The maternal history of the sable antelope (Hippotragus niger) inferred from the g enomic analysis of complete mitochondrial sequences Joana Maria Laranjeira Rocha Mestrado em Biodiversidade, Genética e Evolução Departamento de Biologia 2014 Orientador Raquel Godinho Assistant Researcher at CIBIO/InBIO Invited Assistant Professor at University of Porto Co -orientador Pedro Vaz Pinto Ph.D. student at CIBIO/InBIO Researcher at ISCED – Huíla, Angola Todas as correcções determinadas pelo júri, e só essas, foram efectuadas. O Presidente do Júri, Porto, ______/______/_________ “It is a cursed evil to any man to become as absorbed in any subject as I am in mine” Charles Darwin Acknowledgments First I would like to thank to my supervisor Dr. Raquel Godinho for accepting and trusting me with such an outstanding project, and also for her extraordinary guidance. Thank you, Raquel, for dealing with my overachieving paranoia, my fears and insecurities. Thank you for being patient with me and trusting me so fiercely. I could not have found a better supervisor, or a better friend. Secondly I would like to thank to Pedro Vaz Pinto, for giving me the chance to study a species so close to his heart and for all the support given as my co-supervisor. Thank you Pedro for all the discussions, extensive email exchanging and strong enthusiasm. It is imperative to thank to Professor Nuno Ferrand, for the warm welcoming to CIBIO and for his wise advices during the most difficult and undecided times since the beginning of this master thesis. In particular, I would like to thank him for the life-changing opportunity to work abroad at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig. I would also like to thank to Dr. Matthias Meyer for receiving me at his group at the MPI-EVA. In particular, for providing all the means necessary for me being able to do my work in the most comfortable and friendly working environment a student could possibly wish for. I would also like to thank him for his guidance, suggestions, and for taking the time to sit with me and discuss my project. I never felt treated differently than any of his PhD students and for that I will always feel grateful. I would also like to thank to the technical staff of CTM-CIBIO. In particular, to Susana Lopes for making me fell at ease to come to her in any circumstances, to Diana Castro for ordering and putting together all the museum samples I needed to take to Leipzig, and Patricia Ribeiro, who helped me a lot during my bachelor’s thesis, introducing me to all basic laboratorial techniques, and for teaching me skills that proved to be most valuable during the time I spent in the lab at the MPI-EVA. I would also like to thank to Diana Lobo for all the help given from Portugal while I was in Germany, and for being always available. I would like to thank to the Smithsonian institute (Washington, DC) and to the natural history museum of Vila Viçosa (Portugal) for providing most of the historical samples that integrated the genetic dataset used in this study. I would also like to thank to Banco BES (Portugal) and to ExxonMobil Foundation (USA) for financing all the projects related to the sable antelope and, therefore, allowing me to be a part of a small fraction of these projects. I would also like to thank to my Max Planck friends and colleagues. Thank you Viviane and Mateja for making me feel comfortable enough to come to you with any questions about the lab, in particular Viviane for supervising me during the final step of lab proceedings. Thank you, Alex, for being a nice and quiet desk mate. Thank you Amin for reminding me that Thursday is climbing day. Thank you Philip for not letting me stand alone as the only masters’ student in our group, and for going for a swim with me once in a while. Thank you Manjusha and Rohit for letting me taste the most delicious Indian food ever, and Manjusha for letting me try your sari. I would like to particularly thank to Ana T. Duggan for all the advices given during my staying at the MPI-EVA, and for our email exchanges during the summer to discuss my project, talk about analyses and for motivating me during the final steps of writing. Thank you Ana for your major contribution and suggestions. I could not ask for a better colleague. I would also like to particularly thank Gabriel for all the support given during the bioinformatics part, for our discussions about the best way of assembling the data, for letting me be the first person to use schmutzi (which I have no doubt it will be a tremendous success in the field of bioinformatics), and for our late night conversations at the institute. Thank you for not letting me stand alone as the most workaholic person in that department. Thank you for being an amazing colleague, and even better friend. If there is someone that has contributed enormously for the success of this project, even