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GMELIN, 1788 -.:University of Limpopo PHYLOGEOGRAPHY OF A POLYMORPHIC SOUTHERN AFRICAN ENDEMIC SPECIES, THE SOUTHERN BOUBOU LANIARIUS FERRUGINEUS (GMELIN, 1788) by DIKOBE KAREN MOLEPO RESEARCH DISSERTATION Submitted in fulfilment for the degree of MASTER OF SCIENCE in ZOOLOGY in the SCHOOL OF MOLECULAR AND LIFE SCIENCES FACULTY OF SCIENCE AND AGRICULTURE at the UNIVERSITY OF LIMPOPO SUPERVISOR: DR TG MANDIWANA-NEUDANI CO-SUPERVISOR: DR J FUCHS (Muséum National d'Histoire Naturelle, Paris, France) CO-SUPERVISOR: PROF RCK BOWIE (University of California, Berkeley, California, USA) 2019 Southern Boubou Laniarius ferrugineus (Courtesy: Bowie et al. 2005) DEDICATION I dedicate this dissertation to my parents Mr and Mrs (Legohu and Masemola Molepo) whose love carried me through every phase of my study. Without them this work would never have started. To my son Peakanyo who unknowingly gave me courage and a reason to see through this study. DECLARATION I declare that the work presented in this dissertation titled: PHYLOGEOGRAPHY OF A POLYMORPHIC SOUTHERN AFRICAN ENDEMIC SPECIES, THE SOUTHERN BOUBOU LANIARIUS FERRUGINEUS (GMELIN, 1788) reflects my work in design and in execution. All the referenced information contained herein has been duly acknowledged. This work has not previously been submitted by me for examination at this or any other university. I therefore present this dissertation for the examination for the degree of Master of Science in Zoology at the University of Limpopo. Dikobe Karen Molepo ………………………............ ……………………………. Full name Student number 11 April 2019 ………………………………. ........................................ Signature Date ACKNOWLEDGEMENTS First, I give praise to the Lord who provided me with the strength to complete my study; all this was possible through him. I am indebted to the various institutions and people who contributed to the success of this study. Firstly, I am grateful to my supervisors (Dr Tshifhiwa G Mandiwana-Neudani - University of Limpopo; Dr Jérôme Fuchs - Muséum National d'Histoire Naturelle, Paris, France and Prof Rauri CK Bowie - University of California, Berkeley, California, USA) for their trust in offering me this research project, their consistent professional guidance, encouragement and financial support. In addition, they demonstrated patience throughout all the stages of the study including the production of this dissertation. The support I received from the directors of national and international museums and the curators of various ornithological collections was immense, allowing me access to their bird study skin collections. They are: Mr David Allan (Director - Durban Natural Science Museum); Dr Phil Whittington (Head of Department - East London Museum); Mr Greg Davies (former Curator - Ditsong National Museum of Natural History); Ms Denise Hamerton (Curator - Iziko Museums of Cape Town, Natural History); Dr Jérôme Fuchs (Professor and Curator - Muséum National d'Histoire Naturelle, Paris, France); Prof Rauri Bowie (Professor and Curator - Museum of Vertebrate Zoology, University of California, Berkeley, California, USA); Drs Shannon Hackett and John Bates (Associate Curators - Field Museum of Natural History, Chicago, USA); Ms Viola Makanzana (Curator - Natural History Museum of Zimbabwe, Bulawayo, Zimbabwe), Drs Helen James and Gary Graves (Curators - Smithsonian National Museum of Natural History). A large number of DNA samples analysed in this study were provided by my co-supervisors (Dr Jérôme Fuchs - Muséum National d'Histoire Naturelle, Paris, France and Prof Rauri Bowie - Museum of Vertebrate Zoology, University of California, Berkeley, California, USA). The gaps in DNA sampling were filled with toe pad snips sub-sampled from the study skins housed at Durban Natural Science Museum with the permission of the Director, Mr David Allan. All the DNA samples were analysed in a molecular laboratory at the Muséum National d'Histoire Naturelle, Paris, France under the guidance of Dr Jérôme Fuchs and Céline Bonillo was my second stop. Drs Sean Marr (former Postdoctoral fellow i – Biodiversity Department, University of Limpopo) and Selaelo A Ramoelo (Council for Scientific and Industrial Research - CSIR) are thanked for their assistance with statistical analyses and mapping, respectively. This research project would not have materialised if it were not for the funds provided by National Research Foundation (NRF) to pay for my study and my visit to Muséum National d’Histoire Naturelle in France where I carried out DNA sequencing. The Department of Biodiversity and the University of Limpopo are also thanked for supporting and funding to in undertaking my trips to some natural history museums in South Africa and trips to attend project-related workshops and to present work at national conferences. The