Title Page Variation in Y chromosome, mitochondrial DNA and labels of identity in Ethiopia Christopher Andrew Plaster The Centre for Genetic Anthropology Department of Genetics Evolution and Environment University College London 1 Declaration of ownership I, Christopher Andrew Plaster, 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. Statement of work performed by Christopher Plaster Approximately 20% of all DNA extractions, 40% of all Y chromosome genotypings and 65% of mtDNA sequencing data was generated by myself, with the remainder generated by technicians and students (as part of other and ongoing projects at TCGA) prior to the commencement of my PhD studies. I checked all previous data generated by others for consistency with the data generated by myself. All processing of mtDNA data, and all statistical analysis was performed by myself. All DNA samples and ethnographic information was collected in the field by Dr Ayele Tarekegn. 2 Abstract There is a paucity of genetic studies of Ethiopia. This thesis aims to establish the extent and distribution of variation in NRY and mtDNA genetic markers as well as ethnic and linguistic labels of identity in 45 ethnic groups. A wide range of NRY and mtDNA haplogroups were observed, including both those typically observed in Africa and those more frequently observed outside Africa. Significant correlations were revealed between NRY and mtDNA diversity. Nearly all ethnic groups were significantly differentiated from each other, although the pattern of similarities indicates some recent gene flow between northern ethnic groups and some groups to the south. Significant correlations were observed between almost all measures of linguistic and ethnic similarity and measures of NRY and mtDNA genetic distance. A wide range of values for diversity of sample donors’ ethnic and linguistic identity was observed across groups. There was no evidence that the language of the sample donor is more likely to be inherited from parents of one sex rather than the other. There was a general decrease in the proportion of sample donors speaking the traditional language of their ethnic groups compared with the donor’s parents and grandparents, with a corresponding increase in the proportion of sample donors speaking Amhara as a first language. Restricting analysis to samples from donors with ethnic identity in common with their parents and grandparents had significant effects on the degree of genetic distinctiveness of ethnic groups. Increasing the level of resolution of NRY and mtDNA haplotypes did not substantially alter the patterns of diversity and distance observed in and amongst ethnic groups. This thesis makes an important contribution to understanding the distribution of genetic diversity in Ethiopia. 3 Acknowledgements I would like to thank all the individuals who donated samples, as well as those who helped collect them. I would particularly like to thank Dr Ayele Tarekegn, for spending so much time in the field collecting samples and recording data, and also for his invaluable knowledge while writing this thesis. He is the only man I know to have met and interviewed 10,000 Ethiopians (which has to be some kind of record). I would also like to thank all the people at UCL who have made the time pass very quickly indeed. Some of the people I’d like to thank, in no particular order, include Krishna Veeramah, Adam Powell, Yuval Itan, Sarah Browning, Naser Ansari Pour, Abi Jones, Kate Ingram, Laura Horsfall, Bryony Jones, Lauren Johnson, Andrew Loh, Anna Texieira, Rosemary Ekong and many others. I’d also like to thank Maria Elevant, Ripudaman Bains, and Olivia Creemer for their extreme patience (with me) and dedication to a task (at times), in helping me check the questionnaires of a few thousand Ethiopians. I also appreciate it that they have kindly ignored that I had promised them dinner as payment for helping me out. Thanks again. I’d also like to thank all the undergraduate students I have supervised over the years for the comic relief that they have provided. In particular Rohan Wagle and Farzeen Rauf. The knowledge that one is now a commercial pilot, and the other will be a physician, is terrifying. I would very much like to thank my sponsor, and my supervisors Neil Bradman and Mark Thomas, without whom none of this would have been possible. I’d also like to thank my family for their love and support they have given me. Lastly, I am deeply indebted to Michelle, for her continued love and support she has provided over the years, and especially over the past few months, as my own personal standards have dropped of late, and without whom I would by now be a particularly unwashed and undernourished individual. 4 Contents Title Page ..........................................................................................................................1 Declaration of ownership..................................................................................................2 Statement of work performed by Christopher Plaster...................................................2 Abstract .............................................................................................................................3 Acknowledgements...........................................................................................................4 Contents ............................................................................................................................5 Abbreviations..................................................................................................................10 Chapter1: Introduction ....................................................................................................11 1.1 A brief history of Ethiopia .................................................................................11 1.1.1 The geography of Ethiopia..........................................................................11 1.1.2 Early hominids in Ethiopia .........................................................................13 1.1.3 Modern human history in Ethiopia .............................................................13 1.2 The contemporary peoples of Ethiopia ..............................................................20 1.2.1 Afar .............................................................................................................20 1.2.2 Agaw ...........................................................................................................21 1.2.3 Alaba ...........................................................................................................21 1.2.4 Amhara........................................................................................................21 1.2.5 Anuak..........................................................................................................21 1.2.6 Ari ...............................................................................................................22 1.2.7 Basketo........................................................................................................22 1.2.8 Bena ............................................................................................................22 1.2.9 Bench ..........................................................................................................22 1.2.10 Burji ..........................................................................................................23 1.2.11 Busa...........................................................................................................23 1.2.12 Dasanach ...................................................................................................23 1.2.13 Dawuro......................................................................................................23 1.2.14 Dirasha ......................................................................................................24 1.2.15 Dizi............................................................................................................24 5 1.2.16 Dorze.........................................................................................................24 1.2.17 Gamo.........................................................................................................25 1.2.18 Ganjule......................................................................................................25 1.2.19 Gedeo ........................................................................................................25 1.2.20 Genta .........................................................................................................25 1.2.21 Gewada......................................................................................................26 1.2.22 Gobeze ......................................................................................................26 1.2.23 Gofa...........................................................................................................26 1.2.24 Gurage.......................................................................................................26 1.2.25 Hadiya .......................................................................................................27 1.2.26 Hamer........................................................................................................27 1.2.27 Kefa...........................................................................................................27