A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy 29 July 2013 in Johannesburg, South Africa / Effective management of protected areas and communal rangelands, which are often juxtaposed in developing countries, is essential to prevent biodiversity decline and ensure a sustainable resource base for rural communities. However, in human-modified landscapes, there are complex interactions between factors that determine woody vegetation structural patterns. While the underlying biophysical template continues to influence vegetation patterns in a predictable manner; the intensity and type of disturbances that are the result of resource extraction, fire and herbivory can have an overriding impact. In order to effectively conserve biodiversity and plan for sustainable resource use, an understanding of land-use and land management is required. A case study of adjacent protected areas (Kruger National Park (KNP), a national protected area and Sabi Sand Wildtuin (SSW), a private game reserve) and communal rangelands (in Bushbuckridge Municipality (BBR) with varying intensities of use) in north-eastern South African savannas was used to study the spatio-temporal patterns of three-dimensional (3D) woody vegetation structure as a result of natural resource management and abiotic drivers. The aim of this PhD thesis is to advance our understanding of the effects of management of natural resources on spatio-temporal patterns of 3D woody vegetation structure across land uses in a heterogeneous semi-arid savanna system. Vegetation structure was measured using small-footprint, discrete-return LiDAR (Light Detection and Ranging) collected by the CAO (Carnegie Airborne Observatory) Alpha System over 35 000 ha across the study area. 3D woody vegetation structure was compared both within land uses (KNP versus northern SSW, and within BBR) and between land-uses (southern SSW versus BBR) to address two objectives, namely 1. Can LiDAR be used as a monitoring tool for management of woody vegetation structure and biodiversity in semi-arid savannas and 2. What is the impact of land use and the corresponding management of resources on woody vegetation structure in semi-arid savannas? Different land-use legacy timelines and current management objectives at sites in KNP and northern SSW has resulted in an average of 2.5 times higher vegetation density <3 m and >6 m in SSW. These differences in vegetation structure are exacerbated by current management practices, with implications for faunal biodiversity conservation across all scales. Not all reserves are equal in their ability to conserve biodiversity and such knowledge should be considered in conservation planning and management. In the communal rangelands, intense fuelwood harvesting has resulted in coppiced trees <3 m in height, and the only trees >5 m are preserved for cultural reasons, producing similar vegetation patterns to Sabi Sand Wildtuin. Disturbance (extraction and grazing) gradients occur with distance from settlements, with utilization intensity affecting vegetation cover within the size class distributions, but not the shape. Gradients diminish under heavier utilization resulting in a more structurally homogenous landscape, which may be used as an early warning sign of woodland degradation. The increase in >3 m tall trees was twice as high in low intensity use CRs adjacent to SSW compared to those in southern SSW from 2008 to 2010, indicating the impacts of treefall from megaherbivores and fire management reducing plant recruitment/regeneration in the protected area. Knowledge from investigation of socio-ecological drivers in the two land-uses were used to construct an ecologically relevant 3D woody vegetation structural classification which can be used by land managers to plan for sustainable resource use and effective conservation of biodiversity. The management of natural resources, including direct use of fuelwood and the management of herbivory and fire affects woody structural dynamics; however, a lack of knowledge exists around the social and ecological context of natural resource management. The use of remote sensing, the knowledge of savanna ecology and an understanding of community-based natural resource management is integrated in this thesis to contribute to the context specific understanding of drivers of woody vegetation structure in two socio-ecological systems (protected areas and communal rangelands) which can be used in sustainable natural resource management plans.

