BIOGEOGRAPHY AND COMMUNITY STRUCTURE OF FISHES IN SOUTH AFRICAN ESTUARIES A thesis submitted in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY of RHODES UNIVERSITY by TREVOR DAVID HARRISON February 2003 i ABSTRACT The biogeography and community structure of the fishes of South African estuaries was investigated. In all, 109 systems were examined representing two broad types: temporarily closed and permanently open estuaries. Multivariate analyses of the fish communities identified three biogeographic regions. A cool-temperate region extended along the west and southwest coasts; a warm- temperate zone stretched along the south, southeast and east coasts and a subtropical region occurred along the east coast. The boundaries of these biogeographic regions were also delineated. The general physico-chemical characteristics of the estuaries within the three biogeographic regions also reflected regional differences in climate, rainfall and ocean conditions. Estuarine temperatures followed the trend for marine coastal waters, decreasing from subtropical estuaries toward cool-temperate systems. The low rainfall and runoff in the warm-temperate region together with high evaporation rates and strong seawater input resulted in higher salinities in these estuaries. These factors also accounted for the predominantly clearer waters in warm-temperate estuaries. The estuaries in the three biogeographic regions were also shown to contain somewhat distinctive fish assemblages. Temperature and salinity appeared to be the two main factors affecting the distribution and abundance of fishes in South African estuaries. Subtropical systems were characterised by fishes mostly of tropical origin as well as certain south coast endemic species. Warm-temperate estuaries were dominated by endemic taxa with some tropical species also present. The fish fauna of cool- temperate estuaries mostly comprised south coast endemic species with cosmopolitan and temperate taxa also present. Certain functional components of the ichthyofauna also exhibited slight differences between regions. Freshwater fishes were a major component of closed subtropical estuaries while estuarine resident species were more abundant in warm-temperate estuaries. Overall, estuarine-dependent marine species dominated the fish fauna of the estuaries in all biogeographic regions, signifying that South African estuaries perform ii a vital nursery function for this group of fishes. Slight differences were also apparent in the trophic structure of the fishes; these were related to environmental differences between regions. Zooplanktivores and fishes that feed on aquatic macrophytes/invertebrates assumed a relatively higher importance in warm-temperate systems. Overall, detritivores dominated the estuarine fish fauna in all regions, indicating that detritus forms the main energy source in South African estuaries. iii ACKNOWLEDGEMENTS I am grateful to the South African Department of Environmental Affairs and Tourism, for funding the project that generated the data for this research. I am also grateful to the Division of Water, Environment and Forestry Technology (Environmentek), CSIR, for its support throughout this project. Thanks are also due to the various national and regional conservation authorities for permission to sample the estuaries and for logistical assistance. A study of this scale would be impossible without the assistance of those who volunteered (or were volunteered) to help with field sampling. The fieldwork alone took over six years to complete, often under very demanding conditions. For their assistance, I would like to extend my sincere thanks to John Allen, Jerome Andrew, Iain Bickerton, Alan Blair, Keith Blair, Andrew Cooper, Paul Cowley, Sean Fennessey, Tim Maera, Darrel Matodes, Stuart McLeod, Emile Plumstead, Arjoon Singh, Heath Thorpe, Mike Webster and Alan Whitfield. For help in the laboratory, thanks are due to Iain Bickerton, Alan Blair, Michelle Binedell, Eve Boettiger, Basil Clarke, Allan Connell, Roland David, Sean Fennessey, Jason Gessner, Sabelo Gumede, Bruce Mann, Shamilla Pillay, Leslie Power, Liz Simpson, Murray Simpson, Arjoon Singh, Avendhra Singh, Natasha Stoltz, Heath Thorpe, William Underwood, and Mark Zunckel. I am also grateful to Dr Phil Heemstra from the South African Institute for Aquatic Biodiversity (formerly JLB Smith Institute of Ichthyology) for assistance in the identification and verification of fish specimens. Thanks are due to Dr Bob Clarke and Dr Richard Warwick from the Plymouth Marine Laboratory for their help in the multivariate analyses using PRIMER. I am also grateful to Professor Sarah Radloff, Rhodes University for her assistance in some of the statistical analyses. A special thanks is extended to Arjoon Singh for generating the maps and figures. Thanks are also due to Iain Bickerton, Allan Connell, Andrew Cooper, Sean Fennessey, Bruce Mann, David Marshall and Alan Whitfield, for their contribution iv through various discussions and helpful