without being directly involved in it, was Homa Papoli. Thank you, Homa, for receiving me so well in our home at Ostraβe, during a time of my life where everything seemed lost. Thank you for inviting me for a tea in your Persian red carpet, for teaching me your beautiful language, for all the intellectual discussions and Poirot movies, for the diners and happy moments at the city center, for the opera, for the classic concerts, and walking on the park. You became my new family while my old one was falling apart. Thank you. I would also like to thank Alice for dealing with my stress during the final countdown of the thesis’ delivery. Thank you for the help given with minor, yet extremely important, details. Most importantly, thank you for being my friend and never let me down. Finally I would like to thank to my friends in Porto, master colleagues and family for all the support given during this year. In particular to Pedro, Diogo and Maria João for being at the airport with wide open arms to receive me back in Porto, and for helping me in re- adapting to my life in Porto once again. Abstract The sable antelope is a savanna woodland species with a distribution confined to the central, southern and eastern part of the African continent. Previous studies focused on assessing the patterns of genetic variation within H. niger have been limited by the scant resolution associated to analyzing short fragments of the mitochondrial genome, and by the lack of representative specimens covering the species whole geographic range in Africa. This has foreclosed the accurate estimation of divergence times between the different sable antelope subspecies and, thus, the explicit testing of phylogeographic hypotheses regarding the species evolutionary patterns. With the current development of target-enrichment methods for next-generation sequencing, whole mitochondrial genomes are increasingly being used for population genetics and phylogeography. The ability to provide higher levels of variability and resolution than those obtained when using mtDNA fragments, has been having dramatic impact in solving long-standing questions about the evolutionary history of iconic species. In this study, we made use of next-generation sequencing methods to capture 215 complete mitochondrial genomes from a representative set of modern samples, and samples from African museum collections, covering the species whole geographic range. This allowed us to generate the most comprehensive dataset of H. niger to date and, therefore, to re-assess the phylogeographic history of the species in Africa with an unprecedented accuracy. In contrast to previous studies that failed to explain the deep divergence found between a clade of sables from western Tanzanian populations and the remainder H. niger, our study suggests that this highly divergent clade is the result of an old mitochondrial introgression from a currently extint Hippotragus species that diverged from H. niger around 1.7 mya. The complete absence of nuclear introgression, in contrast to mtDNA, suggests that strong gender-related asymmetries were involved. Our results also point to climatic shifts and geomorphological changes occurring during the Pleistocene as responsible for most of the species phylogeographic history in central, southern and eastern Africa. This allowed us to formulate an explicit hypothesis to explain the close phylogenetic relationship between the critically endangered giant sable antelope of Angola and sables from western Tanzania and Malawi. We believe that the ancestral population(s) to these sables might have been expanded in savanna habitat regions in between their current distribution, presumably in the Congo basin or northern Zambia, during a glacial period around 150 thousand years ago, followed by dispersal into northern Angola in the subsequent warm period, in which rainforests would have displaced savanna habitats. Ultimately, our study could integrate future comparative phylogeographic studies that would allow the reconstruction of the major trends in the histories of vicariance and dispersal in central, southern and eastern Africa, which are still poorly understood. We believe this is a 8 compelling contribution to phylogeography in Africa as most of available literature is focused on study systems from the Northern Hemisphere. Overall, the results obtained in this study can be used as empirical evidence that the use of complete mitochondrial genomes allows achieving higher phylogenetic resolution, and more accurate divergence estimates to assess intraspecific relationships. Therefore, we strongly advise the use of complete mitochondrial genomes in studies that wish to address complex intraspecific relationships or simply to provide higher phylogenetic resolution, and more precise divergence estimates, than those obtained using traditional shorter fragments.