Ph.D., Faculty of Science, University of the Witwatersrand, 1997

A dissertation submitted in fulfilment of the academic requirements for the degree of Master of Science in the School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg. June 2016 / The African baobab (Adansonia digitata) is a charismatic and iconic tree. This keystone species has highly specific moisture requirements for recruitment, a very slow life history, low dispersal capabilities, and is exposed to heavy, often destructive utilization by baboons, elephants and humans. These characteristics result in the reduced ability for baobabs to accommodate and respond to changing environmental conditions. During periods of unfavourable conditions, baobabs rely on the persistence of established individuals for the survival of the population. The Kruger National Park (KNP), South Africa falls within the southern-most distribution of the baobab. A perceived lack of recruitment together with high numbers of dead large baobabs recorded in aerial surveys prompted concern over local population decline in the early 1990s. Long-term monitoring is necessary in order to quantify changes occurring within the KNP baobab population. For this reason Dr Ian Whyte sampled 424 baobab trees in northern KNP in 1995/1996 to describe population size-class distributions and elephant damage. Nearly all of these baobabs, with the addition of 486 individuals were resampled in 2001 by Michele Hofmeyr. This study resampled the majority of these 910 baobabs plus 126 individuals within 50m of those previously sampled, culminated in a data set spanning 18 years and most of the dominant vegetation and climatic zones within the baobab’s KNP range. Photographs taken in 1995/6 and repeated in 2013 allowed for simultaneous direct visual comparisons of elephant damage to baobab stems. This study aimed to record the temporal and spatial changes in the demographics of, and damage to, this sample of 1036 baobabs in order to define and evaluate the factors threatening KNP baobab persistence. The overall population stem diameter structure of baobabs in the KNP showed a healthy inverse J-shaped distribution, with a high proportion of smaller trees and a decreasing proportion of larger trees at each sampling snapshot. However no seedling recruitment was observed during intensive searches within 50m of sampled trees, accumulating in a total area of 4km2. Growth was only noticeable in sub-adult trees >0.15m and <1m in stem diameter. Annualised mortality increased three-fold between the periods 1995/6-2001 (0.25%) and 2001-2013 (0.79%). It is speculated that this increase in mortality is due to the cumulative effect of increased elephant damage, together with below average rainfall years of 2002 to 2013. Trees that had previously sustained severe and very severe damage contributed the highest proportion (32%) of mortality. When comparing sizeclasses, the majority of mortality (61%) was recorded within the <1m stem diameter size-class. However, a high proportion of very large trees (21% of the 4- 4.5m and 29% of the 5-5.5m stem-diameter baobabs sampled) had died from unknown causes. With no recruitment of seedlings evident and little recruitment between size classes, mortality alone was not enough to significantly change the baobab population structure between 1995/6, 2001 and 2013. This might change should more very large (>4m stem-diameter) trees die, as these size classes make up less than 2% of the population. At a spatial scale, maximum fire return interval, level of elephant damage and mean annual temperature all had significant impacts on the size-class distribution of baobabs. Longer (>30 years) maximum fire return intervals and higher mean annual temperatures (23°C) supported an inverse J-shaped baobab population structure whilst shorter (<30 years) maximum fire return intervals and lower mean annual temperatures (21-22°C) supported a bell-shaped population structure. Increases in bark damage over time correlated with increased elephant density (primarily attributed to mature male elephant density). Smaller baobabs – those less than <1m in stem diameter, generally escaped elephant utilization altogether, or suffered very severe damage by elephants. Despite a 3-fold increase in mortality and no recruitment over the 18 year study period, the KNP baobab population has maintained its inverse J-shaped population structure. The high proportion of mortality in the >4m stem diameter is however concerning as the persistence of these large baobabs is essential for the survival of the population during unfavourable conditions for recruitment.

MSc., Faculty of Science, University of the Witwatersrand, 2011 / Abundance counts of ungulate species which are carried out using an aerial census are susceptible to measurement errors. These measurement errors result from environmental factors such as vegetation cover and the resultant effect that factors, such as the annual rainfall pattern, have on the accuracy of the count. Given these measurement errors, models of population abundance that are based on these counts should not only account for the population dynamic process - they need to model the measurement error process simultaneously in order to produce plausible estimates. In addition to this, the recorded counts from these censuses do not give a breakdown of the total count into the different gender and life-history stages of the animals counted. This research report investigates the usefulness of a hierarchical Bayesian hidden process modelling approach at explicitly including the measurement error process and a sub-model for the gender and life-history stage of the animals counted into a population dynamics model based on the aerial census counts. The data used are aerial counts of Kudu in the Kruger National Park from 1983 to 1993. The result is a model which estimates the measurement error in each year of the census and also breaks down the overall count into the numbers in each gender and life-history stage. The usefulness of the model is evaluated based on statistical model diagnostics.

