Electronic Theses and Dissertations (PhDs)

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The application of machine learning methods to satellite data for the management of invasive water hyacinth
(University of the Witwatersrand, Johannesburg, 2023-06) Singh, Geethe; Reynolds, Chevonne; Byrne, Marcus; Rosman, Benjamin
Biological invasions are responsible for some of the most devastating impacts on the world’s ecosystems, with freshwater ecosystems among the worst affected. Invasions threaten not only freshwater biodiversity, but also the provision of ecosystem services. Tackling the impact of invasive aquatic alien plant (IAAP) species in freshwater systems is an ongoing challenge. In the case of water hyacinth (Pontederia crassipes, previously Eichhorniae crassipes), the worst IAAP presents a long-standing management challenge that requires detailed and frequently updated information on its distribution, the context that influences its occurrence, and a systematic way to identify effective biocontrol release events. This is particularly urgent in South Africa, where freshwater resources are scarce and under increasing pressure. This research employs recent advances in machine learning (ML), remote sensing, and cloud computing to improve the chances of successful water hyacinth management. This is achieved by (i) mapping the occurrence of water hyacinth across a large extent, (ii) identifying the factors that are likely driving the occurrence of the weed at multiple scales, from a waterbody level to a national extent, and (iii) finally identifying periods for effective biocontrol release. Consequently, the capacity of these tools demonstrates their potential to facilitate wide-scale, consistent, automated, pre-emptive, data-driven, and evidence-based decision making for managing water hyacinth. The first chapter is a general introduction to the research problem and research questions. In the second chapter, the research combines a novel image thresholding method for water detection with an unsupervised method for aquatic vegetation detection and a supervised random forest model in a hierarchical way to localise and discriminate water hyacinth from other IAAP’s at a national extent. The value of this work is marked by the comparison of the user (87%) and producer accuracy (93%) of the introduced method with previous small-scale studies. As part of this chapter, the results also show the sensor-agnostic and temporally consistent capability of the introduced hierarchical approach to monitor water and aquatic vegetation using Sentinel-2 and Landsat-8 for long periods (from 2013 - present). Lastly, this work demonstrates encouraging results when using a Deep Neural Network (DNN) to directly detect aquatic vegetation and circumvents the need for accurate water extent data. The two chapters that follow (Chapter 3 and 4 described below) introduce an application each that build off the South African water hyacinth distribution and aquatic vegetation time series (derived in Chapter 2). The third chapter uses a species distribution model (SDM) that links climatic, socio-economic, ecological, and hydrological conditions to the presence/absence of water hyacinth throughout South Africa at a waterbody level. Thereafter, explainable AI (xAI) methods (specifically SHapley Additive exPlanations or SHAP) are applied to better understand the factors that are likely driving the occurrence of water hyacinth. The analyses of 82 variables (of 140 considered) show that the most common group of drivers primarily associated with the occurrence of water hyacinth in South Africa are climatically related (41.4%). This is followed by natural land cover categories (32.9%) and socio-economic variables (10.7%), which include artificial land-cover. The two least influential groups are hydrological variables (10.4%) including water seasonality, runoff, and flood risk, and ecological variables (4.7%) including riparian soil conditions and interspecies competition. These results suggest the importance of considering landscape context when prioritising the type (mechanical, biological, chemical, or integrated) of weed management to use. To enable the prioritisation of suitable biocontrol release dates, the fourth chapter forecasts 70-day open water proportion post-release as a reward for effective biocontrol. This enabled the simulation of the effect of synthetic biocontrol release events under a multiarmed bandit framework for the identification of two effective biocontrol release periods (late spring/early summer (mid-November) and late summer (late February to mid-March)). The latter release period was estimated to result in an 8-27% higher average open-water cover post-release compared to actual biocontrol release events during the study period (May 2018 - July 2020). Hartbeespoort Dam, South Africa, is considered as a case study for improving the pre-existing management strategy used during the biocontrol of water hyacinth. The novel frameworks introduced in this work go a long way in advancing IAAP species management in the age of both ongoing drives towards the adoption of artificial intelligence and sustainability for a better future. It goes beyond (i) traditional small-scale and infrequent mapping, (ii) standard SDMs, to now include the benefits of spatially explicit model explainability, and (iii) introduces a semi-automated and widely applicable method to explore potential biocontrol release events. The direct benefit of this work, or indirect benefits from derivative work outweighs both the low production costs or equivalent field and lab work. To improve the adoption of modern ML and Earth Observation (EO) tools for invasive species management, some of the developed tools are publicly accessible. In addition, a human-AI symbiosis that combines strengths and compensates for weaknesses is strongly recommended. For each application, directions are provided for future research based on the drawbacks and limitations of the introduced systems. These future efforts will likely increase the adoption of EO-derived products by water managers and improve the reliability of these products.
South African Podocarpaceae distribution interpreted from a physiological and population genetics perspective
(University of the Witwatersrand, Johannesburg, 2023-09) Twala, Thando Caroline; Fisher, Jolene T.; Glennon, Kelsey L.
Podocarpaceae (podocarp) are the most diverse conifer family with a Southern Hemisphere distribution. Podocarps occur in Afrotemperate and Afromontane forests at high elevations that are cool and humid. Podocarps once dominated the forest canopy but due to their slower growth rate and photosynthetic rates they have are in competition withangiosperms which have faster growing and higher photosynthetic rate. Due to the competition between podocarps and angiosperms, Bond (1989) proposed that podocarps were excluded to nutrient poor and unfavourable environments due to their limited competitive ability. However, podocarps persist under the forest canopy until conditions become favourable. This power dynamic shifts with climate oscillations where podocarps distributions expand and dominate when conditions become cooler. Owing to podocarps being the most diverse and widespread conifers they make for a good study system. This thesis focuses on understanding the climatic variables driving the current and future distribution of podocarps, how their seedling physiology may influence their ability to recruit and establish under climate change, and how this can influence their ability to disperse in their South African distribution. Ensemble species distribution modelling was used to characterise the current and future distribution of podocarps and identify the climatic variables that influence their distribution. The current and future environmental niche was quantified using environmental niche modelling. I found that variables predicting rainfall seasonality were the most important at determining the distribution of podocarps in South Africa. Afrocarpus falcatus and P. latifolius were predicted to have the largest geographic distribution, with P. henkelii and P. elongatus having restricted distributions. Both A. falcatus and P. latifolius were predicted to occur in the Limpopo, Mpumalanga, KwaZulu-Natal, Eastern Cape and Western Cape provinces of South Africa. Podocarpus henkelii was predicted to occur in the KwaZulu-Natal and Eastern Cape provinces. Podocarpus elongatus is endemic to the Western Cape Province. All four podocarps were predicted to expand to higher altitudes (up the escarpment) under climate change and contract in its coastal distribution. Although P. elongatus was predicted to occupy the smallest geographic distribution it was predicted to have the widest environmental niche than the other species, which was predicted to contract under climate change. The environmental niche of P. latifolius and P. henkelii was predicted to remain stable. Afrocarpus falcatus, P. latifolius, and P. henkelii showed niche conservatism, however, P. elongatus under RCP 4.5 → current and the RCP 8.5↔ current niche comparisons showed niche divergence. Podocarpus elongatus was predicted to expand to an environment it currently does not occupy. Ecophysiological and morphological experiments were conducted to understand how podocarp seedlings respond to drought and elevated temperatures. The experiments indicated that P. henkelii seedlings were more drought and heat tolerant than A. falcatus seedlings. Conditions are predicted to become hotter and drier in some parts of South Africa, and this study has shown that P. henkelii seedlings will be able to tolerate these conditions better than A. falcatus seedlings. Furthermore, this suggests that the distribution of P. henkelii is not constrained by its physiology but rather by other mechanisms such as competition, reproductive biology, and/or shade tolerance. Microsatellites were used to inform us about possible podocarp dispersal patterns in A. falcatus, P. latifolius and P. henkelii in South Africa. The results suggested that podocarp populations in South Africa were shown to have higher genetic diversity than other podocarps globally, however these results may be due to the limited number of microsatellites used in this study, smaller population sizes in comparison to other studies and methods used to measure population structure and diversity. As expected, the geographically widespread species (A. falcatus and P. latifolius) are more diverse than the geographically restricted P. henkelii. Geographically distant A. falcatus and P. henkelii populations showed higher differentiation than geographically proximal populations. In P. latifolius South African populations, there was strong isolation by distance. Although the distribution of podocarps is disjunct, there is dispersal between populations. Podocarps are resilient to climate change as was demonstrated by the work in this thesis, and by their paleodistribution expanding and contracting with climate oscillations. In this thesis I considered climate, ecophysiology and genetics as determinants of podocarps distribution. Under climate change, podocarps are predicted to expand to higher elevations to track favourable climatic conditions. Seasonal drought is the most important climatic determinant of podocarp distribution. The ability of these species to tolerate drought and heat stress suggests that the seedlings might be able to tolerate short periods of drought and heat stress, however prolonged exposure may lead to seedling mortality, but populations will then be maintained by adults. Populations show evidence of gene flow, indicating they will be able to persist through changing climates, as they have done in the past. This thesis has highlighted that the factors constraining podocarp distributions might be demographic, and future works should investigate the role of fire in podocarp seedling establishment and longevity, as well as their interactions with angiosperm competitors.
