Comparative biogeography and ecology of freshwater fishes in the Breede and associated river systems, South Africa by Albert Chakona Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown Supervisors: Dr. Ernst R. Swartz (South African Institute for Aquatic Biodiversity) Dr. Gavin Gouws (South African Institute for Aquatic Biodiversity) Prof. Paulette Bloomer (Department of Genetics, University of Pretoria) October 2011 Declaration I, the undersigned, hereby declare that the work contained in this thesis is, to the best of my knowledge, original. This thesis has not been previously submitted, either in part or in its entirety, for the award of any other degree at any other university. Signature: ………………………… Date: ……………………… ii Thesis summary Distribution patterns and levels of genetic diversity in extant taxa are a product of complex palaeogeographic processes and climatic oscillations as well as the species’ intrinsic ecological adaptations. The Cape Floristic Region of South Africa presents a unique system for studying the processes that promote species diversification and distribution patterns. This region has a high degree of endemism of both terrestrial and aquatic biota and is clearly isolated from neighbouring areas by the Cape Fold Mountains and the Great Escarpment. The objective of this study was to firstly examine the ecology of freshwater fishes belonging to the genera Galaxias, Pseudobarbus and Sandelia in the south-western CFR. This was followed by an assessment of the genetic diversity of these taxa. Unique lineages were identified and their distribution was mapped. The work aimed to explore the role of the region’s complex palaeogeographic and climatic history as well as the role of the species’ ecological adaptations in driving lineage diversification and shaping contemporary distribution patterns. The four main components of the study can be summarised as follows: 1. Habitat associations of three widely distributed lineages of Galaxias zebratus Pseudobarbus burchelli and Sandelia capensis were evaluated at multiple localities in minimally disturbed mountain tributaries of the Breede, Duiwenhoks and Goukou River systems. The lineages have distinct habitat associations which were related to differences in their morphological traits. The slender-bodied Galaxias ‘nebula’ and the fusiform- shaped Pseudobarbus ‘Breede’ are capable of exploiting upper reaches with faster water iii velocity. By contrast, the laterally compressed Sandelia ‘eastern’ is restricted to lower reaches, making this lineage more susceptible to a wide array of impacts. 2. A recently discovered lineage of Galaxias zebratus, (Galaxias ‘nebula’), was found to be capable of tolerating emersion for a prolonged period of time. This is the first time that such capabilities have been documented in an African galaxiid. These adaptations have implications for the interpretation of Galaxias ‘nebula’s wide distribution range. 3. The phylogeography of Galaxias ‘nebula’ across its entire distribution range was investigated using two mitochondrial genes (cytochrome c oxidase subunit I (COI) and cytochrome b (cyt b)). This lineage has a complex evolutionary history that was influenced by both intrinsic and extrinsic factors. Rare events such as episodic drainage connections during Pleistocene and Holocene pluvial periods, possibly augmented by river confluences during periods of lower sea-levels and river capture events seem to be the most credible explanation for the extensive contemporary distribution and the relatively shallow genetic divergence between different river systems. 4. Mitochondrial cyt b sequences were used (i) to assess genetic diversity in G. zebratus, P. burchelli and S. capensis from the south-western CFR and (ii) to determine the roles of intrinsic ecological adaptations and extrinsic landscape and climatic changes in promoting genetic diversification and shaping present day distribution patterns of lineages in the three taxa. Marine incursions during periods of major sea-level transgressions are proposed to have isolated populations in upland refugia, thereby iv driving allopatric divergence in these species. Subsequent connections of rivers during wetter periods and lower sea-levels are proposed to have facilitated post-speciation dispersal of lineages to attain present day distribution patterns. While detailed morphological studies and further genetic analysis are needed to substantiate the taxonomic status of the newly discovered lineages of Galaxias zebratus, Pseudobarbus burchelli and Sandelia capensis, results of the present study indicate that the south-western CFR represents a previously unrecognised centre of freshwater fish diversity and microendemism in the