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The Basques in the Genetic Landscape of Europe

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The Basques in the Genetic Landscape of Europe The Basques in the Genetic Landscape of Europe by Copyright 2009 Kristin Leigh Young M.A., University of Kansas, 2001 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 Michael H. Crawford Chairperson James Mielke Deborah Smith Ivana Radovanovich William Woods Date Defended: June 16, 2009 The Dissertation Committee for Kristin L. Young certifies that this is the approved version of the following dissertation: The Basques in the Genetic Landscape of Europe by Copyright 2009 Kristin Leigh Young M.A., University of Kansas, 2001 Michael H. Crawford Chairperson James Mielke Deborah Smith Ivana Radovanovich William Woods Date Approved: June 16, 2009 ii Abstract This study examines the position of the Basques in the genetic landscape of Europe using molecular genetic systems. Biparental markers (autosomal STRs and classical genetic markers) and uniparental markers (mtDNA haplogroups and HVS-I sequences, as well as Y-chromosome STR haplotypes) are used to address the origin and structure of the Basque population of Spain, as well as their role in the peopling of Europe. Three hypotheses of Basque origins are tested: 1) The Basques share a recent common ancestor with populations of the Caucasus; 2) The Basques are descendants of ancient Iberian populations who migrated from North Africa during the Neolithic; and 3) The Basques are a remnant population, the descendants of Paleolithic Europeans, who evolved in situ, with little gene flow from Neolithic farmers. The question of heterogeneity within the Basque population is addressed, and uniparental markers are examined for evidence of Neolithic ancestry in the Basque Provinces. Analysis of the molecular systems does not support a recent common ancestor between the Basques and populations either from the Caucasus or North Africa. While analysis of classical markers reveals the effects of genetic drift on the Basque population as a whole, AMOVA analysis of molecular markers demonstrates genetic homogeneity and little genetic structure between provinces (autosomal STRs: Va = -0.095, FCT = -0.0036, p = 0.878; Y-STRs: 1.71%, p = 0.0369; HVS-I sequences: 1.03%, !ST = 0.0103, p = 0.0308). In addition, heterozygosity versus rii of autosomal STRs reveals that the impact of genetic drift is mediated by the influence of gene flow in three of the Basque Provinces. Gene and haplotype diversity levels in the Basque population are on the low end of the European distribution (autosomal STRs: 0.0805, Y-STRs: 0.9421, mtDNA: 0.0114), but other European populations have equivalent or lower levels. Distribution of uniparental haplogroups demonstrates varying levels of Neolithic admixture in the Basque population, with both Neolithic maternal lineages (J) and paternal lineages (E1b1b, G2, J2a) present. While these results do not suggest that the ancient Basque population had direct contact with Neolithic farmers, the presence of these markers cautions against using the Basques as a proxy Paleolithic population in genetic studies. However, the Basques do have high frequencies of other uniparental haplogroups considered to be of Paleolithic origin (Y-chromosome: R1b, mtDNA: H, U5), and analysis of demographic processes using HVS-I sequences places the date of population expansion among the Basques squarely in the Paleolithic, arguing against the complete replacement demic diffusion model of the Neolithic transition. iii This dissertation is dedicated to my father, for saying I could be anything I wanted to be, and actually believing it. To my mother, for her unconditional love and support. To my children: Kaity, Brae, Hannah, and the little one on the way, for their inspiration and encouragement of my life outside of graduate school. To my husband, Brandon, my cheerleader, therapist, and best friend. To John, who was always proud of me. And to my grandmothers, Dennia Faye and Mary Ann, whose courage and independence were my guiding light. iv Acknowledgements I would especially like to thank the Basque participants whose participation made this study possible. I would also like to thank Dr. Arantza Apraiz-Gonzalez, a Basque post-doc in our laboratory who spent three field seasons in her home country collecting samples. In addition, I would like to thank my committee members: Dr. Michael Crawford, Dr. James Mielke, Dr. Deborah Smith, Dr. Ivana Radovanovic, and Dr. William Woods; my collaborators: Dr. Ranjan Deka, Dr. Guangyn Sun, Dr. Eric Devor, and Dr. Mike Grose; my fellow graduate students in the Laboratory of Biological Anthropology: Geetha Chittoor, Kristie Beaty, Anne Justice, Chris Krawczak, Norberto Baldi-Salas, Jennifer Rack, Dr. Rohina Rubicz, Dr. Phillip Melton, Dr. Mark Zlojutro, and Orion Graf, for their continued friendship and encouragement; the departmental office staff, Judy Ross, Carol Archinal, and Kathleen Womack, who do their best to make this process as smooth as possible; and my family, for their unwavering support. This research was funded by a National Geographic Society Grant to the University of Kansas Laboratory of Biological Anthropology (Project 6935-00) and a Carroll D. Clark award to the author. v Table of Contents CHAPTER ONE: INTRODUCTION....................................................................................................... 1 CHAPTER TWO: LITERATURE REVIEW .........................................................................................7 POPULATION HISTORY...............................................................................................................................7 BASQUE GENETIC STUDIES: CLASSICAL MARKERS...............................................................................17 Blood Groups...................................................................................................................................... 17 Erythrocyte Enzymes..........................................................................................................................23 Plasma Proteins ................................................................................................................................. 25 Human Leukocyte Antigens ...............................................................................................................33 BASQUE GENETIC STUDIES: MOLECULAR SYSTEMS .............................................................................44 Microsatellites .................................................................................................................................... 45 Y-Chromosome ................................................................................................................................... 46 Mitochondrial DNA............................................................................................................................48 BASQUE ORIGINS: HYPOTHESES .............................................................................................................52 Basque-Caucasian Hypothesis ..........................................................................................................52 Vasco-Iberian Hypothesis..................................................................................................................54 Pre-Indo-European Hypothesis.........................................................................................................67 CHAPTER THREE: MATERIALS AND METHODS....................................................................... 78 SAMPLE COLLECTION ..............................................................................................................................78 LABORATORY METHODS .........................................................................................................................79 DNA extraction................................................................................................................................... 79 Autosomal STR Analysis ....................................................................................................................79 Y-chromosome Analysis.....................................................................................................................81 Mitochondrial DNA Analysis ............................................................................................................82 ANALYTICAL METHODS ..........................................................................................................................86 Genetic Diversity and Population Substructure...............................................................................86 Genetic Distance Measures ...............................................................................................................90 Heterozygosity and distance from centroid......................................................................................92 Analysis of Molecular Variance (AMOVA)......................................................................................93 Spatial Analysis of Molecular Variance (SAMOVA)....................................................................... 95 Network Analysis................................................................................................................................95 Mismatch/Intermatch Analysis..........................................................................................................96 Ordination and Visualization Techniques
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