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.

Scholars have engaged actively with the link between customary practices and ecological conservation in Africa as part of a broader debate on governance approaches for natural resource management. To a large extent, this is in response to a growing voice articulating the need to integrate traditional institutions and customary practices into a more contemporary form of governance for Africa’s democratic and socio-economic transformation. To date, however, the integration of customary and statutory approaches to governance has yielded only modest progress in the forest sector and knowledge remains limited about the interface between these governance systems and the effect of this dualism on natural resource management. Using the lens of the baobab tree, this research set out to address these gaps and to elucidate understanding of the interplay between customary and statutory governance in managing natural resources; the influence of such interactions on ecological sustainability and livelihoods; and the contextual factors that shape such approaches. Uses of the baobab tree as well as factors affecting access were analysed. Two study sites were selected on the basis of similarities in resource endowment and contrasting use patterns and forms of governance. Both quantitative and qualitative methods were used. Quantitative methods included an ecological survey to examine the relationship between different indicators of ecological sustainability and different tenure regimes. A household survey was also carried out to examine the extent to which households use and benefit from baobab products. Qualitative methods included focus group discussions, institutional mapping, ranking and scoring, and oral histories. The study engaged with debates around governance, bricolage, non-timber forest products, bifurcation, livelihoods and access. Findings show that the baobab tree is used in multiple ways by households, and has both consumptive values as well as intrinsic values which are typically overlooked in the discourse of natural resource governance. The study illustrates that the interest of traditional institutions in regulating baobab use and access has been informed by reasons relating to sustainable livelihoods, ecological sustainability and the need to maintain a delicate link between environmental sustainability, the spirits of the land and resource users. Local arrangements are robust, dynamic and are entrenched in the day to day lives of the resource users. These arrangements may not fit into existing technical toolkits or environmental blueprints, and policy from the top may not be connecting with reality on the ground. Although traditional authorities and customary practices have remained relevant for local people in the realm of resource governance, they are weakening in the face of commercial baobab use. Where statutory forms of governance are overlaid onto existing customary forms of governance without due regard for local practices, unintended consequences arise. A key finding is that history profoundly informs the way local people harvest and use resources due to the long trajectory of the interplay between customary and statutory forms of governance that spans back to the colonial era. The main conclusion from the study is that both customary and statutory systems of governance are important, but need to be used in a graduated manner. Statutory forms of governance can be introduced to assist customary practices on a demand-driven basis. Results emphasise the importance of considering seemingly peripheral forms of governance such as customary practices within the continuum of resource governance in rural areas.

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

Increased urbanization coupled with the effects of urban stream syndrome and urban informal settlements are degrading rivers and causing a decline in habitat integrity and the delivery of ecosystem services. There is a need to implement river restoration programmes to alleviate the negative impacts on stream ecosystems. This study aimed to determine the ability of a contaminated urban stream, draining Langrug, an informal settlement, to enrich the biodiversity of species and organisms, following a rehabilitation intervention. It was investigated how nature, in the form of biodiversity of diatoms and macro-invertebrates, were observed in the Stiebeuel River when a range of habitats were created and restored through the replanting of indigenous vegetation within the Stiebeuel River channel. The focus of the study is on understanding the value of different types of bio-assessment and water quality methodologies for informing the rehabilitation of a river system. It also illustrates how a combination of methods as opposed to a single method is able to inform the ecological integrity of habitat restoration.The results showed the current physical and biological condition of the Stiebeuel River to be heavily degraded, critically modified, with poor river health and an ecological category between D and E/F. The low DO levels and high EC levels are correlated to low SPI scores and high %PT scores, which infers that there is a significant amount of organic pollution and nutrients in the wastewater discharges from Langrug, informal settlement. The miniSASS scores link to the SPI scores, such that the low sensitivity and low SPI scores are attributed to the highly polluted water quality dictating the abundance of pollutant tolerance species. The inflow of highly polluted water from Langrug, informal settlement is responsible for driving the distribution of species in the Stiebeuel River. This highly contaminated water as a result restricted the success of the habitat intervention to enrich biological diversity and improve the ecological status of the Stiebeuel River. The results from the bio-assessment and water quality monitoring overlap and confirms the link between the three monitoring methods

Marine Protected Areas (MPAs) are an increasingly important tool for sustainable marine governance. However, their effectiveness is improved if designed to consider how people value and interact with coasts and marine resources designated for protection. This research critically examines the different perceptions of stakeholders towards the rezoning of Africa’s oldest MPA, the Tsitsikamma National Park (TNP) MPA. In South Africa, MPAs created prior to 1994 under the Apartheid regime disregarded local communities’ rights to the coast and in some cases removed or restricted access, with no consultation. In December 2016 the TNP MPA was rezoned from a 'no-take’ MPA to a partially open protected area with the aim of readdressing historical exclusion and to provide managed access and benefits to adjacent communities. This thesis explores the perceptions of different stakeholders to the rezoning process and the underlying values, worldviews and beliefs that influence these perceptions. The research also examines the nature of participation in the rezoning process, including issues of representation, trust and legitimacy. Data collection is based primarily on 55 semi structured key informant interviews from the nine different communities adjacent to the Tsitsikamma MPA, scientists, NGO and government officials, as well as a focus group with eight representatives from South African National Parks. Data sources are supplemented with census and mapping information, field observations and a participatory film project. Findings from this research identified and examined the diverse perceptions of stakeholders about the re-zoning and highlighted how different groups have very different perceptions about the benefits of the rezoning for either marine conservation objectives or community economic, livelihood and wellbeing aspirations. What emerged clearly was that perceptions are influenced by values, worldviews and beliefs and that failure to recognize and incorporate these perceptions in planning, discussions and decision-making leads to ongoing contestation and conflict. The research thus highlights the challenge of balancing community rights and needs with conservation goals in a rapidly changing marine context, and highlights that understanding different perceptions and values that underlie these perceptions and providing the space to allow these different views to be shared is important for collaborative governance of MPAs in South Africa. Based on an enhanced understanding of perceptions, recommendations are made regarding the importance of recognizing and incorporating perceptions in planning and decision-making and promoting greater participation in governance.

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.