The past, present and future of cactus invasions in South Africa in response to rising atmospheric CO2 and climate change
(University of the Witwatersrand, Johannesburg, 2023) Venter, Nicolaas; Byrne, Marcus
Cactaceae originate from the Americas and over the past 250 years have been introduced into South Africa and elsewhere for agricultural and horticultural purposes. Numerous species, including useful taxa, have become important invasive weeds that have serious socio-economic and environmental impacts. Fortunately, management strategies, in particular biological control, have been successful in controlling certain species. However, with rising atmospheric CO2 invasive cacti are likely to pose a renewed threat, whereby evidence shows that cactus species are responsive to CO2 fertilisation, which is likely to increase their vigour, mainly through improved water use efficiency (WUE). Additionally, studies show that plant quality declines with increasing CO2 which in general has negative effects on their arthropod herbivores. This study sought to determine the effect of CO2 on two functionally different invasive cactus species and how they may respond to predicted increases in atmospheric CO2. Opuntia stricta (a succulent shrub) is an obligate CAM photosynthetic species that invades grasslands and savannas across semi-arid to subtropical environments whereas Pereskia aculeata (a scrambling woody vine with well-developed leaves) is a CAM-cycling photosynthetic species that invades forest type habits across subtropical environments. Plants were grown at three CO2 concentrations that represented pre-industrial (sub-ambient - 250 ppm), current (ambient - 400 ppm) and future (elevated - 600 ppm) atmospheric CO2 conditions. Plants were also subject to suboptimal and optimal watering treatments for the duration of the experiments to determine the ameliorative effect of CO2 on productivity in response soil moisture deficits. In addition, an experiment was conducted on O. stricta to test the effects of the three CO2 concentrations on plant quality and the subsequent effect on the fitness and efficacy of its insect biological control agent, Dactylopius opuntiae. Growth and productivity of O. stricta and P. aculeata responded positively to increasing CO2, however the responses varied with CO2 concentration. Increasing atmospheric CO2 concentration from date of introduction to present possibly facilitated O. stricta invasion whereas this was less likely for P. aculeata. In both species WUE increased with increasing CO2. Under suboptimal watering, there was partial amelioration of productivity at 600 ppm CO2, but the plant traits that benefitted varied according to species. Plant quality declined for both species, most notably cladode nitrogen (N) content decreased, and carbon/nitrogen ratios (C/N) increased. When D. opuntiae were exposed to O. stricta grown at elevated CO2 (only tested on well-watered plants), D. opuntiae fitness was reduced which in turn reduced the rates of plant mortality due to the insect damage. Using the WUE results from O. stricta, a mechanistic species distribution model (SDM) created here predicted greater increases in its potential distribution in South Africa under climate change relative to the SDM that did not include WUE as a predictor variable. This suggests that improved WUE under future CO2 concentrations can offset the effect of declining rainfall in certain regions of South Africa. Overall, these results suggest that O. stricta and P. aculeata will show more vigorous growth and are also likely to expand their ranges into regions where rainfall currently limits their distribution. This expanded distribution may be further facilitated by reduced biocontrol agent efficacy as host plant quality declines. These findings suggest that management of these two species and other invasive cacti is likely to become more challenging with increasing atmospheric CO2 and climate change.
The Impact of different levels of organic plant-based compost on the macro and micro elements, secondary metabolites and water soluble vitamins content of Moringa oleifera leaves
(University of the Witwatersrand, Johannesburg, 2023) Ngwenya, Nkazimulo; Risenga, Ida M.; Chimuka, Luke
Moringa oleifera leaves are a high source of phytochemicals and nutrients inclusive of macro and micro elements, secondary metabolites and water-soluble vitamins. All the M. oleifera plant parts inclusive of its leaves have been widely utilised for nutritional and/ medicinal properties because of its high levels of minerals and phytochemicals. Studies have been conducted targeting the improvement of the quantity of M. oleifera nutrient content. However, with increased consumer awareness of high quality organic, consumer and environmentally safe products there is increased need to improve the quality of M. oleifera products. One of the major factors impacting the quality and quantity of M. oleifera leaf nutrients is cultivation practices. Particularly soil amendments applied to improve plant biomass have also been found to significantly improve nutrient content of M. oleifera leaves. However, the popularly used soil amendments which are in the form of synthetic fertilisers or animal based compost have raised environmental and product safety concerns. They contain, among other contaminants, traces of heavy metals and other toxins which are harmful to both the environment and consumers of the produce. Producers of herbal plants such as M. oleifera are looking for sustainable, environmental safe ways of improving the quantity and quality of the produce. Application of organic plant based compost was therefore investigated as a potential soil amendment source in improving M. oleifera nutrients in an organic, clean sustainable way, and thus improving the quality of the produce. The use of plant based compost to improve the nutritional content of M. oleifera grown in South Africa was reported in this thesis. The primary objective of the study was to assess the impact of the plant-based organic compost on the macro and micro elements composition, secondary metabolite accumulation and distribution and water soluble vitamins content in M. oleifera leaves. This work is novel and worth exploring as it seeks to investigate for the first time the correlation between the use of plant-based organic compost and quality improvement in terms of nutrient content of M. oleifera leaf biomass. Furthermore, this research is the first of its kind which looks at the impact of compost on the nutritional content encompassing, macro and micro nutrients, secondary metabolites and water soluble vitamins in M. oleifera grown in South Africa. In addition, the developed and validated high performance liquid chromatography (HPLC) method for the simultaneous quantification of five B vitamins was successfully used in the identification and quantification of the vitamins. Clay soil and M. oleifera seeds used in the study were obtained from the M. oleifera community farm in Hammanskraal, Gauteng, South Africa. The clay soil was amended with plant-based organic compost purchased from the local nursery store. The amendments achieved four treatment levels namely 15 % compost / soil amendment, 30 % compost / soil amendment, 45 % compost / soil amendment and 60 % compost / soil amendment. Moringa oleifera seeds used were obtained from the same farm. Plant samples were grown in the School of Animal, Plant and Environmental Sciences (APES), University of the Witwatersrand, greenhouse under ambient temperatures. Harvesting of the leaf biomass was done after six months and nutrient analysis was carried out. Analytical techniques such as Spectroscopy and Chromatography were used for the nutrient analysis. Presence and quantity of macro and micro elements in the soil and leaves was analysed using the Inductively Coupled Plasma Optical Emission spectroscopy (ICP-OES). Whilst, the Ultra high-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS) was used to determine plant metabolites, and for the quantification of water-soluble vitamins by coupling it with the diode array detector (DAD). The nutrient analysis revealed that the use of organic plant-based compost for the amendment of clay soil improved the quality of the soil and M. oleifera leaves harvested from each soil amendment. The addition of the organic plant-based compost improved the macro and micro nutrients. Comparison of the different compost levels revealed that addition of plant based compost increased the bioavailability of macro and micro nutrients in the soil and increased their accumulation in M. oleifera leaves. Metabolic fingerprinting of M. oleifera leaf samples using UHPLC-ESI-QTOF-MS followed by untargeted compound analysis exposed variation in the identified metabolites. Further use of multivariate analysis in the form of PCA clustered the samples into five distinct clusters indicating diversity in the distribution of secondary metabolite as influenced by the addition of plant-based compost to the soil. The developed HPLC method was suitable for the simultaneous quantification of five B vitamins based on the low LOD and LOQ values, recovery of 97.8- 99.58% and good linearity. Application of the validated method revealed that, the addition of plant based compost significantly improved the quantity of the tested vitamins (Vitamin B1, B2, B3, B6 and B9). The 30% plant-based organic compost and clay soil combination was identified and recommended as the best compost-soil combination in improving nutrients in M. oleifera leaf biomass. It had the highest level of macro and micro nutrients. Leaves harvested from this soil/compost combination had higher concentration of Ca (45 042.5 mg/Kg), Mg (17 430 mg/Kg), P (8802. 5 mg/Kg). In addition leaves, harvested from 30% compost treatment exhibited the highest number of identified secondary metabolites and had the highest concentration of two of the five tested water soluble vitamins. This knowledge will make great contribution in the M. oleifera industry in South Africa and worldwide particularly for farmers who are into organic M. oleifera production.
