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The Mitochondrial DNA Heritage of the Baganda, Lugbara and Acholi from Uganda

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The Mitochondrial DNA Heritage of the Baganda, Lugbara and Acholi from Uganda Thesis for Doctor of Philosophy (Ph.D.), 2010 The mitochondrial DNA heritage of the Baganda, Lugbara and Acholi from Uganda Dan Isabirye North-west University (Potchefstroom Campus), South Africa The mitochondrial DNA heritage of the Baganda, Lugbara and Acholi from Uganda BY DAN ISABIRYE, M.Sc. Thesis submitted for the degree Philosophiae Doctor (Ph.D.) in Biochemistry at the North-West University PROMOTOR: Dr Gordon Wayne Towers Centre of Excellence for Nutrition, North-West University (Potchefstroom Campus) September 2010 Die mitokondriale DNS erfenis van die Baganda, Lugbara en Acholi van Uganda DEUR DAN ISABIRYE, M.Sc. Proefskrif voorgelê vir die graad Philosophiae Doctor (Ph.D.) in Biochemie aan die Noordwes-Universiteit PROMOTOR: Dokter Gordon Wayne Towers Sentrum vir Uitnemendheid in Voeding, Noordwes-Universiteit (Potchefstroom Kampus) September 2010 This thesis is dedicated to Dan Waiswa (my son), Rebecca Babirye and the Family of Mrs Alice & Rev. Can. Capt. Samuel Isabirye. ABSTRACT The mtDNA genetic relatedness between and within 13 Baganda, 14 Lugbara and 13 Acholi individuals from Uganda was investigated in this research program. The complete mtDNA sequences of the 40 Ugandan samples were established and a phylogeographic analysis of these sequences was conducted using both a Neighbour-Joining and a Maximum Parsimony tree together with a global sample of 387 African sequences. Prior to this study, only two complete and six partial mtDNA sequences of Ugandans had been established. A total of 563 polymorphisms were determined of which 276 were synonymous, 75 were nonsynonymous, 26 were novel and 208 occurred in the control region. The Lugbara sequences clustered more closely with the Acholi sequences than the Baganda sequences within the Neighbour-Joining and Maximum Parsimony tree. A phylogeographic analysis of the sequences demonstrated that the Acholi and Lugbara individuals in this investigation originated from Southern Sudan while the Baganda samples had a diversified origin which comprised of the Niger-Congo basin, Ethiopia and Sudan. Furthermore, the clustering of the Ugandan sequences with sequences from African American and Hispanic individuals was evidence of slave trade involving the shipping of people from Uganda to North America. It was intriguing that the deepest branch in the phylogeny was L5 (instead of L0) suggesting that the Khoi-San may not be the ancestral origin of anatomically modern man. There was increased resolution of macrohaplogroup L (especially for the small haplogroups) as new branches and nodes were formed in the tree. The results also demonstrated that East Africa was the origin and source of dispersal of numerous small macrohaplogroup L haplogroups. These mtDNA sequences from Baganda, Acholi and Lugbara individuals have a potential for forensic, nutrigenomic and pharmacogenomic application and will serve as useful references in assessment of mtDNA sequences in other Ugandan and East African populations. Key words: mitochondrial DNA, phylogenetics, human migration, Uganda, macrohaplogroup L, African. OPSOMMING Die genetiese verwantskap tussen en binne die mtDNS van 13 Baganda, 14 Lugbara en 13 Acholi individue van Uganda, was ondersoek in hierdie navorsings projek. Die volledige mtDNS volgorde van die 40 Ugandan deelnemers was vasgestel en ‘n filogeografiese analise van hierdie volgordes saam met ‘n wereldwye steekproef van 387 Afrikaanse volgordes was onderneem deur middel van “Neighbour-Joining” en “Maximum Parsimony” bome te teken. Voor hierdie ondersoek onderneem was, was daar net twee volledige en ses gedeeltelike mtDNS volgordes van Ugandans beskikbaar. ‘n Totaal van 563 polimorfismes was bevind, waarvan 276 sinoniem , 75 nie-sinoniem en 26 nuwe veranderinge was, en 208 in die beheer gebied van die mtDNS voor gekom het. Die Lugbara volgordes het nader aan die Acholi volgordes gekluster as die Baganda volgordes in die finale “Neighbour-Joining” en “Maximum Parsimony” bome. ‘n Filogeographiese analise van die volgordes het gewys dat die Acholi en Lugbara individue in hierdie ondersoek, van Suidelike Sudan ontstaan het, terwyl die Baganda individue ‘n afwisselende voorsprong gehad het wat uit die Niger-Kongo stroomgebied, Ethiopië en Sudan saamgestel is. Die klustering van die Ugandan volgordes met die van die Afrikaner- Amerikaner en Hispaniese individue was ‘n bewys van moontlike slawehandel tussen Uganda en Noord Amerika. Dit was interesant, die diepste tak van die fillogenie was L5 (in stede van L0) wat demonstreer dat die Khoi-San miskien nie die voorvaderlike oorsprong van anatomiese moderne man was nie. Daar was groter resolusie van Makrohaplogroep L (hoofsaaklik die klein