Includes bibliographical references (p. 207-227) / Currently heavy fishing is recognized as one of the major threats to the structural and functional organization of marine ecosystems in many coastal nations. The threat is mainly the result of the inherent nature of the various fishing activities: size selectivity, habitat destruction, biomass removal, and uncertainty in resource status and management of the resource. Thus this thesis investigates structural changes that result from fishing. This thesis aims to answer whether there were changes in the structure of fish communities off the of South Africa using two case studies, to explore the response of fish communities to the proposed creation of Marine Protected Areas and to investigate the alternate application of spatially uniform and heterogeneous fishing mortalities. The research questions of the thesis are answered through empirical analysis of landing data for the line fishery and analysis of demersal trawl survey data from the south coast of South Africa, and analysis of output of the Individual Based Model OSMOSE applied to the southern Benguela. Structural changes in the landings from the line fishery and south coast survey data are assessed using a variety of ecosystem indicators believed to capture such changes: size-based indicators {mean size, slope and height of the size spectra, mean Lmax7, proportion of size classes), species-based indicators (ordination by multidimensional scaling, and dendrograms, various diversity indices, dominance curves). Inferences are based on the reference directions of the indicators, according to the expected response of indicators to heavy fishing. Structural changes in the fish communities are observed, over the spatial and temporal bounds of the two case studies, to be the most likely cause of the observed changes is heavy fishing, although the influence of environmental factors cannot he ruled out. investigation of alternative implementation fishing mortality using the simulation model OSMOSE showed that the system and species biomass do differ between the two implementations, but the variability in the system remains the same. The modelled response of fish communities to the introduction of Marine Protected Areas is an overall increase in relative biomass of large predatory fishes and a decline in the biomass of prey and competitor species.

Includes bibliographical references / Animals at Marion Island can be affected by logistic disturbance (especially helicopter noise), incidental pedestrian disturbance and research disturbance. The responses of wandering albatrosses (Diomedea exulans) and king penguins (Aptenodytes patagonicus) were investigated through standardised pedestrian approaches. Intensity of behavioural responses and levels of prolactin (females only) indicated that adult wandering albatrosses had become sensitised by high levels of chronic disturbance. Responses were greatest during the Prospecting and Early Incubation phases. Frequency of disturbance did not influence behavioural responses, but birds visited most often over three consecutive days had the lowest chick survival. Guarding king penguins were less likely to move away during disturbance than non-breeding groups. Visit duration and approach distance affected behavioural responses. There was evidence of habituation by king penguins to current levels of incidental disturbance. Grey-headed albatross (Thalassarche chrysostoma) adults and chicks showed short-term behavioural responses to research disturbance, and recovery times were variable. Level of chronic disturbance did not explain breeding success differences between colony sections. Instantaneous scans or counts of guarding and brooding gentoo penguins (Pygoscelis papua), incubating Crozet shags (Phalacrocoraxmelanogenis), pre-fledging grey-headed albatross chicks and non-breeding king penguins were made before and during helicopter operations.

Includes abstract. / This thesis presents an examination of the relationship between floods as disturbances, the disturbance regime and the temporal dynamics of invertebrate assemblages, over the short term and at intra- and inter-annual time scales in the Molenaars and Berg Rivers in the Western Cape of South Africa. Invertebrate responses to individual floods were investigated by a field study that links the displacement of river-bed stones by a flood to change in invertebrate densities and community and population structure from before to after flood events. The magnitude of the hydraulic force acting on each marked stone during the peak of each flood was also calculated, providing a second measure of physical disturbance. Multivariate analyses of similarity, hierarchical clustering and multidimensional scaling were used for analysis of invertebrate patterns before and after floods. Size frequency data for 28 species or genera were analysed to explore changes in population structure over the flood season. Flood records were developed from the daily discharge hydrological record of both study rivers collected by the South African Department of Water Affairs and Forestry. Flood frequency analysis and descriptive statistics were combined with graphical methods to describe the flood regime and to test flood predictability in these rivers. Quantitative monthly samples of invertebrates from the Molenaars River collected over 17 months were used together with a further 2 ½ years of semi-quantitative monthly data, to identify intra- and inter-annual patterns in communities. Multivariate analysis of community patterns was combined with a range of indices that reflect community persistence and stability over periods longer than one generation. Population dynamics of the common species were also studied. Life history attributes, specifically seasonality of life cycle stages and generation time, were explored using size frequency data from the samples.

