Over the past decade there has been global concern about the bycatch of seabirds, turtles and sharks in fishing operations, in particular longline and trawl fisheries, which have been widely held responsible for their declining population s and threatened conservation status. This thesis addresses the issue of bycatch in a holistic manner, taking into account that species, whether they be target or non-target, do not exist in isolation from each other and their environment. South African fisheries incidentally catch approximately 21 000 seabirds, 165 turtles and 43 000 pelagic sharks per year, including 21 Endangered species. Decreasing CPUE and size-frequency data for Blue Prionace glauca and Short- finned Mako Sharks Isurus oxyrinchus caught in the large pelagic longline fishery suggests exploitation of these species is unsustainable. A decreasing trend in the biomass index was also observed for the Yellow-spotted Catshark Scyliorhinus capensis and the Biscuit Skate Raja. straeleni. An argument for the likelihood of fisheries mortality contributing to the slower than expected turtle population recovery rates is presented, which is supported by results from satellite tracking of Leatherback Turtles Dermochelys coriacea indicating a high degree of overlap with fishing effort. Satellite tracking of Black-browed Thalassarche melanophrys and White-capped T. steadi Albatrosses reveal striking differences in their foraging patterns and presents evidence that Black-browed Albatrosses, in particular, forage to a large extent on natural prey, despite the availability of discards from fishing vessels in the Benguela. Therefore, given the high albatross mortality in the trawl fishery, the benefit of a management decision to limit discarding as a mitigation measure is likely to outweigh the disadvantage of reduced food supply. Reducing bycatch is dependent on the development of effective and relatively inexpensive methods which do not impact on target catches and/or other vulnerable species. In the demersal longline fishery, two methods of optimising line sink rates to reduce seabird bycatch were investigated: increasing mass of weights and decreasing the spacing between weights. This study indicated that while the target species is unlikely to be affected by increased weighting, other vulnerable species of fish and sharks may be affected. Other mitigation experiments investigated line sinking rates and the use of circle hooks in pelagic longline fisheries. The implications of night setting on Swordfish Xiphias gladius catches, fishery closure during full moon and the appropriateness of the international standard 5% fin to trunk ratio for the South African fishery, were also investigated. Lastly, the spatial and temporal overlap of catches of seabirds, turtles and sharks were investigated through a conservation planning exercise using MARXAN and potential areas for closure identified.

Includes abstract. / Includes bibliographical references (leaves 164-187). / An examination of characteristics extreme precipitation in the greater Cape Town region is undertaken. Thereafter, an investigation into the characteristics of these changes is made using two approaches. The first is an empirical methodology to explore the historical attributes of extreme events and the second a numerical method. These are used to demonstrate an approach to produce high resolution forecasts of extreme precipitation if computational resources are scarce. Initially, changes in the characteristics of extreme precipitation in the greater Cape Town region is documented. Then self organizing maps are used to identify archetypal synoptic circulations that are associated with extreme precipitation over the region. Thereafter, days whose synoptic state matched those of the synoptic archetypes are simulated at a resolution of one kilometer to capture regional topographic modification of extreme precipitation. Following this, the simulated precipitation is validated against observed data and the model performance is assessed. These approaches were tested over Cape Town, South Africa which has complex topography where extreme rainfall is not well predicted. As this methodology is computationally relatively inexpensive, it has applicability to regions of the world where these resources are limited, more especially Africa where the state of climate science is poor. An analysis of historical station data from three locations in the greater Cape Town region showed mixed trends in extreme rainfall where extreme rainfall was taken as that in the 90th percentile. One station, located in the lee of topography, showed a statistically significant increase in the intensity of extreme rainfall and another, at a relatively topography-free location, a significant decrease. The third station showed no significant trend. Decadal changes in monthly precipitation show a shift in the start and end of the extreme rainfall season to starting later in winter and continuing into the early spring. The station with the significant increase in extreme rainfall intensity also showed an increase in 99th percentile rainfall intensity. Synoptic states associated with extreme rainfall in the greater Cape Town region were then examined. These were identified as mid-latitude cyclones with centers at relatively low latitudes. They were characterized by strong pressure gradients at the surface and in the upper air high as well as high regional humidities. Precipitation characteristics of the frontal systems ranged from precipitation that fell over a number of days in relatively low daily amounts to very heavy precipitation that fell in one day. Over the twenty-three year test period examined, there are changes