Effects and consequences of natural and artificial light at night on small mammals in peri-urban Johannesburg, South Africa
(University of the Witwatersrand, Johannesburg, 2024) Oosthuizen, Tasha; Pillay, Neville; Oosthuizen, Marietjie
Studies investigating artificial light at night (ALAN) have increased over recent years. However, research examining the influence of ALAN on southern African small mammal species are lacking and even information on their basic biology is scarce. To close this knowledge gap, I investigated the effect of ALAN on different facets of animal behaviour in African small mammals. Firstly, I evaluated the impact of the natural (lunar cycle) and ALAN on the community composition and species abundance in two populations of small mammals. I chose two field sites: one facing Johannesburg (exposed to ALAN) and one facing away. I conducted mark-recapture trapping to ascertain the occurrence and abundance of small mammals. The Light site had both a higher species composition and a higher animal abundance when compared to the composition and abundance of the Dark site. The lunar cycle had an effect; on nights with a full moon, the species composition and animal abundance of both study sites declined, while on new moon nights, the opposite occurred, with an increase in both the species composition and abundance on the Light and Dark sites. The absence of a negative ALAN effect on the Light site can potentially be ascribed to the availability of microhabitats for small mammals to escape illumination, leaving them seemingly unaffected. Next, I assessed the locomotor activity of three species of commonly occurring rodents on the study area, one crepuscular (19 single-striped grass mice, Lemniscomys rosalia), one species with reportedly variable activity (19 angoni vlei rats, Otomys angoniensis) and one nocturnal (19 southern multimammate mice, Mastomys coucha). They were captured at a different location than the mark-recapture study sites and tested in captivity under natural (exposed to natural light and temperature changes), laboratory (standard laboratory conditions; 12h light:12h dark and constant temperature) and ALAN treatments. Lemniscomys rosalia exhibited crepuscular activity under all three experimental treatments, Otomys angoniensis was mostly nocturnal with some diurnal activity. The temporal activity profiles of the two species that showed some activity during the light hours were unaffected by ALAN. Mastomys coucha displayed strictly nocturnal activity during the natural and laboratory treatments, but during ALAN treatments the temporal activity profiles of some animals shifted so that they were active during the start of the day. Lemniscomys rosalia and O. angoniensis were more active under the natural treatment, whilst M. coucha was more active in the laboratory treatment. When exposed to 2 Lux ALAN presented remotely, there was no effect on the level of activity in O. angoniensis, L. rosalia showed a reduction of about 20% in its activity, whereas M. coucha reduced its activity by more than 50%. Finally, I studied how ALAN impacted the foraging behaviour of the three species under four treatments (during the day, at night, 2 Lux ALAN and 10 Lux ALAN). Foraging behaviour differed in the three species under different light conditions. Lemniscomys rosalia was risk-averse when feeding during the diurnal and nocturnal (no light at night) treatments. Otomys angoniensis showed irregular responses in their foraging behaviour under all foraging treatments. Mastomys coucha showed no differences when feeding under any of the nocturnal treatments, but it was inactive under the diurnal treatment. Overall, my study revealed that the effect of ALAN is not similar for all small mammalian species and appear to depend on both the spatial and temporal niches that the different species occupy. Strictly nocturnal animals seem to be affected the most, whereas animals that are active during the day showed lesser responses. Given the rapid increase in urbanisation and anthropogenic disturbances, more and more species are exposed to ALAN. Species that prefer darker, more secluded habitats appear to be more vulnerable and at higher risk of local extinctions as a result of disturbances, such as ALAN and habitat transformation. My study highlights that ALAN affects both nocturnal and diurnal rodents to the extent that it can have fitness consequences, including changed active times, foraging efficiency, movement patterns and susceptibility to predation. Finally, the disruption of rodent behaviour can have cascading effects for ecosystems and my study also emphasises the importance of safeguarding our night skies to protect biodiversity.
The effects of concurrent extreme temperature and water deficit on the phytochemical profile and phytopharmacological activities in Portulacaria afra Jacq
(University of the Witwatersrand, Johannesburg, 2024) Adeleye, Oluwafunbi Christianah; Risenga, Ida
In nature, all plants are exposed to stress which are mostly biotic and abiotic stress factors. Previous studies have demonstrated the impact of various abiotic stress factors on the production of secondary metabolites in therapeutic plants. Plant responses to stressors brought on by a combination of antagonistic abiotic factors have shown to be phenomenal compared to when plants are exposed to single a factor. According to latest climate change models, it is believed that plants would suffer unique or demanding concurrent abiotic stresses in the years to come. South Africa has been experiencing increasing temperatures over last 40 years and being regarded as a climate change ‘hot spot’ by the Intergovernmental Panel on Climate Change (IPCC). Therefore, it is critical to conduct research on the impact of climate change on the bioactive compounds in therapeutic plants. The overarching aim of this study was to establish and scientifically document, for the first time to our knowledge, the phytochemical profile, medicinal properties and phytopharmacological attributes of Portulacaria afra, a widely renowned medicinal plant used for treating several skin conditions and oral infections which also includes the assessment of the effects of concurrent extreme temperatures and water deficit/drought on species’ biological activities. In this study, South African Portulacaria afra plants were selected from healthy parent plants and propagated from cuttings. Samples were allowed to grow and establish a root system in the greenhouse for up to three months. After three months, 180 potted plant samples were exposed to treatments and not watered for up to 144 hours (6 days), and 45 control samples were placed under 25oC (ambient) and watered every second day with 500ml of water. The control samples were kept at 25°C maximum night-time temperature (7pm to 5am) and 27°C maximum day time temperature. Plants undergoing treatment (coded as treatment A, B, C, D) were treated as follows: A and B were exposed to 0/10ºC (night/day) and 5/15ºC (night/day) respectively, while C and D were exposed 20/40°C (night/day) and 35/45°C (night/day), respectively. Five potted plants were harvested in each treatment three times for up to 6 days (144hrs). Sample harvesting was scheduled episodically every 48hrs (48, 96, 144) and were then airdried under 40°C for 2 to 3 days. The aqueous (water) extracts at a temperature of 60°C, alongside methanol, n-hexane, and ethyl acetate extracts were derived from the leaves, stems, and roots. The extracts were then used to investigate the phytochemical composition, antibacterial efficacy, antioxidant capacity and antidiabetic potential. The qualitative phytochemical screening encompassed the preliminary assessment of saponins, flavonoids, glycosides, quinones, phenols, terpenoids, steroids, phytosteroids, volatile oil, carbohydrates, amino acids, and coumarins. The quantitative analyses were performed to determine the total phenolic content (TPC), total flavonoid content (TFC), while the antioxidant assays were performed to determine the reducing, scavenging and chelating abilities against DPPH, H2O2 and metal (Iron) chelating. The antibacterial activities against gram-negative Escherichia coli and gram-positive Staphylococcus aureus, Streptomyces griseus were assessed through agar well diffusion assay. The antidiabetic potential was evaluated using In vitro inhibitory α-amylase assay. Chemical profiling of various extracts from the leaves, stems, and roots of P. afra was conducted to identify and quantify some secondary metabolites. The methanolic leaf extracts exhibited a notable presence of quinones, phenols, steroids, and coumarins, whereas the aqueous leaf extracts contained moderate presence of saponins, terpenoids, quinones, and coumarins. Ethyl acetate leaf extracts were characterized by a strong presence of tannins and a moderate presence of phytosteroids. Conversely, n-hexane leaf extracts showed considerable saponin levels, moderate tannins, and terpenoids. Significantly strong presence of secondary metabolites was observed in methanolic stem extracts, particularly terpenoids, steroids, phenols, and coumarins. Notably, coumarins, known for their anticancer properties, were prominently present in methanolic leaf and stem extracts, with a moderate presence in root extracts, hinting at potential pharmaceutical applications and future roles in public health. Aqueous stem extracts exhibited strong glycoside presence, while ethyl acetate and n-hexane stem extracts exhibited few fewer secondary metabolite groups, ranging from moderate to weak presence. Distinctive chemical profiles were observed in root extracts, with ethyl acetate extracts showing significantly stronger quinone presence. Methanolic root extracts displayed moderate presence of coumarins and glycosides, whereas aqueous root extracts showed a low glycoside presence. The highest total phenolic contents (TPCs) and total flavonoid contents (TFCs) were found in methanol stem extracts and aqueous root extracts, respectively. Notably, aqueous root extracts exhibited the highest TPC and TFC among all root extracts. Antibacterial activity assays showed a wide range on inhibitory effects of n-hexane extracts from leaf, stem, and root against test microorganisms. Ethyl acetate leaf extracts demonstrated considerable inhibitory efficacy against Staphylococcus aureus, while methanolic extracts showed zero zone of inhibition. Aqueous root extracts showed strong antibacterial activity against Staphylococcus aureus, whereas other extracts showed no significant activity. Inhibition zones ranged from 13 to 24 mm for the plant extracts. The assessment of antioxidant potential through DPPH, H₂O₂ scavenging, and metal chelating assays showed varied activity among extracts. Ethyl acetate root extracts showed the strongest H₂O₂ scavenging activity, while aqueous stem extracts showed the strongest antioxidant activity against DPPH radicals. Aqueous and n-hexane root extracts showed the strongest metal chelating ability. The in vitro antidiabetic activity showed that all plant parts were active against α-amylase, with the highest inhibitory action recorded from the methanolic leaf extracts, followed by the methanolic root extracts
Uncovering genetic changes underlying adaptation in southern African dwarf chameleons (Bradypodion)
(University of the Witwatersrand, Johannesburg, 2024) Taft, Jody M.; Alexander, Graham J.
