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 INFLUENCE OF HYDRAULICS, HYDROLOGY AND TEMPERATURE ON THE DISTRIBUTION, HABITAT USE AND RECRUITMENT OF THREATENED CYPRINIDS IN A WESTERN CAPE RIVER, SOUTH AFRICA Bruce Randall Paxton Town Submitted in fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY In the Department of Zoology UNIVERSITY OF CAPECape TOWN Capeof Town October 2008 University Supervisors Dr. Jackie King (Freshwater Research Unit, UCT) Dr. Jim Cambray (Albany Museum) Town Cape of University THE INFLUENCE OF HYDRAULICS, HYDROLOGY AND TEMPERATURE ON THE DISTRIBUTION, HABITAT USE AND RECRUITMENT OF THREATENED CYPRINIDS IN A WESTERN CAPE RIVER, SOUTH AFRICA Bruce Randall Paxton October 2008 ABSTRACT This study aims to explore the relationships between river flow and fish ecology in the context of the riverscape model of river ecosystems by examining the seasonal distribution of two endangered fish species, i.e. the Clanwilliam yellowfish and Clanwilliam sawfin, in relation to their physical (structural) and hydraulic habitat requirements at several scales, and to assess the importance temporal changes in flow and temperature in relation to the timing of key life history events and recruitment. From these findings it aims to recommend water management strategies to ensure the persistence of remaining populations, as well as to suggest a way forward for fish habitat studies in South Africa. The study was conducted on the Driehoeks River, a tributary of the Doring River system, which rises in the Cederberg mountains of the Western Cape, South Africa. A 5.9 km segment of this river was selected for the study. Town Seasonal variations in the relative abundances and distribution of larval, juvenile and adult sawfin along the longitudinal profile of the study segment were investigated prior to, during and after the spring spawning period (November to January) and these variations were interrogated in terms of the spatial arrangement of physical habitat units within the segment. Dive surveys servedCape to identify the location and extent of critical reproductive and nursery habitats, as well as to characterise the dispersal and/or movement of larval and juvenile fish to nursery habitats following the spawningof season. Habitat Suitability Criteria (HSC) were used to describe the hydraulic (velocity and depth) as well as substratum habitat use by Clanwilliam yellowfish and sawfin. The study included habitats deemed most limiting to fish production, i.e. those used for foraging, early life stages and reproduction. The suitability of a two-dimensional hydraulic modelling programme (River2D) for simulating habitat of the Clanwilliam yellowfish and sawfin was investigated. HSC derived for Clanwilliam yellowfish and sawfin were combined with the simulated depthsUniversity and velocities generated by River2D and measured substratum particle sizes to produce Combined Suitability Indices (CSIs). To evaluate the consequences of alternative flows on habitat availability, Weighted Usable Area (WUA) – an aggregate of the product of the CSI at each node in the model and the area associated with that node (CSI × surface area) – was then calculated for each species and life stage and for each site over a range of discharges. To test the ability of River2D to accurately predict microposition choice by yellowfish and sawfin, the correspondence between observed fish positions and the spatial distribution of the simulated habitat suitabilities was investigated. The rate of daily increment deposition on otoliths was validated using known-age larvae reared under laboratory conditions and the early development stages of sawfin eggs and larvae were recorded. Age-length relationships for larval and early juvenile sawfin were then established from wild-caught fish. Younger fish could be aged more accurately than older fish (>20 days) since increment spacing was more compressed in older fish. The results of the aging study were used to investigate the influence of environmental conditions, particularly flow and water temperature on the spawning and recruitment patterns of sawfin in the Driehoeks River. This was achieved by back-calculating spawning dates using the age-length models developed in the aging study of random samples of fish collected from the Driehoeks River towards the end of the low-flow season in two consecutive years. Since Clanwilliam yellowfish did not spawn over the study period, it was not possible to include them in the study. The principle findings were that sawfin require access to a broad range of critical habitat units in a river to complete the different stages of their life cycle. Although sawfin used deeper habitats (> 1.2 m) throughout the year, faster-flowing, shallower habitats (< 1.2 m) were only occupied by fish over the spawning period (November to January). It was established that sawfin are non-guarding, open substratum, lithophilic spawners, selecting riffles and runs with loosely embedded cobble substrata, shallower water (0.13-0.36 m). Current speeds measured in spawning habitats were the highest recorded for this species (0.3-0.8 m s-1). Large differences in habitat use were found between larval, juvenile and adult fish. Sawfin larvae and juveniles lay down increments on their otoliths at a rate of one per day, and the first visible increment is laid down approximately two days post-fertilisation, or upon hatching. Once they hatch larvae attach themselves to the substratum by means of an adhesive pad. Swim-up occurs after a period of 10-13 days when they are washed into downstream slackwaters. Sawfin spawned over a period of roughly 100 days between November and January. Peak recruitment events were associated withTown temperature of ~19 °C and continuously rising temperatures over seven days or more. The HSC derived in this study were compared with Flow Classes currently used to describe fish habitat in South Africa. Several points emerged from this comparison:Cape (1) both sawfin and yellowfish use a much smaller subset of the habitat defined by each Flow Class; (2) there are considerable differences between life- stages as well as differences between behaviours (e.g.of feeding vs spawning) and (3) connectivity between habitat patches is an important consideration. Flow Classes provide a useful alternative to HSC where these are not available. The risk of applying Flow Classes arbitrarily, however, is that habitat may not be perceived by a fish species in exactly the same way leading to reduced availability or elimination of certain critical categories of habitat. There was a discrepancy between the discharges required for optimal spawning habitat as predicted by River2D and the conditions under which the sawfin actually spawned as suggested by spawning-date distributions. These differences serve to highlight the limitations of hydraulic habitat modelling and the value ofUniversity hydrological information for identifying flows of ecological importance. An over- reliance on instantaneous measures of habitat is therefore not advised. By examining the seasonal distribution of sawfin in relation to key habitat units and at a range of scales, as well as the timing of life history events in relation to flow and temperature conditions, this study successfully demonstrates that sawfin depend on certain key components of the annual flow and temperature regime and access to a range different habitats through the year – definable at a range of scales – for their successful reproduction and recruitment. The usefulness and importance of placing flow-ecology relationships in the riverscape context is thereby reinforced. Town This thesis is dedicated to my parents Leith and Lynette Paxton whose support and encouragement through my studies has made this all possible Cape of University Town Cape of University ACKNOWLEDGEMENTS A special thank you to Dr. Jackie King my mentor and supervisor for her faith in my abilities and for her steadfast support of my research career. Thank you to Mr. Ben Jacoby and Mr. Western Barwise (Pinelands High School 1986) who planted the seeds of a passion for science and the natural world. Thank you also to Dr. Jim Cambray (co-supervisor) for dispensing freely of his knowledge, experience, and on occasion manpower, particularly with regards to early life history studies. The contribution of a number of individuals and organisations is also gratefully acknowledged: Dr. Steve Mitchell (South African Water Research Commission) for his unwavering support of the research reported on in this document; The success of the hydraulic models were principally due to Mr. Peter Hirschowitz’s diligence, attention to detail and patience. Dr. Angelina Jordanova (Golders Associates Africa) gave generously of her inexhaustible energy, time and expertise to the topographic survey work. Thank you to Frans Mouski and Louwtjie de Wet (Department of Water Affairs and Forestry, Western Cape) for their willingness to contribute to this research by providing the labour to install the stage logger on the Driehoeks River. The following people contributed significant theoretical and technical expertise to the study: Dr Jackie King (University of Cape Town); Dr.