The El Niño Southern Oscillation (ENSO) is a major driver of southern Africa droughts, but the nonlinearity of ENSO variation inhibits accurate prediction of droughts. While studies have identified multiple patterns of ENSO, most drought predictions over southern Africa are still based on only two ENSO patterns. This study examines the relationship between southern African droughts and eight ENSO patterns: four El Niño SST conditions (EN1 - EN4) and four La Niña SST conditions (LN1 - LN4). In this study we analyzed multi-forcing ensemble simulations from SPEEDY (a general circulation model from the International Centre for Theoretical Physics) and used two drought indices (SPEI: Standardized Precipitation Evapotranspiration Index; SPI: Standardized Precipitation Index) to characterize drought. The capability of SPEEDY in reproducing southern Africa climate was evaluated by comparing the historical simulations (1979- 2008) with the Climate Research Unit (CRU) observation. To obtain the influence of ENSO patterns, we forced the SPEEDY simulations with SST of each ENSO pattern, analyzed the impacts on the simulated drought indices (SPEI and SPI), and studied the atmospheric dynamics that link each ENSO pattern to southern Africa droughts. The results show that SPEEDY generally captures the temporal and spatial distribution of climate variables over southern Africa well, although with warm and wet biases across the region. However, in most cases, these results are comparable with those from more complex atmospheric models. In agreement with previous studies, the results show that El Niño SST conditions weaken the Walker circulation and cause drier conditions over parts of southern Africa, whilst La Niña SST conditions strengthen the Walker Circulation and cause wetter conditions. However, the results show that the differences in the El Niño SST conditions (EN1 - EN4) alter the circulation, thereby influencing the spatial pattern and intensity of drought over the region. For instance, while EN2 induces the most severe drought in the tropical area, EN4 produces it in the southwestern region, because the two patterns feature different characteristics of anticyclonic moisture flux over southern Africa. The same is true of the La Niña SST conditions. Although, LN1 and LN4 show wet conditions across the southern part of the region, LN1 produces drought in the northern part, while LN4 induces it along the western coast. Hence, this study shows that accounting for the differences in El Niño (or La Niña) conditions may improve drought predictions in southern Africa.

Includes abastract. / Includes bibliographical references. / This study highlights the importance of including all biomass burning emissions, from the aerosols directly released from fires to the precursor gases, as different radiative forcings will be obtained from different chemical species, and, therefore, different circulation patterns are likely to be induced over all seasons, regardless of how large the emissions loading and/or concentrations are.

Includes bibliographical references. / The importance of vegetation feedbacks to the atmosphere has been highlighted in many recent research studies. The influence of climate on vegetation has long been established, and climate has regularly been used to predict vegetation distribution. However, the influence of vegetation on climate is a relatively new research area. The need to understand vegetation-atmosphere interactions is growing in light of the increasing atmospheric carbon dioxide concentrations and the change in climate associated with these increases. These linkages are analysed over southern Africa with the use of sophisticated computer models of the climate and vegetation. The models are used to explore some of the vegetation-atmosphere interactions for this region, but without attempting a definitive study of either system.

Includes abstract. / Includes bibliographical references. / In a water scarce country like South Africa with a number of large consumers of water, it is important to estimate evapotranspiration (ET) with a high degree of accuracy. This is especially important in the semi-arid regions where there is an increasing demand for water and a scarce supply thereof. ET varies regionally and seasonally, so knowledge about ET is fundamental to save and secure water for different uses, and to guarantee that water is distributed to water consumers in a sustainable manner. Models to estimate ET have been developed using a combination of meteorological and remote sensing data inputs. In this study, the pre-packaged Surface Energy Balance System (SEBS) model was used for the first time in the South African environment alongside MODerate Resolution Imaging Spectroradiometer (MODIS) satellite data and validated with eddy covariance data measured in a large apple orchard (11 ha), in the Piketberg area of the Western Cape. Due to the relative infancy of research in this field in South Africa, SEBS is an attractive model choice as it is available as open-source freeware. The model was found to underestimate the sensible heat flux through setting it at the wet limit. Daily ET measured by the eddy covariance system represented 55 to 96% of the SEBS estimate, an overestimation of daily ET. The consistent underestimation of the sensible heat flux was ascribed to sensitivities to the land surface air temperature gradient, the choice of fractional vegetation cover formula as well as the height of the vegetation canopy (3.2 m) relative to weather station reference height (2 m). The methodology was adapted based on the above findings and was applied to a second study area (quaternary catchment P10A, near Grahamstown, Eastern Cape) where two different approaches for deriving surface roughness are applied. It was again demonstrated that the sensible heat flux is sensitive to surface roughness in combination with land surface air temperature gradient and again, the overestimation of daily ET persisted (actual ET being greater than reference ET). It was concluded that in complex environments, at coarse resolution, it is not possible to adequately describe the remote sensing derived input parameters at the correct level of accuracy and at the spatial resolution required for the accurate estimation of the sensible heat flux.