haplogroepe) omdat nuwe takke en knoppe in die bome gevorm het. Die uitslae van hierdie ondersoek het gewys dat Oos Afrika die oorsprong en die bron van verspreiding van meetalige klein Makrohaplogroep L haplogroepe was. Hierdie mtDNS volgordes van die Baganda, Acholi en Lugbara individue het ‘n potensiaal vir forensiese, nutrigenomiese en farmakogenomiese gebruik en sal as nuttige verwysings in die skatting van mtDNA volgordes in ander Ugandan en Oos Afrikaanse bevolkings gebruik kan word. TABLE OF CONTENTS Page no. LIST OF ABBREVIATIONS AND SYMBOLS ....................................................................... i LIST OF FIGURES .............................................................................................................. v LIST OF TABLES .............................................................................................................. viii ACKNOWLEDGEMENTS ................................................................................................... ix CHAPTER ONE INTRODUCTION ................................................................................................................. 1 CHAPTER TWO THE PHYSICAL AND GENETIC STRUCTURE OF THE MITOCHONDRION .................... 5 2.1 STRUCTURE OF THE MITOCHONDRION ............................................................ 8 2.1.1 Physical structure of the mitochondrion .................................................................. 8 2.1.2 Genetic structure of the mitochondrion ................................................................... 9 2.1.2.1 Inheritance pattern ............................................................................................ 10 2.1.2.2 Replication, transcription and translation of the mitochondrion ......................... 11 2.2 MUTATION RATE OF MITOCHONDRIAL DNA ................................................... 12 CHAPTER THREE THE EVOLUTIONARY AND PHYLOGENETIC ASPECTS OF MTDNA .......................... 15 3.1 HUMAN ORIGIN ................................................................................................... 15 3.1.1 Origin of the people of East Africa ........................................................................ 19 3.2 HUMAN MIGRATION ........................................................................................... 20 3.2.1 Human migrations from and into Africa ................................................................. 21 3.2.1.1 Human migrations from and into East Africa .................................................... 23 3.2.1.1.1 Migrations and settlements of the East African Bantu .................................. 24 3.2.1.1.2 Migrations and settlements of the East African Nilotes ................................. 25 3.2.1.1.3 Migrations and settlements of the East African Moru Madi ........................... 26 3.3 MITOCHONDRIAL PHYLOGENIES ..................................................................... 26 3.3.1 mtDNA phylogenetic analysis of African populations ............................................ 28 3.3.1.1 mtDNA phylogenetic analysis of East African populations ................................ 31 3.3.1.2 mtDNA phylogenetic analysis of Ugandan populations .................................... 32 3.4 OBJECTIVES OF THE STUDY ............................................................................ 34 3.4.1 Specific objectives ................................................................................................ 34 CHAPTER FOUR MATERIALS AND METHODS .......................................................................................... 35 TABLE OF CONTENTS 4.1 ETHICS AND REGULATORY APPROVAL ......................................................... 35 4.2 SAMPLE POPULATION ....................................................................................... 35 4.3 EXTRACTION OF DNA FROM WHOLE BLOOD ................................................. 36 4.4 DETERMINATION OF DNA CONCENTRATION .................................................. 37 4.5 DNA AMPLIFICATION .......................................................................................... 38 4.6 AGAROSE GEL ELECTROPHORESIS ................................................................ 40 4.7 PURIFICATION OF PCR PRODUCTS ................................................................. 40 4.8 AUTOMATED SEQUENCING ANALYSIS ............................................................ 41 4.9 SODIUM DODECYL SULPHATE (SDS) CLEANUP OF THE SEQUENCED PRODUCTS .......................................................................................................... 42 4.10 PURIFICATION OF SEQUENCED PRODUCTS .................................................. 43 4.11 ANALYSIS OF SEQUENCED DNA SAMPLES .................................................... 44 4.11.1 Construction of phylogenetic trees .......................................................................
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