South African Journal of Science

Celebrating multidisciplinarity

Invasion science in South Africa: The definitive collection

The University of Cape Town: Between apartheid and academic freedom

In the footsteps of famous family forebears to a respected polymath through moral courage

What the science of child and adolescent development contributes to understanding the impacts of COVID-19

Artificial intelligence enhanced molecular databases can enable improved user-friendly bioinformatics and pave the way for novel applications

Snapshot Safari: A large-scale collaborative to monitor Africa's remarkable biodiversity

Engagement for airborne geophysical survey within a transdisciplinary baseline programme in the Eastern Cape Karoo

Karoo research update: Progress, gaps and threats

Opening the floor for discussion: A perspective on how scholars perceive attitudes to science in policymaking in South Africa

Professor D.P. Mason (MASSAF, FRSSAF) on the occasion of his 75th birthday: A lifetime contribution to the development of Applied Mathematics in South Africa

Lightning monitoring and detection techniques: Progress and challenges in South Africa

Globally, lightning causes significant injury, death, and damage to infrastructure annually. In comparison to the rest of the world, South Africa has one of the highest incidences of lightning-related injuries and deaths. The latest available lightning detection techniques and technologies are reviewed and include current research in South Africa and South Africa's lightning detection challenges. Technological advances have contributed towards improving lightning detection and monitoring activities in many countries. South Africa has made considerably more progress in the field of lightning research than other African countries and possesses one of the three ground-based lightning detection networks in the southern hemisphere. However, despite these developments, rural communities in South Africa, and indeed in Africa, remain vulnerable to lightning, the occurrence of which is predicted to increase with climate change. A large proportion of the population of African countries resides in rural areas, where citizens participate in subsistence farming, and built infrastructure is not lightning safe. We recommend a call for the integration of indigenous and scientific knowledge as well as for the development of a participatory early warning system. Investigations into determining the most effective way to utilise existing monitoring networks - but with warning dissemination to rural communities - are also required. Lastly, future research on the development of lightning-safe rural dwellings or shelters, especially in lightning prone areas, is needed.SIGNIFICANCE: • Climate change projections of increases in lightning incidence highlight an increased risk for vulnerable communities. • There is a lack of literature focusing on lightning detection within rural communities. • Technological advances now allow for better dissemination of lightning information and early warning within rural communities. • The South African Lightning Detection Network is operational at a national level; however, there is no dissemination at a local level. • There are currently no recommended design guidelines for informal dwellings and no safety protocols for rural communities.

The altitude of sprites observed over South Africa

Sprites are mesospheric optical emissions that are mostly produced by large, positive cloud-to-ground lightning discharges. Sprites appear in different morphologies such as carrot, jellyfish and column, and are typically in the altitude range of ~40-100 km above the Earth's surface. Sprites are a subset of transient luminous events and they contribute to the global electric circuit. South Africa has large convective thunderstorms, which typically occur in the summer months of every year. Peak current, time and geographical position of lightning strokes were obtained from the South African Weather Service. Sprite observations were recorded in South Africa for the first time on 11 January 2016 from Sutherland in the Northern Cape using a night-vision television camera from the South African National Space Agency's Optical Space Research laboratory. We report the first estimates of the top altitude, and the altitude of maximum brightness, of 48 sprites over South Africa. We found that the average top altitude and the altitude of maximum brightness of sprites are approximately 84.3 km and 69 km, respectively, which is consistent with estimates made elsewhere. We also found a moderately high positive and a weak positive correlation between the top altitude and the altitude of maximum brightness, respectively, of sprites and the lightning stroke charge moment change.SIGNIFICANCE: • We present the first altitude estimation of sprites observed over Africa. • The altitude of sprites observed over South Africa is in agreement with observations made elsewhere. • There is a positive correlation between the top altitude of sprites and the parent lightning charge moment change. • Sprite maximum brightness is observed near the stratopause.