Natural selection acting on the available range of phenotypes in a population will favour alleles beneficial to an organism’s fitness, resulting in adaptation. Characterizing patterns of adaptive genetic variation in wild populations is a fundamental first step toward understanding the potential for adaptation in response to selection. With recent advances in sequencing technology, the increased availability of high-quality genomic resources has made efforts to identify loci under selection across the genome more tractable. As a result, there is a growing body of research challenging the notion that adaption takes place over deep evolutionary timescales, with evidence of rapid adaptation occurring in a range of taxa. Examples of rapid adaptation are rife within reptiles, particularly in response to contemporary environmental changes such as urbanization. Despite this, insights into the genetic architecture of adaptation in reptiles remain limited as appropriate genomic resources are currently lacking. The southern African dwarf chameleons, Bradypodion, are the most recently diverged lineage in Chamaeleonidae. These arboreal lizards are well known for their high capacity for adaptation, especially in response to environmental change. Bradypodion are known to have undergone rapid diversification linked to habitat specialization resulting in the emergence of few convergent phenotypes, or ecomorphs, across the genus. These lizards occupy a variety of habitat types, from closed-canopy forests to open-canopy habitats such as grasslands, but are also known to occur within urban environments. As ecomorphs of various Bradypodion species display phenotypic convergence in similar habitat types, populations may also converge phenotypically in urban habitats. However, the underlying genetic architecture of these phenotypes remains unknown for Bradypodion, further constrained given the absence of appropriate genomic resources for these lizards. To facilitate insights into the genetic architecture underlying adaptation in Bradypodion, two de novo assembled whole genomes were produced using Pacific Biosciences long-read sequencing data. These assemblies are among the highest-quality squamate genomes published to date. In addition, coalescent analyses of these assemblies indicated that historical changes in effective population size correspond to notable shifts in the southern African environment. Furthermore, the high-quality annotations of both Bradypodion genome assemblies were generated and used to describe the genetic feature landscapes and evaluate the gene family evolution of Bradypodion. Findings indicated that expanded gene families within this genus are likely the result of responses to changing environmental conditions, facilitating the diversification of Bradypodion. In addition, differences in gene family composition at the species level provide insights into underlying genetic pathways resulting in adaptive traits possibly promoting ecomorph divergence across the genus. Lastly, to detect loci under selection, population structure and genetic diversity were assessed in five species of Bradypodion known to have populations in natural and urban habitats using a pairwise comparative approach. While there is evidence of allele frequency differentiation between urban and natural populations, it is uncertain that this is due to selection pressures experienced by the urban population. While links between genes containing outlier loci and the phenotypic traits known to be associated with adaptation in urban habitats are made, it is recommended that these genes be used as candidates for targeted gene modification to evaluate the phenotypes generated by those modifications and contrasted with phenotypes present in urban populations. This thesis provides insights into the mechanistic genomic basis of adaption in Bradypodion. The high-quality genomes and annotations produced here will hopefully serve as a resource for further assessments of genetic adaptation in chameleons and reptiles more broadly. Furthermore, these findings present a framework from which to formulate robust hypotheses to assess candidate genes presented here as likely underlying adaptive phenotypes in urban populations
Factors limiting karoo shrub populations in the Nama-Karoo
(University of the Witwatersrand, Johannesburg, 2023-09) Hebbelmann, Lisa; O’Connor, Tim; Witkowski, Ed
The Nama-Karoo Biome occupies the central and western region of South Africa. Nama-Karoo shrublands are dominated by karoo dwarf shrubs and in the wetter eastern regions annual and perennial grasses are interspersed among shrubs. Rainfall and grazing are the main drivers of vegetation change in the Nama-Karoo. Stocking rate, season of grazing and animal type are important influences on vegetation community composition, and rainfall determines shrub growth and the abundance of grass. More recently, fire has been identified as a driver of vegetation change. Understanding vegetation change is important for land managers in the Nama-Karoo as changes in karoo shrub communities have implications for forage availability. This thesis is focused on understanding how grazing, fire, grass-shrub competition, and soil moisture and temperature affect the composition, structure, growth and phenology of karoo shrubs in the Eastern Upper Karoo. Livestock type and stocking rate vary greatly over the greater Nama-Karoo area. Plant composition data from the Afrikaner-Hereford grazing trial at Grootfontein show that grazing has a strong legacy effect on Karoo rangelands and grazing-induced compositional and structural changes are clear many years after grazing has ceased. Different sheep breeds affect karoo shrub communities in different ways. There was a severe negative effect of heavy stocking with dorper sheep on karoo shrub communities and their structure; the impacts of merino sheep were significant but less severe. Effects of animal type and stocking rate were not consistent across the sites but appear to be dependent on edaphic factors. Soil physical properties appear to play an important part in determining the long term effects of grazing on karoo shrub communities. Fire is a novel disturbance in the Karoo. Nine sites which had experienced fire for the first time in history were studied for the effect of fire on the composition and structure of their shrub communities. The immediate effect of fire on karoo shrub communities was severe and the legacy effect of fire was significant. The nature of recovery after a fire depended on the abundance of fire-intolerant obligate reseeder shrubs that are killed by fire compared to the abundance of fire-tolerant resprouting shrubs. Rainfall and grazing management were important determinants of shrub recovery after a fire. As rainfall increases, grass biomass is predicted to increase, and this may result in fire becoming a more frequent occurrence in the Nama-Karoo. During periods of high rainfall, the biomass of grass in the Nama-Karoo increased at the expense of shrub cover. The effect of grass-shrub competition on shrub growth and phenology is not adequately explained by existing hypotheses of niche separation and succession. A field experiment which examined the growth and phenology of karoo shrubs in the presence of grass (unclipped control) and the absence of grass (grass removed by clipping) did not provide evidence of a competitive effect from grass on shrub growth or phenology. It did, however, provide valuable insight into how shrub growth and phenology are influenced by soil moisture and temperature. Rainfall in the Nama-Karoo is sporadic and a karoo shrub’s ability to utilise soil moisture will determine its ability to grow and successfully recruit. Shrub growth, with or without grasses in the vicinity, was strongly correlated with rainfall, but this was modified by temperature. Similarly, soil moisture and temperature were important for stem growth and phenology. Flowering occurred in response to soil moisture all year round but seeding occurred mainly during summer. Patterns of growth and phenology can be used by land managers to optimise shrub production while allowing phenological processes to take place. The findings of this study provide further insight into how grazing, fire, competition, soil moisture and temperature influence shrub populations and their structure, and these are discussed in the context of an existing state-and-transition model for the Eastern Upper Karoo. The importance of animal type and stocking rate, and how they vary across Nama-Karoo landscapes, is highlighted. The legacy of both grazing and fire reveal that the transitions between the alternate states of Nama-Karoo shrublands are not easily reversed in a management timeframe. It may take decades for a community changed by grazing or fire, acting independently or in conjunction, to return to their former state even under benign management. These findings along with a description of how soil moisture and temperature influence shrub growth and phenology have been used to make ecologically sound recommendations for the management of Nama-Karoo rangelands. Future research is needed to improve our understanding of how edaphic factors limit and influence karoo shrub populations across a variety of karoo landscapes, how repeat fires might change karoo vegetation, and whether temperature and the presence of pollinators influences shrub seed set. An assessment of the economic implications of vegetation change in the Nama-karoo is warranted so that management recommendations can be made with both ecology and economy in mind.
