Trees alter the environment by affecting microclimate, soil properties and adding structural complexity to an otherwise single stratum system. It is known that the herbaceous understory of Savanna ecosystems is most productive at intermediate tree density, where the shade and nutrients from the tree are more influential than the competition with the tree. Tree density varies in savannas due to disturbances, such as fire and herbivory. Yet, disturbances do not only alter density but can affect entire tree structure. It has been found that chronic ungulate browsing influences whole tree size, as well as canopy size and shape. Giraffe in south of Kruger National Park browse heavily on Acacia nigrescens found on basalt-derived soils. I studied the influence of trees above the giraffe browse trap (>6 m) as opposed to trees in the browse trap (< 6 m) on savanna ecosystem properties. I compared grass biomass, soil moisture, soil organic matter, soil carbon and soil nitrogen beneath tall trees vs. short trees, as well as in the open vs. underneath trees. Ecosystem properties were estimated and compared between a giraffe impacted to a giraffe absent area. Giraffe impacted area overall yielded lower grass biomass, soil moisture, soil nitrogen and soil carbon. The consequence is a trophic cascade of events from increased giraffe decreasing fires and in tum increasing tree density and hence carbon sequestration. As giraffes replace a single large tree by several small trees, shows that their population size is key determinant of ecosystem properties.

Includes bibliographical references / Eastern high - altitude grasslands of South Africa are centres for endemism and harbour fauna and flora of regional and international conservation concern. This area also provides important ecological services such as provision of water to communities downstream. Sweet and sour veld support beef livestock farming during summer months. The aesthetic beauty of the region makes the area a prime tourist destination too. More recently the area is becoming a target of other agricultural projects such man - made forests. Other new developments that need to be mitigated against are development of renewable energy projects such as pumped water schemes to generate electricity or wind farms. Additional habitat is lost when these projects are connected to the national grid. In this thesis, I use bird data and vegetation data to compare, contrast and suggest management tools to manage this area. I present data that I collected at Ingula Pumped Storage Scheme spanning five years from the beginning of the construction of the scheme to near its completion in 2012 as a case study to manage similar habitats. Chapter 1 presents a brief overview of ecological importance of this area and the history behind the construction of pumped storage scheme at Ingula. A literature review in Chapter 2 investigates management tools to manage these grasslands for avian diversity. Fire and grazing is a key management tool cited to make habitat suitable for birds. While few studies from this type of grassland exist, studies from outside South Africa suggest that fire and grazing supplement each other as management tool to make habitat suitable for species with contrasting ecological requirements. A mosaic of grass heights and cover across the landscape translates to species habitat suitability. Chapter 3 explores species richness through years, seasons and impact of grass height and cover on bird species richness. Species richness was highest in summer suggesting that management should make habitat for species suitable in summer when most priority species are likely to use the habitat. The main disadvantage of using bird species richness is that fieldworkers must know their species well. Secondly, use of species richness must be treated with caution because this method does not account for species detectability in time and in space. In Chapter 4 I use hierarchical distance sampling models which take into account both the detection and the biological process. To demonstrate this I used common grassland bird species which can easily be identified during monitoring. The downside of this approach is that because these species are common and therefore occur almost everywhere, they may not easily respond to lack of habitat heterogeneity. The technical disadvantage of using this method is to accurately allocate species to within distance bands, making this method challenging for fieldworkers. Chapter 5 presents random plot occupancy which records only detection - nondetection of birds during repeated plot surveys. This method accounts for observational and biological processes too and in addition implements rigorous statistical inferences to predict how birds respond to habitat variable s as influenced by management decision on fire and grazing. Finally, adverse weather conditions may hamper surveying all plots in some years. Through occupancy modelling it is possible to predict species occupancy on plots that were not surveyed during some years and finally this method has been improved to include rare species. This is my preferred method to monitor management effect on habitat suitability for birds at Ingula. Adaptive management, a pillar of which is adaptive monitoring is a new paradigm shift in conservation. In Chapter 6, I capture interactions between burning and grazing and effects on grass height and cover to predict habitat suitability for birds including large threatened Ingula birds using a simulation models. This model sets a stage for implementing adaptive management through experimental plots to capture a set of management uncertainties regarding the use of fire and grazing as management tools. Chapter 7 summarizes the thesis and acknowledges that Ingula consists of other equally important habitat and ecosystem such as cool moist mountain forest and matrix of grassland wetland that equally need to be conserved.

