Faculty of Science (ETDs)

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    The Taxonomy and Phylogeny of Varanopidae from the Middle Permian of outh Africa
    (University of the Witwatersrand, Johannesburg, 2024-08) Sibiya, Zoleka; Rubidge, Bruce; Benoit, Julien
    Varanopidae are the only pelycosaur-grade tetrapods from the Abrahamskraal Formation of the Beaufort Group. Although four varanopid species are described from the middle Permian of South Africa (SA), their validity has been questionable. Moreover, Ford and Benson recently proposed that varanopids belong to the Diapsida rather than Synapsida. Given this taxonomic and phylogenetic turmoil, this study i) describes two newly discovered and well-preserved varanopid specimens from the middle Permian of SA using CT scanning and ii) re-assesses the validity of the four species from the Karoo Basin in the light of new data from these specimens. The phylogeny of the group is addressed by updating two pre-existing cladistics matrices. The two new specimens exhibit a mosaic of features that overlap the diagnoses of several species of SA varanopids. In addition, some diagnostic traits of the four SA varanopid genera and species are found to be variable across ontogeny. For instance, dorsal osteoderms and the extent of ornamentation on the angular bone co-vary with size. It is therefore proposed that all varanopid specimens currently described from the middle Permian of South Africa belong to a single valid species, Heleosaurus scholtzi, with differences between specimens being accounted for by ontogenetic changes. The phylogenetic analysis supports Ford and Benson’s hypothesis but contra the prediction of this hypothesis, no differences in cranial fenestration during ontogeny are observed. Morphological characters preserved in the manus of the newly discovered specimen BP/1/8499 suggest that Heleosaurus was arboreal.
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    Investigating the impact of the land reform policy on land use and land cover changes, in Ngaka Modiri Molema district of the North West province
    (University of the Witwatersrand, Johannesburg, 2024) Mmangoedi, Molebogeng Precious; Adam, Elhadi
    The purpose of this study was to assess how land reform policies affected changes in land use and land cover in the province of North West's Ngaka Modiri Molema district municipality. The study employed remote sensing technologies to analyse changes in land use and land cover (LULC) resulting from the implementation of land reform programs between 1985 and 2015. The primary objective of the research was to systematically map Land Use and Land Cover types across five-year intervals spanning from 1985 to 2024, leveraging Landsat earth observation data in conjunction with a random forest classifier. These methodologies were employed to facilitate the identification of spatial patterns and trends associated with the implementation of land reform policies within the study area. Furthermore, the study utilized Landsat data and advanced change detection algorithms to quantitatively assess LULC changes over the specified timeframes. Through the application of spatial analysis techniques, the research aimed to elucidate the relationship between the implementation of land reform measures and corresponding shifts in LULC patterns across the research study area. The findings of the investigation indicated a noticeable expansion in built-up areas between the years 1985 and 2024 which was approximately 10.86%. This expansion was primarily attributed to the growth experienced by the municipality during this period. Additionally, more opportunities might have risen from the agricultural farming activities and also from the land reform policy being implemented. However, as the ownership changed due to land redistribution and more land was being acquired by black people through the land reform policy, agricultural farming decreased slightly throughout the years. The reduction was due to the factors that arose from inefficient policy implementation. The study also recommends that remote sensing techniques should be utilised to carry out studies to determine LULC changes that derive from land policies aiming at dealing with socio-economic factors and urbanisation. An incorporated agrarian reform sustainable programme has vast potential in cultivating the production of the projects, particularly if it involves packages in rural infrastructure, support services, and co-operatives. The major role of such an approach should be in the trainings conducted for the farmers, obtaining, and distributing agricultural resources and equipment to agrarian reform or beneficiaries of the land reform projects. Additionally, there should be an allowance for special grants which will be useful in supporting the government’s efforts.