The North-West University's High Altitude Radiation Monitor programme

Since the discovery of cosmic radiation by Victor Hess in 1912, when he reported a significant increase in radiation as altitude increases, concerns about radiation effects on human bodies and equipment have grown over the years. The secondary and tertiary particles which result from the interaction of primary cosmic rays with atmospheric particles and commercial aircraft components, are the primary cause of the radiation dose deposited in human bodies and in electronic equipment (avionics) during aircraft flights. At an altitude of about 10 km (or higher) above sea level, the dose received by frequent flyers, and especially flight crew, is a serious concern. Also of concern is the possible failure of sensitive equipment on board commercial aircrafts as a result of flying through this mixed radiation field. Monitoring radiation in the atmosphere is therefore very important. Here we report on the first measurements by the High Altitude Radiation Monitor (HARM) detector during a commercial flight from Johannesburg (O.R. Tambo International Airport) to Windhoek (Hosea Kutako International Airport). As part of a public awareness activity, the HARM detector was placed on a high-altitude balloon, and these measurements are also shown here. Model calculations (estimations) of radiation levels for the commercial aircraft flight are shown and the results are used to interpret our measurements.SIGNIFICANCE: • Measurements of the Regener-Rfotzer maximum in South Africa and dosimetric measurements on board a commercial flight are presented. • These radiation measurements are compared to model calculations which can be used to predict the radiation dose during commercial flights. • This study also aims to raise public awareness about the atmospheric radiation environment from ground level to the Regener-Rfotzer peak at high altitude.

Constraints on improving higher education teaching and learning through funding

In the midst of massification, targeted funding has been used in various countries to address inefficiencies in teaching and learning. In South Africa, arguments have been made for significant investments to be made and the University Capacity Development Grant (UCDG) in particular is being used as a driver for improved outputs. Prior to its implementation in 2018, the UCDG comprised the Research Development Grant and the Teaching Development Grant. The Teaching Development Grant was intended to address low retention and throughput rates and ZAR5.5 billion was spent to this end over a 12-year period. The analysis presented here of all Teaching Development Grant budget plans and progress reports from 2007 to 2015 shows that the undifferentiated implementation of the Teaching Development Grant within a differentiated sector limited its potential for system-wide gains. Institutions without adequate resources tended to divert Teaching Development Grant funds to attend to backlogs rather than to address teaching and learning practices and such universities lost much of their allocation through the withholding of unspent funds. This blanket practice addressed the symptoms of underspending but not the structural, cultural and agential mechanisms that led to such under-expenditure. Uneven access to the limited teaching development expertise also impacted on the use of the grant. This call for a context-based approach to funding has been identified as a key success factor in grant interventions in both African and European universities. We recommend a sector-wide response in the form of a national body or plan for the benefit of all universities and investment in financial management enhancement.SIGNIFICANCE: • The study contributes to a better understanding of how government funding interventions can achieve intended goals. The study calls for a more contextualised approach to funding and to greater collaboration across the sector to maximise limited capacity.

Predicting take-up of home loan offers using tree-based ensemble models: A South African case study

We investigated different take-up rates of home loans in cases in which banks offered different interest rates. If a bank can increase its take-up rates, it could possibly improve its market share. In this article, we explore empirical home loan price elasticity, the effect of loan-to-value on the responsiveness of home loan customers and whether it is possible to predict home loan take-up rates. We employed different regression models to predict take-up rates, and tree-based ensemble models (bagging and boosting) were found to outperform logistic regression models on a South African home loan data set. The outcome of the study is that the higher the interest rate offered, the lower the take-up rate (as was expected). In addition, the higher the loan-to-value offered, the higher the take-up rate (but to a much lesser extent than the interest rate). Models were constructed to estimate take-up rates, with various modelling techniques achieving validation Gini values of up to 46.7%. Banks could use these models to positively influence their market share and profitability.SIGNIFICANCE: • We attempt to answer the question: What is the optimal offer that a bank could make to a home loan client to ensure that the bank meets the maximum profitability threshold while still taking risk into account? To answer this question, one of the first factors that needs to be understood is take-up rate. We present a case study - with real data from a South African bank - to illustrate that it is indeed possible to predict take-up rates using various modelling techniques.

