School of Geosciences (ETDs)
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Item Taphonomy and palaeoecology of a monospecific microvertebrate bonebed: behavioural implications for the late Permian (Lopingian) parareptiles(University of the Witwatersrand, Johannesburg, 2024-06) Mukwevho, Lutendo; Choiniere, Jonah; Smith, RogerSociality in the vertebrate fossil record is a dynamic and fast-expanding area of research. Natural history observations of living animals are crucial for understanding and categorizing sociality, but these observations are not feasible for extinct species. Monotaxic bonebeds provide unique opportunities to conceptualize the social behaviours of these extinct animals. An unusual bonebed (SAM-PK-K11289) discovered in the uppermost Permian strata of the Balfour Formation, Karoo Supergroup, in the Eastern Cape presents a window into the sociality of Late Permian reptiles. The use of propagation phase-contrast synchrotron X-ray microcomputed tomography permitted the 3D reconstruction of skeletal elements in SAMPK-K11289, allowing the taxonomic identification of the individuals in the bonebed as most likely belonging to Owenetta. This is the largest aggregation of Owenetta individuals known to date, with a minimum number of 31, which are all very similar in body size. The ontogenetic profile of SAM-PK-K11289 was interpreted by analysing the size distribution of duplicate elements and by making comparisons with other Owenetta and procolophonid specimens. The specimens in the bonebed are all osteologically immature, indicating that they are juveniles. The bonebed occurs in a pedogenically modified ripple cross-laminated siltstone suggesting that a low-energy fluvial sedimentation likely contributed to the modification, disturbance and disarticulation of elements before the bonebed was buried at or very close to the death site. This bonebed provides novel information that directly challenges the popular belief that reptiles and their ancestors are non-social or asocial. Considering the overall circumstances of the bonebed, I hypothesize that Owenetta rubidgei juveniles were socially gregarious and this behaviour may have been induced or influenced by environmental changes during the early extinction phase of the end Permian mass extinction in the Karoo Basin.Item Nutrient and Salinity Loading Based On The Temporal And Spatial Water Quality Data In The Upper Crocodile River Basin(University of the Witwatersrand, Johannesburg, 2024-03) Mistry, Nikhil Jayant; Ali, K. Adam; Abiye, TamiruThe Upper Crocodile River Basin has undergone a drastic change through anthropogenic factors such as rapid urban growth, industrial activities, agriculture and mining in the past thirty-eight years. This has led to an increase in nutrient and salinity loads with decreasing water quality. The Upper Crocodile River Basin wastewater treatment works struggle to maintain loading rates, causing partially treated wastewater to enter the river systems that increased the salinity loads. Water chemistry and discharge data from the DWS were collected, cleaned and processed; data were summated across the necessary river channels in which they are located to determine the nutrient and salinity loads in all rivers in the Upper Crocodile River Basin. The results indicated that the Hennops, Jukskei and Crocodile Rivers are responsible for the largest nutrient and salinity loading rates. Changes in land use activities and climate over the past thirty-eight years, since 1980, have drastically impacted the rate at which nutrient and salinity loads enter into the UCRB. During the early 1980s to 1990s a significant drop was observed in nutrient and salinity loading rates, spiking in the late 1990s and early 2000s, influenced by changes in water management and climatic events like the La Niña and the El Niño phenomena. The inter-basin transfer in the early 2000s and subsequent two decades have led to an overall rise in nutrient and salinity loading rates, posing serious water quality and health risks to people in the UCRB area. Mining activities, poor landfill management and leaking tailing storage facilities have resulted in increased sulphate loading rates into the UCRB. Nitrogen loading has risen due to uncontrolled waste disposal from informal settlements, industrial activities and sewage spills in the Johannesburg region. Phosphorus loading rates have risen due to agricultural fertiliser runoff, with the Jukskei River being the largest contributor to these loads in the Upper Crocodile River Basin. The loads entering the Hartbeespoort dam during summer and winter seasons in the 2016-2018 period for sulphate