South African DST, NRF in partnership with the US NSF, Howard University funded my trip to present research at the international Women in Science, Technology, Engineering and Mathematics (STEM) conference at Howard University, Washington DC, USA. I have no words to repay what my family did for me. My parents (Mr Legohu G. Molepo and Mrs Masemola N Molepo) are the reason for my accomplishment. My son, Peakanyo Molepo has always been the source of my strength. I cannot forget my life partner Mr Morongwa G. Mohubedu for his love and support. I am truly grateful to the love and generosity of my brother and sister-in-law (Mr Mokgatla D and Mrs Maleopeng R. Molepo, respectively and my nieces (Dikobe Jnr. Mokgadi, Kobela and Legohu Jnr). Lastly, I am thankful to all my friends for their encouragement. Without the assistance and support from all the institutions and people, this work would never have seen the light. ii GENERAL ABSTRACT It cannot be overemphasised that birds, which form a group of animals that are conspicuous in many habitats, occur worldwide, and are ecologically diverse and better known than any other vertebrate groups. Some species present no geographical variation while others exhibit complex geographic variation rendering them polytypic. The Southern Boubou Laniarius ferrugineus (Gmelin, 1788) is a polymorphic and highly vocal resident species endemic to Southern Africa. It overlaps with the Tropical Boubou Laniarius aethiopicus in the extreme north of South Africa. The taxonomic circumscription presents six subspecies of L. ferrugineus which vary in size and plumage colourations. Although L. ferrugineus is of least concern (LC), its wide distribution range calls for its precise taxonomic delineation and our knowledge of its genetic structure hence the need to investigate the status and level of morphological, genetic and vocal differentiation in this species complex. Morphological, genetic and song variation were analysed from museum study skins, DNA sequences spanning one coding mitochondrial gene and three non- coding nuclear introns generated from modern and ancient samples and songs from various sound libraries respectively. While morphometric analyses and Bayesian phylogenetic inference recovered two major lineages in L. ferrugineus: 1) L. f. ferrugineus / L. f. pondoensis / L. f. natalensis (southern clade) and 2) L. f. transvaalensis / L. f. tongensis / L. f. savensis (northern clade), L. f. transvaalensis overlapped between the two lineages in MDS and Box and whisker plots. The 95% parsimony ATP6 network similarly revealed two distinct lineages with the population demographic histories of the two clades showing expansion. The divergence between the two lineages occurred approximately 1.5 million years ago during the Pleistocene epoch. Laniarius ferrugineus pondoensis is the most distinctly dark morph. The moist habitat of L. f. pondoensis could be having an effect on plumage while there is no genetic basis for the difference in plumage colouration. Almost all L. ferrugineus subspecies render a tonal song duet made up of ‘bou’ and ‘whistle’ elements with the significant difference being observed in maximum peak frequency. Laniarius ferrugineus (Gmelin, 1788) should at best be split into two species, one representing members of the southern clade to be named Laniarius ferrugineus (Gmelin, 1788) and another species representing members of the northern clade iii named Laniarius transvaalensis Roberts, 1922 based on the Principle of Priority. The current study expanded our knowledge base as far as ornithology is concerned and shed light on the phylogeographic patterns of the Southern Boubou Laniarius ferrugineus (Gmelin, 1788). The findings significantly contributed to our understanding of the evolutionary processes governing the geographical variation in Laniarius ferrugineus complex and the findings could possibly be extrapolated to other species. It was critical that the taxonomic affinities of L. ferrugineus were investigated due to its extensive distribution range for better management and conservation. Future work should further unravel the less differentiation within the south and north lineages with additional songs being analysed to understand the song pattern across the range. iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ----------------------------------------------------------------------------- i GENERAL ABSTRACT ------------------------------------------------------------------------------ iii TABLE OF CONTENTS ------------------------------------------------------------------------------- v LIST OF FIGURES, TABLES AND APPENDICES ------------------------------------------ vii CHAPTER 1 ---------------------------------------------------------------------------------------------- 1 General Introduction.
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