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Evolutionary History of the Critically Endangered Giant Sable Antelope (Hippotragus Niger Variani)

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Evolutionary History of the Critically Endangered Giant Sable Antelope (Hippotragus Niger Variani) FCUP i Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) “Black among black shadows” Gilbert Blaine, 1922 FCUP ii Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) FCUP iii Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) Foreword In compliance with the no. 2 of article 4 of the General Regulation of Third Cycles of the University of Porto and with article 31 of the Decree-Law no. 74/2006, of 24 March, with the alteration introduced by the Decree-Law no. 230/2009, of 14 September, the results of already published work were totally used and included in some of the chapters of this dissertation. As these studies were performed in collaboration with other authors, the candidate clarifies that, in all these works, participated in obtaining, interpreting, analysing and discussing the results, as well as in the writing of the published forms. This thesis should be cited as: Vaz Pinto P (2018) Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani). Insights into its phylogeography, population genetics, demography and conservation. PhD Thesis, University of Porto, Porto, Portugal. FCUP iv Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) FCUP v Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) Aknowledgements This dissertation is a milestone on a long, yet unfinished, journey that I have initiated many years back in the wonderful Angolan bush, and it would not have been possible without a vast array of contributions from many friends. I will try my best to recognize here at least some of the most relevant contributors. First and foremost to my supervisor Nuno Ferrand, for his brilliance, friendship and enthusiasm while guiding me through this enterprise, and also by adding new layers to my views of the natural world. But most of all because he came up with the idea and convinced me to do the PhD, so quite literally, this work could never have materialized without Nuno. To my co-supervisor Raquel Godinho, for her guidance, patience and warm hospitality. She forced me to raise my standards, and her pragmatic and hard-working attitude was inspirational and proved crucial for the success of this work. To my informal co- supervisor Pedro Beja for sharing his knowledge and adding several key contributions in critical stages. I must address special thanks to Luis Veríssimo, with whom I have shared so many brainstorms that provided answers to outstanding questions and new lines of research. And Luis has always been available, donated some of his free time, and ended up kindly producing the majority of maps presented in this work. Also to Joana Rocha for spearheading many tasks in several papers, and to Hugo Fernandes for his artwork. Thank you, to my good friend Filippo Nardin, who has always been there for me and provided critical assistance at various stages of this work. To my friend Vladimir Russo, for his cool head and by putting down numerous “fires”. To Sendi Baptista for being a wonderful companion and precious collaborator in so many bush trips. To Abias Huongo, for his friendship and precious assistance. A very special thank you to generals João Traguedo and Afonso Hanga for their friendship, unrelentless continuing support to my work and to the giant sable conservation, and commitment to the cause. I must also aknowledge my many other Angolan friends who were instrumental in different ways for the success of various stages related to the conservation project on the ground, starting with Kalunga Lima who I have deerly missed, Henriette Koning, FCUP vi Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) Wolfram and Werner Brock, Nito Rocha, Harold Roberts, João Sousa, Miguel Morais, Carlos Cunha, David Schaad and Kostadin Louchanski. They were always supportive. The team of local shepherds and rangers in Cangandala and Luando played a decisive role on the ground throughout the project, and several have become friends. A special thanks is due to Manuel Sacaia, for his enthusiasm and good humour, with whom I hope to share many more camp fires in the wilderness under Angolan starry nights. To Brian Huntley, Richard Estes, Jeremy Andersen and John Walker, for being inspirational and for having shared with me their passion and immense knowledge on the giant sable antelope. And I am hugely indebted to Peter Morkel for his incredible skills and professionalism, and for his truthful and unrestricted commitment to conservation. It has been a privilege to know all of you. To all the staff at CIBIO, particularly at the lab in CTM, making the magic of transforming tiny biological samples into quantifiable data. A special mention is due to Carina Matos, Dario Martins, Valdemar Pinto and rest of the staff at Kissama Foundation for their continuing support for many years. To the Catholic University of Angola and all my good friends at CEIC. To