Includes bibliographical references. / Freshwater fishes are among the most threatened taxa in the world. Increasing demand for freshwater, habitat degradation and the introduction of non-native species, will continue to place pressure on the remaining native freshwater fishes. A meta-analysis estimated that more than 90% of river habitat in three major catchments has been invaded by non-native fish and that catchments covering less than 1% of Cape Floristic Region have no recorded non-native fish introductions, the major rivers containing 10 or more non-native species. The majority of the native fishes continue to be threatened by the presence of non-native fish.

It is the intention of this thesis to bring together the existing scattered data concerning the Amphipoda of southern Africa, to add records from unidentified collections and to present the whole in a form that will provide a firm basis for future work in this field. The collections examine d are principally those of the University of Cape Town, the South African Museum and the National Institute for Water Research. These collections are together much larger than any previously reported from southern Africa (in excess of 90 000 specimens from several thousand stations). Findings are presented in a series of five regional papers. Each paper includes brief descriptions of principal collecting areas and their faunas and an analysis of species collected. Station data, references and distributions are provided for all species, while a short diagnosis is given with the first reference to each species. A total of 299 gammaridean and caprellid species is recognised. One family (Temnophliidae), four genera (Chaka, Cunicus, Dikwa, Janice) and 39 species are described as new to science; while 21 others are recorded from southern Africa for the first time. Nine existing species are relegated as synonyms. Following the five regional taxonomic papers, a synoptic guide to the benthic amphipods of the region is provided. This is intended to provide the non-specialist with a means of identifying his own material. A brief guide to methods of collection, storage and examination is provided and is followed by comprehensive fully illustrated keys to the families, genera and species of gammaridean and caprellid Amphipoda recorded from Africa south of 20 degree S, 0-1000m. The figures cover virtually all species, including many never before illustrated and will hopefully reduce the need for exhaustive knowledge of morphological nomenclature, or of extensive reference facilities, before identifications can be made. An appendix provides reference to more detailed descriptions of each species, gives their distributions world-wide and within southern Africa, and lists common synonyms. A concluding chapter discusses modes of dispersal of amphipods and possible origins of the southern African fauna. The region can apparently be divided into tropical, subtropical and temperate provinces, the first two dominantly populated by species of tropical origins and the third rich in endemic forms. This pattern is paralleled in other groups such as the polychaeta. It is concluded that although southern Africa is rich in endemic species and genera it is not a centre for the evolution of major taxa but rather an evolutionary outpost where immigrant forms have evolved under reduced pressure.

The Eerste River is situated in the south-western Cape Province, South Africa. Its upper reaches have a stony substratum, and can be divided into three physical/biotic zones: The Mountain Stream, Upper River and Lower River zones. Investigations of the abundance, biomass, species diversity and species composition of the benthic macro-invertebrates in the three zones were carried out in 1975/76. Spatial and temporal changes in these factors can be correlated with changes in the physico-chemical quality of the water. Abundance and biomass generally increased downstream, but were low below a dam construction-site, because of the blanketing effects of silt on the substratum. Seasonal changes in abundance and biomass differed in the three zones, but always included a peak in spring. The highest values of both were in the Lower River in summer, reflecting the build-up of organic pollutants there during times of low flow. Diversity of the Ephemeroptera, which was felt to be representative of a change in.diversity of the fauna as a whole, generally decreased downstream, with a major drop at the town of Stellenbosch, and another at a sewage-farm outfall. A misleading increase in diversity occurred, however, in the silt-laden waters below the dam site,. due to the fleeting occurrence of individuals of several different species. Composition of the fauna was typical of local rivers with mountain sources. Figures for abundance, biomass and calorific values of species are given in appendices

The globally Near-threatened Damara Tern Sterna balaenarum is little known and faces several conservation issues. The aim of this study was to provide a description of the ecology and numbers of the species and discuss conservation management plans that will effectively ensure its survival.