Understanding disturbance, vegetation density, seed banks and pollination for the conservation of Protea curvata
(University of the Witwatersrand, Johannesburg, 2023) Mabuza, Precious Gugulethu Babalwa; Balkwil, Kevin
Background Aims: Protea curvata (Proteaceae) is a threatened species endemic to Mpumalanga, South Africa. Previous records of the species showed discrepancies in location data and information on population demographics was sparse. At the time of the study (2018), the last IUCN assessment of P. curvata was 20 years ago and one subpopulation of the species was reported to have a low number of mature individuals. In 2017, a census of another subpopulation indicated that the mature individuals were the most abundant cohort and there was no recruitment of P. curvata seedlings. Thus, there was uncertainty regarding how population size, population demographics and threats faced by the species may have changed over the last 20 years. The study aimed to update the IUCN status of P. curvata and to assess factors relating to P. curvata recruitment, namely the breeding biology of the species and the woody species composition on P. curvata sites. Methods: A census was conducted on P. curvata sites. Census data and site composition was compared between sites with contrasting management. Soil samples were collected from six sites. Pollination modes in P. curvata were investigated by manually pollinating inflorescences that were covered at bud phase to exclude animal pollinators. Five treatments were tested: autogamous selfing, tree geitonogamous selfing, inflorescences geitonogamous selfing, natural outcrossing and pollen supplemented outcrossing. Seeds from each treatment were weighed and tested for viability using TTZ staining. Animal pollinators were observed in the field and through camera traps positioned in front of non-covered inflorescences. Key Results: Five subpopulations were identified. P. curvata recruitment was low in two subpopulations and absent in three subpopulations. When comparing the site with the lowest recruitment (Site A) to the site with the highest recruitment (Site C), woody cover and tree density was higher on the site with low recruitment – indicating bush encroachment. This was attributed primarily to long intervals between fires at Site A. Site A showed a concerning net decline in subpopulation size (3% loss per year). Despite having more P. curvata juveniles, Subpopulation C showed a similar rate of decline (2% loss per year). The species was identified as endangered; with severe hailstorms and delayed, intense fires posing the major threats. Hailstorms compounded fire-induced damage on P. curvata bark. Flowering declined significantly after a hailstorm. (x̄pre-hail = 10.94 inflorescences per tree, x̄post-hail = 4.28 inflorescences per tree, p-value = 0.0031). During pollination experiments, Protea curvata was able to self-pollinate. However, seed mass and viability were significantly higher in outcrossed treatments. Viability in naturally outcrossed treatments (x̄=42.7%) was similar to pollen-supplemented outcrossed treatments (x̄=32.1%), but significantly higher than treatments of autogamous selfing (x̄=21.95%), geitonogamous selfing within inflorescences (x̄=27.1%) and geitonogamous selfing within trees (x̄=26.2%) [C.I= 95%; d.f.= 4, 95; Fcalc= 4.5; p = 0.0021]. Colletid bees and Apid bees contributed to P. curvata pollination via geitonogamy and early removal of self-pollen from stigmas. Birds were the most frequent visitors of P. curvata and were the most effective pollinators due to their prominent role in natural outcrossing. Bats infrequently visited inflorescences but may possibly complement outcrossing since they make contact with stigmas and do not spend their visit time restricted to one inflorescence or tree. P. curvata was non-serotinous and possessed a short-lived, soil seed bank. Across all sites, the average viability of seeds in the soil was well below that of freshly collected seeds from pollination experiments (4–9% for soil seed bank; 22.0–42.6% for fresh seeds). Seed bank size was surprisingly low in subpopulations with high flowering. Conclusions: Reducing seed loss after release from the canopy appeared to be more important than high flowering for maintaining a large seed bank. Therefore mild, frequent fires will be essential for reducing bush encroachment, making way for seed deposition and encouraging seedling survival
Tracing multiple aquatic ecosystem stressors across a land-use intensification gradient: A multi-tooled environmental forensic approach
(University of the Witwatersrand, Johannesburg, 2024) Levin, Jonathan Chaim; Woodford , D.J.; Curtis, C.J.
South Africa requires advanced freshwater management approaches to address complex catchment stressors acting on aquatic ecosystems. An environmental forensics toolbox could help disentangle pollution sources, informing stressor-focused adaptive management. Existing national, spatial resource strategies that define aquatic resource objectives, overlook modelling different aquatic stressor-linked components across spatio-temporal scales to disentangle individual stressor effects along land-use intensification gradients. This thesis investigated how spatio-temporal, physico-chemical water quality parameters, dissolved and sediment-bound trace metals as well as fish tissue δ34S all collected from 15 river sites in the tributaries of the Gwathle River Catchment, positioned in the Platinum Belt of South Africa across a land-use intensification gradient, can be used to disentangle aquatic stressors. Through using a spatio-temporal generalised linear mixed effects model (GLMM) approach, the importance of employing a multi-hydrological-spatial (sub-basin, cumulative basin and riparian buffer) scale approach to link stressors (drivers) to changes in key catchment water quality parameters as opposed to a single scale approach was identified. At the sub-basin scale, ammonium concentrations were best explained by urban stress through wastewater effluent, Cu increased with mining via leaching from pollution control dams and mineral discharges, while turbidity increased with higher agricultural coverage, following greater tillage practices and irrigation. River pH was positively predicted for by slope heterogeneity at the cumulative-basin scale, while sulfate increased with mining at the cumulative 100 m riparian buffer, from leaching and discharges. Dissolved inorganics, including trace metals, are routinely assessed in national aquatic resource assessments, yet metals in sediments demonstrating legacy effects, are yet to be integrated. Using geo-spatial models across seasons, dissolved and sediment Cr concentrations were found to be driven primarily by mining both at the sub-basin scale, while dissolved Zn concentrations reflected sub-basin lithology and sediment-bound Zn reflected cumulative basin scale urban stress and lithology. Concordance correlation indicated that the Cr had a substantial positive stress-tracking agreement between the two media, with both tracking Cr land-use intensification gradient inputs while Zn displayed negligible concordance. While fish tissue δ15N has been used to trace nutrient pollution, no local or international research has assessed time-integrated fish tissue δ34S as a sulfur stress-tracer from interacting urban, agricultural and mining stressors. Using a spatio- temporal GLMM modelling approach, it was found to be possible to distinguish key agricultural and mining stressors on aquatic ecosystems, with δ34S being relatively enriched following sub-basin scale agriculture and relatively depleted following cumulative basin scale mining activities. The outcomes of this research expands our knowledge base on using aquatic physico-chemical parameters, inorganic media indicators, and biotic tracers, towards the development of a potential environmental forensic toolbox to elucidate complex pollution sources and pathways for enhanced catchment management and freshwater governance in South Africa.