I describe the spider biodiversity for a savanna ecosystem, assess sampling techniques, investigate surrogate measures of species richness and measure the biotic and abiotic processes affecting spider diversity. Spiders were sampled at Makalali Game Reserve, Northern Province, South Africa from February to December 1999 using pitfall traps, sweep netting, beating and active searching. A total of 4832 individuals from 268 species (14 potentially new), 147 genera (8 endemic and 2 new records for South Africa) and 37 families (1 new record for South Africa) were recorded. There was no overall significant difference in spider diversity among different physiognomic habitat types. However, analysing the results at a functional group level revealed that the web builders were significantly affected by the habitat type. Mopane woodland habitat type had the greatest number of web builders and general bushveld the least. Sweeping and active searching sampled the greatest number of individuals and species respectively. I recommend a combination of at least beating and active searching, which together sampled the highest number of unique species, for efficient and cost effective surveys. There was a significant relationship between the spider species richness and other invertebrate richness. However, the relationship is not significant when functional groups are considered separately. There was also a significant relationship between the number of species and families and species and genera. However, species level identifications remain ideal for conservation purposes. Inexperienced participants significantly overestimate the number of species. The use of surrogates is not supported by the work conducted in this study. It is still unclear what biotic and abiotic processes or combination of processes influence spider diversity patterns at the local scale. Different spider functional groups are significantly influenced by different factors. However, habitat diversity (branches and vegetation density) was the most common factor influencing spider diversity . Predicted diversity (modelled using GIS and beta-coefficients from multiple regression analyses) was higher than measured diversity values. While further research into the role of other environmental variables is clearly required, current reserve management should aim to maximise microhabitat structural diversity. / Thesis (M.Sc.)-University of Natal, Durban, 2000.

The feeding of the cichlid fish Sarotherodon mossambicus in Lake Sibaya, KwaZulu, was studied in relation to various biotic and abiotic features of the l ake environment from January, 1973 to July, 1975. The primary goal of the study was to determine the cause of stunting and poor condition of adults in this population. Juvenile and adult S. mossambicus feed on a mixture of detritus, bacteria and diatoms that occurs as a flocculent layer on sand substrates throughout the lake. Concentrated gastric acid, commonly at pH values of 1.5 and lower, lyses diatoms and bacteria which are subsequently digested in the intestine. This is the first report of digestion of bacteria by a fish, and the nutritional significance of the finding is discussed. Juveniles feed predominantly on shallow sand terraces found along the margin of much of the lake, while adults usually feed in offshore waters at depths of 3 m and greater. Benthic floc from feeding areas of juveniles and adults have similar concentrations of organic matter, total carbohydrate, soluble carbohydrate and calories, but differ markedly in respect to diatom and protein concentration. Diatom concentrations are generally high in terrace floc but are consistently low in floc from deep water. Protein concentration of benthic floc decreases with increasing depth from 0 - 5 m. Partial correlation analysis shows that protein and diatom concentrations have no correlation independent. of their common relationship to depth, and the evidence implicates detrital bacteria as the primary source of protein in benthic floc. Probable causes of the observed distributions of diatoms and protein are discussed. The protein content of benthic floc profoundly influences its nutritional value. A comparison with available data on animal nutrition shows that the ratio of digestible protein to digestible energy in floc in the shallows is high enough that this food resource would be expected to support good growth, but the ratio for deep water floc is so low that it would be expected to result in conspicuous malnutrition. Thus, inadequate dietary protein is identified as the principal cause of stunting and poor condition of adult S· mossambicus in Lake Sibaya; It is argued that the ratio of digestible protein to digestible calories can be expected to determine the food value of particulate organic matter that includes amorphous detritus in other ecosystems. Despite stunting and poor condition of adults, S. mossambicus are abundant in Lake Sibaya. The precocious breeding of this population is discussed as an adaptation that allows it to maximize reproductive output given the limited resources available to adults. Juvenile S. mossambicus perform daily movements from deep water onto the terraces where they feed and then back into deep water. During periods of relatively low lake level when terrace waters were usually less than 1.5 m deep (1-73 to 1-74), juveniles were present on the terrace throughout daylight hours. At relatively high lake levels (7-74 to 8-75), juveniles were present on the terraces for only about five hours following sunset. Periods of heavy wave action interrupt feeding activity and result in reduced numbers of fish in terrace waters. The possible roles of predator avoidance and temperature in determination of daily feeding behavior are discussed. Daily energy assimilation by juveniles, estimated by a field technique, is approximately 115 cal per g fish dry weight.

