The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgementTown of the source. The thesis is to be used for private study or non- commercial research purposes only. Cape Published by the University ofof Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University The phylogenetics, taxonomy and biogeography of African arid zone terrestrial birds: the bustards (Otididae), sandgrouse (Pteroclidae), coursers (Glareolidae) and Stone Partridge (Ptilopachus) Callan Cohen Town Thesis presented for the degree of DOCTOR OF PHILOSOPHY Faculty of ScienceCape DST/NRF Centre of Excellence at the Percy FitzPatrick Instituteof of African Ornithology Department of Zoology UNIVERSITY OF CAPE TOWN University Supervisor: Professor Timothy M. Crowe, DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology, University of Cape Town Co-supervisor: Professor Rauri C.K. Bowie, Museum of Vertebrate Zoology & Department of Integrative Biology, University of California Berkeley, CA, USA February 2011 Declaration: The phylogenetics, taxonomy and biogeography of African arid zone terrestrial birds: the bustards (Otididae), sandgrouse (Pteroclidae), coursers (Glareolidae) and Stone Partridge (Ptilopachus) I, Callan Cohen, hereby (a) grant the University of Cape Town free licence to reproduce the above thesis in whole or in part, for the purpose of research; (b) declare that: (i) the above thesis is my own unaided work, both in concept and execution, and that apart from the normalTown guidance from my supervisor, I have received no assistance except as stated in the Acknowledgements. Cape (ii) neither the substance nor any part of the above thesis has been submitted in the past, or is being, or is to be submitted for a degree at this Universityof or at any other university. I am now presenting the thesis for examination for the degree of PhD. SIGNED: ________________________________ DATE: __________________________________University Dedication To my parents, Mark and Alice, whose encouragement for me to follow my interests from an early age made starting this PhD possible, and to Deirdre, whose continual support has made completing it a reality. Town Cape of University Acknowledgements This research would not have been possible without the generous support of many people over a number of years, and I’d like to thank each of you for your help (and I apologise if I have inadvertently missed anyone off the list below). Collecting the samples required for this research was the largest logistical challenge and I would like to especially thank the following people who either accompanied me in the field in various places across Africa, assisted with logistics, permissions and permits, or provided samples from their own collections: Tim and Laurel Osborne, Michael Mills, Claire Spottiswoode, Kirsten Louw, Steve and Louise Braine, Renate Kersing, Alfred Simiyu, Eladio L. García de la Morena, Bob Drewes, Jon Fjeldså, Graeme Oatley, Ray Jansen, Dusty Millar, Richard Schodde, Angus Anthony, Paulette Bloomer, Bob Dawson, Miles Coverdale, Peter Huth, Mike Picker, Jonathan Colville, Ian Little, Sarah Hallager and Penn Lloyd, as well as thoseTown from the following institutions: Leon Bennun, George Amutete and Muchane Muchai from the National Museums of Kenya, Nairobi; John Bates and Dave Willard from the Field Museum of Natural History, Chicago; Deon Hignett from Capethe Western Cape Nature Conservation Board who also assisted with CITES permits; Mark Anderson, Maxie Jonk and Marileen Badenhorst from the Northern ofCape Nature Conservation Service; and the Kenyan Wildlife Service. I’d especially like to highlight the important contributions of Renate Kersing and Claire Spottiswoode for their help with sandgrouse samples, Alfred Simiyu and Steve Braine for their help in Kenya and Namibia respectively, and Tim and Laurel Osborne, undoubtedly the world’s best bustard catchers, for their hospitality, trainingUniversity in how to capture bustards in nets, providing many samples, and discussions on Kori Bustards in particular. Eric Sande and Christine Dranzoa provided the Francolinus nahani samples and Brian Finch provided additional sound recordings of this species; Ian Parker and Pedro vaz Pinto provided additional galliform samples. Thanks, too, to Keith Barnes, Jon Rossouw and Adam Riley right at the start of this project for their companionship on the epic 4x4 drive across Africa, from the south-west to the north-eat arid zone, along the path of the hypothesised ‘arid corridor’. I’d like to thank those at the following museums which I visited for providing access to their skin collections, additional tissue samples (the former four listed here allowed limited toepad-skin sampling), and useful discussions: British Natural History Museum, Tring (Robert Prys-Jones, Mark Adams); National Museums of Kenya, Nairobi (Leon Bennun); American Museum of Natural History, New York (Joel Cracraft, George Barrowclough, Paul Sweet); Royal Museum for Central Africa, Tevuren, Belgium (Marc Herremans and Michel Louette); Smithsonian Museum, Washington (Carla Dove); Durban Natural Science Museum (David Allan); and Iziko Museum, Cape Town (Denise Hamerton). Many thanks to Elaine Cook and Rollo Turner who provided accommodation and lent me their car to visit the British Natural History Museum at Tring; Marc and Diane Herremans for accommodation and support in Belgium; Dawn Hannay, Peter and Mary Shen, Brad Klein and Danielle Gustafsen for accommodation and assistance in New York City; and David Wilcove for his help in Washington. Paul Goriup is thanked for access to the Bustard Morphometrics Database. I’d like to Marion Sandwith for her help with illustrating Fig. 5.5 (and Nik Borrow and Ron Hoff for allowing us to useTown their photographs as a basis for those line drawings) and Tari Cohen who modified Figs 1.4 – 1.7. For assisting me in the laboratory in CapeCape Town, I’d like to thank Tracey Nowell, Pamela Beresford, Colleen O’Ryan, Terry Hedderson and Tony Verboom. Sampath Lokugalappatti provided adviceof and invaluable assistance with the extraction and sequencing of bustard samples and I am tremendously grateful for his help. Jérôme Fuchs really took me under his wing in Berkeley and I could never have completed my genetic sequencing or analyses without his invaluable assistance, advice and tutoring – merci beaucoup! Anna Seles was always on hand in Berkeley to offer advice andUniversity assisted with some samples once I had left, and I also received helpful support at Berkeley from Verna Bowie, Carla Cicero, Lydia Smith, Stephen Long, Anna Ipollito, Sandra Nieto, Allison Shultz, Krystle Chavarría, Mitzy Pepper, Hanneline Smit and Mat Fujita. Joerns Fickel and Christian Pitra are thanked for assisting with getting funding for me to work collaboratively with them in Germany, even though we did not get the funding in the end; thanks too to Tina Sommer and Silke Kipper for accommodation and orientation in Berlin. The samples for Chapter 5 were largely sequenced by Julia Wakeling, Tshifhiwa Mandiwana, Rauri Bowie and Tracey Nowell. Many thanks to Julia Wakeling for her important contributions to the Ptilopachus research. Thanks to David Allan and Nigel Collar (“FYFT”) for general discussions on bustard relationships. Scott Lanyon and Bob Zink gave me some useful phylogenetics advice at the IOC in Durban 1998 which led me down this path. I’d like to thank my friends Claire Spottiswoode, Michael Mills, David Winter, Giselle Murison and Kirsten Louw for many discussions on African birds and who shared of their knowledge and experience. I am very grateful to J. Salvador Arias for his tutorial assistance with setting up and running my datasets in VIP. The Percy FitzPatrick Institute (University of Cape Town) has been my base for many years and I’m grateful to everyone there for their support and assistance. Morne du Plessis is especially thanked for his patient encouragement and advice, without which this dissertation would never have been completed. Phil Hockey also provided essential Fitz support in his directorship role. Pete Ryan has always provided advice and support throughout the years. Margaret KoopmanTown has always gone out of her way to assist with bibliographical matters at the Niven Library. Chris Tobler, Hilary Buchanan, Lionel Mansfield and Sandy Dewberry assisted in many ways with admin and logistics. Cape The Percy FitzPatrick Institute, ofSouth Africa’s Department of Science and Technology and National Research Foundation, Frank M. Chapman Memorial Fund at the American Museum of Natural History, African Biodiversity Information Centre (Royal Museum for Central Africa, Tervuren, through a framework agreement of the latter institution with the Belgian Development Cooperation) and Birding Africa are thanked for financialUniversity support. A special thanks to my supervisor Prof. Tim Crowe for his years of support and mentorship, facilitating access to samples and the AMNH, assistance with parsimony analyses, and checking my entire dissertation while he was on medical leave. I’m sure he can’t believe that I’ve finally finished! It would have been impossible to have completed this Ph.D. thesis without the supervision, support, commitment and generosity of my co-supervisor, Rauri Bowie, and his wife Verna. He arranged for me to complete my sequencing in his laboratory in Berkeley, assisted with analyses, commented on all my drafts and provided critical input. On top of all of this, Verna and he invited me to stay with them at their house on my first visit to Berkeley and made me feel right at home. Rauri and Verna, I cannot thank you enough for your generosity. On a personal level, I’d like to especially thank my parents, Mark and Alice Cohen, for encouraging and supporting my childhood interest in birds which transformed into a career. Thanks very much to Marje Hemp for assisting with numerous things, and to Guy and Jay Louw, thanks you for your encouragement. My biggest debt must go to Deirdre Vrancken, without whose caring and unfailing support over these many years, I would never have been able to complete this research.