Includes bibliographical references. / This research investigates the role of horizontal cooperation in the adaptive management of regional socio-ecological systems (SESs). Horizontal cooperation refers to the collaborative, non-hierarchical interactions of actors across sectors, modes of governance and spatial scales. It can allow diverse actors to deal with the complexity and uncertainties that characterize SESs and to co-produce public benefits. The research question is, When does horizontal cooperation contribute to adaptive management in complex governance arrangements? The Berg River catchment in South Africa serves as a case study to analyze such complex systems. The empirical focus is on the operational level which is responsible for maintaining key functions of the water resources in the SES. A formal social network analysis is employed to describe and analyze the management of the Berg River catchment. The analysis focuses on (i) cohesion and (ii) heterogeneity, which are two network characteristics that affect learning and collective action in actor networks. Horizontal cooperation is further investigated by examining selected collective action initiatives with the help of Ostrom’s eight design principles (1990). Constraints affecting collective action and the capacity to self-organize are identified, and the robustness of the governance arrangements arising from horizontal cooperation is evaluated. The study finds that the behavior of actors towards each other and the SES is influenced by incentives provided by informal network structures, market mechanisms and bureaucratic hierarchies. Hence, modes of governance intersect at the operational level and consequently influence the nature of horizontal cooperation. While the quality of the management of the SES is largely determined by the patterns of interactions among the actors that manage the SES, these interactions are influenced by other institutional and organizational structures in which they are embedded. Unexpectedly, market mode incentives stimulate collective action in the Berg catchment and accentuate the need for addressing degrading water quality. Informal relations and emerging inter-organizational platforms matter for learning and for providing opportunities for collective action. Yet, the incentives (or lack thereof) created through hierarchical steering of the South African water governance system by the national government department are often counterproductive. That is, so far the self-organizing efforts at sub-catchment level could not be transformed into functioning governance arrangements because of constraints imposed by the hierarchical mode. The study confirms that self-organization and collective action that arise from horizontal cooperation are important for the adaptive management of regional SESs.

Summary in English. / Bibliography: leaves 263-292. / This thesis presents new palaeoenvironmental evidence from the semi-arid lowlands of the West Coast Sandveld, which prompts a fresh synthesis as to the nature of late Quaternary environmental changes in the southwestern Cape's fynbos biome. The study is centred on Verlorenvlei, a remote coastal lake and swamp system which is ideally situated to investigate the complex interactions between late Holocene climate change, vegetation change, sea-level fluctuation, lacustrine/estuarine/fluvial sedimentology and human activity in the Sandveld region. In addition, this region of the West Coast has provided Quaternary scientists with a rich archaeological record against which independent lines of palaeoecological evidence can be evaluated. In support of the study, a wide range of palaeoenvironmental techniques has been applied to sediments sampled from the Verlorenvlei area. Organogenic deposits have been radiocarbondated and subjected to pollen analysis and assorted sedimentological and geoarchaeological assessments. Preliminary fossil pollen data from Elands Bay Cave, assembled for the period following the Last Glacial Maximum until approximately the terminal Pleistocene, are suggestive of moister and possibly cooler conditions in the Sandveld at this time. This is in contrast to prevailing evidence from the summer rainfall region of the subcontinent. Particle size analysis and an assessment of the in situ fossil Mollusca from vibracores, derived from the estuarine reaches of Verlorenvlei, reveal substantive evidence for rapid sea-level fluctuations along the West Coast during the mid-Holocene. Further inland, several mid-Holocene higher sea-levels are reflected in the palynology of lacustrine cores derived from Grootdrift and Klaarfontein. Detailed pollen diagrams, presented from Grootdrift, Klaarfontein, Muisbosskerm and Spring Cave, reflect the regional vegetation history during several periods over the last 7 000 years. There is convincing evidence from these data that the first half of the Holocene - commensurate with the Holocene hypsithermal - was associated with reduced moisture availability, and hence arid conditions along the West Coast. By contrast, there is evidence from the latter half of the Holocene that conditions ameliorated in the Sandveld around 3 000 BP and that moisture was, at this time more freely available. Following a hiatus in sedimentation some time after 4 000 BP, marine conditions are no longer visible in Verlorenvlei, having been replaced by fresh water as the dominant hydrological regime. A high resolution palynological investigation of the Grootdrift wetland sediments has contributed to a detailed palaeolimnological reconstruction of the upper Verlorenvlei system since the time of colonial expansion into the area, some 300 years ago. The picture reveals a sequence of rapid ecological changes in the face of progressive human disturbance. Arising from these insights, a number of recommendations for the management of dryland aquatic ecosystems such as Verlorenvlei, are presented. The significance of these late Quaternary palaeoenvironmental changes, in terms of the biogeography of plants and animals and also in terms of human occupation of the region, is examined.

