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An Examination of Population History, Population Structure, and Biological Distance Among Regional Populations of the Kenyan Coast Using Genetic and Dental Data

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An Examination of Population History, Population Structure, and Biological Distance Among Regional Populations of the Kenyan Coast Using Genetic and Dental Data AN EXAMINATION OF POPULATION HISTORY, POPULATION STRUCTURE, AND BIOLOGICAL DISTANCE AMONG REGIONAL POPULATIONS OF THE KENYAN COAST USING GENETIC AND DENTAL DATA Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of the Ohio State University By Amelia R. Hubbard, B.A., M.A. Graduate Program in Anthropology The Ohio State University 2012 Dissertation Committee: Professor Debbie Guatelli-Steinberg, Adviser Professor Douglas Crews Professor Paul Fuerst Professor Joel Irish Professor Paul Sciulli Copyrighted by Amelia Robin Hubbard 2012 ABSTRACT This study tests the long accepted assumption that non-metric dental traits and genetic variants provide similar information about population history through reconstructions of biological distance and population structure. Further, it examines whether these biological data agree when comparing populations within a geographically restricted region. Using non-metric dental morphology, microsatellite repeat variation, and genealogical data from four contemporary coastal Kenyan populations (n=295), the goals of the project are twofold: 1) To determine if there is concordance between dental and genetic based reconstructions of biological distance (a measure of biological similarity between populations) and population structure (a measure of the contributions of gene flow and genetic drift to variation within and between populations), and 2) To determine if genetic and dental reconstructions of biological distance and population structure agree with known population histories for the region. The results of this study indicate that there is agreement between dental and genetic reconstructions of regional population structure and biodistance when examining general patterns in the relationships among groups; however, when testing more detailed relationships, non-metric dental traits are not as sensitive as genetic variants to differences among populations. This finding has important implications for how bioarchaeologists approach studies of regionally restricted populations. ii To my rock, Jason Von Ville, and my academic (and actual) parents, Dennis Hubbard and Karla Parsons-Hubbard. iii ACKNOWLEDGMENTS No scientific research is done in isolation. As such, the following people must be recognized for their contributions to the current project. First and foremost, I owe a great debt of gratitude to Debbie Guatelli-Steinberg, my mentor and adviser for the past eight years. Her untiring commitment to my professional development as a researcher, a teacher, and a colleague cannot be repaid. Second, to my committee, thank you for your tireless assistance in answering my many questions during this arduous process, for reading through and making comments on this document, and for your general guidance throughout the process. Dr. Douglas Crews provided a great deal of assistance prior to beginning fieldwork, recommendations for my Institutional Review Board application, and meticulous comments on this manuscript. Dr. Paul Fuerst graciously provided me with the space needed to complete the genetic analysis of this project, trained me in the myriad genetic programs available for analyzing genetic datasets, and provided a solid framework for my understanding of human genetic variation. Dr. Joel Irish assisted with my training in scoring non-metric dental traits (particularly those that I found difficult to score), provided statistical assistance and recommendations, and spent countless hours discussing aspects of the project over the phone. Dr. Paul Sciulli provided invaluable assistance with the analytical portion of this project, including sharing his programs in SAS for calculating biodistance and population structure among other things. I certainly attribute the vast majority of the knowledge I have gained in statistical methods and iv methodology to Sciulli. Thank you also to Dr. Yuan Zheng, who served as my outside committee member for the dissertation defense. While having a dental implant installed in 2008 I was fortunate to meet the wonderful Dr. Burak Yilmaz. In addition to receiving proper occlusion and the purported “Cadillac of dental crowns,” Burak provided me with extensive training in taking dental impressions from living people and recommended materials for my traveling “clinic”; I have also gained a lifelong friend. Sağ olun! Upon returning from the field I could not have completed the labwork without the tireless assistance of my undergraduate research students: Crystal Alford, Vince Caicco, Justin Fryer, Alexis Goots, Laura Layne, Chris Parker, and Caitlin Rak. Crystal, Vince, and Chris were with me from the very beginning and deserve special recognition for their patience, attention to detail, and long hours making dental casts in the lab without question or complaint. Various statistical gurus also must be recognized for their assistance including Paul Sciulli, John Relethford, Lyle Konigsberg, Bridget Algee-Hewitt, and John Blangero. Thanks to Graciela Cabana and Keith Hunley for recommendations on this project at various stages. To Chap Kusimba, thank you for opening my eyes to the wonders of Kenya. Several people also assisted me in securing materials and the space needed to complete this project including Ryan Raaum (thanks for the spit tubes!), Paul Fuerst (for making space for me in his genetics laboratory), the people of Prevention Genetics (for a reduction in my analysis costs), and Dr. Bandeen for donating toothpaste and brushes for my participants. A great deal of thanks is also due to my colleague and friend, Dr. Evelyn Wagaiyu, for her assistance in securing the necessary permits, ethical approvals, and v affiliations in Kenya. To my friend and research assistant, Antony Mwambanga, I cannot thank you enough for keeping me on track and introducing me to your community. Youwere a great help and a fantastic travel companion on the arduous journeys between locations. To my other assistants and friends while in Kenya, Yusuf Muhaji Badru (and faithful driver), Michael Mwananyumba, Stanly Kimonge, Dorkus Maza, Abraham Jumapili, and the women of the Bungule Basketweavers Guild a big thanks as well. Finally, to the Mchula family thank you for housing and feeding me during my stay in Old Town and to Ilham for inviting this mzungu to be a part of your wedding. Finally, this project would not have succeeded without the willingness and kindness of the many participants who enrolled in this study. To the people of Lamu, Old Town, Kasigau, and Dawida, nawashukuru sana kwa wema wenu. vi VITA 16 April, 1980 Born- St. Croix, US Virgin Islands, USA 2002 B.A. (with honors) Anthropology Beloit College 2006 M.A. Anthropology The Ohio State University 2004-2005 Editorial Assistant American Journal of Physical Anthropology 2007 Assistant Editor American Journal of Physical Anthropology 2011 Presidential Fellow Present, 2005-2010 Graduate Teaching Associate The Ohio State University PUBLICATIONS Hubbard, A.R., Guatelli-Steinberg, D., and Sciulli, P.W. 2009. Under restrictive conditions, can the widths of linear enamel hypoplasias be used as relative indicators of stress episode duration? American Journal of Physical Anthropology 138: 177-189. Guatelli-Steinberg D, Ferrell R, Spence J, Talabere T, Hubbard A.R., and Schmidt S. 2009. Sex differences in anthropoid mandibular canine lateral enamel formation. American Journal of Physical Anthropology 140: 216-233. FIELDS OF STUDY Major field: Anthropology vii TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii DEDICATION ................................................................................................................... iii ACKNOWLEDGMENTS ................................................................................................. iv VITA ................................................................................................................................. vii LIST OF TABLES ............................................................................................................ xii LIST OF FIGURES ......................................................................................................... xiv CHAPTER 1: INTRODUCTION ........................................................................................1 1. Research problem and project development ........................................................................2 2. Objectives ................................................................................................................................4 3. Hypotheses ...............................................................................................................................7 3.1 Testing agreement between biodistance and known population history ...........................8 3.2 Testing agreement between population structure and known population history .............9 3.3 Testing agreement between dental and genetic estimates of biodistance ........................12 3.4 Testing agreement between dental and genetic estimates of population structure ..........12 4. Significance of the study .......................................................................................................13 5. Organization of dissertation ...............................................................................................14 CHAPTER 2: LITERATURE REVIEW ...........................................................................16
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