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    Diversity and Abundance of Arthropods on Conventional Sugarcane under Field Conditions in South Africa
    (University of the Witwatersrand, Johannesburg, 2024-09) Smith, Roshay; Malinga, Lawrence; Bouwer, Gustav
    Insect diversity and abundance are often the base for formulating strategies that involve the appropriate application of pest control methods, considering the ecosystem services provided by insects. Therefore, the aim of this study was to provide recent baseline data on the diversity and abundance of insects in conventional sugarcane based on two sugarcane fields in KwaZulu-Natal. Three sampling methods, namely pitfall, sticky and water pan traps, were used to sample insects in rain-fed and irrigated sugarcane in Gingindlovu and Pongola from March to October 2022. This study collected 12 493 insects belonging to 14 insect orders and 88 families in rain-fed sugarcane and 22 309 insects belonging to 14 orders and 94 families in irrigated sugarcane. Significant differences in the diversity indices were found between the sampling methods and the sampling periods. This study provides recent baseline data on the diversity and abundance of insects in sugarcane.
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    Machine Learning Algorithms-Based Classification of Lithology using Geophysical Logs: ICDP DSeis Project Boreholes, South Africa
    (University of the Witwatersrand, Johannesburg, 2024-09) Atita, Obehi Chapet; Durrheim, Raymond; Saffou, Eric
    One of the most significant geosciences tasks is the accurate classification of lithologies for metal and mineral resources exploration, characterization of oil/gas reservoir(s), and the planning and management of mining operations. With the availability of abundant, huge and multidimensional datasets, machine learning-based data-driven methods have been widely adopted to assist in solving geoscientific problems such as the efficient evaluation and interpretation of large datasets. The adoption of machine learning-based methods aims to improve lithological identification accuracy and extract information required for accurate and objective decision-making with respect to activities such as exploration, drilling, mine planning and production. Practically, this helps to reduce working time and operating costs. We aim to evaluate the feasibility of machine learning-based algorithms application to geophysical log data for the automated classification of lithologies based on the stratigraphic unit at the formation level for the purpose of distinguishing and correlating the quartzites between boreholes, and mapping key radioactive zones within the mining horizon. This study implemented four different machine learning algorithms: gradient boosting decision trees, random forest, support vector machine, and K-means clustering models. Analyzed features and labelled datasets are multivariate downhole geophysical and lithology logs from the two ICDP DSeis project boreholes drilled in the Klerksdorp gold field, respectively. To mitigate misclassification error and avoid model overfitting/underfitting, the optimal combination sets and optimal values for each implemented supervised model’s hyperparameters were obtained using the Grid search and 10-fold cross-validation optimization methods. The input dataset was randomly split automatedly into training and testing subsets that made up 80% and 20% of the original dataset, respectively. The models were trained and cross-validated using the training subset, and their performances were assessed using the testing subset. The classification performance of each model was evaluated using F1 scores and visualized using confusion matrices. The best supervised classification model for our study area was selected based on the testing subset F1 scores and computational cost of training models. The testing subset results shows that Random Forest and Support Vector Machine classifier models performed much better relative to the Gradient Boosting Decision Trees classifier model, with F1 scores over 0.80 in borehole A and B. In borehole A and B, Random Forest classifier has the least computational training time of about 14- and 6- hours, respectively. The feature importance results demonstrate that the logging feature P-wave velocity (Vp) is the highest predicting feature to the lithology classification in both boreholes. We find that the quartzite classes at different stratigraphic positions in each borehole are similar and they are correlated between the DSeis boreholes. The K-means clustering revealed three clusters in this study area and effectively map the radioactive zones. This study illustrates that geophysical log data and machine learning-based algorithms can improve the task of data analysis in the geosciences with accurate, reproducible and automated prediction of lithologies, correlation and mapping of radioactive zones in gold mine. This study outputs can serve as quality control measures for future similar studies both in the academic and industry. We identified that availability of large data is the major factor to high accuracy performance of machine learning-based algorithms for classification problems.
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    An initial estimation of the concentrations of methane (CH4) emitted from the Wakkerstroom wetland and Majuba power station in Mpumalanga province, South Africa
    (University of the Witwatersrand, Johannesburg, 2024-08) Bobo, Christine; Scholes, Mary C.; Furniss, David. G.