Performance assessment of four HIV self-test devices in South Africa: A cross-sectional study

HIV self-testing (HIVST) has been introduced to supplement existing HIV testing methods to increase the number of people knowing their HIV status. Various HIVST kits have been developed; however, in many countries, their entry into the market is contingent on either being listed as World Health Organization (WHO) prequalified diagnostics/products or being approved by that country's health device regulator or both. In this cross-sectional study, we evaluated the usability, sensitivity and specificity of HIVSTs, as directed by the WHO prequalification literature. A boxed, sealed HIVST kit was provided to enrolled lay users with no further instruction, who then performed the test under observation. For each HIVST, a product-specific semi-structured checklist was used to calculate a usability index, while the sensitivity and specificity of each HIVST were calculated by comparing the HIVST results to the 'gold standard' -fourth-generation ELISA laboratory blood test. The average usability index was 97.1% (95.9-97.8%), while the average sensitivity and specificity were 98.2% (96.8-99.3%) and 99.8% (99.4-100.0%), respectively. We also diagnosed 507 (15.1%) HIV-positive participants from the general population. The average usability index, sensitivity and specificity were all comparatively high, and these results corroborate previous usability and performance studies from other regions. These results suggest HIVSTs are appropriate for the South African market and can assist manufacturers with readying their devices for final WHO prequalification evaluation.SIGNIFICANCE: • This study has followed the WHO Technical Specification Series for the prequalification of HIV self-test devices, so the usability, sensitivity and specificity results may be used to inform the WHO prequalification process. • The average usability index (97.1%), sensitivity (98.2%) and specificity (99.8%) were all very high, and these results support previous usability and performance studies from other regions, which suggest HIV self-tests are appropriate for WHO prequalification, and subsequently, the South African market. • This study also diagnosed 507 (15.1%) HIV-positive participants from the general population - slightly higher than the national prevalence of 13.1%.

Hominin lower limb bones from Sterkfontein Caves, South Africa (1998-2003 excavations)

We describe late Pliocene and early Pleistocene hominin fossils from Sterkfontein Caves (South Africa), including two femoral specimens, as well as a partial tibia and a partial fibula. The fossils are likely assignable to Australopithecus africanus and/or Australopithecus prometheus and the morphology of each corroborates previous interpretations of Sterkfontein hominins as at least facultative bipeds.SIGNIFICANCE: • A recent series of papers by our research team describes the morphology of a hominin skeleton from Sterkfontein Caves (South Africa), nicknamed 'Little Foot'. Based on its unique skull morphology, R.J. Clarke, the skeleton's discoverer, places it in the species Australopithecus prometheus, as distinct from the better-known and co-occurring Australopithecus africanus. Here we describe additional hominin thigh and leg fossils from Sterkfontein that, when considered in a comparative context, support the hypothesis that there was significant (probably interspecific) variation in South African hominin postcranial morphology during the late Pliocene and early Pleistocene.

**The cryptic case of Otomys sloggetti (Sloggett's vlei rat): Interpreting murid molar morphology in the fossil record**

Vlei rats (Family: Muridae; Subfamily: Otomyinae) have a widespread distribution in southern Africa. They are favoured prey of barn and spotted eagle owls, and frequently become associated with archaeological deposits when the owls roost in cave sites. The phylogeny of several Otomyinae species is enigmatic, and Otomys sloggetti (Sloggett's vlei rat) is no exception. This species has been referred to as the 'ice rat' and present distribution ranges are seemingly limited to mountainous areas, at high altitude, in Lesotho, Drakensberg and the Karoo. It was thus surprising and unexpected when specimens closely resembling Otomys sloggetti (identification was based on molar morphology) were found in several archaeological sites on the south and west coasts of South Africa, and also in modern owl pellet assemblages - all extralimital to the current reported distribution. However, further examination of and comparison between these specimens, as well as extensive differences observed between comparative Otomys sloggetti specimens from museum collections, highlighted potential problems associated with the common practice of using tooth morphology to identify fossil murid species. We identified six molar morphotypes from the fossil and modern material, all of which bore a morphological resemblance to O. sloggetti. The material discussed in this paper suggests that cryptic, undescribed vlei rat species, or subspecies, have been in the past, and may yet be, co-occurring with modern populations of O. karoensis and O. irroratus. Phylogenetic studies need to be done in conjunction with morphological studies, as, currently, the relationship between the huge variation seen in interspecific morphology with genetics is little understood, different Otomys species are not always distinguishable morphologically, and considerable chromosomal polytypes have been found. Our findings highlight the need for extensive cladistic and genetic research on the Otomyinae.SIGNIFICANCE: • Mice and shrews from fossil sites are frequently used by archaeologists as indicators of past climatic and environmental conditions. Research into the species present in fossil assemblages is usually done on a single site basis and intersite comparisons are rare. The taxonomic conundrums presented by a vlei rat found in several South African archaeological sites indicates that such comparisons could result in the re-evaluation of identifications, and/or indicate the presence of cryptic species/subspecies. Phylogenetic studies are needed in conjunction with morphological studies, as the relationship between variations in interspecific tooth morphology (used to identify taxa) with genetics is little understood. This in turn will help to elucidate the relationship between morphology, biogeography and local adaptations.

