South Africa has 3650 km of coastline that spans the boundary between the Atlantic and Indo-Pacific biomes. The coastal waters boast a remarkable array of biological diversity and high levels of species abundance and endemism. Currently around 23% of the coastline is formally protected via marine protected areas (MPA) with 9% enforced as no-take zones. Even with this relatively high level of protection (as compared to other nations globally) the MPA network is still relatively sparse with protected areas that are on average ~110 km apart and unevenly distributed with the majority of MPAs situated along the species-rich east coast. This has led to concerns that the current MPA network is not protecting a representative sample of the genetic diversity among marine species nor is it sufficiently genetically connected via dispersal and gene flow to ensure their long-term persistence. To test a number of questions regarding the distribution of genetic diversity and degree of population genetic structuring along the South African coast we analyzed mitochondrial DNA sequence data for 10 sessile rocky-shore species and one reef-fish that represent three distinct life history strategies. We find that the distribution of genetic diversity across the South African coastline closely mirrors the distribution of species richness, increasing from west to east. We also find similar levels of population genetic structure among brooders, broadcast spawners and live-bearers, demonstrating that life histories are a poor predictor of genetic connectivity for South African marine species. Finally, we find that estimates of effective dispersal distance for taxa from each of the life history categories are low (~0.5-1.5 km per generation) suggesting that populations within MPAs are reliant on populations in unprotected areas via a steppingstone model of genetic connectivity. In light of these findings, we discuss a number of recommendations to enhance the role of the existing South African MPA network and echo previous calls for the establishment of protected areas along the west coast.

The Western Cape population of Blue Cranes (Anthropoides paradiseus) is of great importance as the largest and most stable population throughout its range. This species is strongly associated with agricultural lands in the Western Cape, and therefore may come into conflict with farmers who perceive them as damaging to crops. Blue Cranes are suspected to be locally nomadic, but little information has been collated to support this and they are also relatively understudied in terms of demographic parameters. This project investigates the viability of the Blue Crane population in three ways: exploring farmer attitudes towards cranes in two regions of the Western Cape (Swartland and Overberg) using 40 semi-structured interviews, generating estimates of survival using Mark-Recapture methods and exploring movement patterns using a long-term data set of resightings of marked individuals. These three components all add important aspects to the overarch ing goal of achieving a better understanding of threats to Blue Cranes in the Western Cape, and thus the population's long-term viability. Perceptions of cranes differed widely between regions: farmers in the Swartland perceived cranes to be particularly damaging to the feed crop sweet lupin (65% of farmers reported some level of damage by cranes), and 40% of these farmers perceived cranes as more problematic than other common bird pests. Farmers in the Overberg did not perceive cranes as highly damaging, although there was concern about cranes eating feed at sheep troughs. Survival was age-structured: individuals in their first year had a survival of 0.6, those in their second and third years that of 0.87 and adult individuals (4+) that of 0.72. The adult survival estimate is suspected to be underestimated due to ring loss. Resightings of colour-ringed cranes suggest that movements in the Western Cape were localized, with an average displacement of 24.6 km from their natal point. Only 3.8% of marked individuals were resighted in both the Overberg and the Swartland regions, indicating that movement between these regions was low and regional fidelity was high. There was significant movement within the Overberg however, and 90% of movements of >10 km were made within this region. This species therefore appears to be resident to locally nomadic in nature. Evidence for natal philopatry was also found: 57% of adults returned at least once to the area where they were ringed as juveniles. These results highlight the need for location-specific management solutions to crop-damage by cranes, and contribute to the understanding of basic demographics for this vulnerable species.

Includes bibliographical references. / Alien species are the second most important cause for the loss in biodiversity globally, after habitat destruction. Marine alien species are transferred across the globe through various vectors, including ballast water, hull fouling, aquaculture facilities and the aquarium and pet trade. Ballast water has previously been considered as the primary vector of alien species transfer. However, fouling is becoming widely recognised as an important vector for the transfer of marine alien species both internationally, as well as in South Africa, where it has been reported to contribute 48% of marine species introductions. The objectives of this study were to document alien species from fouling assemblages in six South African harbours (St Helena Bay, Saldanha Bay, Table Bay, Hout Bay, Gansbaai and Mossel Bay) and to use the data collected to identify factors (such as vectors and other harbour characteristics and activities), that could be used by management authorities to target harbours upon which to focus monitoring efforts. This was done by taking subtidal scrape samples and visual samples from harbour walls and pillars. The prioritisation of harbours was obtained through the use of regression tree models utilising CART (Classification and Regression Trees).

