Electronic Theses and Dissertations (PhDs)

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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.
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.
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.
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.
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.
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.

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