Donkeys are used extensively in Namaqualand and other rural areas in South Africa for pulling carts, carrying loads, ploughing and threshing grain. There is, however, an ongoing debate among farmers, agriculturalists and the wider population about the implications of keeping donkeys, particularly on communal lands. Donkeys are reported to cause more damage to the veld than other animals, and it is commonly said that one donkey eats as much as seven goats. This project was initiated as a case study to investigate the impacts of donkeys in a communal area in the succulent shrublands of Namaqualand, and to generate suggestions for the management of donkey populations. The degree of competition between goats and donkeys was investigated by predicting daily food intake using a model based on ruminant and non-ruminant digestion, which takes into account the animal's body weight and digestibility characteristics of its diet. The ratio predicted food intakes is discussed in the light of the degree of dietary and habitat overlap, which were obtained from field observations. Habitat use was scored using dung frequency transects, and feeding was directly observed. It was found that in the wet season, one donkey eats as much as 5 / 7.6 goats (donkey weight set at 200 and 250 kg respectively). In the dry summer, this ratio increases to 7.6 / 8.6 because in ruminants, the passage of food through the gut slows down as the digestibility of the diet decreases. Habitat overlap is concentrated in the riverine areas and sandy pediments, which make up 15 % of the landscape and are strongly favoured by donkeys. No significant differences were found to exist between the intensities of goat use of the different habitats. The botanical composition of the diets of donkeys and goats were found to be similar, but there is a great difference in the quality of the diet consumed by each species as goats are able to select plant parts of a higher quality. The implications of this are that whereas a donkey takes in as much dry matter as 5 - 8.6 goats, the diet of this food is not high enough to satisfy the dietary requirements of goats, and hence fewer goats than predicted can be supported for every donkey that is eliminated. Donkeys are commonly reported to have destructive feeding habits; little of this was directly observed, but donkeys were found to bite deeper into the wood of shrubs, which may damage the plants in the long term. There are two main management measures that should be applied. The feral donkey population in Paulshoek, estimated at 50-100 animals, must be eliminated - even at a conservative estimate, these animals could be replaced with 250 goats. However, one must look beyond the number to the processes taking place to make management effective. Even if one donkey can be replaced with fewer than 5 goats, the vegetation is relieved of the indirect effects donkeys have through their feeding habits. Control of working donkeys should focus on the riverine and flat, sandy areas, as they are potentially of high nutritional importance (especially the riverine areas which support grass throughout the year), and which are also the most susceptible to erosion due to their sparse vegetation cover. These areas are small and valuable, and plans should be made to protect some areas through the growing season.

The Namaqualand area in the North Western Cape, South Africa is unique in comparison to other similar semi-arid areas of the world. It has a high biodiversity and endemism and is consequently an area of interest for a growing number of conservation initiatives. Climate plays an important role in influencing the phenology and growth of the vegetation in the area. Remote sensing techniques were used to reveal the vegetation patterns in the greater Namaqualand area and to relate them to climatic variables. To do this we used the normalised difference vegetation index (NDVI) to relate biomass to altitude, rainfall and vegetation type. Each vegetation type in the area had a unique temporal signature and the climatic variables influencing the summer rainfall and winter rainfall vegetation types differed significantly from each other. Mean annual NDVI was significantly correlated to precipitation and potential evapotranspiration (PET) (r = 0.60, -0.63 respectively). A multiple regression model explained 52% of the variance when Mean Annual NDVI was related to climatic variables. Mean NDVI in August (the month of maximum NDVI in most of Namaqualand) was significantly related to PET and the current plus two previous months of precipitation (r = -0.72 and 0.74 respectively). A multiple regression model for mean NDVI in August and climatic variables explained almost 58% of the variance. The results suggest that NDVI can be used successfully as a measure of growth and phenology in the Namaqualand area and that NDVI could be used in climate models, drought prediction, desertification predictions and a number of other applications in the future.

