Includes abstract. / Includes bibliographical references. / At the root of this thesis was the Benguela Current Large Marine Ecosystem (BCLME) Programme’s project "Top Predators as Biological Indicators of Ecosystem Change in the BCLME" (LMR/EAF/03/02). The objectives of this project were to assess the utility of top predators as biological indicators of ecosystem change in the Benguela Current Ecosystem, and implement an appropriate, integrated, system-wide monitoring programme based on top predators, to support ecosystem-based management in the Benguela Current Ecosystem.

The fossil sites Swartkrans, Sterkfontein and Kromdraai are situated in close proximity, not more than three kilometres apart, in the Sterkfontein valley near Krugersdorp, Transvaal. Excavation at these sites has yielded abundant faunal remains, including hominids, as well as stone artefacts.For a comprehensive review of various aspects of these sites the reader is referred to Brain (1958). The many hundreds of cranial fragments, belonging to the mammalian family Bovidae Gray, from these assemblages, form the basis for this study.

Includes abstract. / Includes bibliographical references (leaves 115-126). / This thesis focuses on these raised concerns and attempts to refine the modelling approach used to test the WTH. This is achieved by investigating squid paralarval survival and their specific gravity using aquarium experiments together with an improved ocean model and IBM. The influence of temperature on yolk utilization was assessed through experimentation. Tank experiments found that yolk utilization rates in chokka squid paralarvae are directly affected by temperature with faster rates at high temperature and slower rates at low temperature.

Includes abstract. / Includes bibliographical references (leaves 157-175). / This study focused on the parasite assemblages of three catshark (Elasmobranchii: Scyliorhinidae) species: the dark shyshark, Haploblepharus pictus, the puffadder shyshark, H. edwardsii and the pyjama shark, Poroderma africanum, all endemic to Southern Africa. These sharks are found from Namibia to Agulhas (H. pictus), Cape Point to Northern KwaZulu-Natal (H. edwardsii) and St Helena Bay to KwaZulu-Natal (P. africanum), and reach maximum total lengths of 60, 60 and 105 cm respectively. Sharks were collected by SCUBA divers and rod and line fishing from four sites between Saldanha Bay and De Hoop Nature Reserve. Parasites from the skin, gills, body cavity, spleen, stomach and intestine were counted, removed, and fixed as appropriate.

Includes bibliographical references. / Most HIV vaccines currently in development aim to protect people from infection or disease by eliciting strong anti-HIV cytotoxic T lymphocyte (CTL) responses. Evolved evasion mutations that undermine host immune responses pose a major challenge to the development of such vaccines. Understanding the mechanisms that selectively favour the emergence of CTL evasion mutations in vivo and the impact of these mutations on both disease progression and long-term HIV evolution will not only contribute to our understanding of HIV pathogenesis, but will also inform vaccine design strategies. This study aimed at investigating CTL escape mutations in HIV-1 Gag and Nef, during the acute and early phases of infection and the impact of these mutations on subsequent disease progression in a cohort of recently HIV-1 subtype C infected females. Of 36 women recruited into the study within 12 weeks of infection (median 6 weeks) and followed for six months, 32 were infected with single viruses. Two participants were infected with epidemiologically unlinked viruses (dual infection), and in a further two individuals the viruses were highly divergent suggestive of dual infection and/or recombination. These individuals were excluded from further analysis as it was difficult to predict CTL escape due to high degrees of diversity between sequences. In the remaining 32 study participants, there was a high frequency of CTL escape with putative escape mutations identified in 21 of 32 individuals (66%). Twelve of these 21 (33%) harboured viruses which developed escape mutations in Gag, and 17 (53%) developed escape mutations in Nef. In the conserved structural protein, p24, potential reversion mutations were more frequent than potential escape mutations. During the first six months of infection whereas potential reversion mutations occurred at low entropy sites, potential escape mutations occurred at high entropy sites. Although there was no detectable association between the timing of escape mutations and disease progression, there was an association between the degree of deviation of the p24 sequence from the subtype-C population consensus (a measure of escape mutation load) and CD4+ counts. Analysis of the earliest sampled viruses from HLA-B*57/B*5801 negative study participants for viral genetic markers associated with disease progression identified two iv polymorphisms, A146X (n = 9) and T242N (n =6), that were associated with improved viral control. The polymorphisms are well-known escape mutations in HLAB* 57/B*5801 restricted epitopes. This suggested transmission of these variants from individuals carrying these alleles. Further evidence that viruses carrying the T242N and/or A146X mutations had been previously passaged through B*57/B*5801 positive individuals came from the fact that the observed T242N mutations reverted to wild type during follow-up. There was no significant change in viral load and CD4+ counts upon reversion of the T242N mutations. In vitro replication assays using chimeric viruses containing gag sequences from one of participants showed that the virus harbouring the T242N mutation was fitter than that carrying the reversion mutation. These viruses harboured other T242N associated compensatory mutations suggesting that these compensatory mutations may themselves carry a fitness cost in the absence of the T242N mutation. This suggests that there possibly exist networks of B*57/B*5801 associated mutations and that reversion of some of these mutations in isolation does not necessarily restore viral fitness. Lastly, the kinetics of CTL escape in HLA-B*5801 positive participants (n = 6) and the impact of escape on disease progression was investigated. CTL escape within B *5801 positive individuals was found to predominantly occur within the TW10 in Gag (n = 4) and KAF9 in Nef (n = 6) epitopes. The emergence of the T242N mutation in TW10 was always preceded by mutations elsewhere in the epitope and was associated with the occurrence of previously described compensatory mutation upstream of the epitope. The targeting of TW10 and the emergence of T242N escape mutations were associated with higher CD4+ counts at 12 months postinfection in the B*5801 positive individuals (p = 0.0231 and p = 0.0282, respectively). Independent of host HLA genotypes, the presence of the A146X and T242X mutations was associated with higher CD4+ counts (p = 0.0495). This study provides some useful insights into HIV-1 subtype C pathogenesis. The notion that CTL escape mutations do not invariably result in less fit viruses is evidenced by the observation that escape was not obviously associated with disease progression in this cohort, while escape mutations in the Gag p24 region within B*5801 positive individuals v in particular, was associated with improved viral control. There is therefore evidently a complex interaction between escape and compensatory mutations and further work is required to identify the impact of compensatory mutations on viral fitness. Overall, this study provides further evidence that vaccines need to elicit responses that specifically target the functionally constrained regions of the HIV proteome.