The value of large trees and their protection where elephants and trees co-exist
(University of the Witwatersrand, Johannesburg, 2024) Cook, Robin Michael; Henley, Michelle; Witkowski, Edward
Increasing African elephant (Loxodonta africana) numbers in many southern African protected areas have raised concerns about their impact on large tree species and subsequent effects on biodiversity. However, sustainable strategies for managing elephant impact on particular large trees of concern require stakeholder support. Concerned stakeholders in South Africa's Associated Private Nature Reserves (APNR), a protected area containing a high density of waterholes and elephants, are implementing tree protection methods to protect large trees from elephant impact, but few studies have assessed these methods’ efficacy. This thesis aimed to understand stakeholder perception of the value of large trees. Thereafter, I investigate elephant impact on the large tree component within the APNR over a 12-year period while also assessing the relationship between the persistence of the nests of large tree nesting birds and that of the trees themselves. Lastly, I assessed the effectiveness of various implemented tree protection methods to mitigate against elephant impact. A combination of qualitative and quantitative analysis was used to measure stakeholders’ values on large tree and elephant population dynamics, as well as management strategies to reduce the impact on large trees. The results show that stakeholders were concerned about the loss of large trees and its impact on other species. However, they disagreed on the most effective management strategy to minimise elephant impact, with varying values across stakeholder generations and professions. The persistence trends of 2,758 large trees comprising three species of concern were analysed between 2008-2020 to understand the impact of elephants and other environmental factors on tree mortality. The annual large tree mortality rate from 2008-2020 was 5.6%, with varying declines among tree species and the most significant declines occurring during dry periods. Furthermore, the long-term impact of elephants on trees nested in by the critically endangered white-backed vulture (WbV, Gyps africanus) was studied in riparian and woodland habitats to investigate both tree and nest persistence. Ten tree species were utilised for nesting sites, with woodland trees more at risk to elephant impact verses those in the riparian habitat. However, there was no direct correlation between WbV nest loss and tree fall. Lastly, when considering tree protection methods, about half of the 2,758 trees surveyed were wire-netted as potential elephant impact mitigation strategy. Trees with a stem diameter >40 cm that were wire-netted had the highest persistence rates, but the wire-netting needed replacing after four years. Overall, wire-netting was the most practical method for larger- scale implementation, particularly on larger trees elephants cannot push over. Of the four tree protection methods evaluated in this study in terms of their effectiveness and practicality as a mitigation strategy, beehives were found to be the most effective at protecting trees but proved to be the most expensive in comparison to wire-netting, concrete pyramids and creosote jars
An essential variable approach for integrated social-ecological systems monitoring to determine sustainability in a South African catchment
(University of the Witwatersrand, Johannesburg, 2024-05) Itzkin, Adela; Clifford-Holmes, Jai Kumar; Coetzer, Kaera; Scholes, Mary
This thesis presents an essential variable (EV) approach tailored for integrated social ecological systems (SES) monitoring within the Tsitsa River Catchment (TRC) in South Africa. The study addresses the conceptual and methodological challenges inherent in SES integration and monitoring to provide insights into sustainable landscape management. The research methodology employed a transdisciplinary social learning process, integrating systems thinking and participatory research methods across three related publications. In the first publication, systems diagramming, qualitative interviews, and participatory data collection provided a systemic snapshot of the interconnected social and biophysical drivers of land degradation in the TRC. The findings underscored the dual benefits of changes in land use and grazing practices for landscape improvement and sustainable livelihoods, informing the identification of monitoring variables crucial for sustainable land management. In the second publication, a social learning process, termed participatory self-observation, explored approaches to enhance integration and monitoring of biophysical and social data for adaptive management. The process identified data integration, overload, scale, learning oriented monitoring, and relationship-building as key challenges in SES monitoring Recommendations included participatory approaches focusing on applied work, identifying essential data for SES monitoring, and improving transdisciplinary collaboration. In the third publication, a transdisciplinary process guided by EV development identified Essential Social-ecological System Variables (ESEVs) for the TRC, emphasising the relational connection between social and ecological aspects of SESs. ESEVs were prioritized based on essentiality scores and participant consensus, facilitating integrated planning and management at the catchment scale. The ESEVs identified for the TRC include 'soil erosion related to human actions on the land,' 'participation in natural resource governance,' 'grazing and rangeland sustainability,' and 'land cover and condition. Participants proposed three additional ESEVs, 'access to water,' 'local natural resource governance system,' and 'human well-being in the landscape'. The study concludes that collaborative learning informed by diverse transdisciplinary perspectives can guide adaptive monitoring approaches, with lessons from the TRC applicable to diverse contexts. The ESEV approach offers wider application value, addressing the question of the minimum variables needed for integrative landscape management in complex SESs. Overall, this thesis pioneers a transdisciplinary mixed-methods approach for efficiently monitoring social-ecological sustainability outcomes. Through advancements in conceptualizations of integrated, contextually grounded monitoring, it offers a novel perspective for understanding the implications of development interventions, bridging critical gaps in SES monitoring.
Environmental impact assessment performance in an african context: case studies from Southern Africa (South Africa, Namibia, Malawi, and Tanzania)
(University of the Witwatersrand, Johannesburg, 2024) Aljareo, Abdulhakim; Schwaibold, Ute; Watson, Ingrid
The Environmental Impact Assessment (EIA) system is a worldwide environmental policy tool, which has been introduced and adopted both in developed and developing countries. The EIA system is internationally acknowledged as an essential instrument to support sound decision-making in pursuit of sustainable development. Many countries have established the requirement for EIAs in their respective environmental legislative frameworks. However, considerable concerns are often raised about the inadequate performance of the EIA system in developing countries. The African developing countries have introduced EIA as an environmental policy implementation tool to their environmental policy and legal framework for environmental protection and management, as well as sustainable development promotion. However, the EIA system performance in the African developing country context is regarded as limited. The country context of the developing countries has been perceived to influence the performance of the EIA system. Fundamentally, the assessment of EIA system performance focuses on particular key EIA systemic components and EIA report, having limited consideration of the country context influence on the EIA system performance, and so does not provide a thorough understanding of the real causes of the limited EIA performance in the African context. Focusing on the EIA system performance in the African developing country context, an evaluation approach for EIA system performance and country context was developed. The developed approach was applied to four case studies from the southern African context (South Africa, Namibia, Malawi, and Tanzania). This was to evaluate EIA system components, EIA report, and country context. The research findings indicate that EIA system performance is limited due to the influence of the context of the case study countries. It was found that, despite the presence of the EIA legislative frameworks, EIA competent authorities, EIA procedural steps, and EIA reports in the case studies, different shortcomings have been identified such as misinterpretation of EIA provisions, limited EIA timeframes, incomprehensive EIA guidelines, insufficient provisions for conducting EIA follow-up and auditing. A further finding was the insufficient EIA report legal requirement which mirrored in the inadequate quality of the evaluated EIA reports. The most important v finding of this research is that EIA system performance depends on its country context. There is a clear relationship between country context of the case studies and EIA system development, implementation, and enforcement, thereby influencing EIA system performance. The key country context elements that were found to affect EIA system performance are the country legal, political, and socio-economic context, and the EIA stakeholders’ capacity. The consequences of the limited EIA stakeholders ‘capacity coupled with the inadequate country legal context due to insufficient laws to support justice in the administrative decisions, and access to information, had a significant impact on EIA system implementation and enforcement. The developmental state pressure on the EIA administration due to socio-economic challenges associated with political context issues such as interference and pressure also affected EIA system implementation and enforcement. The EIA system development was also influenced by the development state presented by the demand for economic development due to issues such as poverty and unemployment and the lack of political will and commitment to the EIA system. Based on this, a comprehensive understanding of the relationship between EIA system performance and the country context in Africa is required which can be achieved by using the developed evaluation approach in this study, to identify the possible measures for improving EIA system performance.
