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Cisticola Spp.) University of Cape Town Doctoral Thesis Taxonomy, phylogeny and biogeography of cisticolas (Cisticola spp.) Supervisors: Author: Prof. Timothy M. Crowe Owen R. Davies Prof. Rauri C. K. Bowie A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the Faculty of Science DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology UniversityDepartment of of BiologicalCape Sciences Town November 2014 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 Declaration of Authorship I, Owen R. Davies, declare that this thesis titled, ‘Taxonomy, phylogeny and biogeog- raphy of cisticolas (Cisticola spp.)’ and the work presented in it is my own, unless otherwise stated. Apart from the guidance received from my supervisors, assistance from all institutions and individuals in this dissertation is acknowledged. This disserta- tion has not been previously submitted for the degree at this or any other university and I therefore present it for examination for the degree of Ph.D. I hereby grant the University free license to reproduce the above thesis in whole or in part, for the purpose of research. Signed: Date: i "With the loss of their chief, all the birds claimed to be the new king. Confident in his abilities, the vulture suggested a competition; whichever bird that could fly the highest, would be the king of the birds. When all the other birds had dropped to earth, exhausted, the vulture remained soaring high. While the vulture was claiming victory, a tiny Cloud Cisticola emerged from its hiding place amongst the vultures feathers and soared higher than the vulture could manage, shouting ‘I am king’. The Cloud Cisticola realised that the rest of the birds were unhappy with this trickery and quickly dropped to earth and hid in a snake hole." — Traditional Xhosa folklore Abstract Faculty of Science DST/NRF Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology Department of Biological Sciences Doctor of Philosophy Taxonomy, phylogeny and biogeography of cisticolas (Cisticola spp.) by Owen R. Davies A review of the genus Cisticola was published in 1930 by Rear-admiral Lynes. While subsequent authors have modified Lynes’ original groupings, his work remains the basis for modern syntheses of cisticolas. This study tests Lynes’ hypotheses by analysing data that he presented in his review and with measurement and plumage data collected from museum specimens. Lynes’ groupings were well recovered (98%) when data captured from his review were analysed phenetically, suggesting that he grouped species mostly by similarity. In contrast, when morpho-behavioural data were analysed using cladistic methods, many of his groupings were not monophyletic and the resultant cladogram had very little nodal support due to their highly conservative morphology. To resolve the structure of the genus and the relationships within it, two mitochondrial and four nuclear regions were sequenced from toe-pad samples taken from museum specimens. The molecular analyses included 44 of the 49 currently recognised species and repre- sents the most taxon-dense molecular phylogeny of the genus. The resultant phylogeny separates species into five main clades, but many of Lynes’ groupings were not mono- phyletic and there was also very little support for more recent groupings. Vocalisation analyses indicated that frequency components of songs were correlated with habitat type and body size. These correlations, though, disappeared when phylogeny was controlled for indicating that phylogenetic history rather than habitat preference influenced song character distribution. Some song types are mismatched to their environment, and some sympatric sister species appear to give similar calls. Cisticolas may overcome these at- tenuation and identification difficulties with behavioural adaptations and aerial displays. The biogeographic distribution of closely related species does not agree with many of the previously proposed hypotheses and a dated phylogeny estimates that most of the diversification in the genus has occurred within the last five million years. Most of the mean divergence date estimates correlated with periods of climate variability and episodes during which there is evidence for high lake levels in Africa, rather than cor- relating with Plio-Pleistocene glaciation, offering evidence that open habitats may have become fragmented during extremes of both arid and humid climates. Acknowledgements The historical work of Rear-admiral Hubert Lynes must surely be acknowledged first and foremost; without his huge effort and detailed descriptions I would not have had a foundation upon which to build this thesis. I must thank Prof. Timothy M. Crowe and Prof. Rauri Bowie for their guidance and supervision as well as their financial and technical support with data collection and analyses. I am indebted to the Director of research at the Museum of Natural History in Stockholm, Dr. Per G. P. Ericson, as well as the head of the Molecular Systematics Laboratory, Dr. Pia Eldenäs, for allowing me access to their laboratory facilities and additional financial and technical support during my trip to Sweden. A huge amount of effort was made by Dr. Martin Irestedt who offered technical assistance to me in the Molecular Systematics Laboratory and passed on his skills by taking the time to teach me the technical expertise required to successfully sequence DNA from samples collected from old museum specimens, an invaluable skill which I have been able to bring back to South Africa and consequently reproduce successful DNA extractions of museum specimens in local laboratories. In addition to the technical assistance, I must thank Martin for going out of his way to be hospitable and welcoming to me from the moment I arrived in Sweden, including inviting me for birding trips and social events; hopefully I shall be able to return the favour one day. Many hours of fieldwork were spent with Dr. Jérôme Fuchs and Dr. Graeme Oatley who passed on their knowledge of skinning, field preparation and taxidermy of birds. I could not have asked for two nicer people to spend time with in the bush. Thanks to Dr. Jérôme Fuchs and Ms. Lisa Nupen for assisting with molecular analyses and Dr. Patrick R. A. Lindop for his hospitality and Mr. Charles Owen, Dr. Hanneline Smit- Robinson and Dr. Ben Smit for additional assistance in the field. Thanks to Dr. Fenton Cotterill for many hours of discussion and to Mr. Mike Mills for access to his vocalisation recordings. Thanks must go to Prof. Peter Ryan for his comments on various drafts of this manuscript, as well as Assoc. Prof. Sugnet Lubbe of the Statistical Sciences department at the University of Cape Town, Prof. François Husson of the Applied Mathematics department of Agrocampus Ouest in France and Mr. Toby Goodworth for their invaluable input and patient guidance in the statistical analyses, particularly with multiple factor and multiple correspondence analyses. Thank you also to Assoc. Prof. Rebecca R. Ackermann at the Archaeology Department at the University of Cape Town for her assistance with the analyses and interpretation of geometric morphometric data. Thanks must also be extended to the staff of Natural History Museum at Tring for their hospitality and assistance with their cisticola collections, particularly senior curator of birds Mark Adams and collections manager Dr. Robert Prys - Jones. Thanks to Ms. Petra Muller, Mr. Chris Tobler, Ms. Tania Jansen and Ms. Hilary Buchanan and the rest of the administrative and support staff at the Percy FitzPatrick Institute iv of African Ornithology and the Department of Biological Sciences at the University of Cape Town for their help in the logistics and planning of my various trips both locally and abroad. Thanks to my family for financial and emotional support, including my fiancée Ms. Jennifer Waters for her continued support, patience and the invaluable comments and corrections made to thesis drafts. Thanks also to the late Prof. Phil A. R. Hockey for support, conversation and inspiration. The majority of the financial support for this project was provided by the South African Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence at the Percy FitzPatrick Institute of African Ornithology and the Clancey Trust. Contents Declaration of Authorshipi Abstract iii Acknowledgements iv Contents vi List of Figures ix List of Tables xi Summary xiii 1 Status quo ante: Taxonomic history of the genus Cisticola 1 1.1 Introduction ................................... 1 1.1.1 Morphology ............................... 1 1.1.2 Sexual dimorphism ........................... 2 1.1.3 Breeding and seasonal plumage variation ............... 2 1.1.4 Juvenile plumage ............................ 3 1.1.5 Habitat ................................. 3 1.1.6 Vocalisations .............................. 4 1.2 Taxonomic history ............................... 5 2 Cisticolas? They all look the same to me – The problem of similarity. An assessment of Lynes’ (1930) review on the genus and a reassessment of morpho-behavioural data using phenetic and cladistics methods 18 2.1 Introduction ..................................
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