The study of the biology of the Cape Weaver Ploceus capensis was carried out mostly in the winter rainfall area of the S. W. Cape in South Africa. This report shows that the species has conspicuous plumage dimorphism and some physical dimorphism in the sexes, and that the male only achieves full plumage at about 22 months old. The female reproduces at one year of age. Possible reasons for this deferred maturity in the male are discussed. It is concluded that the high competition for mates and the advantage to the young male in nest-building and territorial activities on the periphery of the colony are the main pressures for deferred maturity. A detailed investigation of breeding seasons in the species is reported and it is shown how aspects of the clutch-size and incubation strategy are apparent adaptations to polygyny and its concomitant fluctuating food source. The ultimate and proximate factors influencing the breeding season are also discussed. This study presents the first comprehensive study of moult in passerines in southern Africa. The more important findings are that moult is slower than in the northern hemisphere and that there are differences in the start of moult in different age/ sex classes. The food situation in the Cape Weaver is reported and it is shown how the species is adapted to a wide variety of insect and vegetable foods. The chicks are fed almost entirely on insect food except towards the end of the season. Weight fluctuations throughout the year are small and it is suggested that this shows that food fluctuations are smaller and present a much less difficult situation for the passerine in South Africa than in the northern hemisphere. Evidence is presented which shows a sex ratio of 1 : 1 in nestlings though there are some interesting tendencies revealed in the data. In full-grown birds, there is a slight excess of males probably throughout the year. It is pointed out that this is the opposite to what would be "required" by a polygynous mating system. Contrary to general theories, it is proposed that males do not suffer higher mortality than females during the breeding season. In fact it is suggested that females suffer higher mortality both in and out of the breeding season, partly as a result of their subordinate social position in all circumstances except at the nest. The territorial and courtship behaviour of the Cape Weaver are described and it is shown how aspects of the behaviours vary according to the time in the season and the pair-bond circumstances. A social hierarchy study on the species is discussed. Finally, the special aspect of the study, the unusual polygynous mating system is investigated in detail. A possible evolutionary sequence for the development of polygyny in passerines is proposed. This stresses the importance of the type of food source and the development of coloniality or gregariousness as the primary prerequisite. A feature of the thesis is the attempt to keep the theme of the adaptations to polygyny in mind through all the studies of the other parts of the Cape Weaver's biology.