Unravelling the speciation process in barking geckos (Ptenopus: Gekkonidae)
(University of the Witwatersrand, Johannesburg, 2024) Becker, Francois S.; Tolley, Krystal A.; Graham J. Alexander
Barking geckos (genus Ptenopus) are a group of terrestrial, burrowing lizards endemic to southern Africa, with three currently recognised species: P. kochi, P. carpi, and P. garrulus, the last containing the subspecies P. g. garrulus and P. g. maculatus. Males produce uniquely loud vocalisations to attract females to the burrows, a trait which is involved in mate recognition. I produced the first comprehensive phylogeny for the genus, which supported several deep divergences and the presence of unrecognised species. I then applied the unified species concept in an integrated taxonomic framework to delimit species within Ptenopus. I used multiple lines of evidence including genetic-spatial analyses, advertisement calls, ecological divergence, and morphology to test the evolutionary independence of putative species suggested by phylogenetic species delimitation analyses. Based on these findings, I suggest there is a total of eight species of Ptenopus, and that the two subspecies P. g. garrulus and P. g. maculatus should be elevated to full species. I provide provisional descriptions of four additional species. The advertisement calls and preferred habitats were clearly distinct among these proposed species, while morphological characters were generally less reliable for species identification. I also tested various candidate hypotheses of divergence drivers in the genus using multiple regression on matrix models (MRMs). The MRMs supported the hypothesis that substrate specialisation was the main factor over other factors as the key driver of divergence. Geographic barriers, including rivers and mountains or ridges, also appear to be important drivers of some of the more the recent divergences. The Namib Desert is the centre of diversity for the genus Ptenopus, containing seven of the eight proposed species. There was also strong evidence for reproductive character displacement in the advertisement calls of sympatric species, indicating the importance of calls in mate recognition and the maintenance of species boundaries. This is the first study to show evidence for reproductive character displacement of vocal traits in a non-avian reptile.
Cognition in urban-dwelling yellow mongoose, Cynictis penicillata
(University of the Witwatersrand, Johannesburg, 2024) Muller, Mijke; Pillay, Neville
Cognition involves perceiving and processing environmental cues and devising appropriate behavioural responses to act on the acquired information. Studying animal cognition in an urban setting provides insight into the occurrence of behavioural changes in urban-adapted animals. This thesis aimed to investigate the cognitive abilities of a population of yellow mongoose, Cynictis penicillata, inhabiting locations with differing extents of urbanisation in South Africa. First, I investigated whether mongooses could learn to solve a puzzle box problem of increasing complexity. The mongooses were able to solve the problem at each stage of complexity, but took longer in a residential ecological estate than those frequently visiting a residential garden. These results indicated that mongooses were capable of innovation, but their problem-solving abilities were influenced by the level of disturbance in their environment. Secondly, I investigated whether mongooses exhibited cognitive flexibility. The mongooses were able to inhibit a non-rewarding behaviour, even when it was previously rewarded, in favour of a newly rewarded behaviour during the puzzle box task. Additionally, they could solve the puzzle box problem during distraction, but took longer with the most distraction, likely splitting their attention between solving the problem and remaining vigilant. Combined, the mongooses were capable of reversal learning and divided/alternating attention, providing evidence of cognitive flexibility in this mongoose population. Thirdly, I investigated the effects of a direct human approach on the problemsolving ability of mongooses. In areas of heightened human disturbances, the mongooses had reduced tolerance to humans, but were equally efficient at solving the puzzle box problem following human disturbance than those in areas of reduced human disturbance. Those more tolerant of humans improved their problem-solving efficiency, likely adapting to the disturbance. Finally, I investigated whether mongooses experienced a paradox of choice (i.e. whether too much choice can be cognitively challenging). The mongooses in my study appeared to experience cognitive difficulties when presented with extensive choice, providing support for a paradox of choice. These results provide evidence that urban-living yellow mongooses’ successful adaptation to an urban habitat may be attributed to their cognitive abilities, allowing them to exploit novel resources and flexibly adapt to the rapid environmental changes associated with urbanisation. However, the disturbance associated with urbanisation may negatively affect problem-solving efficiency, which may impact successful food acquisition, and the increased availability of resources may be cognitively challenging for urban-living yellow mongooses.
Farming systems in South Africa beyond 2020: a scenario-based study, using systems analysis, of the connectivity between farming systems in the Vhembe district, Limpopo, South Africa
(University of the Witwatersrand, Johannesburg, 2024) Materechera-Mitochi, Fenji; Scholes, Mary
Agriculture is a significant contributor to the South African economy and overall development as it contributes to poverty reduction and food security. It is against this backdrop that agricultural development becomes a focus area for decision making amongst stakeholders, as it is directly linked to food systems. The traditional approach to agricultural production in the country has been one that views farming as mainly based on land ownership and yield in isolation from the broader context of the four drivers of production namely land, labour, capital and enterprise. The concept of farming systems provides a broader perspective on farming and encompasses the entire value chain for a commodity which includes production, management practices, marketing, value addition, financial resources, and policies. The South African agrarian structure is characterised by a dualism in which large-scale commercial farmers co-exist alongside small-scale farmers. This is a legacy of the apartheid system of governance. Large-scale commercial farmers, who are mostly capital intensive, have historically been regarded as the main drivers of national food security while small-scale farmers on the other hand are viewed as significant contributors to food security at a household level. Both farmers are therefore important contributors to the national agricultural economy. Research on the two types of farmers in the South African context is usually focused on the respective farmers’ approaches to production individually and does not consider them as joint ventures. This study was aimed at providing an alternative approach to viewing South Africa’s farming systems by evaluating current farming systems in the Vhembe district of Limpopo, South Africa, using systems analysis as a tool to highlight the connectivity of the interactions within and between them. The study also aimed to conceptualize scenarios for sustainable future farming systems in South Africa. The Vhembe district in the Limpopo province was chosen for the study because both largescale commercial and small-scale farmers occur and due to the favourable sub-tropical climate, the area has become a hub for the farming of numerous high value crops that contribute positively to the country’s agricultural economy. The study made use of a mixed methods approach that combined the analysis of primary data obtained from in-depth interviews and secondary data obtained from an agricultural database to identify and characterize large-scale commercial and small-scale farming systems in the Vhembe district. The study examined the drivers of production for three different commodities, macadamia nuts, mangos and avocado iii pears, the two types of farming systems and their connectivity. The study was grounded on the conceptual framework of systems thinking and used a systems analysis tool i.e., causal loop diagrams to analyse the connectivity between the two farming systems. Lastly, the study developed conceptual scenarios using a deductive scenario method to conceptualise scenarios for the future of the two farming systems and the different commodities. Key findings of the study showed that farming systems need to be understood through the lens of the four drivers of production. Land as a driver of production interacts with multiple other factors in shaping the management of a sustainable farming system. Examples of these factors include the link between land availability, ownership and farm size, decision-making and resource allocation tied to land management practices, and socio-economic considerations including the diversification of livelihoods by incorporating non-farm income and the farmers’ adaptability to uncertainties such as climate change. The findings also revealed that there are interconnections between the two types of farming systems presenting potential for enhanced production and commercial opportunities. The conceptual scenarios developed in the study and the systems thinking tool of causal loop diagrams proved to be valuable tools to inform decision making and policy development. The study’s main conclusion points to the potential of large-scale commercial and small-scale farming systems in South Africa operating as joint ventures in the future and enhancing the sustainability of agricultural production and livelihoods. It also recommends the use of systems thinking that includes social, financial and environmental values and impacts in decision making for agricultural development.
Extreme weather events and human health in South Africa: implications for climate services
(University of the Witwatersrand, Johannesburg, 2022) Manyuchi, Albert Edgar; Erasmus, Barend; Wright, Caradee; Vogel, Coleen
Extreme weather events (EWEs), defined as ‘weather events that are rare at a particular place and time of the year’, have increasingly been affecting many countries worldwide (IPCC 2014). The increased occurrence and intensity of EWEs, among other factors, has increased public interest and demand for climate information. More detail is needed on EWEs and how they can be more effectively coupled to climate services in Africa. This study brings a compendium of empirical evidence, conceptual clarity and transdisciplinary approaches to policymakers, researchers and practitioners dealing with these crucial issues. The main aim of this study is to explore the human health effects of EWEs, particularly heat and the delivery of climate services for health in Africa. Through a systematic review, the study examines the potential impacts of heat on human health in Africa. Using a case study approach heathealth effects are evaluated including the status of climate services in the Agincourt subdistrict of South Africa. A novel systems theory-based conceptual framework and an inclusive analytical framework are employed to explore climate services delivery within the context of climate change adaptation. The study produces two main findings. First, EWEs particularly heat, potentially affects human health in Africa by changing mortality and morbidity patterns. In the Agincourt sub-district in particular, heat may be associated with adverse health effects on vulnerable populations, including inter alia the elderly, children and outdoor workers. Despite this, Africa-specific heat-health interventions and policy suggestions are scarce. Second, climate services are generally in embryonic stages of development and climate services for health in Agincourt subdistrict are non-existent. Within the South African context, the main barriers to delivery of climate services for health are paucity of interagency coordination and gaps in meteorological data. One of the key conclusions of the study is that African countries can promote development of climate services to adapt to EWEs such as heat. Heat, and heatwaves, for example, are already affecting populations, and are projected to increase in frequency and intensity with concomitant adverse effects on health outcomes on vulnerable population groups. The three key recommendations from this study are as follows. First, African policymakers and practitioners must avoid a reductionist approach to analysis of EWEs, especially heat impacts and start viewing these as harmful to human health. Therefore, governments must prioritise interventions, create institutions and formulate policy measures to deal with the health effects of heat within their national adaptations plans. Second, African countries must prioritise policy mixes that promote climate services in general and climate services for health in particular. And finally, further policy-science research that generates empirical evidence for African policymakers and practitioners engaged in international negotiations and programmes for climate change adaptation and climate services should be encouraged.