Water security and rangeland sustainability: Transdisciplinary research insights from Namibian-German collaborations

The Global South is facing severe challenges in ensuring livelihood security due to climate change impacts, environmental degradation and population growth as well as changing lifestyles. These complex problems cannot be solely solved by single scientific disciplines - they require transdisciplinary research (TDR). Stakeholders from civil society, the corporate sector, government and science need to pool their knowledge to find solutions for sustainable transformations. In Namibia, we have been involved in TDR projects on water supply, and sanitation services as well as livestock management in rangeland systems. In this paper, we review two TDR projects that differ in multiple ways and hence allow us to carve out structural differences and critically discuss research outcomes, lessons learned and the challenge of North-South collaborations. Our review builds upon published and unpublished project documents as well as expert interviews with Namibian and German researchers who were involved in the projects. Our results show that TDR can be put into practice in different ways, depending on the research focus and the period available. The TDR phases of problem framing, inter- and transdisciplinary integration were implemented with different tools and foci points. We discuss the role of project length and funding conditions for project success and outcome generation. In addition, we critically consider the role of Namibian and German researchers in these international collaborations. The conclusions we draw touch upon the points of preparatory research funding, the equal acknowledgement of Global South contributions to joint research projects and the explicit handling of TDR components in project work.SIGNIFICANCE: • The current social-ecological challenges are complex and require TDR as a mode of knowledge co-production, particularly in a development context. • Inter- and transdisciplinary integration are critical processes for a project to be successful and require the allocation of adequate time and monetary resources. • Longer-term projects with a funded preparatory research phase constitute a structural model for TDR as project outcomes can evolve over time. • Global South researchers carry a hidden burden in international collaborations that has to be adequately acknowledged upfront in project planning and final products.

Identified main fire hotspots and seasons in Cote d'lvoire (West Africa) using MODIS fire data

Biomass burning has become more frequent and widespread worldwide, with a significant proportion occurring in tropical Africa. Fire dynamics have been generally studied at global or regional scales. At local scale, however, fire impacts can be severe or catastrophic, suggesting local analyses are warranted. This study aimed to characterise the spatio-temporal variations of vegetation fires and identify the main fire hotspots in Cote d'lvoire, a country of West Africa, one of the world's burn centres. Using MODIS-derived fire data over a 10-year period (2007-2016), the number of fire days, active fires and fire density were assessed across the entire country. In the southern part dominated by forests, fire activity was low. Three main fire hotspots were identified between 2°30'-8°30'W and 7°00'-10°30'N in the North-West, North-East and Central areas all dominated by savannas. In these areas, Bafing, Bounkani and Hambol regions recorded the highest fire activity where fire density was 0.4±0.02, 0.28±0.02 and 0.18±0.01 fires/km²/year, respectively. At national scale, the annual fire period stretched from October to April with 91% of fires occurring between December and February, with a peak in January. Over the decade, there was a decreasing trend of fire activity. Fire density also was negatively correlated with rainfall >1000 mm for the synchronic analysis, whereas fire density was positively correlated with rainfall in the previous years. Results suggest that the positive relationship between the previous year's rainfall and fire activity could operate on a cycle from 1 to 4 years.SIGNIFICANCE: • Three fire hotspots were found primarily in savanna vegetation, which burns more regularly than forest-dominated vegetation. • The fire season occurs over 7 months, the majority of active fires (91%) occurring in just 3 months (December-January-February) with a peak in January (39%). • Fire activity has declined over the past decade with a return time of above-average fires from 1 to 4 years. • Fire density is positively correlated to the amount of rainfall in preceding years, whereas fire density and rainfall of the same year were negatively correlated in the region of rainfall >1000 mm.