    The continuous increase in methane (CH4) emissions to the atmosphere poses a formidable challenge to Earth's climate resilience and exacerbates the impacts of global warming. This study compared microbial CH4 concentrations from the Wakkerstroom wetland to fossil fuel concentrations from the coal stockpiles at the Majuba power station in Mpumalanga, South Africa, using three methodological approaches: flexfoil bags, isotopic analysis, and satellite data. Seasonal ground measurements were collected in 3L flexfoil bags and analysed for CH4 mole fraction using a Picarro 2301 calibrated to the WMO X2004A CH4 scale. Samples were prepared for isotopic analysis by continuous-flow isotope-ratio mass spectrometry using an Isoprime Trace Gas system. Findings from ground sampling measurements showed that for three out of the four seasons, Phragmites australis at the Wakkerstroom wetland had the highest CH4 concentration [spring (0.209 ± 0.076 ppm), autumn (0.537 ± 0.239 ppm), and winter (0.132 ± 0.065 ppm)], and the coal stockpiles at the Majuba power station had the lowest CH4 concentration [summer (0.022 ± 0.021 ppm), autumn (0.014 ± 0.053 ppm), and winter (0.002 ± 0.004)]. Isotopic measurements, which identify and differentiate gas sources by examining distinct isotopic signatures, showed that the Wakkerstroom wetland had consistently light, 13C depleted isotopic signatures seasonally ranging between -61.4‰ to -55.6‰. In contrast to this, the Majuba power station coal stockpiles had inconsistent isotopic signatures through the sampling seasons- heavier CH4 emission isotopic signatures with 13C enrichment during spring and summer at -35.3 ± 1.0 ‰ and -43.5 ± 3.5 ‰ respectively, and lighter isotopic signatures with 13C depletion during autumn and winter of - 62.0 ± 1.6 ‰ and - 87.0 ± 10.3 ‰ respectively. On a larger temporal and spatial scale, satellite-based measurements from the Tropospheric Monitoring Instrument (TROPOMI) showed no significant differences between Wakkerstroom (1855.4 ± 18.0 ppb) and Majuba power station (1857.1 ± 22.9 ppb) in terms of the total column averaged dry-air mole fraction of methane (XCH4). An increasing trend in CH4 mole fraction, in Southern Africa as measured at Cape Point Global Atmospheric Watch (GAW) station over a 39-year period was also observed. Meteorological variables, particularly wind direction, had a more significant impact on CH4 mole fractions at Cape Point than at the Wakkerstroom wetland. The multi-faceted approach of utilizing the three measurement techniques provided a comprehensive view of atmospheric CH4 showing that wetlands could be more significant CH4 hotspots in comparison to coal stockpiles at power stations. Measuring methane concentrations is challenging due to its inherent complexity, thus the utilisation of different measurement methodologies further highlighted the spatial and temporal variability of CH4 concentrations at both the wetland and the coal stockpiles.
