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Study of Mitochondrial Dna Variabilityin Four Ethnic Groups Within the Southern Part of Kaduna State Nigeria

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Study of Mitochondrial Dna Variabilityin Four Ethnic Groups Within the Southern Part of Kaduna State Nigeria STUDY OF MITOCHONDRIAL DNA VARIABILITYIN FOUR ETHNIC GROUPS WITHIN THE SOUTHERN PART OF KADUNA STATE NIGERIA. BY JAMES ABRAK TIMBUAK DEPARTMENT OF ANATOMY AHMADU BELLO UNUIVERSITY, ZARIA NIGERIA. JUNE, 2015 STUDY OF MITOCHONDRIAL DNA VARIABILITY IN FOUR ETHNIC GROUPS WITHIN THE SOUTHERN PART OF KADUNA STATE, NIGERIA. BY James AbrakTIMBUAK, B.Sc.2000(A.B.U.), M.Sc.2008(A.B.U.) Ph.D/MED/01123/2008-2009 ADISSERTATION SUBMITTED TO THE SCHOOL OF POSTGRADUATESTUDIES, AHMADU BELLO UNIVERSITY, ZARIA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE AWARD OF THE DEGREE OF DOCTOR OF PHILOSOPHY (Ph.D.) IN HUMAN ANATOMY. DEPARTMENT OF HUMAN ANATOMY, FACULTY OF MEDICINE AHMADU BELLO UNIVERSITY, ZARIA NIGERIA JUNE, 2015 ii DECLARATION I declare that the work in this dissertation entitled, “STUDY OF MITOCHONDRIAL DNA VARIABILITYIN FOUR ETHNIC GROUPS WITHIN THE SOUTHERN PART OF KADUNA STATE, NIGERIA”has been carried out by me in the Department of Human Anatomy, Faculty of Medicine. The information derived from the literature has been duly acknowledged in the text and a list of references provided. No part of this Dissertation was previously presented for another degree or diploma at this or any other Institution. ____________________________________ ______________ _________ Name of StudentSignature Date iii CERTIFICATION This dissertation entitled “STUDY OF MITOCHONDRIAL DNA VARIABILITY IN FOUR ETHNIC GROUPS WITHIN THE SOUTHERN PART OF KADUNA STATE, NIGERIA” by James Abrak TIMBUAK, meets the regulations governing the award of the of Doctor of Philosophy (Ph.D)degree of the Ahmadu Bello University, and is approved for its contribution to knowledge and literary presentation. Prof.S.S.AdebisiB.Sc., M.Sc. ,Ph.D_____________________________ Chairman Supervisory CommitteeSignature Date Department of Anatomy Faculty of Medicine Ahmadu Bello Univeristy, Zaria Dr. B. DanbornoB.Sc., M.Sc.,Ph.D ______________________________ Member Supervisory Committee Signature Date Department of Anatomy Faculty of Medicine Ahmadu Bello University Zaria Prof. A.J. Nok B.Sc., M.Sc., Ph.D., MFR_____________________________ Member Supervisory Committee Signature Date Department of Biochemistry Faculty of Medicine Ahmadu Bello University, Zaria Prof. S.S.AdebisiB.Sc., M.Sc. Ph.D___________________________ Head of Department Signature Date Department of Anatomy Faculty of Medicine Ahmadu Bello University, Zaria Prof. A.Z. HASSAN DVM, M.Sc. Ph.D_____________________________ Dean, School of Postgraduate studies SignatureDate Ahmadu Bello University, Zaria iv DEDICATION I dedicate this work to the loving memory of our son Ethan Bisan, rest on in the loving bosom of our Lord. v ACKNOWLEDGMENTS I give thanks to God Almighty who made all this possible. I also wish to thank all the participants who provided samples for this research, without you this research would not have been possible. I would like to thank all the members of my supervisory committee namely, Prof. SS Adebisi, Dr. B. Danborno and Prof. A.J. Nok for their commitment, guidance, encouragement and patience. Much appreciation goes to the Tertiary Education Trust Fund (TETFUND) and the management of Ahmadu Bello University for providing part of the funds for this research. I would like to thank Prof. M.H. Crawford of the Laboratory of Biological Anthropology (LBA), Kansas, through the connection established by Dr B. Danbornofor giving me the opportunity to experience molecular genetics on hands on basis. I also wish to thank other members (past and present) of the LBA Dr. A. Justice, Stephen Johnson, Kristie Beaty and Orion Graf, you all contributed to my rich laboratory experience. I wish to appreciate Dr. Pat Williams and Torrey Parish, of Evogen Inc., who made their facility available to me without charge. I am also extending my gratitude to Dr. Sarah Tishkoff and JibrilHirbo for their advice and I wish to thank my sister Mrs. Alheri Timbuak Bala and lateMr. Tauna for their invaluable assistance throughout the sample collection period. I also wish to thank my dearest wife Mrs. Rose Sharon A. Timbuakwho not only brought my long search to an end but also went the “whole nine yards” withme through the nights and days of proof reading this work. I will not forget my lovely son Ethan B. Timbuak who has broughtme so much joy and hope. vi I am also expressing my gratitude to Dr. (Mrs)Danborno and her children for providing me with a support system far from home and for giving me the rare experience of a tiny bit of family responsibility. Be assured all the lessons learnt are safely tucked away for the inevitable future. I also wish to thank my senior colleaguesDr. U.E