Okhombe is a ward in the Northern Drakensberg where community based restoration of degraded lands has been conducted for over a decade. In this important water supply region, payment for ecosystem services has been suggested as a means through which to conserve biodiversity, improve veld condition, provide income to local communities, and ensure water security. However, before such alternative market mechanisms can be considered, the effects of community based restoration must be properly quantified. The primary aim of this study was to determine some of the ecological impacts of community based restoration in these communal grasslands.

Eutrophication, one of the leading global water pollution challenges, can be addressed with nature-based solutions (NBSs). NBSs use or mimic natural processes (ecosystem services) to improve water quality, for example microorganisms, plants and filter feeders have already been shown to mitigate eutrophication. However, burrowing endobenthic organisms have not yet been considered as a NBS, despite their potential to greatly impact water quality. Therefore, the purpose of this study was to determine whether these endobenthic organisms could be effective as NBSs, more specifically whether the activities of the common sandprawn (Callichirus kraussi) can improve water quality in terms of pelagic nutrient, microalgal and suspended solids concentrations. C. kraussi is a benthic ecosystem engineer that, like other endobenthic crustaceans, affects water flow, sediment biogeochemistry and benthic-pelagic fluxes through bioturbation and bioirrigation. Their elaborate burrow systems may act as biological filters for pelagic microalgae, but they may also be a source of nutrient-rich excrement inputs into the water column. To determine the effects of C. kraussi on water quality, a laboratory mesocosm experiment and comparative in situ analysis were used in this study. In the mesocosm experiment, water quality at 3 increasing C. kraussi densities (0 [control], 100 and 200 individuals·m-2 ) were compared. At the end of the experiment, the water column NH4 + concentration in the high density C. kraussi treatment was 2.6 times greater compared to the controls. Despite this increase in the NH4 + concentration, the water column chl-a concentrations were 42.8% (50% density treatment) and 44.3% (100% density treatment) lower compared to the controls. Additionally, microalgal biomasses in the sediment were less concentrated on burrow mounds created by C. kraussi compared to the adjacent sediment between mounds and within the burrows. However, the overall chl-a concentrations in the sediment did not differ between treatments. This suggests that C. kraussi has the effect of breaking up microalgal mats on the sediment surface with their burrow mounds without changing the overall sediment surface chl-a concentration, thereby maintaining benthic-pelagic coupling. C. kraussi did not affect suspended solids concentrations in the water column over the 12-day study period. For the in situ component, water quality was compared at sites where C. kraussi was present and the adjacent sections where it was absent in the Zandvlei Estuary Nature Reserve. The findings from the mesocosm experiment were reflected in situ: Chl-a concentrations in C. kraussi habitats were reduced by 43.1% from upstream areas without C. kraussi, and again increased by 32.9% from C. kraussi habitats to downstream canalised areas without C. kraussi. Differences in suspended solids concentrations were also not explained by C. kraussi presence in situ. The conclusion from this study is that ecosystem engineering by C. kraussi has an overall positive effect on water quality in urban estuaries, principally by reducing chl-a concentrations in the water column and maintaining benthic-pelagic coupling. Therefore, C. kraussi should be conserved for its water purification ecosystem services. This can be achieved by maintaining soft sediments in estuaries, rather than constructing concrete canals in which C. kraussi cannot burrow. Regulation of C. kraussi extraction for fishing bait is also necessary to prevent the loss of their filtration function. Furthermore, this study supports the use of C. kraussi as a NBS to eutrophication and encourages the consideration of similar endobenthic organisms for this purpose. Endobenthic ecosystem engineering should not be underestimated in addressing the global challenge of eutrophication.

Includes bibliographical references.

Includes bibliographical references. / Seabird bycatch in commercial fisheries is one of the major factors causing decreases in many seabird populations. In trawl fisheries, high mortalities have been recorded as a result of seabirds being struck by trawl warps (the cables used to tow the trawl net). Tori (bird-scaring) lines have been used to decrease seabird mortality in some trawl fisheries by up to 90%. However, tori lines are not effective at reducing the number of birds that drift towards the trawl warps while feeding on factory discards alongside the vessel. The Albatross Task Force (ATF) helped to develop and test a new device, the Rory Line (RL), to be used in conjunction with tori lines, and designed to reduce warp strikes by placing a physical barrier between the scupper (where factory discards are released) and the danger zone (where the trawl warps enter the water) at the stern of the vessel. This study tests the efficacy of the RL at reducing the number of birds drifting into the danger zone and the number of birds being struck by the trawl warps.