Bibliography: pages 243-268. / Cordylus giganteus is a large, terrestrial, viviparous lizard, endemic to the Highveld grasslands of South Africa. Its distribution is limited and its conservation status is vulnerable. Autopsy and mark-recapture methods were used to study the seasonal aspects of its reproductive cycle, diet, energy reserves, growth, population dynamics, daily activity and thermoregulation. Reproduction is distinctly seasonal in both sexes. Females may reproduce biennially. Vitellogenesis commenced in autumn (March), and continued through hibernation with ovulation in spring (October). Two or three young are born in autumn. A functional placenta is implicated. Seasonal steroid hormone profiles are presented. Males exhibit a postnuptial spermatogenetic cycle. Spermatogenesis commences in spring with peak spermiogenesis in autumn and testicular regression following in late autumn. Spermatozoa are stored in the epididymis and ductus deferens for seven to eight months. A bimodal plasma testosterone profile is reported, consistent with spermiogenesis in autumn and mating behaviour in spring. C. giganteus feeds during 8 months of the year and prefer Coleoptera as prey. Fat bodies are utilized for winter maintenance and reproduction. Hatchlings grow 20-30mm during the first year and maximum growth rates occur in summer. Males and females attain sexual maturity at about 165 mm SVL in the fourth year. Seasonal affects on growth rate resulted in poor fit by either logistic-by-length or von Bertalanffy models and a seasonal oscillating model was introduced. Adult males are smaller than females; head sizes are the same but allometric slopes differed significantly. Population size and structure remained stable in the study area. Densities ranged from 9 - 11 lizards/ha. The age structure is marked by the low relative abundance of juveniles. Survivorship during the first year varied among years. Mortality was highest during summer months rather than winter months. Average annual survival of adults 'was high, but varied with sex and years (ranged from 58%-80%). A life table yielded a net reproductive rate (Ro= 1) sufficient to sustain the population, if the reproductive life of an adult female is at least 12 years. Lizards remain in their burrows during winter. In summer, activity was bimodal on sunshine days but unimodal on cool overcast days. Body temperature is regulated by behavioural means (postural and orientation changes) and by shuttling to the cool burrow microclimate. The life history strategy corresponds partially to that of K-selection.

Aspects of the feeding strategies and digestive invertebrate-microbial interactions of two saltmarsh thalassinid detritivores, the mudprawn Upogebia africana (Ortmann) and the sandprawn Callianassa kraussi Stebbing were examined. Resources available in their respective habitats were investigated together with the feeding apparatus, diet and digestive enzymes necessary for hydrolysis of refractory compounds of detritus. U. africana inhabits the upper reaches of Langebaan lagoon (Geelbek),. while C. kraussi was sampled near the mouth (Oesterwal). Both species occur intertidally. Physical characteristics of sediment and water fluctuate more widely at Geelbek than at Oesterwal. Geelbek also has higher mud and clay content in the sediment, and greater particulate load in the water. The resources available in both sediment and water from Geelbek were of greater quality (assessed by proportion of living component, C:N ratio) and quantity. In terms of distribution ofthe resource, quality was highest in surface sediments, while quality was greatest at burrow linings. The mode of feeding, gut structure and diet of the two prawn species differ, although gut throughput rates are similar (ca. 6h). U. africana is a filter feeder which non-selectively ingests small particles which are further sorted in the modified filtertype gastric mill into larger particles which enter the midgut, and smaller particles which are channeled into the hepatopancreas. U. africana has a relatively large throughput gut (fore, mid, hind) allowing large meals to be taken. This may be related to its reliance on vascular plant detritus for both carbon and nitrogen requirements, as shown by stable isotope analyses. By contrast, C. kraussi feeds by a combination of deposit feeding and filter feeding.

Heterotrophic bacterial activity and nitrogen fixation are fundamental to nutrient regeneration and nitrogen cycling in saltmarsh ecosystems. Ecological and physiological aspects of bacterial production and nitrogenase activity in marine sediments and water were examined in Langebaan Lagoon, a temperate saltmarsh ecosystem. Emphasis was placed on factors modulating rates and patterns of nitrogen fixation. Nitrogen fixation appeared to be dominated by heterotrophic bacteria. Rates of nitrogen fixation (estimated by the acetylene reduction technique), and bacterial production (estimated by tritiated thymidine incorporation, Tri) were higher in fine, muddy sediments near the head of the lagoon (Geelbek) than in coarser, sandy sediments near the mouth of the lagoon (Oesterwal). These comparisons (between sites) reflected the higher bacterial abundance and organic content of sediments from Geelbek. Examinations of five sedimentary microhabitats at each site (including those associated with beds of the seagrass Zostera capensis, burrows of the sandprawn Callianassa kraussi at Oesterwal, and burrows of the mudprawn Upogebia africana at Geelbek) showed that bacterial activity was higher in surface sediments than in subsurface sediments. Highest rates of nitrogen fixation (annual mean, 0.28 + 0.07 nmol C2H4 g-1 dry sediment h-1) were measured in Zostera bed sediments at Geelbek. Thymidine incorporation activity and nitrogenase activity were higher in burrow linings than in adjacent subsurface sediments, suggesting that burrow linings provided an improved subsurface environment for bacterial activity. Burrow linings also had a higher organic content than subsurface sediments away from burrows. Nitrogenase activity was not detected in lagoon water.

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