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Human Genetic Variation, Relationships of Peoples of Sub- Saharan Africa and Implications for Healthcare

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Human Genetic Variation, Relationships of Peoples of Sub- Saharan Africa and Implications for Healthcare Title Page Human genetic variation, relationships of peoples of sub- Saharan Africa and implications for healthcare By Naser Ansari Pour SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY (Ph.D.) SEPTEMBER 2010 MINOR CORRECTIONS SUBMITTED APRIL 2011 The Centre for Genetic Anthropology Department of Genetics, Evolution and Environment University College London (UCL) Supervisor: Prof Mark G Thomas Second Supervisor: Prof Dallas M Swallow 1 Declaration of Ownership I, Naser Ansari Pour, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Abstract Sub-Saharan Africa is thought to have the most genetic variation of any continent and to be the place of origin of anatomically modern human. Nevertheless it is the subject of relatively few studies of human genetic variation. This thesis contributes to redressing this imbalance. Sex-specific genetic systems (non-recombining portion of the Y chromosome (NRY) and mitochondrial DNA (mtDNA)) along with functional nuclear loci were characterised in multiple sub-Saharan African populations with large sample sizes to infer relationships of peoples and identify implications for healthcare. This thesis contains four projects which addressed questions in genetic anthropology, human evolution and pharmacogenetics utilising human genetic variation. In chapter 2, NRY analysis shows that a hypothesised paternal Yombe (Congo) ancestry of Palenque (Colombia), based on linguistic and historical evidence, is consistent with genetic data. Chapter 3, based on NRY data, demonstrates that a) multiple waves of migration occurred southwards during the expansion of Bantu-speaking peoples (EBSP), b) the eastern route displayed more recent migrations than the western route and c) the absence of substantial east to west NRY gene flow in sub-Saharan Africa over the past millennium. Chapter 4 suggests an eastern route out of Africa for the CASP12 truncated variant is more likely than a western route. (The stop-codon mutation was also dated to around 120,000 YBP). Chapter 5 demonstrates that a potentially functional CYP1A2 variant which has not been reported outside Africa is present at considerable frequencies in sub-Saharan African population groups and that exons associated with active sites in CYP1A genes are well conserved. 3 Acknowledgements I owe a special thanks to the NERC for funding me, and to all sample donors and individuals involved with sample collections. I would also like to thank Dr Yves Moñino for collaborating with me on the Palenque project. I also thank those individuals who have made my experience at UCL, and TCGA in particular, over the last four years an enjoyable one. This includes (in somewhat chronological order) Sarah Browning, Christopher Plaster, Krishna Veeramah, Catherine Ingram, Adam Powell, Andrew Loh, Lauren Johnson, Olivia Clark, Bryony Jones, Laura Horsfall, Rosemary Ekong, Olivia Creemer, Ripu Bains and Gurjeet Rajbans. I am also indebted to (this time in no particular order) Professor Andres Ruiz-Linares, Professor Sue Povey and Dr Mike Weale for their invaluable guidance during the different works described in this thesis. However my main thanks are reserved for my industrial sponsor, Dr Neil Bradman, my supervisors, Professor Mark Thomas and Professor Dallas Swallow, my precious parents, Dr Mohammad-Ali Ansari Pour and Tayebeh Sedigh Orai and my adorable wife, Sajedeh Mohaghegh Hazrati. Without their support and encouragement I would have simply been unable to undertake and complete this work. 4 Table of Contents Title Page ........................................................................................................................... 1 Declaration of Ownership ................................................................................................ 2 Abstract.............................................................................................................................. 3 Acknowledgements ........................................................................................................... 4 Table of Contents .............................................................................................................. 5 List of Figures.................................................................................................................... 9 List of Tables ................................................................................................................... 10 Abbreviations .................................................................................................................. 13 1. Introduction................................................................................................................. 15 1.1. Geography, peoples and languages of sub-Saharan Africa ................................... 15 1.2. Genetic studies in sub-Saharan Africa................................................................... 19 1.2.1. Classical genetic markers................................................................................ 19 1.2.2. DNA markers .................................................................................................. 20 1.2.2.1. Autosomal markers ...................................................................................... 20 1.2.2.2. Sex-specific NRY and mtDNA markers...................................................... 21 1.3. Rationale of the thesis:........................................................................................... 22 1.4. Overview of result chapters: .................................................................................. 24 2. The origins of the Palenque: a Kikongo speaking community in rural Colombia 26 2.1. Introduction............................................................................................................ 26 2.1.1. The history and language of Palenque............................................................ 26 2.1.2. Genetics and origin of African Diasporas....................................................... 28 2.1.3. Expectations of sex-specific genetic variation in the Palenque and EBSP..... 30 2.1.4. Aims................................................................................................................ 31 2.2. Materials and Methods........................................................................................... 32 2.2.1. Sample Collection........................................................................................... 32 2.2.2. DNA Extraction .............................................................................................. 34 2.2.3. Y-chromosome typing .................................................................................... 34 2.2.4. mtDNA typing ................................................................................................ 36 2.2.5. Statistical analysis........................................................................................... 38 2.3. Results.................................................................................................................... 39 2.3.1. Frequencies of NRY haplotypes and NRY-based genetic distances .............. 39 2.3.2. Comparisons of NRY datasets........................................................................ 43 2.3.3 Yombe and Chewa........................................................................................... 43 2.3.4 Principal Component Analysis ........................................................................ 44 2.3.5. The distribution of mtDNA variation ............................................................. 44 2.3.6. Comparison of mtDNA across datasets .......................................................... 46 2.3.7. Intra-village analysis of Palenque................................................................... 46 2.3.8 Abajo and Arriba in the context of sub-Saharan Africa .................................. 47 2.4. Discussion.............................................................................................................. 48 2.4.1 Answering the principal questions of the study............................................... 48 2.4.1.1. Are genetic data consistent with a Yombe speaking paternal founding group of the Palenque?........................................................................................................ 50 5 2.4.1.2. Is there any pattern in the distribution of maternal ancestry based on mtDNA HVR-1 haplotypes or K2P distances similar to that displayed by analysis of the NRY? ........................................................................................................................ 51 2.4.1.3. Can the two groups of residents of Palenque de San Basilio occupying Abajo and Arriba respectively be distinguished from each other and, if so, are the residents of Arriba more similar to the peoples of the Congo than are the residents of Abajo? ....................................................................................................................... 51 2.4.2 Additional observations ................................................................................... 52 2.4.2.1 European and African contributions to the Palenque NRY gene pool ......... 52 2.4.2.2 NRY distribution in sub-Saharan Africa....................................................... 55 2.4.2.3 Analysis of mtDNA variation in Palenque and sub-Saharan Africa............. 55 2.4.2.4 Differentiation
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