Acacia cyclops A. Cunn. ex G. Don is an invasive alien plant that invades fynbos and coastal dunes. Several acacia species are grown commercially in South Africa and this has limited biocontrol agents to those that reduce only reproductive capacity. Dasineura dielsii was released in 2002 as a biocontrol agent for A. cyclops. This gall-forming midge destroys inflorescences and prevents seedpods from forming, but allows continued harvesting. Insects overwinter as larvae within their galls. This study examined the levels of parasitism experienced by dormant D. dielsii larvae, as well as the trigger that causes them to break dormancy. Gall clusters were sampled over autumn and early winter, and were dissected to determine occupancy. The effects of temperature and light on dormant larvae were also examined. Observations showed that as the season progressed, more D. dielsii larvae entered dormancy. At the same time, a greater proportion of dormant larvae were parasitized. Parasitism was highest, at 18.5%, at the end of the study period, but this level of parasitism is not enough to reduce the biocontrol power of D. dielsii. A positive relationship between mass of gall clusters and the number of galls they contain was established. Larval dormancy could not be artificially broken by either light or temperature, and it appears that neither factor alone can trigger a break in dormancy.

Protea witzenbergiana possesses some features common to that of therophilous Proteas in the Cape Floristic Region, such as a cup-shaped, downwards-hanging inflorescence surrounded by red involucral bracts, which emits a yeasty, musky odour. The flowering season occurs in the winter and the plants occur in small, localized and isolated stands in the Witzenberg fynbos. However, the species has never been investigated as to whether it is pollinated by small mammals. This study investigated whether the plant is rodent-pollinated, and if so to what extent by various species. Fieldwork was carried out over three days of live trapping, during and after the flowering season. Exclosure experiments were set up in order to assess seed set. Mammal droppings were collected, processed and pollen grains were counted. All small mammal species excepting one (Otomys irroratus) contained pollen grains in their faeces. Oendromus melanotis, Mus minutoides and Aethomys namaquensis were found to be the most important pollinators. The small mammal community showed a distinct change in size and composition after flowering season had ended, suggesting that the availability of nectar resources may be an important food supply to small mammals in the area. Implications of these findings could be relevant for conservation and co-evolutionary studies.

Their high energetic demands make seabirds sensitive to changes in prey availability, which is often reflected in their diet and energetic expenditure during breeding. Populations of the three seabirds endemic to southern Africa's Benguela upwelling ecosystem that rely on small pelagic fish have decreased dramatically over the last decade. In contrast, the population of the greater crested tern Thalasseus bergii has increased. To understand these conflicting trends, I investigated the foraging ecology and energy requirements of greater crested tern breeding in the Western Cape, South Africa. Diet was assessed by a novel non-invasive methodology developed in this study, using digital photography. More than 24,000 prey items from at least 51 different prey taxa were identified, with 34 new prey species recorded, revealing a high degree of foraging plasticity for this seabird. Greater crested terns rely mainly on anchovy Engraulis encrasicolus (65%), which averaged 84 mm long. Prey composition differed significantly between breeding stages, with anchovy especially dominant at the onset of the breeding period and the diet becoming more variable as the season progressed. Time-energy models for breeding terns were built based on activity budgets collected from non-invasive video-recordings and focal observations. Foraging trips were significantly longer during incubation than the chick provisioning stages, and feeding rates doubled from early to late chick provisioning. This study illustrated a steady increase in energy needs of adults throughout the breeding season, due to their increased foraging effort to meet chick energy needs. In comparison to other Benguela endemic seabirds that also rely on small pelagic fish, terns displayed substantially lower energy requirements at both individual and population levels. I also explored the benefits underlying interactions within mixed-species aggregations by investigating the costs induced by kleptoparasitism between mixed colonies of greater crested terns and Hartlaub's gulls Chroicocephalus hartlaubii and colonies with greater crested terns alone. Video-recordings coupled with focal observations showed that terns suffer direct costs to chick provisioning rates and indirect costs through energy expenditure in a mixed-species colony, suggesting that these breeding assemblages may be a form of parasitism rather than a mutualistic association. Despite the detrimental effects of interspecific kleptoparasitism, the marked foraging plasticity and low energetic requirements of greater crested terns, described in this study, coupled with specific life history traits such as low fidelity to breeding sites and extended post-fledging care, are key factors that allow this species to cope with changes in the availability and abundance of their main prey. Understanding species-specific behavioural responses to ecosystem variations in the Benguela upwelling system is vital for assessing the impact of commercial fisheries on seabird populations and fish stocks. Finally, the implementation of the method developed in this study, in long-term monitoring programmes, may provide crucial knowledge for conservation plans and key input to realising an ecosystem approach to fisheries management.

