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Phylogeny, Phylogeography And The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Phylogeny and Phylogeography of the Chacma Baboon (Papio ursinus): The role of landscape in shaping contemporary genetic structure in the southern African baboon Riashna Sithaldeen ape Town Supervisors: Assoc. Prof. Rebecca Ackermann, Department of Archaeology Dr. Jacqueline Bishop, Department of Zoology UniversityThesis Presented of for Cthe Degree of DOCTOR OF PHILOSOPHY in the Department of Archaeology Faculty of Science UNIVERSITY OF CAPE TOWN March 2011 ape Town The Big Baboon The Big Baboon is found upon The plains of Cariboo: He goes about with nothing on University(A shocking of thing C to do). But if he dressed up respectably And let his whiskers grow, How like this Big Baboon would be To Mister So-and-so! Hilaire Belloc DECLARATION This thesis reports the results of the original research I conducted under the auspices of the Department of Archaeology in the Faculty of Science at the University of Cape Town, between 2004 and 2011. All the assistance that I received has been acknowledged. This work has not been submitted for a degree at any other university. Signature Removed ______________________________________ Riashna Sithaldeen ape Town University of C i Author: Riashna Sithaldeen Thesis title: Phylogeny and Phylogeography of the Chacma Baboon (Papio ursinus): The role of landscape in shaping contemporary genetic structure in the southern African baboon Date: 04 March 2011 ABSTRACT Baboons (genus Papio) have evolved over the course of the Plio-Pleistocene, and remain widely distributed throughout Africa. This thesis contributes to our understanding of the role of climate and landscape change in structuring diversity within chacma baboons (Papio ursinus). The data set comprises molecular sequences from two mitochondrial DNA markers: the Brown region and the hypervariable D-loop. Faecal samples were collected from 261 free living chacma baboons across southern Africa from which DNA was extracted and processed. Phylogenetic and phylogeographic techniques, including coalescent modeling, are used to examine past and present population dynamics of chacma baboon populations. Bayesian tree constructions provide a timeline of diversification for the sample. Results recover a major diversification event at ~1.6 Ma which divides chacma baboons into two major mitochondrial lineages, a northern lineage (NL) and a southern lineageape (SL). This Town is coincident with the aridification of southern Africa and a period of genetic isolation between populations, due to the expansion of the Kalahari Desert. Two monophyletic clades are nested within these lineages. The first is a clade of Namibian baboons which diversified at ~1.0 Ma, most likely in response to fluctuations in levels of the Orange River. The second is a northeastern clade (NeC) which diversified at ~420 ka in response to a warmer and wetter climates. Although the phylogenetic placement and geographic distribution of NeC relative to NL suggests that it was founded by a minority fragment of NL, the limited sample cannot confirm this. A sudden expansion event is recovered for SL, mostUniversity likely out of the southwestern of C Cape, which was used as a glacial refuge for the species. This expansion is dated to ~15 ka which coincides with the end of the last glacial maximum. Estimates of the contribution of the geographic parameters shaping modern genetic structure were inconclusive. The results of this study support a model of climate driven diversification for Papio in which periods of isolation drive genetic and phenotypic differentiation. Although the ecological drivers of ongoing differentiation remain unclear, it has been shown that population contractions and expansions have also played a significant role in driving regional genetic structure within the species ACKNOWLEDGEMENTS I will be eternally grateful for the support and encouragement of my supervisors Assoc Prof. Becky Ackermann and Dr. Jacqui Bishop. Your wisdom and patience in guiding me though the preparation of this thesis has been invaluable. Thank you. I would also like to thank: The Palaeoanthropological Scientific Trust, the South African National Research Foundation, the Wenner-Gren Foundation and the University of Cape Town for financial support. Professor Raj Ramesar and the staff and students of the Department of Human Genetics (UCT Medical School) who provided lab space, resources and advice. Professor Judy Sealy and the Department of Archaeology at UCT for creating a supportive and stimulating environment to work in. South African National Parks for providing permits