The Genetic Structure of the Kuwaiti and Failaka Island Populations: Y-chromosome & Mitochondrial DNA Variation By Jasem Bader Theyab M.A., University of Kansas, 2010 Copyright 2013 Submitted to the graduate degree program in Anthropology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. ________________________________ Chairperson, Dr. Michael H. Crawford ________________________________ Dr. Majid Hannoum ________________________________ Dr. Deborah Smith ________________________________ Dr. Bartholomew C. Dean ________________________________ Dr. John Kelly Date Defended: May 28, 2013 The Dissertation Committee for Jasem Bader Theyab certifies that this is the approved version of the following dissertation: The Genetic Structure of the Kuwaiti and Failaka Island Populations: Y-chromosome & Mitochondrial DNA Variation ________________________________ Chairperson, Dr. Michael H. Crawford Date approved: May 31, 2013 ii Abstract Recent studies applying multidisciplinary approaches suggest that the Anatomically Modern Homo sapiens (AMHS) passed through the Arabian Peninsula in their major diaspora out of Africa. The Arabian Peninsula is connected to three continents: Africa, Asia, and Europe. In addition to the major diaspora, the Arabian Peninsula has witnessed numerous migrations among the three continents. The populations of the Arabian Peninsula have been investigated to better understand their evolutionary history. This dissertation investigated the paternal genetic structure of the Kuwaiti and Failaka Island populations using 15 loci Y-STR data. In addition, the maternal genetic structure of Failaka Island has been investigated using mtDNA HVS-I sequence data. This is the first genetic study to characterize Failaka Island population. The result showed that the Kuwaiti population has a high frequency of Y- haplogroup J1 (37%) similar to other Arabian populations. the highest Y-haplogroup frequency in Failaka Island is J2 (26%). According to the MDS plot, the Kuwaiti population is clustered with neighboring populations, including Iran and Saudi Arabia, and Failaka Island. However, maternal and paternal genetic structures of Failaka Island are closely related to Kuwait and Iran than Saudi Arabia. The paternal and maternal genetic structures of Kuwait are highly diverse and experienced more gene flow compared to Failaka Island which has experienced genetic drift with limited gene flow. Finally, Mantel tests show insignificant correlation between genetic and geographic distance matrices. iii This dissertation is dedicated to my mother, father, wife, lovely daughter Mariam, and the rest of my family for their support, encouragement, and patience iv Acknowledgment I would like to thank my academic father and mentor Prof. Michael H. Crawford who gave me unlimited support, guidance, and encouragement during my M.A. and PhD studies. It is easy to be admitted to any graduate program, but it is difficult to have such a mentor. I would like thank Dr. Suzanne Al-Bustan from Kuwait University for her support during my research, and for giving me access to her lab to do my analyses. I would especially like to thank the Kuwaiti and Failaka Island participants whose participation made this study possible. I would like to thank Dr. Yaqoub Al- Kandari for his continues support and encouragement since my acceptance of a Kuwait University scholarship. I would like to thank Dr. Mohammad Alenizi, forensic genetics specialist at the Ministry of Interior, and the forensic technician Mr. Ahmed M. H. Saleh, Senior Medical Laboratory Practitioner, for analyzing the electropherogram data using GeneMapper software. I would like to thank my committee members for their guidance and support throughout my PhD program: Prof. Michael H. Crawford, Dr. Majid Hannoum, Prof. Deborah Smith, Dr. Bartholomew C. Dean, and Prof. John Kelly ; my fellow students including: Dr. Kristin Young, Dr. Phillip Melton, Kristine Beaty, Dr. Norberto Baldi, Orion Graf, Stephen Johnson, Jacob Boyd and my other friends and fellow students in the Department of Anthropology and the Laboratory of Biological Antrhopology; the Department of Anthropology office staff: Le-Thu Erazmus, Carol Archinal, and Kathleen Womack. v I would like to thank Mrs. Mariam Al-Khamis at the Department of Cultural Relations of Kuwait University for answering all my questions regarding my scholarship. Finally, I am in debt to my mother, father, wife, daughter, and the rest of my family and friends for their support and encouragement during my studies. vi Table of Contents Chapter One: Introduction .......................................................................... 1 Chapter Two: Literature Review ................................................................ 6 Archaeological Background: ........................................................................................ 7 History of the Arabs: .................................................................................................. 10 The origin of the word Arab .................................................................................. 10 Arabia before Islam ................................................................................................ 11 Arabia and the rise of Islam ................................................................................... 15 Occupation of Arabia: Genetic evidence .................................................................. 17 Mitochondrial DNA (mtDNA) ............................................................................... 19 Y-chromosome ......................................................................................................... 21 Genetic Structure of Arabia ....................................................................................... 24 Archaeology of Kuwait: .............................................................................................. 30 History of Kuwait: ...................................................................................................... 33 Utub Families Migration ........................................................................................ 34 Al-Sabah…The Ruling Family .............................................................................. 37 Economic Development .......................................................................................... 38 Kuwait’s Social Structure ...................................................................................... 40 Kuwait in the 20 th Century: ................................................................................... 42 Oil Discovery & its Impact ..................................................................................... 43 Chapter Three: Material and Methods .................................................... 47 Sample .......................................................................................................................... 47 Comparative Populations: ...................................................................................... 47 Laboratory Methods ................................................................................................... 49 DNA Extraction ........................................................................................................ 49 Y-chromosome STRs: Amplification and Sequencing ........................................... 51 Mitochondrial DNA: Amplification and Sequencing ............................................. 52 Statistical Analyses: .................................................................................................... 54 Chapter Four: Results ................................................................................ 60 Y-chromosome DNA ................................................................................................... 60 Y-chromosome STRs Haplotype and Population Diversities ................................. 60 Y-chromosome Haplogroup Frequencies ............................................................... 67 Y-chromosome Median-Joining Tree ..................................................................... 73 Neighbor-Joining Tree ............................................................................................ 74 Multidimensional Scaling ........................................................................................ 74 Gene Diversity vs. Distance from the Centroid (r ii ) ................................................ 79 Analysis of Molecular Variance (AMOVA) ............................................................ 80 Mitochondrial DNA (mtDNA) ................................................................................... 81 Sequence Diversities and Neutrality Test Statistics ................................................ 81 Mismatch Distribution ............................................................................................. 82 Neighbor-Joining Tree ............................................................................................ 83 Multidimensional Scaling ........................................................................................ 83 Gene Diversity vs. Distance from the Centroid (r ii ) ................................................ 88 Analysis of Molecular Variance (AMOVA) ............................................................ 89 Mantel Test: .............................................................................................................