The subtidal seaweed communities of the KwaZulu-Natal coast are poorly understood. A recent collaborative research project between Belgian and South African phycologists, however, is currently investigating the diversity and biogeographical affinities of the marine benthic algal flora of this region. The newest leg of the project is focusing on correlating biogeographic patterns with abiotic factors in the area between the St. Lucia estuary and Sodwana Bay, where it has become evident that there is a huge turnover in species composition. The present study examines seaweed community change along a depth gradient (1-30 m depth) at Sodwana Bay on the KwaZulu-Natal (KZN) coast, South Africa. All seaweed cover within 25 x 25 cm quadrats was collected, identified and weighed. The environmental variables, depth and % sand cover, were also measured. Both biomass and presence/absence data were ordinated to show community differentiation related to the environmental variables. The seaweed communities are largely red turfs, with a total of 82 Rhodophyte, 14 Chlorophyte, and 8 Phaeophyte taxa recorded. These turf communities showed exceptional diversity with 105 taxa (>25 % of recorded KZN flora) occurring in the total sample area of 1.56m². Seaweed communities clearly change with depth, but the biggest change occurs between the shallow subtidal zone (approx 1 m depth) and deeper waters (>5 m depth), mostly likely due to the effects of wave action; thereafter communities do change with depth, but the effects are less pronounced. Biomass (p=0.049, significant) and seaweed diversity (p=0.078, not significant) were both shown to decrease, and % bare (seaweed-free) cover (p=0.002, significant) increased, with increasing depth. It is likely that these changes with increased depth can be attributed to the effects of increased light attenuation on ecological functioning in the subtidal communities. Sand inundation patterns are shown to be important in determining seaweed community structure, but do not appear to be predictable along a depth gradient (p=0.544, not significant).