The Berg River is a pivotal source of fresh water for domestic, industrial and agricultural use as well as for in stream ecology, therefore knowledge of what impacts this rivers water quality and assessing whether ecological resilience has been surpassed are of the utmost importance. Since diatom assemblages are inextricably linked to the chemical, physical and biological characteristics of their environment, they were chosen for this study to investigate long-term changes in water quality and availability and suggest potential drivers of such changes at an agricultural site (Rhenostervlei Farm) adjacent the Berg River in the Cape lowlands through fossil diatom analysis of a sediment core (RV3). Diatoms were extracted along the length of the RV3 core, chemically and physically treated to remove unwanted material and then were mounted on a slide to be counted. Twenty abundant diatoms were chosen as environmental indicators for the analysis. Their abundances were plotted against depth and age and changes in water quality and availability were inferred based on their autecological characteristics. The most prominent shift in the indicator diatoms at Rhenostervlei Farm as shown by the stratigraphic diagrams, CONISS analysis and the PCA occurred at the onset of the 20th century CE and was characterised by a shift from a saline, dry and nutrient-poor environment (ca. 1790-1890 CE) to a more turbid, nutrient-rich environment with increased freshwater influence that was prone to periodic flooding (ca. 1890-2011 CE). Through the chronological analysis and the interpretation of the historical record (climate and land-use) as well as other environmental proxies (sediment accumulation rate and macro-charcoal), the causes of the detected change in water availability and quality at the floodplain site were likely related to land-use change in the form of agricultural intensification at Rhenostervlei Farm and potentially in the Berg River catchment as a whole. This could have involved burning, clearance of natural vegetation, soil disturbance and fertilizer use - all of which contributed to increased surface runoff, erosion and nutrient and sediment loading into the site. Furthermore, water extraction and diversion in the 1950s could explain the decreased flooding signal (i.e. lower abundance of Aulacoseira granulata). Although no evidence of a catastrophic regime shift was identified, if land-use practices continue to intensify (e.g. increased fertilizer use) and future climate change interacts and influences the agricultural alterations to hydrological systems, we may expect increased vulnerability to global change and unexpected ecological outcomes such as regime shifts. In order to improve the interpretation of fossil diatom records in terms of changing water quality and availability, a study with multiple proxies should be undertaken to help infer environmental conditions in a complex environment that has many potential drivers, such as the Berg River.

Includes bibliographical references (p. 97-104).

In this thesis I determine how an emphasis on tourism may have both a top-down and bottom-up affect on the two most dominant tree species in the southern Kalahari Desert of central southern Africa. Both tree species are considered as keystone species especially along ephemeral rivers. My focus is on the impact of the introduction of an extralimital megaherbivore, Giraffa camelopardalis, (top-down) and anthropogenic water abstraction (bottom-up) on the reproductive output and vegetation structure of Acacia erioloba and Acacia haematoxylon in the Kgalagadi Transfrontier Park. I determine the impact of giraffe on canopy structure and reproductive potential of the two tree species by comparing three zones of giraffe density (high, medium and low) along the Auob River. I do this through a series of transects through the river to determine both giraffe and tree density and also photographed several trees to determine change in canopy width, percentage canopy death and change in the number of flowers and pods between the three zones and between species. My results show a significant negative impact of giraffe browse on canopy structure, specifically for A. haematoxylon. I did not however find any significant differences in recruitment between the different giraffe density zones. However, a noticeable decrease in numbers of flowers and pods in the giraffe browse height of trees (2 - 5 m) between zones suggest that giraffe will have a negative effect on the A. haematoxylon population but not the A. erioloba population in the future. I use stable hydrogen and oxygen isotope ratios to determine the water source for the two tree species. I do this relative to the stable isotope ratio of the water extracted from nearby boreholes. I also determine how close to physiological stress the trees are (using specific leaf area, leaf δ¹³C values, canopy death and midday xylem pressure potentials) both upstream and downstream of active boreholes used for two tourist camps. One camp, Nossob, in the Nossob River is abstracting at a high rate while the other camp, Urikaruus, in the Auob River is abstracting at a lower rate. My results for water isotope ratios show that both A. erioloba and A. haematoxylon are using deep groundwater. My results also show that in the dry season, A. erioloba in the Nossob are losing contact with groundwater and have to rely on some as yet unmeasured water source in the soil profile. This 'stress' is not reflected in canopy dieback as yet. The trees continue to transpire in the dry season suggesting that they are physiologically able to adapt to fluctuations in the water table of between 4.5 - 5.2 m between the wet and dry season by closing their stomata but are prone to drought-induced carbon starvation, specifically for trees in the Nossob. Overall, my results show that the impact of giraffe on vegetation structure is already evident for A. haematoxylon, indicative of future negative effects on reproduction. My research also shows that although current levels of water abstraction are as yet not affecting vegetation structure below the abstraction points, the trees are edging closer to thresholds of water stress that would be exacerbated with drought. These findings are discussed within the context of ecosystem health and management implications for the giraffe population and water use within the Park.