the Ministry of Environment and Provincial Government of Malanje for having authorized the various research lines, and to all the good people in these institutions that have supported the activities. And of course to the various branches of FAA, the Angolan military forces, in particular the air force, for the outstanding efforts that made possible some of the more challenging initiatives. I must also express my sincere gratitude to the institutions that have contributed financially to various components of the project, namely Sonangol, Esso Angola, Angola LNG, Whitley Award, Tusk Trust, Fondation Segré. In Particular, Laurentino Silva, Bill Cummings, Fernando Pegado, Miguel Cordeiro, David Mallon have never doubted the value of the project from the onset and ensured continuation of support when needed. The financial donations received from the ExxonMobil Foundation specifically addressed several of the research lines covered by this thesis, and proved to be a critical contribution to the end result. Finally but not least to my dearest, to my recently deceased father for having exposed me to the bush and wildlife while I was still a little kid, and to my mother for having always been tolerant and supportive. And of course to my lovely wife Paula, and our wonderful kids Beatriz, Afonso, Margarida and Frederico. I hope this work will make them all proud. FCUP vii Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) Summary The African continent is renowned for a remarkable diversity of bovid taxa, the end product of an explosive taxonomic radiation that was sparked by environmental changes during the Miocene. Having adapted to the vast array of ecological niches present in Africa, extant members of this highly speciose family come in many forms and sizes, but arguably none is as rare, revered and poorly known as the giant sable antelope (Hippotragus niger variani), which occupies the centre stage of this dissertation. Described as late as in the early twentieth century, the giant sable has never been found outside a small region confined to the Kwanza River basin in central Angola, and in spite of carrying a high cultural and iconic value, it is also one of the most endangered mammals in the world. Because of its rarity, historical background and the recent political turmoil that affected the country, few studies have focused on this taxon and conservation has been neglected, these constituting critical shortfalls that the current thesis aims to address. On a wider level, the sable antelope could be seen as a model species for biogeographical studies in Africa because it is one of the most highly specialized antelopes, closely associated with particular habitats, and yet widely distributed across the continent. In addition, the economic interest on sable has boomed in recent years, becoming one of the most prized high value species for the fast-growing multi-million dollar game farming industry in Southern Africa. Despite its importance and the increasing attention received by researchers over the years, we have identified various gaps on the species knowledge. Recent studies have relied on mitochondrial DNA fragments and limited datasets to infer phylogeographic patterns and intraspecific taxonomy, yet the results may not have improved much on previous data published by zoologists before the advent of DNA and based on morphological analyses. By adopting new tools and expanding the sampling effort, we expect this dissertation will much improve current knowledge on the species. Within this framework we started by targeting the conservation crisis facing the giant sable antelope in Angola. The use of new molecular tools, namely autosomal markers not yet available for Hippotragus was considered crucial, and by developing a panel of 57 species-specific microsatellites, also successfully tested on congeneric roan antelope H. equinus, we were able to address specific questions affecting the giant sable, and provide for the first time estimates of genetic diversity further interpreted within the context of other populations. These initial efforts evidenced the giant sable as being seriously depleted of genetic diversity when compared to other sable populations. In FCUP viii Evolutionary history of the critically endangered giant sable antelope (Hippotragus niger variani) addition, analyses of allele frequency spectrums and allele sharing between populations, proved to be consistent with an evolutionary history of giant sable characterized by population bottlenecks and long-standing isolation. A more decisive application for these nuclear markers consisted in providing support to specific conservation initiatives already unfolding on the ground. Here we report on how the sustained use of extensive field research methods based on field, aerial and trap- camera surveys, combined with modern molecular tools, has uncovered and allowed the documentation in unprecedented detail, of a remarkable case of interspecific introgressive hybridization between giant sable and roan antelope in Cangandala National Park.
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