Includes abstract. / Includes bibliographical references (leaves 336-353). / The broad aims of this research, following the establishment of a firm taxonomic base for the southern African Notonemouridae, were to investigate species boundaries and to infer phylogenetic relationships in the Aphanicerca capensis Tillyard species complex using morphological, behavioural and molecular data (mtDNA), and to model historical biogeographic patterns and drivers of cladogenesis. Additionalaims included an evaluation of the cytochrome oxidase subunit I gene as a molecular barcode in the Notonemouridae, a test of the monophyly of the genera, the construction of a phylogeny for the southern African Notonemouridae and the identification of clade synapomorphies.

Includes bibliographical references (p. 209-274). / The biogeography and ecology of benthic shallow subtidal reef communities in the western Indian Ocean is poorly known, particularly in north-eastern South Africa and southern Mozambique. This thesis uses quantitative information to resolve biogeographic patterns, define reef community types, elucidate potential abiotic determinants of community composition, and evaluate whether subsidies of riverine-derived particulate organic matter (POM) support filter-feeder biomass and drive biogeographic patterns. A large-scale biogeographic analysis was conducted using quantitative biomass data derived from 55 shallow subtidal reefs spanning five countries in the western Indian Ocean. Two statistically distinct marine provinces, Tropical Indo-West Pacific and Subtropical Natal, were recognised by differences in community composition and separated by a biogeographic break in the vicinity of Cape Vidal, South Africa. The biogeographic break took the form of a transitional or overlap area corresponding in location to the Delagoa Bioregion, one of three bioregions also revealed by post-hoc analyses. Significant differences in total average biomass and trophic structure were evident among bioregions, with a number of inter-bioregional trends in trophic groups being apparent. In total, 12 reef community types were recognised, based on similarity profile permutation tests. Most reefs in the Subtropical Natal Bioregion were dominated by a community type characterised by a high biomass of the filter-feeding ascidian Pyura stolonifera and various species of articulated coralline algae. In the Delagoa Overlap Bioregion, a comparatively high diversity of community types was defined, many dominated by algal turf, P. stoloniferaand various Alcyonacea and Scleractinia. Further north, P. stolonifera diminished and the contributions of Scleractinia, especially Porites spp., Pocilloporaspp. and Galaxea spp. increased. Many of these community types are not represented within protected area networks, particularly those in southern Mozambique. When the biomass data were correlated with nine abiotic variables, likely determinants of community composition emerged at both inter- and intra-regional scales. Sea surface temperature, significant wave height, chlorophyll-a and suspended inorganic sediment were the variables highly correlated with community composition and therefore most likely to drive biogeographic differences. Within each bioregion, different sets of abiotic variables were found to be important in driving community differences among sites, including turbidity, chlorophyll-a, reef susceptibility to sand inundation, reef heterogeneity and sea surface temperature. Striking differences in the oceanographic conditions of bioregions were evident, especially between Subtropical Natal and Delagoa Overlap bioregions. In particular, the strong influence of wave height emerged as a novel and unexpected correlate at a biogeographic scale. These differences initiated a trophic study conducted in the Subtropical Natal Bioregion, aimed at determining the importance of riverine-derived POM subsidies in supporting the high filter-feeder biomass in this bioregion. Using carbon, nitrogen and sulphur isotopes and a three-source Bayesian mixing model to calculate proportional contributions, I determined that marine-derived POM formed the bulk of the diets of four species of filter-feeders, but the assimilation of riverine-derived POM was nevertheless notable, ranging from 8 to 33 %. I concluded that riverine POM is likely to play an important but secondary role to factors such as increased levels of turbidity and productivity in explaining the high filter-feeder biomass in the Subtropical Natal Bioregion. These findings provide the first evidence of riverine-inshore-pelagic coupling in filterfeeder communities in this bioregion, and throw light on the factors linked to large-scale biogeographic patterns.

The phylogenetics and biogeography of the following four groups of unrelated terrestrial non-passerine birds, that have endemics in both the south-west and north-east arid-zone lowlands (and Sahel), and which also encompass taxa with differing habitat tolerances, mobility and life-history traits, were examined: the bustards (Otididae), sandgrouse (Pteroclidae), coursers (Glareolidae) and Stone Partridge (Ptilopachus). Another aim of this research is to use insights from the evolutionary relationships of these families to assess the current state of their taxonomy, as well as to assess character evolution and other life history attributes (including evolution of their mating systems).