is 6819.24 kg/hr, 4873.62kg/hr; for nitrogen 4179.24 kg/hr, 4021.55 kg/hr and for phosphorus 40.08 kg/hr, 34.724 kg/hr, respectively. Salinity loads entering the Hartbeespoort dam during summer and winter are 42952.87 kg/hr and 27548.39 kg/hr, respectively. According to the findings, water resource management must act quickly to improve the overall quality of the water; in the upcoming ten years, as loading rates are expected to rise exponentially as a result of increased demand and stressed water use, which will lead to poor water quality. This will pose serious health and economic risks to the people of the Upper Crocodile River Basin and the populace of South Africa.Item Baseline Hydrogeology of Dolerite Dykes in Lesotho, Mafeteng District as a Case Study(University of the Witwatersrand, Johannesburg, 2024-06-10) Monyane, Napo Shadrack; Shakhane, Teboho; Abiye, TamiruGroundwater is a vital alternative resource due to the increasing demand for water supply in Lesotho’s rural and urban areas as surface water faces threats from population growth and climate variability. For instance, groundwater serves the demands of Lesotho's growing textile industry and agricultural sectors. The 3D form of the dolerite dykes widespread throughout the Karoo rocks in Lesotho may have an impact on the groundwater occurrence, flow, and yield characteristics of the region. However, specific research on their hydrogeology has not been extensively undertaken. This study aimed at characterising the hydrogeology of the dolerite dykes in the lowlands of Lesotho using selected places namely, Boluma-Tau, Ha Lumisi, Ha Mofota, Ha Maoela, Ha Mofo, Malumeng, Qalabane, Matlapaneng, Thabana Mohlomi, Ha Mohlehli, Malimong, Tsoeneng and Ha Lenonyane as case studies for the research. This research adopted the desktop and walkover survey in developing information on the region’s broad geological and hydrogeological setting within the Karoo lithologies. Included also was the use of ground magnetics in ascertaining the existence and determining the geometry of the dykes, using the D-8 algorithm for flow directions, and drilling and pumping tests for aquifer analysis. The dykes dominating the focal area in the Mafeteng District generally trend NE-SW, NNE-SSW and NW-SE. The magnetic results outlined negative anomalies along the dyke’s contact with the country rocks as surveyed from Qalabane, Mafeteng Lesotho, these magnetic lows imply fracture gaps along the strike of the dyke. A generalised dip, width, and depth could not be easily inferred due to inconsistent magnetic anomaly shapes, but forward modelling indicated a thin (10 m wide) shallow (10°) dyke trending NE-SW intruding both the Burgersdorp and Molteno Formations at Qalabane, Mafeteng. As per the D-8 results, the dolerite dykes in Mafeteng are distributed in the intermediate basin flow values due to a gentle hydraulic gradient. Certain dyke sites exhibit a groundwater flow direction towards the north, whilst others display a radial groundwater flow direction. The derivative analysis revealed the boreholes were drilled in a fractured dyke system, also the dominant radial flow regime and double porosity dip at different pumping durations, and the possible recharge boundary were revealed in some drilled dyke sites. Further analysis from the drawdown versus time curves resulted in average yields of 0.1 – 1.25 l/s with transmissivities ranging from 1 – 14 m2/day, insinuating that a limited extraction of the local water supply is suggested from the dolerite dyke lithologies in the lowlands of Mafeteng Lesotho, given the groundwater yielding capacity and magnitude of the transmissivities. Even though the drilled boreholes from the dyke sites indicated a fractured dyke setting, estimated transmissivity values are variable and low, this is indicative of the inconsistent apertures and lack of interconnectivity of the available secondary hydrogeological features in the lowlands of Lesotho.Item 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, JulienVaranopidae 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.Item Palaeoclimate Reconstruction Using Charcoal from a Mid-Holocene Stratum 4b, Wonderwerk Cave, South Africa(University of the Witwatersrand, Johannesburg, 2024-06-18) Hlophe, Busisiwe; Bamford, MarionCaves are often sources for palaeoenvironmental information in the dry interior regions of southern Africa. The Wonderwerk Cave, located in Northern Cape, is a national heritage site with a well-preserved, nearly complete record of the local Holocene LSA techno-complexes and past environmental indicators. Hence, it has the potential to provide valuable insights