Various aspects of the feeding ecology of zooplankton are described for hypertrophic Hartbeespoort Dam, where the phytoplankton is dominated by the cyanophyte Microcystis. The study considers zooplankton succession, community grazing rates, and speciesspecific filtration rates on Microaystis colonies and natural bacterioplankton. Seasonal abundance of the main herbivorous zooplankton between 1981 and 1986 is described both in respect of biomass and specific densities. In situ community grazing rates were measured from January 1983 to March 1985 using 14C-Iabelled Chlorella . Zooplankton succession and community grazing rates are examined in relation to food quantity and quality. Experiments measuring species-specific filtration rates on labelled Chlorella and Microcystis colony fractions revealed low filtration rates for small-bodied cladoceran species on cyanophyte colonies. Daphnia fed significantly on Microcystis colonies up to 60-100 ).μm but Daphnia filtration rates on Chlorella were suppressed by ~707. during the mid-summer increase in Microcystis abundance. Filtration rates of small cladoceran species were not suppressed by MicpocystisJ which was not an important food resource . Cladoceran filtration rate:body length models were developed for Chlorella and Microcystis colony fractions as food. Multiple regression models explained variance in filtration rates on these foods as a function of body length, food type and size, grazer species and temperature (in order of significance). Inclusion of food quality factors such as cyanophyte colony size seems justified in models of plankton feeding in eutrophic or hypertrophic lakes. Methods for in situ measurement of zooplankton filtration rates on 'H-thymidine-Iabelled natural bacteria were improved for use under hypertrophic conditions, and associated isotope-adsorption errors were measured. Community, species-specific and length-specific filtration rates on bacterioplankton were measured (late-spring to late-summer 1986-87) . Ceriodaphnia exhibited no preference for bacteria or Chlorella. Other cladocerans preferred the algal food . Algal/bacterial selectivity coefficients of the zooplankton community revealed an increased algal preference following the mid-summer shift to phytoplankton dominance by largely inedible Microcystis. This implies that bacterioplankton is not an important food resource for the summer cladoceran community. Estimates of the contribution of bacterial carbon to the daily zooplankton carbon requirements are low. The implications of all results are discussed in relation to seasonal succession, the clear-water phase', and biomanipulation in this hypertrophic reservoir.

Benthic filter feeders have a key functional role in the dynamics of coastal food web as an intermediate trophic level and bioengineers. A wide variety of factors, operating across multiple spatial scales (e.g. hydrographic regime, human activities), can affect the composition of the water column and thus the availability of food for benthic populations. Food availability in turn affects the growth, reproductive rates and survival of benthic organisms, and consequently, can influence the functioning of the entire ecosystem. This study aims to evaluate how various environmental factors may modify the diet of intertidal filter feeders living along the South African coast. Specifically, the effects of biogeography, upwelling, urbanization and freshwater input on the dietary regimes of five species of filter feeders (two mussel and three barnacle species) were investigated using fatty acid (FA) and stable isotope (SI) analyses.Strong interspecific differences were found among the five species considered. However, all species responded to factors operating at large (100s km) and meso (10s- 100s km) scales (i.e. biogeography and upwelling respectively). The barnacles exhibit habitat segregation and showed different FA and SI signatures from each other, while the two mussel species, an invasive and native species that co-occur in the same mussel beds, had partially overlapping diets. Differences in their diets were found only using FA analysis, while their SI signatures differed on only one occasion. This highlights the importance of using the appropriate tool, and ideally combined techniques, to investigate diets.FA and SI signatures of all species considered changed among the three biographical provinces (west, south and east coasts of South Africa) exhibiting similar patterns that reflect the two oceanographic regimes that characterize the coastline: the eutrophic Benguela Current on the west coast and the oligotrophic Agulhas Current on the other two coasts. Upwelling had a significant effect on FA and SI signatures, with stronger effects on the west coast than the south coast. The results indicate that benthic filter feeders at upwelling areas consumed a mix of coastal macroalgal detritus and phytoplankton, which was probably brought onshore during downwelling events. At smaller spatialscales and using repeated sampling, the influence of upwelling on the west coast was found to be pervasive, rather than discrete, so that it may be more appropriate to categorize upwelling by referring to upwelling centres and downstream areas. SI underlined a significant effect of urbanization on the diet of filter feeders with an enrichment in the δ¹⁵N being characteristic of anthropogenic effect. Although a large number of rivers characterize the South African coast, no distinct effect of freshwater input was found for either the SI or FA signatures of the filter feeders. This contrasts with earlier work on demersal species and suggests that freshwater input does not significantly affect food availability for intertidal filter feeders, and that other factors (e.g. hydrogeography) are more important in determining the diet of these populations. These results highlight that environmental and anthropogenic factors operating at different spatial and temporal scales have a profound effect on benthic ecosystems, and that they control the relationship between primary production and primary consumers in coastal areas. Above all, this work highlights the importance of understanding the spatial and temporal scales at which different factors affect feeding regimes, and their critical role in coastal food webs.