Umana and Dr. W.O.Hammanfor their friendship and support.Many thanks go to my Parents, Mr. and Mrs. Timbuakfor the joy and travails of parenting me. My siblingsAlheri, John, Yamai, Dinatu, Timo and Priscilla, for always being there and knowing I just cannot ask for a finer set of siblings. I wish to thank my colleaguestoo for the contributions they towards the completion of this study. I will not forget to mention the staff of the department of Human Anatomy and all those who assisted me in one way or the other urged me on in this endeavor. I really do appreciate you all. vii ABSTRACT The middle-belt of Nigeria is known for its ethnic diversity and linguistic complexity. Studies on biological variation within the region have been mostly based on anthropometry but with recent advances in anthropological genetics, newer tools now provide greater resolution on human variation. This study examined the efficacy of the mitochondrial DNA (mtDNA) as a genetic marker to characterize the genetic structure of four ethnic groups of Benue-Congo affiliations from Kaduna State. Column and propriety salting based methods were used to extract mtDNA hypervariable segment-I (HVS-I) sequences from samples belonging to four ethnic groups, the Bajju, Chawai, Atyap and Kagoro. Sequences were amplified and amplicons purified using ExoSap. Sequencing for the light strand was done followed by sequence alignment, restriction fragment length polymorphism (RFLP) andsingle nucleotide polymorphism (SNP) analysis. Nucleotide positions 16050-16460 were compared to the revised Cambridge Reference Sequence (rCRS) and 91 haplotypes were observed. A total of 107 polymorphic sites characterized the haplotypes. The African specific HpaIcut site at 3592 defined the L1 and L2 haplotypes which were most frequent but absent for the L0 and L3 haplotypes. Subclade L3e had the highest frequency while other sub clades of the sub Saharan haplogroups werealso present across the study populations in appreciable frequencies, indicative of substantial gene flow between them and other neighbouring populations.A fewsamples, however failed to cluster with the majority as they lacked SNPs belonging to the region and were merely identified as Non-L haplogroups.The Nucleotide diversities (π) were 0.019, 0.026, 0.025 and 0.020 for the Atyap, Bajju, Chawai and Kagoro respectively. The haplotype diversities (HD) were viii high and consistent with the regional and overall African values, with the Atyap having the leastdiverse value (0.960) while the Bajju had the most diverse haplotypes(0.992). Sub-clade analysis based on L0, L1, L2 and L3, for haplotypediversity (HD) and nucleotide diversities, π, exhibited greater diversity for L3 and L2 while L0 had the least diversity. Mismatch distributions for the major haplogroups showed stable demographic patternsfor L0, L1 and L2 but the more recent L3 clade exhibited an expansion pattern as expected. The same expanding demographic was observed for the Atyap, Chawai and Kagoro with the Bajju having a more stable population. Partitioning the genetic variation using the linguistic group model using the analysis of molecular variance (AMOVA) revealed little variation among the populations (3.66%) but showed a high level of variation (94.6 %) within each population.This study has revealed the presence of a shared genetic structure among the Atyap, Bajju, Chawai and Kagorousing molecular markers, which is indicative of close genetic relationship due to common history, substantial gene flowand geographical proximity. ix TABLE OF CONTENTS Cover Page ........................................................................................................................... i Title page ........................................................................................................................... iii Declaration ......................................................................................................................... iv Certification ....................................................................................................................... iii Dedication ............................................................................................................................ v Acknowledgements ........................................................................................................... vii Abstract ............................................................................................................................ viii Table of Contents .......................................................................................................... ix-xx List of Abbreviations ....................................................................................................... xxi CHAPTER ONE 1.0 Introduction .................................................................................................................
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