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    Behavioural and physiological responses of sable antelope to heat and aridity
    (University of the Witwatersrand, Johannesburg, 2024-10) Haylock, Kiara Avelyen; Hetem, Robyn; Parrini, Francesca
    The increased probability of longer, more extreme dry seasons, due to rapidly rising temperatures and the increased frequency and intensity of droughts, threatens water-dependent, selective grazers throughout Africa. Phenotypic plasticity such as behavioural adjustments and physiological flexibility may buffer the impacts of spatiotemporal variations in resource availability and climate. My project aimed to assess variations in home range size, movement distances, behavioural states of movement, fine-scale activity, microclimate selection and body temperature of sable antelope (Hippotragus niger niger), a water-dependent selective grazer, in relation to spatiotemporal variation in vegetation greenness and environmental heat load. To address the aim of my project, I measured body temperature and fine-scale activity using biologging in ten free-living GPS-collared sable antelopes in the semi-arid Bwabwata National Park of Namibia. Each collar was fitted with a miniature black globe thermometer to assess microclimate selection. A weather station with a standard black globe thermometer recorded black globe temperature and air temperature. Data collection spanned 24 months, from May 2016 to April 2018. The dry season was a critical period for sable antelopes, particularly the late dry season when high ambient temperatures compounded reduced resource availability. As conditions became hotter and browner with the progression of the dry season, home ranges elongated towards the Kavango River and increased in size by ~50% from the early dry to the late dry season. In response to increased 24-hour mean black globe temperature and increased exposure to brown vegetation, the 24-hour mean hourly displacement distance of sable antelopes increased with progression of the dry season, mostly due to the increased frequency of long, directed movements to the Kavango River during the late dry season. One sable antelope travelled between 13 and 30 kms every 4-5 days to access water from the river during the late dry season. Using Hidden Markov Models, four behavioural states were identified from the movement tracks of sable antelopes: resting, foraging, local movement and relocating. The long, directed movements to water, classified as a relocating behavioural state, predominated during the late dry season. Sable antelope displayed an increase in relocating behaviour and a decrease in foraging behaviour associated with high 24-hour mean black globe temperature and increased proportion of brown vegetation exposure. Sable antelopes also displayed an increase in local movement with increased exposure to brown vegetation and high 24-hour mean black globe temperature, but a decrease in resting behaviour with an increase in the proportion of brown vegetation exposure. Driven by decreasing vegetation greenness and increasing black globe temperatures, sable antelopes reduced their diurnal proportion of activity with progression of the dry season, associated with a reduction in activity during the heat of the day in response to increased exposure to brown vegetation, high 24-hour mean black globe temperature and an increased proportion of time spent in the shade. Sable antelopes did not fully compensate for lost diurnal activity, despite increased nocturnal activity during hot and dry conditions, as total 24-hour activity decreased with progression of the dry season. Sable antelopes also selected higher quality microclimates (i.e. microclimates that were on average 6.7 ± 0.2 oC cooler than direct sun) when increasingly exposed to brown vegetation and high 24-hour maximum black globe temperature. Fluctuations in 24-hour body temperature increased during the dry season with maximum amplitudes of body temperature rhythm of >5 oC within a single day during the late dry season. Sable antelopes displayed a reduction in minimum 24-hour body temperature in response to decreased 24-hour black globe temperature and increased exposure to brown vegetation during the early dry season, likely due to energy deprivation. While minimum body temperatures remained low during the late dry season, sable antelopes displayed an increase in maximum 24-hour body temperature in response to increased mean 24-hour black globe temperature and increased exposure to brown vegetation, likely due to water deprivation. High maximum 24-hour body temperatures, indicative of dehydration-induced hyperthermia, increased the likelihood of relocating movements to the Kavango River which in turn were associated with a subsequent decline in maximum 24-hour body temperatures. By linking body temperature to a behavioural state of movement, I am the first to demonstrate a direct link between access to a water resource and maximum body temperature in a free-living antelope species. The behavioural flexibility exhibited by sable antelopes during the dry season failed to buffer reduced resource availability as fluctuations in body temperature indicated that sable antelopes experienced nutritional and water stress. My findings highlight the importance of incorporating physiological measurements into behavioural and ecological studies to inform management decisions and improve conservation efforts in the face of climate change.
