genetics and phylogeography to characterize genetic diversity in these populations, and places the results in a molecular anthropological context. Previously, researchers used anthropological, historical, ethnographic and linguistic evidence to categorize the indigenous inhabitants of the Altai into two groups – northern and southern Altaians. Genetic data obtained in this study were therefore used to determine whether these anthropological groupings resulted from historical processes involving different source populations, and if the observed geographical and anthropological separation between northern and southern Altaians also represented a genetic boundary between them. These comparisons were made by examining mitochondrial DNA (mtDNA) coding region single nucleotide polymorphisms (SNPs), control region sequences (including HVS1), and several complete mitochondrial genomes. Variation in the non-recombining portion of the Y- chromosome (NRY) was characterized with biallelic markers and short tandem repeat (STR) haplotypes. Overall, this work provided a high-resolution data set for both unipaternally inherited genetic marker systems. The resulting data were analyzed using both population genetic and phylogeographic methods. Northern Altaians (Chelkan, Kumandin and Tubalar) were distinctive from the southern Altaians (Altai- kizhi) with both genetic systems, yet the Tubalar consistently showed evidence of admixture with southern Altaians, reflecting differences in the origin and population history of northern and southern groups as well as between ethnic northern Altaian populations. These results complement the observation of cultural differences as noted by anthropological/ethnographic research on Altaian populations. These differences likely reinforced and maintained the genetic differences between ethnic groups (i.e., a cultural barrier to genetic exchange). Therefore, biological and cultural lines of evidence suggest separate origins for northern and southern Altaians. Phylogeographic analysis of mtDNA and NRY haplotypes examined the impact of different historical events on genetic diversity in Altaians, including Neolithic expansions, the introduction of Kurgan cultures, the spread of Altaic-speakers, and the intrusion of the Mongol Empire. These insights also allowed for a greater understanding of the peopling of Siberia itself. The cultures of Altaian peoples ultimately helped to shape their current genetic variation. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Anthropology First Advisor Theodore G. Schurr Keywords mtDNA, Y-chromosome, genetic history, molecular anthropology Subject Categories Archaeological Anthropology | Biological and Physical Anthropology | Genetics | Molecular Genetics This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/1545 A MOLECULAR ANTHROPOLOGICAL STUDY OF ALTAIAN mSTORIES UTILIZING POPULATION GENETICS AND PHYLOGEOGRAPHY Matthew C. Dulik A DISSERTATION III Anthropology Presented to the Faculties ofthe University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2011 Dissertation Supervisor Graduate Group Chairperson Theodore G. Schurr Deborah A. Thomas Associate Professor, Anthropology Associate Professor, Anthropology Dissertation Committee Janet M. Monge, Adjunct Associate Professor, Anthropology Victor H. Mair, Professor of Chinese Language and Literature, East Asian Languages and Civilizations A MOLECULAR ANTHROPOLOGICAL STUDY OF ALTAIAN HISTORIES UTILIZING POPULATION GENETICS AND PHYLOGEOGRAPHY COPYRIGHT 2011 Matthew C. Dulik To my parents iii Acknowledgments First of all, I need to thank my dissertation advisor, Theodore Schurr. He allowed me and others in his lab the chance to explore our ideas (the plausible and farfetched) under his auspices, giving us a secure environment to expand our theoretical and technical expertise without getting lost along the way. Aside from my dissertation, the opportunities he afforded to me (both in range and scale of research topics) gave me numerous occasions to broaden my experience as a molecular anthropologist. Under his direction, I have learned what it takes to manage multiple projects and run a busy lab simultaneously. Our exchanges in the field, in grant and publication writing and in everyday interactions will be lessons I carry with me throughout my career. This dissertation would not have been possible had it not been for my dissertation committee members, Janet Monge and Victor Mair. I sincerely appreciate their continued support and diligence in reading every page I gave them. Our discussions helped to shape my ideas more clearly, challenged my perspective and, as a result, strengthened the arguments I wished to make. Undoubtedly, their efforts made for a stronger, more polished dissertation. It was an absolute pleasure working with them. I also owe my deepest gratitude to my first advisor, Richard Zettler, who provided me the opportunity to come to Penn and encouraged my interests in combining Near Eastern archaeology and molecular genetics. I will never forget the patience he showed me and his continued guidance and honesty throughout my time here. None of this research would have been possible without the financial support of numerous institutions and agencies. In particular, the Department of Anthropology and the University of Pennsylvania, the Baikal Project and the Social Sciences and iv Humanities Research Council of Canada, the Russian Basic Fund for Research, the National Genographic Society and the National Science Foundation for my Doctoral Dissertation Improvement Grant. In addition, I want to extend my thanks to the Altaian participants who volunteered to collaborate with us on this project. I would like to express my appreciation to Joe Lorenz for helping to facilitate a goal of mine to blend my interests in archaeology and human genetics through our ancient DNA work (and for helping me gain a better appreciation of “the lab where things work”). I would also like to thank Art Washburn, first and foremost, for great friendship and comaraderie. The opportunity to teach anatomy and share experiences in forensic consulting with him allowed me to apply my knowledge and training as an anthropologist outside of the Department, which has been just as fulfilling as any of my other endeavors at Penn. I am grateful for my friends and fellow graduate students (from my year and others) as well as current and past members of the Schurr lab who have helped make this process more rewarding, especially Samara Rubeinstein, Ömer Gökçümen, Paul Babb, Emily Renschler, and Klara Stefflova. Early on in our graduate school careers, Samara, Ömer and I brainstormed together and challenged each other on everything molecular anthropology, from grandiose theories to the minuscule details of statistical analysis. I still see the result of much of those collective efforts in our bodies of scholarship today. Ömer eloquently characterized the relationship that the three of us shared as that of intellectual siblings – I cannot convey this mutual sentiment more precisely. Words alone cannot express the thanks I owe to my fiancée, Kim Kahle, who has been amazing throughout this whole process. Her encouragement was constant, and her v impeccable advice was given freely and always at the right time. She possessed seemingly endless patience and tolerance during all the working weekends, the inordinate stacks of books and papers, the inescapable attachment to my computer, and the many late-night lab runs. Having received her PhD several years ago, she knew what she was getting into, but despite everything, it didn’t scare her away, and I am wholly grateful for that. I don’t how I would have made it through this process without her, and I can’t wait to embark on the next phase of our lives together. Finally, I owe everything to my family, especially my parents, brothers and sisters. There is no way that I would be where I am today without their unfaltering support and constant encouragement. They scarificed to get me to this point as well and have done everything from proof-reading and computer support to providing required distractions. Most graciously, they stopped asking the dreaded question, “so when are you going to finish?” quite some time ago. My parents have provided me the