suggestions. I am also grateful to my supervisors, Professor Peter Britz and Dr Alan Whitfield for their helpful comments and suggestions. I am particularly indebted to Alan Whitfield for his constant support and encouragement throughout this study. I would also like to extend a special thanks to Andrew Cooper and Alan Ramm for their support. A special thanks is also extended all my friends and family, especially my parents for all their support throughout my studies. Finally, to my wife Eve, for all her love, support, patience and understanding right the way through. v CONTENTS Title Page i Abstract ii Acknowledgements iv Contents vi Chapter 1 General Introduction 1 Chapter 2 Study Area 4 2.1 Climate and Rainfall 4 2.2 Ocean Currents 6 Chapter 3 General Materials and Methods 8 3.1 Field Methods 8 3.1.1 Ichthyofauna 8 3.1.2 Physico-chemical 11 3.2 Laboratory Methods 11 3.3 Data Analyses 11 3.3.1 Estuary classification 11 3.3.2 Sampling effort 13 3.3.3 Ichthyofauna 14 Chapter 4 Biogeography 16 4.1 Introduction 16 4.2 Materials & Methods 20 4.2.1 Species richness and distribution 20 4.2.2 Multivariate analyses 20 4.3 Results 25 4.3.1 Species richness and distribution 25 4.3.1.1 Closed estuaries 25 4.3.1.2 Open estuaries 28 4.3.2. Multivariate analyses 31 4.3.2.1 Closed estuaries 31 4.3.2.2 Open estuaries 35 4.4 Discussion 39 4.4.1 Species richness and distribution 39 4.4.2 Multivariate analyses 46 4.4.3 General 47 4.5 Summary and Conclusions 52 Chapter 5 Physico-chemical Characteristics 53 5.1 Introduction 53 5.2 Materials & Methods 53 5.2.1 Physico-chemical characteristics 56 5.2.2 Multivariate analysis 56 5.3 Results 57 5.3.1 Closed estuaries 57 5.3.1.1 Physico-chemical characteristics 57 5.3.1.2 Multivariate analysis 61 5.3.2 Open estuaries 63 5.3.2.1 Physico-chemical characteristics 63 5.3.2.2 Multivariate analysis 65 5.4 Discussion 67 vi 5.4.1 Closed estuaries 67 5.4.2 Open estuaries 76 5.4.3 General 87 5.5 Summary and Conclusions 92 Chapter 6 Species Composition 93 6.1 Introduction 93 6.2 Materials & Methods 93 6.2.1 Species composition 93 6.2.2 Inter-regional comparisons 94 6.2.3 Physico-chemical relationships 94 6.3 Results 95 6.3.1 Closed estuaries 95 6.3.1.1 Species composition 95 6.3.1.2 Inter-regional comparisons 100 6.3.1.3 Physico-chemical relationships 102 6.3.2 Open estuaries 104 6.3.2.1 Species composition 104 6.3.2.2 Inter-regional comparisons 113 6.3.2.3 Physico-chemical relationships 115 6.4 Discussion 118 6.4.1 Closed estuaries 118 6.4.1.1 Cool-temperate estuaries 118 6.4.1.2 Warm-temperate estuaries 118 6.4.1.3 Subtropical estuaries 119 6.4.2 Open estuaries 120 6.4.2.1 Cool-temperate estuaries 120 6.4.2.2 Warm-temperate estuaries 121 6.4.2.3 Subtropical estuaries 124 6.4.3 Physico-chemical relationships 125 6.4.4 General 129 6.5 Summary and Conclusions 133 Chapter 7 Estuary-Association Analysis 135 7.1 Introduction 135 7.2 Materials & Methods 136 7.2.1 Estuary-associations 136 7.2.2 Multivariate analyses 138 7.3 Results 138 7.3.1 Closed estuaries 138 7.3.1.1 Cool-temperate estuaries 138 7.3.1.2 Warm-temperate estuaries 139 7.3.1.3 Subtropical estuaries 141 7.3.1.4 Multivariate analyses 142 7.3.2 Open estuaries 144 7.3.2.1 Cool-temperate estuaries 144 7.3.2.2 Warm-temperate estuaries 145 7.3.2.3 Subtropical estuaries 146 7.3.2.4 Multivariate analyses 147 7.4 Discussion 149 7.4.1 Cool-temperate estuaries 149 7.4.1.1 Closed estuaries 149 vii 7.4.1.2 Open estuaries 150 7.4.2 Warm-temperate estuaries 151 7.4.2.1 Closed estuaries 151 7.4.2.2 Open estuaries 152 7.4.3 Subtropical estuaries 155 7.4.3.1 Closed estuaries 155 7.4.3.2 Open estuaries 156 7.4.4 General 157 7.5 Summary and Conclusions 164 Chapter 8 Trophic Composition 167 8.1 Introduction 167 8.2 Materials & Methods 168 8.2.1 Trophic composition 168 8.2.2 Multivariate analyses 168 8.3 Results 169 8.3.1 Closed estuaries 169 8.3.1.1 Cool-temperate estuaries 169 8.3.1.2 Warm-temperate estuaries 169 8.3.1.3 Subtropical estuaries 170 8.3.1.4 Multivariate analyses 171 8.3.2 Open estuaries 173 8.3.2.1 Cool-temperate estuaries 173 8.3.2.2 Warm-temperate estuaries 174 8.3.2.3 Subtropical estuaries 175 8.3.2.4 Multivariate analyses 175 8.4 Discussion 177 8.4.1 Cool-temperate estuaries 177 8.4.1.1 Closed estuaries 177 8.4.1.2 Open estuaries 178 8.4.2 Warm-temperate estuaries 179 8.4.2.1 Closed estuaries 179 8.4.2.2 Open estuaries 181 8.4.3 Subtropical estuaries 184 8.4.3.1 Closed estuaries 184 8.4.3.2 Open estuaries 185 8.4.4 General 186 8.5 Summary and Conclusions 192 Chapter 9 General Synthesis 195 9.1 Biogeography 195 9.2 Physico-chemical Characteristics 196 9.3 Species Composition 198 9.4 Estuary-Associations 200 9.5 Trophic Composition 202 9.6 Conclusion 203 Chapter 10 References 205 Appendix 219 viii CHAPTER 1 GENERAL INTRODUCTION The Southern African coast spans a number of climatic zones from humid, predominantly summer rainfall conditions in the east and northeast, to a Mediterranean climate in the south and southwest, to arid conditions in the northwest (Tinley, 1985).