Includes bibliographical references / This thesis investigates water risk in small-to medium-sized agro-processing companies and the public sector. Global interest in water management from the private sector has led to an increase in the development of water risk tools that are available to companies. Not only has the number of tools increased, but also the quality and form of these tools has been refined. Water risks are complex and extensive, and cannot be managed alone. Private sector interest in partnership and collaboration with other actors in managing water risk has increased as a result. The principal aim of this thesis is to investigate and explain the idea of shared water risk, using an adaptive theory process within a case study to investigate the understanding and knowledge of water risks among public and private actors. The study is informed by an assumption that if private and public interests are aware of the collective risks within a catchment, then sustainability of those business enterprises and public services, along with the protection and conservation of water resources may be possible. The case study is located in Grabouw and the Elgin Valley in the Theewaterskloof Local Municipality, Western Cape, South Africa. Private sector actors include agro-processing industries in the region, while the public sector includes local municipality officials and water resources management institutions such as the Catchment Management Agency and the Water Users Association. A conceptual framework of water risk and a sharing typology was developed from an analysis of interviews and the use of secondary sources of documents on the hydrology and socio-economic information on the catchment. The conceptual framework identifies the different water risks of the private and public sector, while the sharing typology indicates the progression of knowledge and understanding of private and public sector water risks, recognising that sharing does not take place in a single form. The framework and the typology together are intended to integrate an understanding of the theory and empirical data. Refinement of the framework and typology found that shared risk is especially pertinent in situations where systemic water risks affect the management of water and where that risk cannot be managed by individual companies or public sector authorities alone. The conceptual framework and typology identify the private and public sector exposure to risks, enabling actors to understand the scale and form of the respective risks in each sector. Where risks are not shared, the process of investigating the knowledge and understanding of risks helps to identify the complexity of the system. Contributions of this thesis include the use of risk as a common language to help bring together diverse sectors, especially when participatory decision-making is required. Not only the technical aspects of water supply and sanitation, but the wider social and environmental factors need to be considered as well. Understanding water security as a risk enables a wider and more diverse stakeholder group. The thesis concludes that collaboration and adaptive management need to be informed by knowledge and understanding of the complexity of risks within the catchment by multiple stakeholders.

Dryland farmers in southern Africa operate under harsh conditions; infertile soils, erratic rainfall regimes, sub-optimal input levels etc. Crop yields have generally been low, negatively affecting food security and livelihoods. Climate change is anticipated to aggravate these already existing challenges. In the recent past, a wide range of studies has sought to understand how climate change will affect crop production. However, there are only few detailed localised studies that focus on understanding climate change impacts and adaptation under heterogeneous conditions that dryland farmers in southern Africa operate. This study sought to understand how climate change will affect food crop production in southern Africa's drylands and to provide insight on the potential of on-farm agronomic management strategies for adaptation. The study focused on three locations representing some of the agro-ecological conditions of southern Africa i.e. Big Bend in Swaziland (low altitude, hot and dry), Mohale's Hoek in Lesotho (high altitude, cool and wet and dry), and Lilongwe in Malawi (mid altitude, wet with moderate temperatures). The study was performed largely using a climate-crop model simulation approach supported by a review of similar approaches in the region, data collected from reported agricultural experimental trials, regional experts, downscaled climate projections (using up to 9 GCMs) and surveys.