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    Accessory REE mineralization of the Nokeng fluorite deposit as distal facies of the adjacent Vergenoeg pipe, Bushveld Complex, South Africa
    (University of the Witwatersrand, Johannesburg, 2024-10) Makhema, Relebohile Edward; Yudovskaya, Marina; Madlakana, Nonkuselo
    The Nokeng Plattekop deposit forms part of the Paleoproterozoic Bushveld Complex and it is located near Rust de Winter, approximately 80 km northeast of Pretoria. This deposit belongs to the Vergenoeg Igneous Complex, which is associated with a violent gas-vapour-rich rhyolitic eruption. The complex comprises the Vergenoeg discordant breccia pipe and a pyroclastic rock suite. Within the breccia pipe and associated pyroclastic rocks, rare earth element (REE) mineralization is observed in minerals like allanite, apatite, bastnasite, monazite, and xenotime. The Plattekop fluorite deposit, which lies 1000 m south of the breccia pipe, is postulated to represent spill-over remnants of the Vergenoeg volcanic edifice. This study performed a comprehensive petrographic and geochemical analysis of ore and pyroclastic breccia of the Nokeng Plattekop deposit, utilizing various analytical techniques, including optical microscopy, XRF, ICP-MS, and SEM. The aim is to characterise the style of accessory REE mineralization at Nokeng as a provisional distal facies of the Vergenoeg volcanic field. The findings of this study suggest that the Nokeng Plattekop deposit comprises a hematite-fluorite unit overlying an ignimbrite unit. Hematite-fluorite ores of the upper unit resemble the Vergenoeg ore, exhibiting elevated CaO concentrations and reduced SiO2 content attributed to high fluorite and hematite proportions. Conversely, the ignimbrite unit displays reduced CaO and elevated SiO2 concentrations, corresponding to lower fluorite content and higher rhyolitic lava fragments. The basal ignimbrite is proposed to have formed during the early stages of rhyolitic volcanism, while Nokeng and Vergenoeg ores formed during later stages dominated by Ca- and F-rich ferruginous magma. Petrographic evidence suggests hematite pseudomorphs after magnetite, indicating mineral assemblage evolution. REE mineralization in the Plattekop fluorite deposit is represented by bastnasite, monazite and xenotime, mostly associated with quartz, goethite, aegirine, hematite and fluorite. The highest REE + Y content (~ 5 890 ppm) is associated with Plattekop hematite-fluorite ores. Comparative analysis of REE distribution patterns suggests similar styles of mineralization between Vergenoeg and Nokeng, indicating both deposits as potential sources of REEs as by-product.
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    Landscape-scale carbon stocks in the subtropical thicket of the Baviaanskloof, South Africa
    (University of the Witwatersrand, Johannesburg, 2024-08) Kooverjee, Neha; Smart, Kathleen; Fisher, Jolene; Scholes, Bob
    South Africa’s subtropical thicket biome has garnered interest for its potential for carbon sequestration through the restoration of degraded land, funded locally and internationally by the carbon market. Accurate carbon estimation of pre- and post-restoration carbon storage is key to monitoring the progress of restoration efforts and determining accurate estimates of carbon increase. Most past thicket studies have based landscape-scale carbon estimates on plot data alone, without accounting for the spatial variation in factors such as soil depth, resulting in overestimates of the average potential carbon that can be stored. The aim of this research was to estimate and create maps showing the spatial distribution of the thicket carbon stocks in the Baviaanskloof Nature Reserve, South Africa, by calculating the amount of carbon stored in the soil, woody biomass, root biomass and litter biomass across the thicket area of the reserve using plot data with remote sensing imagery. Soil organic carbon was estimated using soil profile data collected in the same primary catchment as the Baviaanskloof and extrapolated across the landscape using a Random Forest-based regression model. Woody carbon was estimated using previously recorded in situ carbon recordings. This data was then extrapolated across the landscape using raster data for vegetation height and cover, climate data, and elevation as predictor variables. Root and litter carbon were then calculated individually based on the woody carbon estimates and ratios of root and litter carbon to woody carbon from a past study. The average soil organic carbon (37.7 ± 29 t ha-1), woody carbon (18.1 ± 4 t ha-1), root carbon (3.1 ± 0.7 t ha-1), and litter carbon (2.4 ± 0.5 t ha-1) estimated in this study for intact thicket are all lower to varying degrees than those of past thicket studies that were based solely on plot data, indicating the importance of accounting for variation in the landscape and its effect on carbon stocks. The results of this study indicate that slope position, a proxy for soil depth, has a significant effect on thicket carbon stock. Woody carbon, root carbon and litter carbon estimates significantly decreased downslope, but soil organic carbon, the largest carbon pool in thicket, significantly increased downslope. In general, the results also indicate an increase in carbon after restoration, however, an illogical trend of lower potential root and litter carbon compared to current carbon in degraded thicket is present, indicating that the results of this study are not reliable for restoration planning and decision-making. This may be due to the inaccuracy of global Light Detection and Ranging (LiDAR) products, such as the Global Land Analysis and Discovery (GLAD) canopy height dataset, over non-forested areas such as thicket which are much shorter. Accurate estimates of current and potential carbon and accurate monitoring of restoration is important in tracking South Africa’s progress towards its biodiversity conservation goals under the Convention on Biological Diversity, and carbon emission reduction goals under the Paris Agreement. With access to locally captured LiDAR imagery that is suited to the short, dense structure of thicket vegetation and the topography of the landscape, and a larger database of in situ thicket carbon recordings, the methods used in this study could be employed to calculate more accurate carbon estimates and aid in directing restoration efforts to the most appropriate areas.