broader Cape Floristic Region. Accurate identification of lineages and comprehensive mapping of their distribution is a fundamental pre-requisite for ecological studies, assessing conservation status and implementation of appropriate conservation measures. v Dedication To my daughter Rutendo, my wife and friend Gamuchirai my parents Assumpta and Runesu Chakona … and to all those dedicated to the conservation of the CFR’s unique freshwater fishes … vi Thesis acknowledgements I gratefully acknowledge my supervisors, Ernst Swartz and Gavin Gouws from the South African Institute for Aquatic Biodiversity and Paulette Bloomer from the University of Pretoria, for their support, guidance, mentorship, intellectual input and great working alliance from the beginning of this study until the end. Ernst conceived the research idea, administered the project and helped define its direction. Gavin’s unrelenting patience, assistance and guidance in the early days of my lab work and data analysis is greatly appreciated. Funding for this study was provided by the National Research Foundation (NRF, South Africa), the South African Institute for Aquatic Biodiversity (SAIAB), Rufford Small Grants Foundation (RSGF), International Foundation for Science (IFS) and WWF Prince Bernhard Scholarships for Nature Conservation. Without their generous financial support, neither the project nor my studies in South Africa would have been possible. SAIAB is also thanked for providing all the necessary facilities including laboratory and office space, equipment and research vehicles. I would like to acknowledge CapeNature for permits and for the support they gave to the project. The South African Navy is thanked for providing bathymetry layers that were used to reconstruct palaeoriver systems. I am very grateful to the landowners for allowing us access to their properties for sampling. Their support, enthusiasm and advice are much vii appreciated. Hilda and Doempie Swartz are thanked for providing a base during field trips. Your hospitality is sincerely appreciated. James Merron, Wilbert Kadye, Ernst Swartz and Gavin Gouws assisted for long periods of time during my field surveys. These surveys would have not been possible if it were not for their dedicated support. I would also want to thank Dean Impson, Martine Jordaan, Tom Barry, Mpho Ramoejane, Kit Magellan and Steven Lowe for providing ad hoc assistance with fieldwork. Roger Bills and Olaf Weyl are thanked for some of their field equipment that was used during this study. Further assistance was provided by Unathi Lwana (preparing of DNA tubes), Bafo Konqobe and Vuyani Hanisi (preparing of formalin and ethanol), Willem Coetzer, Sherwyn Mack and Gamuchirai Chakona (help with GIS). I am very grateful to Poogendri Reddy for her assistance, guidance, patience and willingness to help with troubleshooting during my laboratory work. Paul Skelton, Ofer Gon, Monica Mwale, Alan Whitfield, Wilbert Kadye, Mpho Ramoejane, Thabo Maake, Tshoanelo Moloi, Amos Chinomona and Nicodemus Mautsa are thanked for the fruitful discussions about my research. I thank my family, especially my parents, Assumpta and Runesu Chakona, for giving me all the necessary support from my childhood, and for giving me the freedom to pursue my dreams. I am very thankful to my wife, Gamuchirai, for the love and constant support throughout this study. Finally, my daughter, Rutendo, has been such a great inspiration! viii Research outputs Peer reviewed articles Chakona, A., Swartz, E. & Magellan, K. (2011). Aerial exposure tolerance of a newly discovered galaxiid fish. Journal of Fish Biology 78, 912–922. Conference presentations Chakona, A., Gouws, G., Swartz, E. & Bloomer, P. (2011). Vicariance or dispersal: does the distribution pattern of Galaxias ‘nebula’ conform to previous biogeographic hypotheses? (Abstract and oral presentation). 9th SASSB Conference (19-21 January 2011, Rhodes University, Grahamstown. Chakona, A., Swartz, E., Gouws, G. & Bloomer, P. (2009). Genetic differentiation of a widespread Galaxias lineage across currently isolated river systems (Abstract and oral presentation). 10th Anniversary Conference, Southern Africa Society for Systematic Biology, 25-27 July 2009, Natalia, Illovo Beach, KwaZulu-Natal, South Africa. Popular articles and newsletters Chakona, A. (2010). Biodiversity field work in the Cape Floristic Region: Experiences and lessons learned from the Breede River expedition of 2008 to 2009 (Newsletter article). South African Biosystematics Initiative students’ newsletter, March 2010. Chakona, A. (2010). Genetic diversity and habitat requirements of native fish in the Cape Floristic Region. South African Institute for Aquatic Biodiversity (SAIAB) research