into past human behaviour as well as the local palaeoclimate and vegetation. This study examined wood charcoal from stratum 4b, Excavation 1 of the Wonderwerk Cave. The aim was to evaluate the taxonomic composition and the physiognomy of the charcoal to understand the environment around the cave 6.9-5.9 ka. The study also investigated the modern uses of the vegetation to infer how humans may have utilized the woody plants around them during that period. The results indicate the landscape cover included woody plants adapted to dry conditions and summer rainfall. However, the archaeological taxa identified also included two species that thrive in moist environments, Halleria lucida and Olinia ventosa, suggesting fluctuations in climate. The taxonomic composition also suggests an environment similar to the modern bushveld found near the cave. The low conductivity capacity as well as vulnerability and mesomorphy indices of the woods support the implication that the vegetation was adapted to low water availability or aridity. The cave's inhabitants likely used the identified plants for firewood, magical and medicinal purposes, and more between 6.9 and 5.9 ka.Item 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, EricOne 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.Item 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, NonkuseloThe 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.Item 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, TaahirahThe 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.Item Assessing aquifer vulnerability to landfill pollution using drastic method in Gauteng, South Africa(University of the Witwatersrand, Johannesburg, 2023) Mphaphuli, Idah; Abiye, TamiruThis study integrated the DRASTIC method and field investigations into mapping the degree of vulnerability of aquifers to landfill pollution in the Gauteng Province, which is one of the most populated provinces in South Africa. In order to investigate the aquifer vulnerability of Gauteng's heterogeneous and complex geology, the DRASTIC method was used to generate intrinsic and specific vulnerability maps. Three vulnerability classes were generated from the DRASTIC index, namely, low vulnerability, moderate vulnerability and high vulnerability, which covered 46%, 37% and 17% of the study area, respectively. The highly-vulnerable areas were associated with the karst aquifer of Malmani dolomite, permeable vadose zone, high hydraulic conductivity and loamy sand/sandy loam soil type, whilst moderately-vulnerable areas were associated with fractured/weathered aquifers, high recharge and low topography. The intrinsic vulnerability was validated using average NO3+NO2-N (nitrate + nitrite as nitrogen) and the results of water samples from field investigations conducted in Marie Louise and Robinson landfill sites. Elevated NO3+NO2-N concentration (9.85-16.03 mg/l) was observed in the highly-vulnerable areas. Water samples were collected, in order to analyse the water chemistry, stable isotopes and radioactive isotopes (tritium). Gibbs and Piper diagrams were used to evaluate the main mechanism controlling the groundwater chemistry and the dominant major ions that influence it. Pollution by leachate was detected in the Marie Louise landfill site, where the groundwater showed high tritium and ammonia concentration. The main hydrochemical facies detected in Marie Louise were Mg SO4, Ca-SO4, Na-SO4 and Na-Cl. The hydrochemical facies detected in Robinson were Na-SO4, Ca-HCO3, Na-Cl and Ca-Cl. The DRASTIC method was shown to be effective in assessing groundwater vulnerability on a regional scale, provided that there is adequate input data.Item Late Triassic to Early Jurassic ecology: An insight into diet and trophic levels using non-traditional Ca isotopes(University of the Witwatersrand, Johannesburg, 2023-07) Davechand, Priyanka; Bybee, Grant; Choiniere, JonahThe diet and trophic structuring of organisms in deep time is poorly understood, making comparison of ancient and modern ecosystems challenging. Proxy data (e.g., dental morphology, jaw muscle reconstruction) remain the most common mode of palaeodietary inference, but the correlative strength of these proxies remains untested due to a lack of direct evidence and an incomplete sampling of palaeobiodiversity. These major challenges in palaeodietary reconstruction can be overcome using novel geochemical markers in fossilised tooth enamel, which provide direct evidence of palaeodiet and trophic relationships. Traditional stable isotopes of carbon, oxygen, and nitrogen have been used in the past to infer palaeodiets, but these elements are