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    Finite Element Analysis of Dinocephalian Skulls to Address Head-Butting Behaviour in Early Therapsids
    (University of the Witwatersrand, Johannesburg, 2024-08) Bolton, Andrew; Benoit, Julien; Mangera, Taahirah
    The origin of complex social behaviour in the mammalian lineage has been a long-standing enigma. Behaviours do not leave a rich fossil record; however, adaptations to highly specialised complex behaviour can be traced back in some lineages, such as the dinocephalians. Dinocephalians dominated carnivorous and herbivorous niches of terrestrial ecosystems in the Middle Permian (~273-259 million years ago). Species within this clade often have skulls with considerable pachyostosis (overly thickened bones) and cranial ornamentation (horns and bosses). This morphology has been interpreted as evidence for head-butting, but the evidence is circumstantial at best. For this project, I used three-dimensional models of the skulls of four dinocephalians and two outgroups to simulate and investigate the capabilities of these skulls to withstand different magnitudes of head-butting and flank-butting impacts with finite element analyses. Palaeopathological analyses vindicated the accuracy of FEA data, which indicates that dinocephalian skulls modelled here arguably reflect biological truth. As head-butting is a complex social behaviour, this would strongly suggest the presence of dominance hierarchies, territoriality, and gregariousness. This represents the earliest robust evidence of complex social behaviour in tetrapods, preceding all known examples of social interactions in dinosaurs and mammals by hundreds of millions of years.
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    Modelling for Rainwater Harvesting Structures Using Geospatial Techniques
    (University of the Witwatersrand, Johannesburg, 2024-10) Makaringe, Precious Nkhensani; Atif, Iqra
    Climate change poses a significant threat, leading to droughts, floods, and hindering sustainable development. Water scarcity is a growing concern, particularly in developing countries like South Africa, where limited freshwater resources are further strained by climate variability. This research explores the potential of rainwater harvesting (RWH) as a strategy to address water scarcity in such regions. This study aims to model potential rainwater harvesting sites in Lynwood Park, Pretoria, South Africa, utilising geospatial techniques. Object-Based Image Classification (OBIC) was employed to extract building footprints from high-resolution satellite imagery. Microsoft and Google building footprints were utilised to determine the suitable automated building footprints for Lynnwood Park. ArcGIS Pro software served as the primary platform for spatial data analysis and mapping potential RWH sites. Data integration included high-resolution satellite imagery, a Digital Elevation Model (DEM), building footprints, and rainfall data. Additionally, questionnaires were distributed to estimate population and water demand within the study area. The research demonstrates the efficacy of geospatial tools in identifying suitable locations for RWH systems. Indicating that steeper slopes in the southern region of Lynnwood Park have limited collection from large rooftops, while the flatter north offered greater potential. Rainfall graphs and PRWH results suggest that over half of Lynwood Park's annual water demand could be met through rooftop rainwater collection. However, factors such as system losses due to evaporation, inefficiencies in collection and storage, and variability in rooftop sizes across different buildings would need to be incorporated into more detailed models, as well as water quality analysis for rooftop harvested water in future studies. This study highlights the potential of RWH as a viable water security strategy in water-scarce regions. The findings contribute to the development of geospatial approaches for RWH implementation, promoting water security and sustainability in a changing climate.