Genetic Structure of the Iraqi Population at 15 Strs and the Consequent Forensic Applications by © 2017 Sarah D
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Genetic Structure of the Iraqi Population at 15 STRs and the Consequent Forensic Applications By © 2017 Sarah D. Alden 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 Master of Arts. Chair: Michael Crawford, PhD Jennifer Raff, PhD Majid Hannoum, PhD Date Defended: 30 October 2017 The thesis committee for Sarah D. Alden certifies that this is the approved version of the following thesis: Genetic Structure of the Iraqi Population at 15 STRs and the Consequent Forensic Applications Chair: Michael Crawford, PhD Date Approved: 30 October 2017 ii Abstract 1061 individuals were sampled from the cities of Anbar, Baghdad, Basra, Diyala, Najaf, and Wasit in Iraq and typed for 15 forensic STRs to explore the genetic structure of Iraq and develop a forensic DNA database. Analyses found that Iraq is similar to other countries in the Middle East, particularly Iran and Turkey, and is more similar to Europe than either Asia or Africa. Iraq is genetically diverse; a clustering algorithm was used to infer the number of genetic clusters in the population and the best fit was eight genetic clusters. Baghdad provides a good representation of the rest of country while Anbar is the most genetically distinct. This may be because Anbar is the only city sampled in a Sunni-dominant region. Although genetic structure differs significantly between the cities, most of the genetic differentiation is between genetic clusters rather than cities. These loci had an average heterozygosity of 0.779, homozygosity of 0.221, polymorphism information content of 0.77, power of discrimination of 0.927, and power of exclusion of 0.563. At these loci, a matching genotype will occur, on average, in 1 in 8.152 x 1017 individuals. For paternity tests, the average paternity probability for a matching profile is 99.9997%. For both measures, this can be taken as an exact match. These loci are appropriate for use in forensic and paternity testing for this population. iii Acknowledgments I would like to thank the people of Iraq who generously donated their DNA for the project. I must also thank the researchers at the Forensic DNA Center for Research and Training at Al-Nahrain University who collected the samples and performed all the laboratory work and typing: Majeed Arsheed Sabbah, Mohammed Mahdi Al-Zubaidi, Haider K. Alrubai, Dhuha Salim Namaa, Thoalnoon Younis Saliha, Hala Khalid Ibrahem, Salba Jaber Al-Awadi, and Adnan Issa Al-Badran, as well as Basim Muften at the Iraqi Ministry of Interior. I would like to thank my advisor and committee chair, Dr. Michael Crawford, for his support and guidance as well as my committee members, Dr. Jennifer Raff and Dr. Hannoum. I would like to acknowledge the help of Dr. Kristine Beaty, Amanda Kittoe, and Michael Guarino in interpreting various analyses and providing feedback on my thesis, and Corinne Butler for making sure that I knew what needed to be done and when, as well as the Department of Anthropology and the Laboratories of Biological Anthropology. Finally, I would like to thank my family for their support. iv Table of Contents Chapter 1: Introduction ................................................................................................................... 1 Chapter 2: Literature Review .......................................................................................................... 6 A History of Iraq ......................................................................................................................... 6 Population Genetics .................................................................................................................. 18 Inbreeding ............................................................................................................................. 18 Y Chromosome ..................................................................................................................... 19 Mitochondrial DNA .............................................................................................................. 21 Autosomal ............................................................................................................................. 23 Chapter 3: Methods ....................................................................................................................... 25 Sample Collection ..................................................................................................................... 25 Population Structure ................................................................................................................. 25 Hardy-Weinberg Equilibrium ............................................................................................... 26 F-Statistics ............................................................................................................................. 29 Nei’s Genetic Distance ......................................................................................................... 30 Principal Component Analysis ............................................................................................. 31 Analysis of Molecular Variance ........................................................................................... 33 Discriminant Analysis of Principal Components .................................................................. 38 Multidimensional Scaling ..................................................................................................... 43 Forensic Applications ............................................................................................................... 44 Chapter 4: Results ......................................................................................................................... 47 Population Structure ................................................................................................................. 47 Hardy-Weinberg Equilibrium ............................................................................................... 47 v F-Statistics ............................................................................................................................. 47 Nei’s Genetic Distance ......................................................................................................... 48 Principal Component Analysis ............................................................................................. 49 Analysis of Molecular Variance ........................................................................................... 54 Discriminant Analysis of Principal Components .................................................................. 55 Multidimensional Scaling ..................................................................................................... 64 Forensic Applications ............................................................................................................... 66 Chapter 5: Discussion ................................................................................................................... 71 Genetic Structure of Iraq ........................................................................................................... 71 Hardy-Weinberg Equilibrium and F-Statistics ..................................................................... 71 Nei’s Genetic Distance ......................................................................................................... 73 Principal Component Analysis ............................................................................................. 76 Analysis of Molecular Variance ........................................................................................... 78 Discriminant Analysis of Principal Components .................................................................. 78 Multidimensional Scaling ..................................................................................................... 80 Forensic Applications of Population Structure ......................................................................... 81 Limitations of the Study ........................................................................................................... 83 Chapter 6: Conclusions ................................................................................................................. 85 Summary of Conclusions .......................................................................................................... 85 Future Studies ........................................................................................................................... 88 Works Cited .................................................................................................................................. 89 vi List of Figures Figure 1. A map of Iraq with cities marked (Google Maps, 2017). ................................................ 5 Figure 2. Plot of eigenvalues for each principal component. ....................................................... 49 Figure 3. PCA plot showing individuals sampled. ....................................................................... 50 Figure 4. PCA plot with individuals 0812 and 0818 removed. .................................................... 51 Figure 5. PCA plot of the six sampled cities in Iraq. .................................................................... 52 Figure 6. PCA plot of allele frequencies of Iraq and surrounding