Tolerance, uptake, and translocation of platinum (Pt), nickel (Ni), and cobalt (Co) by Tamarix usneoides E. Mey. ex Bunge
(University of the Witwatersrand, Johannesburg, 2022) Mader, Anthony E.; Weiersbye, Isabel M.; Mycock David J.
The intensification of platinum (Pt), cobalt (Co) and nickel (Ni) mining and processing results in the release of salts and metals into the environment. This calls for the identification of halophytes with an ability to tolerate and desalinate metal-contaminated sites while simultaneously allocating metals (Pt, Ni, and Co) into harvestable biomass. Tamarix usneoides E. Mey ex Bunge is an indigenous exo-recretohalophyte that has been used for erosion control and for the desalination and allocation of metals from gold and uranium mine tailings and land contaminated by metallurgical effluent. The aim of this study was to investigate the uptake, translocation, and tolerance of Pt, Ni, and Co by T. usneoides from liquid medium (in vitro) and soil contaminated by base metal refinery effluent spillages and previous overspray from the enhanced evaporation spray system (in situ). More specifically, the in situ study investigated the utility of mature T. usneoides trees in the desalination of soil contaminated by previous metallurgical spillages and overspray emissions through the extraction of sulphur and metals Pt, Ni, and Co into harvestable biomass. Four T. usneoides trees were categorised into different size classes based on tree measurements and allometric equations. Seven soil pits (four “planted” and three “unplanted” – control) were excavated and opposite faces of the soil profile were sampled at 20 different intervals (0 – 340 cm). Soil samples were freeze-dried and analysed for total element concentrations. Root systems were harvested by excavating soil pits (maximum depth of 3.5 meters) using a mechanical excavator. Trees were harvested and immediately separated into above (leaves, twigs, wood, and flowers) and belowground (coarse and fine roots) plant organs. Tree biomass was further separated into different above (outer bark, inner bark, and sapwood and heartwood) and belowground (epidermis, cortex, and stele) tissue types. Plant material was rinsed three times in tap water to remove unbound residual metals and residual substrate from root and shoot surfaces. It must be noted that the determined metal concentrations are a combined measure of metals adsorbed on the root surface, assimilated in planta, and excreted on the plant surface from the foliar salt glands. Metals were allocated in trees (across plant organs and tissue types) in the order: Ni (59.46 ± 4.67 mg/kg) > Co (2.65 ± 0.34 mg/kg) > Pt (50 ± 6 µg/kg) whereas sulphur (S) was hyperaccumulated in tree leaves [39 900 ± 861 mg/kg (3.9% ± 0.7 %)]. Platinum was bioaccumulated [bioconcentration factor (BCF) > 1.5] and translocated [translocation factor (TF) > 1] in the leafy shoots of one individual tree, Ni in one (BCF = 1.03), and Co in another replicate (BCF = 1.02). Soil chemical properties (pH, electrical conductivity, and redox potential) differed between planted and unplanted pits whereby pH and EC were lower in planted pits [pH 6.0; EC = 3 499 µS/cm (34.99 mM NaCl)] compared with unplanted [pH 7.6; EC = 9 644 µS/cm (96.44 mM NaCl)] (ANOVA, p < 0.01). The lower EC, along with S hyperaccumulation (BCF > 20; TF > 1), supports the potential use of T. usneoides for phytoextraction of S and Ni in shoot tissues and Co and Pt in roots. At a spacing of 1333 trees / ha, T. usneoides trees could remove an estimated 2.23 ± 0.30 mg Pt/ha, 3.02 ± 0.83 kg Ni/ha, 1.28 ± 0.90 kg Co/ha, and 1.28 ± 0.09 tons S/ha, excluding excreted salts. Excreted salts were visible but could not be quantified without confounding surface dust contamination. The first in vitro study determined factors influencing the rhizogenesis of T. usneoides in order to develop a mass propagation protocol. Explant establishment in vitro was influenced by various donor plant factors, viz. growing conditions (contaminated < non-contaminated; Kruskal-Wallis (KW), p < 0.05), physiological age (younger > older donor plants; ANOVA, p < 0.05), genotype (KW, p < 0.001), season of culturing (higher establishment in winter; KW, p < 0.05), length of explant (40 mm > 25 mm; KW, p < 0.05), and volume of growth vial (50 mL > 15 mL; KW, p < 0.05) but not pH, chronological age, strength of plant growth medium, or auxin pulse treatments. This study indicates that propagation protocols can be developed by controlling factors influencing explant establishment. A standardised and rapid in vitro protocol was developed for the mass propagation of T. usneoides explants. This in vitro protocol was used for the metal uptake studies whereby established explants were exposed to 25 % Murashige and Skoog standard plant growth medium supplemented with Pt, Co, or Ni (as sulphate complexes) at 0, 25, 50, or 100 mg/L at pH 5.5 or 7.5 over a 14-day exposure period. On completion of the metal exposure period, plantlets were harvested, separated into roots and shoots, freeze-dried, and analysed for metal concentrations. Higher metal concentrations (Ni > Co >> Pt) were accumulated in roots (combined measure of metals adsorbed on the root surface and assimilated in planta) compared with shoots whereby BCF > 1 (excluding Pt) and TF < 1. Metal BCF (Ni > Co >> Pt; KW, p < 0.05) and TF (Co > Ni >> Pt; KW, p < 0.05) increased in a dose-dependent fashion and were not influenced by pH level. Cobalt and Ni (≤ 50 mg/L) uptake dynamics did not v differ suggesting similar uptake dynamics, when treated separately. Platinum (defined in this study as Pt > 1 – 4 mg/kg), Ni (> 1 000 mg/kg), and Co (> 300 mg/kg) were hyperaccumulated in roots (“rhizo-hyperaccumulation”) across treatments with possible Co-hyperaccumulation in shoots by two genotypes. Genotype influenced Co allocation in shoots but not Ni or Pt. Tolerance indices did not differ [Co (97 %) > Pt (82 %) > Ni (77 %)] between pH, metal, treatment concentration, or the interplay between these factors. Metal treatments did not impact measured morphological parameters (excluding Ni treatments which promoted shoot length increment) (KW, p < 0.05). Plantlet survival differed between pH and metals [Pt (90 %) > Ni (81 %) > Co (62 %)] (KW, p < 0.05). Variability in Co accumulation capacity between genotypes indicated that selective breeding, using the developed in vitro mass propagation protocol, for improved rhizofiltration and phytoextraction traits is feasible. Results demonstrate that T. usneoides has the potential for recovery of Ni and Co (and Pt to a lesser degree) from effluents, exhibiting a tolerance to Ni, Co, and Pt at 1, 10, and 10,000 times the average soil crustal abundance, respectively, under moderately acidic (pH 5.5) and alkaline (pH 7.5) conditions and across a wide metal concentration range. Results from the in situ study indicate that 9- year-old T. usneoides trees can be used for the decontamination of sulphate-contaminated soils under study site conditions which are more conducive to the survival of glycophytes. Tamarix usneoides is thus able to assimilate, translocate, and tolerate Ni, Co, and Pt (to a lesser degree) when exposed to metals across a wide pH and metal concentration range, under different (in situ and in vitro) experimental conditions. This opens the possibility for the species to be used in a range of phytotechnologies.
Sex and age related distinctions in the feeding ecology of the African elephant
(2010-01-29T08:19:33Z) Greyling, Michelle Deborah

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