to collect samples and for rangers and conservation officers always ready to lend aape hand. Town Ministry of Environment and Tourism, Namibia, for collection permits. Professor Maarten De Wit and Dr. Woody Cotterill of the African Earth Observatory Network (AEON) unit at UCT for the use of their computational facilities to perform some of the analyses presented here. For samples I am gratefulUniversity to: of C Nicolas Fourie, for going above and beyond the call of friendship. Kurt Ackermann, Shabnum Behari, Jacqui Bishop, Woody Cotterill, Angela Layman, Lieutenant Moton (South African Police Services) and Anthony Roberts (Lapalala Wilderness Game Reserve) for much appreciated help in the field. Becky Ackermann, the Archer family, Esme Beamish (Baboon Research Unit, UCT), Seth Eiseb (National Museum of Namibia), Helena Fitchat (Centre for Rehabilitation iii Acknowledgments of Wildlife), Jacinta Beehner, Thore Bergman, Dorothy Cheney, and Robert Seyfarth of the Dorothy Cheney and Robert Seyfarth 'Lab', Matthew Bond, Geraldine Frasier (Namibia National parks), Gareth Hempson, Eric Hermann, Hannes Marais (Mpumalanga Parks Board), Erin Roberts (Lapalala Wilderness School). Special thanks to: Andy Burrell (New York Consortium in Evolutionary Primatology) and Dietmar Zinner (Deutsche Primatenzentrum) who kindly provided me with P. ursinus sequence data. Ms. Lynn Cable (Department of Archaeology) you have been a pillar of strength to me over these many years. Thank you for assistance with logistics, and for always being willing to listen to the crazy ramblings of put upon graduate students. To my fellow graduate students, for a sympathetic ear, and to all my friends for forgiving my neglect of you, thank you. To my family (Sithaldeen and Archer), I thank you for your unwavering belief that I could finish this. ape Town And finally to my partner Will Archer, your assistance in the field has made a significant contribution to the completion of this project and your personal pursuit of excellence has been a continuous inspiration. For all your support, you have my eternal gratitude. University of C Ethical clearance was obtained from the University of Cape Town Science Faculty Animal Experimentation Committee (AEC #2006/v2/RS) and field samples were collected under Western Cape Nature Conservation Board Permit #001-201-00004. Collection permits were also obtained from the Ministry of Environment and Tourism, Namibia (993/2005) and the Tsitsikamma National Park. iv Table of contents TABLE OF CONTENTS DECLARATION……………………………………………..……………………..….………i ABSTRACT……………………………………………………………………..….….………ii ACKNOWLEDGMENTS…………………………………………………………….............iii LIST OF FIGURES………………………………………………………………………......viii LIST OF TABLES………………………………………………………………………...….xii LIST OF APPENDICES……………………………………………………………………..xiii CHAPTER 1 GENERAL INTRODUCTION…………………………….………..……………………..............1 . CHAPTER 2 AN INTRODUCTION TO BABOONS (GENUS PAPIO) Evolutionary relationships among the African Papioninsape …………….………… Town ..4 The southern African Papionins……………………………………..………….......6 The emergence of Papio………………….………………………..………………..8 Taxonomy and Phylogeny of modern Papio…………………...……….…….… 10 Baboon distribution and ecology……………………………...……………..…….14 Summary………………………………………………………….………………….17 CHAPTER 3 University of C A DESCRIPTION OF THE SOUTHERN AFRICAN CHACMA BABOON (P. URSINUS) AND THE HABITATS ACROSS WHICH THE SPECIES IS DISTRIBUTED Introduction………………………………………………………………...….……...18 Ecological variation across the distribution of chacma baboons……………......18 Phenotypic variation within chacma baboons……………….…………………….22 Modern habitats of the southern African (chacma) baboon………...…………...25 The Kalahari Desert……………………………………………...…….…....26 The Cape Floristic Region (CFR)…………………………………………..27 v Table of contents Climate and habitat change in the southern African Pleistocene……….………28 Palaeoenvironmental change and species distributions in southern Africa………………………………………………………………29 Summary……………………………………………………………………………...31 CHAPTER 4 PHYLOGENY OF THE CHACMA BABOON (PAPIO URSINUS) Preface to chapter 4……………...……………………………………………..….37 Abstract……………………...……………………………………………………….38 Introduction……………………………………………………….....……….………39 Materials and methods…………………………………………………...…………42 Sampling………………………………………………………..……..….………….42 Choosing a marker for intraspecific phylogenetic reconstruction……...44 Molecular methods………………………………………….……...……....47 Phylogenetic tree construction…………………………………...………..49 Results……………………………………………………………………………......56 Discussion……………………………………………………………………….…...ape Town 61 Conclusions…………………...……………....................………………...66
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