Seabirds are considered one of the most threatened groups of birds in the world. They face additional mortality both on their breeding islands from introduced predators and at sea by fishing fleets, as fisheries bycatch, as well as other human impacts. Seabird bycatch has negatively affected many seabird populations worldwide, with trawl, gillnet and longline fisheries considered the most destructive to seabird populations. Seabird bycatch from trawl and gillnet fisheries has been significantly reduced in recent years, but large numbers of seabirds are still killed annually by longline fisheries. Of the two types of longline fisheries (demersal and pelagic), pelagic longlining is considered the most harmful to seabirds as lines remain closer to the surface for longer periods than demersal longlining, and it is harder to weight lines to ensure rapid sinking beyond the depth they are accessible to birds. Seabirds are killed when they swallow baited hooks and consequently drown. Despite the large number of studies investigating seabird bycatch from pelagic longline fisheries, there remain gaps in our understanding of seabird bycatch from pelagic longline fisheries. This thesis addresses some of these knowledge gaps and makes recommendations as to how seabird bycatch from pelagic longliners can be reduced at both a local and global scale. Chapters 2 and 3 investigate the factors affecting seabird bycatch from pelagic longliners off South Africa, provide a summary of seabird bycatch from the fishery for the period 2006–2013 and quantify the structure of seabird assemblages associated with pelagic longline vessels off South Africa. This was achieved by analysing seabird bycatch data collected by fisheries observers as well as data from sea trials onboard pelagic longliners. Seabird bycatch by pelagic longliners off South Africa over the 8-year study period has been significantly reduced from the 8-year period (1998–2005), mainly driven by a significant reduction in seabird bycatch rates from foreign-flagged vessels, which are responsible for c. 80% of fishing effort off South Africa. Seabird bycatch rates from South African vessels still remain high, four times higher than the interim national target of < 0.05 birds per 1000 hooks. The species composition of seabird bycatch off South Africa is best explained by an understanding of the structure of the seabird assemblage associated with longline vessels. For most species, bycatch and attendance ratios were similar, but for some species such as shy-type and black-browed albatrosses there were large mismatches, likely caused by differences in foraging behaviour and foraging dominance hierarchies. In Chapters 4 and 5 the foraging ecology of the most commonly recorded bycatch species off South Africa, the white-chinned petrel (Procellaria aequinoctialis), is investigated. An understanding of the foraging ecology of commonly recorded bycatch species enhances our understanding of seabird bycatch and helps to improve the design of current and future mitigation measures. The year-round movements of white-chinned petrels from Marion Island were investigated with Global Location Sensors (GLS loggers) and GPS loggers. Adult white-chinned petrels undertake only limited east-west movements of, with all birds remaining between southern Africa and Antarctica. These results strengthen the theory that there is limited spatial overlap year-round between white-chinned petrel populations from South Georgia, the southern Indian Ocean islands and New Zealand sub-Antarctic islands, suggesting that these populations can be managed as separate stocks. The diving behaviour of white-chinned and grey petrels (P. cinerea), another common bycatch species in Southern Ocean longline fleets, were examined with the use of temperature-depth recorders (TDRs), deployed on birds from Marion Island and Gough Island. My study was the first to analyse TDR dive data from any Procellaria petrel, and recorded them reaching maximum dive depths of 16 and 22 m, respectively. Current best practise suggests that baited hooks be protected to a depth of 5 m by bird-scaring lines, but my results suggest this depth should be increased to at least 10 m. Although line weighting is a proven mitigation measure to reduce seabird bycatch from pelagic longliners, fishers have concerns that it will compromise fish catches, crew safety and operational efficiency. In Chapter 6 I analyse line weighting data from trials onboard three pelagic longline vessels, to address the concerns of fishermen. My results show that sliding leads can be incorporated into pelagic longline fisheries without compromising fish catch, crew safety or operational efficiency. I thus recommend that sliding leads be used on pelagic longline vessels fishing off South Africa. By incorporating studies investigating the factors affecting seabird bycatch, seabird foraging ecology and the efficacy of seabird bycatch mitigation measures, my thesis has broadened our understating of seabird bycatch from pelagic longliners and makes meaningful recommendations to further reduce bycatch, both locally and globally. Although seabird bycatch rates have declined off South Africa, through the use of a number different mitigation measures, they still remain higher than the South African national target and thus more work is needed to achieve this target. To reduce seabird bycatch from pelagic longliners to acceptable levels, studies from the world's various longline fleets needs to be considered and improved upon, with seabird conservationists and fishermen working together to achieve this goal.

Arid and semi-arid systems comprise one third of the earth's surfaces. The succulent karoo alone comprises approximately 1660 endemic species and is one of the world's hotspots in terms of diversity. Although these areas are of high ecological value less than 10% of arid systems are conserved. This study was conducted in Paulshoek a remote village in the Leliefontein area of the Namaqualand. Historically Paulshoek has been under continuous selective grazing since the 18th century. A fence line contrast is investigated in an area that was fenced three years ago and in one that has been exposed to heavy, continuous, selective grazing over the past century (both areas were fenced prior to fencing). The objective of this study was to investigate the effect of short-term rest on key vegetation demographic parameters as well as the physical characteristics of communal river systems. No significant differences in plant species richness were observed across the fence line. However, the numbers of plants of each species within the plots were significantly different, depending on presence or absence of grazing. The grazed sites had more species tolerant of grazing such as geophytes, annuals and toxic species such as Galenia africana. Heavy grazing in this ecosystem has resulted in increased proportions of unpalatable species with a slow reduction in the number of palatable species. Species cover was significantly reduced on the grazed sites; however, these reductions were insignificant for Lyceum cinereum species due to large standard deviations. Heavy grazing of palatable sedge species (Scirpus nodosus) resulted in significant reductions in the number of flowers of plants, in the grazed sites. Grazing not only reduced the size of the plants, it also reduced flowering, fruit set and recruitment rate. There was no significant difference in the physical and geomorphologic characteristics of the river across the fence-line. This study indicates that short-term rest has major implications for plant recovery. Educating communal farmers to use a farming system that insures temporary rest on certain areas of the rangelands at certain times of the year will go a long way in improving species richness in Namaqualand.