susceptible to diagenetic alteration during fossil preservation and require large sample amounts for assays. In contrast, non-traditional calcium (δ44/42Ca) isotopes are less susceptible to diagenesis and require significantly smaller sample amounts. This, together with the fractionation that Ca isotopes undergo as a bio-essential element, allows δ44/42Ca to be utilised on a broad range of palaeontological questions including assessing dietary range and trophic level. The diverse ecosystems of the Elliot Formation (Karoo Supergroup) in South Africa are represented by abundant fossils of a variety of reptilian and mammalian stem lineages that coexisted during the latest Triassic–earliest Jurassic interval (218–190 Ma). The broad range of body sizes, inferred dietary preferences, and phylogenetic positions make the Elliot palaeoecosystems an ideal natural laboratory in which to apply palaeodietary isotopic tools. This dissertation aims to assess the palaeotrophic divisions of the Elliot Formation vertebrates using non-traditional δ 44/42Ca isotopes. This research uses ion-exchange chromatography on vertebrate tooth enamel to assess the palaeodietary preferences of Elliot Formation reptilian and mammalian lineages. To obtain these data, existing techniques for sample preparation of non-traditional δ 44/42Ca isotopes were modified and optimised at the Wits Isotope Geoscience Laboratory (WIGL) at the University of the Witwatersrand. δ 44/42Ca analysis was conducted on a variety of specimens across a broad range of amniote lineages, ranging from: dinosaurs such as presumed herbivorous sauropodomorphs Massospondylus and Aardonyx, the presumed omnivorous ornithischian (Lesothosaurus and Heterodontosaurus), and the presumed carnivorous theropod Megapnosaurus; to cynodont therapsids (Tritylodon, Pachygenelus and Scalenodontoides); to pseudosuchians such as the crocodylomorphs Protosuchus and Orthosuchus and earlier branching taxa (‘rauisuchians’ and poposauroids). A leaching procedure was also tested to ensure that the results produced were not influenced by diagenetic biases. Once consistent and reproducible methods were finalised, column chemistry and Multicollector-Inductively Coupled Plasma Mass Spectrometery (MC-ICPMS) analysis was conducted on the different Karoo-aged specimens. There are various outcomes from this dissertation. One important outcome was the optimisation of time for Ca separation using ion-exchange chromatography. This allowed for a shorter chemical preparation time and increased the number of analyses completed per session. Another improvement of the method was that the leaching procedure can be used to control for any diagenetic biases by removing secondary calcite in samples as old as those from the Triassic–Jurassic period. Elliot taxa were then analysed, and significant differences were found between δ 44/42Ca values of large carnivorous pseudosuchians (‘rauisuchians’; -0.45 ‰ to -1.17 ‰) and co occurring herbivorous sauropodomorph genera (-0.26 ‰ to -0.69 ‰). These results indicated that non-traditional δ 44/42Ca isotopes can be used to understand trophic structures and palaeodiets in ecosystems at least 210 million years old. We also found that while some taxa had δ44/42Ca isotope values in-line with their presumed diets, other taxa had more diverse diets than initially presumed. δ 44/42Ca-enriched values in this study provide evidence for herbivory in crocodylomorph and the oldest theropod. There is also a possibility of an omnivorous diet for presumed herbivorous Lesothosaurus as the δ 44/42Ca values are relatively depleted to other herbivores. In addition to diet, calcium plays a major role in the formation of reptilian eggs and there are documented changes in δ 44/42Ca values during the reproductive cycle. To assess this in a living system, Crocodylus niloticus, was analysed to understand if δ 44/42Ca could be used to identify the difference in sex based on the δ 44/42Ca values. No isotopic differences were found between the juvenile male and female Crocodylus niloticus samples. Testing these important ecological principles in temporally constrained formations allows us to understand the historical nature of biodiversity changes, especially across periods when environments on Earth were experiencing extreme conditions. The ability to determine factors such as palaeodiet and palaeotrophic range will enable the development and improvement of palaeoecological analysis. This research presents the first ever δ 44/42Ca values on Karoo-aged vertebrate fossils and will have a large impact on how palaeoecological reconstruction is conducted in the future of palaeosciences.