Mangroves in South Africa are prone to anthropogenic pressures such as browsing and trampling by livestock and by natural disturbances such as drought and floods. These mangroves exist at one of the most southerly limits in the world providing a unique opportunity to study recovery and resilience to change. This study used long term data at three South African study sites located in the subtropical (St Lucia Estuary) and warm temperate regions (Nxaxo and Kobonqaba estuaries) to compare mangrove growth rate, population structure and responses to disturbance. The first objective was investigated at St Lucia Estuary where site specific or microhabitat differences were measured to assess the influence of these on mangrove growth and population structure. It was suggested that site - specific variability would ensure mangrove survival and analysis showed that seedlings were present at different sites in different years. There was always some recruitment but often little survival to the next size class. Over time seedling numbers were quite variable and self – thinning of adults was evident. The second objective was to identify the environmental factors influencing population density and growth. Results showed that sediment moisture and salinity influenced seedling and adult density due to fluctuations in estuary water level. Mangrove growth rates for Avicennia marina in terms of height was faster (40 – 75 cm yr-1 ) at Site 1 where conditions were waterlogged and moderately saline and slower (5 – 25 cm yr1 ) in dry and hypersaline conditions at Site 4. Overall mangroves at St Lucia have shown persistence through drought and fluctuations in environmental conditions however resilience may be hindered at sites that are subjected to partially flooding and prolonged waterlogging. The second site was Nxaxo Estuary in the Eastern Cape where cattle exclusion plots (nonbrowsed) and control plots (browsed) were used to assess the recovery of A. marina trees from cattle browsing. Trees in the browsed plots showed no vertical growth while trees in the non-browsed plots grew significantly faster (5.4 ± 0.5 cm yr-1). When cattle were prevented from entering the mangrove area, the trees recovered fairly quickly and within 3 years growth was similar in both the non – browsed (17.9 ± 3.2 cm yr -1) and browsed plots (18 ± 1.6 cm yr -1). Lastly, mangrove recovery was investigated at Kobonqaba Estuary where long-term closure of the mouth to the sea resulted in high water levels, inundation of pneumatophores and die-back of the majority of the mangroves. This study measured the recovery of the mangroves by assessing changes in vegetation cover and sediment characteristics along transects. High initial porewater nutrient concentrations promoted salt marsh growth and plants increased average cover from 0% in 2011 to 18.9% (2013) and 50% in 2015. The total number of A. marina individuals increased from only seven to 27 individuals over four years. Salt marsh competition and facilitation will likely influence mangrove recovery in the future. Overall it was concluded that when a short term pressure (cattle browsing) is alleviated, mangrove forests even at warm temperate sites are able to recovery rapidly by increasing growth and seedling establishment. However, mangroves in the subtropical sites show more resilience and recovery potential to long term pressures such as fluctuating environmental conditions because of faster growth rates.

The Fynbos biome in south-western South Africa is a global biodiversity hotspot vulnerable to climate change. Of the six Fynbos-endemic passerines, Cape Rockjumpers (hereafter Rockjumpers; Chaetops frenatus) are most vulnerable to increases in temperature, with population declines correlated with warming, and low physiological heat thresholds. Rockjumper’s preferred mountain habitat is predicted to decrease as they lack opportunity to move to cooler regions as temperatures warm. As Rockjumpers currently occupy the coldest regions of the Fynbos, I hypothesized their thermal physiology would show cold adaptation at the expense of lowered ability to cope with higher temperatures. I aimed to determine the seasonal 1) maintenance metabolism and cold tolerance, and 2) thermoregulatory responses to high temperatures of Rockjumpers. I measured seasonal maintenance metabolic rate, thermal conductance, and maximum thermogenic capacity. I also measured seasonal resting metabolic rate, evaporative water loss, evaporative cooling efficiency, and body temperature at high air temperatures. In winter, Rockjumpers had higher maximum thermogenic capacity, lower maintenance metabolic rate, and lower thermal conductance. Lower maintenance metabolic rates (and thus, lower metabolic heat production) combined with the decreased thermal conductance, confers substantial energy savings in winter. The increased winter maximum thermogenic capacity of Rockjumpers was expected, although the mean seasonal values fell below those expected for a ~ 50 g bird using a global data set, suggesting Rockjumpers are not especially cold tolerant. I further show that in summer Rockjumpers had higher elevations in resting metabolic rates, evaporative water loss, and body temperature, denoting higher rates of heat production and lower heat thresholds in summer compared to winter. My results suggest that Rockjumpers are best suited for relatively mild Krista Oswald Dissertation Chapter 1: General Introduction temperatures. While I found further support for a physiological basis for declining Rockjumper populations, further studies on other mechanisms Rockjumpers may possess to cope with climate warming (e.g. behavioural adjustments) are needed in order to truly understand their vulnerability to climate change.