Thesis (M.S.)--University of North Carolina at Wilmington, 2005. / Includes bibliographical references (leaves: [74]-79)

Thesis (M.Sc. (Ichthyology & Fisheries Science)) - Rhodes University, 2009.

Thesis (Ph.D.)--University of Wollongong, 2009. / Typescript. Includes bibliographical references: leaf 146-171.

Thesis (M.S.)--University of California, Santa Cruz, 2001. / Typescript. Includes bibliographical references (leaves 69-72).

Thesis (Ph. D.)--University of California, Los Angeles, 2003. / Vita. Includes bibliographical references (leaves 120-136).

Thesis (Ph. D.)--College of William and Mary. / Vita. Includes bibliographical references. Also available online.

Phylogeographic patterns of coastal organisms with different life histories and breeding strategies may reveal patterns not consistent with the current delineation of the biogeographic provinces around South Africa. The subdivision of the South African coastline into these three main climatological or biogeographic regions: namely the cool temperate west coast, the warm temperate south coast and the subtropical east coast, is based on average seawater temperatures and hydrological conditions. Genealogies of two estuarine fish species Atherina breviceps, a marine breeder, and Gilchristella aestuaria, an estuarine spawner, were reconstructed using mitochondrial DNA (mtDNA) control region sequences. The study comprised two components, an assessment of a small dataset of both fish species to compare their population structure along the South African coastline and a more comprehensive investigation of the phylogeography of G. aestuaria collected from 21 estuaries around the coast. The comparative study of A. breviceps and G. aestuaria indicate different population distribution patterns along the South African coastline. Results of the A. breviceps analysis demonstrate substantial gene flow due to the random mixing of alleles, while the comparative G. aestuaria dataset indicates a more structured population and considerably less gene flow. The G. aestuaria population demonstrates geographic separation into four groups, namely the west coast (Great Berg), Bot (south coast), Seekoei (south coast) and east coast (Bushmans, Kasouga and Cefane). Results from the larger G. aestuaria dataset indicate that the phylogeographic patterns observed during this study do not conform to existing biogeographic boundaries along the southern African coastline. The delineation identified during this study between the warm temperate and subtropical regions is further south than originally perceived and this southward extension can be ascribed to the prevailing hydrology. The life history patterns and ecology of these two estuarine fish species appears key to understanding their population structure. These factors interact with environmental characteristics such as physical oceanography and the distribution of estuaries (along the coastline) to explain the observed distribution patterns and population structure of A. breviceps and G. aestuaria.

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 warmtemperate 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 cooltemperate 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 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.

From Introduction: Energy passes through an ecosystem via a multiplicity of interconnected routes, which can be broadly categorised into trophic and detrital pathways. The "metabolic activity" of most lakes will be governed predcminantly at the base of these two routes; namely, the primary producer and decanposer levels, respectively (Wetzel and Allen, 1972). The importance of the littoral primary producers (especially the aquatic macrophytes) in the functioning of the Swartvlei ecosystem has been emphasised in a comprehensive report by Howard-Williams and Allanson (1978) dealing with the lake system fran 1975 to 1978. They noted that although the littoral shelf (<2m below low water level) occupies only 43% of the lake's surface area it contributed 64% of the total annual primary production during the period investigated. This was largely due to the dense Potamogeton pectinatus stands which alone accounted for 52% of the total carbon input into the lake by plants. The fact that the production/biomass ratio for P. pectinatus was only 1,2:1 suggested that its importance as a primary producer in Swartvlei was largely due to its high bianass. (Biomass, or standing stock, is used in this report as defined by Waters (1977); namely, "the amount present at a point in time, expressed best as quantity per spatial unit".)

Early stage fishes, namely larvae and early juveniles, were collected from 12 estuaries and associated habitats in the warm temperate region of South Africa between July 1998 and December 2000. This study served to provide new information and expand on existing knowledge of early stage fish assemblages associated with various types of Eastern Cape estuaries. A total of 65 536 predominantly postflexion fish larvae were collected. Together with early juveniles, taxa comprised 72 species from 25 teleost fish families. Surf zones associated with two intermittently open estuaries showed that estuary-dependent marine species predominated in this zone. Early stage fishes responded positively during natural estuary opening events and concentrated along the estuary outflow plume, suggesting that cueing from estuary and/or river water may be taking place. A habitat study in the Swartkops Estuary, using light traps, showed that newly recruited larval fishes concentrated along the margins of the estuary and unlike their older juvenile counterparts, were poorly represented in eelgrass beds. A multi-estuary comparison, including seven permanently open and five intermittently open estuaries, indicated that early stage fish assemblages were more diverse than indicated by past investigations. Early stage fishes were also shown to concentrate in the mesohaline regions of these estuaries. Studies of estuaries with altered freshwater flow regimes were also included in the research. A regulated release of dam water in the euhaline Kromme Estuary failed to induce a cueing response from estuary-dependent marine fish larvae. This project showed that large amounts of freshwater are required to reverse the negative effects of river impoundments. The release study did show that estuary-resident fishes were sensitive to small natural pulses of freshwater and responded by spawning. However, excessive river supply through an inter-basin water transfer scheme was shown to have a flushing effect on the larvae and early juveniles of the estuary-resident Gilchristella aestuaria in the upper reaches of the Great Fish Estuary. This effect was evident in comparisons with the freshwater starved Kariega Estuary where concentrations of G. aestuaria, a species usually more abundant in freshwater rich estuaries, were considerably higher. This finding suggests that freshwater minima and maxima be considered when assessing and managing estuarine systems.