Rates and patterns of habitat loss across South Africa's vegetation biomes

The loss of natural habitat resulting from human activities is the principal driver of biodiversity loss in terrestrial ecosystems globally. Metrics of habitat loss are monitored at national and global scales using various remote sensing based land-cover change products. The metrics go on to inform reporting processes, biodiversity assessments, land-use decision-making and strategic planning in the environmental and conservation sector. We present key metrics of habitat loss across South Africa at national and biome levels for the first time. We discuss the spatial patterns and trends, and the implications and limitations of the metrics. Approximately 22% of the natural habitat of South Africa has been lost since the arrival of European settlers. The extent and the rate of habitat loss are not uniform across South Africa. The relatively mesic Grassland, Fynbos and Indian Ocean Coastal Belt biomes have lost the most habitat, while the arid Nama-Karoo, Succulent Karoo and Desert have lost the least. Rates of loss increased across all biomes in recent years (2014-2018), indicating that the historical drivers of change (i.e. expansion of croplands, human settlements, plantation forestry and mining) are intensifying overall. We should caution that the losses we report are conservative, because the land-cover change products do not capture degradation within natural ecosystems. Preventing widespread biodiversity losses and securing the benefits we derive from biodiversity requires slowing and preventing further habitat degradation and loss by using existing land-use planning and regulatory tools to their full potential.SIGNIFICANCE: • The loss of natural habitat resulting from human activities is the principal driver of biodiversity loss in terrestrial ecosystems in South Africa. • Monitoring trends and patterns of habitat loss at a national scale provides a basis for informed environmental decision-making and planning, thus equipping civil society and government to address habitat loss and protect biodiversity while also meeting key development and socio-economic needs.

Teatime in Kruger: Tailoring the application of the Tea Bag Index approach to an African savanna

Attempts to obtain standardised decomposition data to determine potential drivers of carbon release have evolved from the use of cotton strips and standardised leaf litter mixtures to the most recent Tea Bag Index (TBI). The TBI is an internationally standardised method to collect comparable, globally distributed data on decomposition rate and litter stabilisation, using commercially available tea bags as standardised test kits. As this index was developed as a citizen science project in the northern hemisphere, we aimed to highlight the potential value - and pitfalls - of its application in a subtropical African savanna. We furthermore aimed to expand on existing protocol details and propose amendments to achieve an enhanced understanding of decomposition dynamics across temporal and spatial scales in African ecosystems. Proposed adaptations include extended incubation periods for long-term monitoring studies, the burial of more tea bags to account for potential losses, and the use of additional equipment to enhance effective sampling. These adaptations provide a system-specific protocol which can facilitate studies aimed to understand the interactions between top-down drivers (e.g. herbivory, fire, climate variability) and bottom-up controls (e.g. decomposition) in carbon flux dynamics of savanna ecosystems. Application of the proposed extended protocol in a semi-arid savanna provided results which reinforce the potential value of the TBI in an African context.SIGNIFICANCE: • The TBI is a relatively easy and cost-effective approach to gather globally distributed data on potential decomposition rate and inherent carbon flux, yet it was developed and primarily tested in boreal and temperate ecosystems. • The use of more paired tea bag replicates and additional equipment is a viable means to mitigate tea bag losses to several savanna-based agents of disturbance, while enabling confident conclusions made from statistical results and improved estimates of the TBI. High recovery success across disturbance treatments and incubation periods suggest that the TBI can be applied successfully to spatial and temporal decomposition studies.

Possible causes of a substantial decline in sightings in South Africa of an ecologically important apex predator, the white shark

A decline in sightings of a top predator, the white shark (Carcharadon carcharias), in South Africa was quantified in order to identify possible causes for this decline. White shark sightings data across 8 years (2011-2018), recorded from a cage-diving vessel in Gansbaai are reported. A significant decline in mean total white shark sightings per boat trip (>6 in 2011 to <1 in 2018) and a 69% reduction in the probability of a sighting were found. Correlating with this decline in sightings is a rise in sightings of sevengill sharks (Notorynchus cepedianus) in False Bay and copper sharks (Carcharhinus brachyurus) in Gansbaai, as well as substantial ecosystem changes. The effects of lethal conservation measures such as the use of shark nets in KwaZulu-Natal; the direct and indirect effects of overfishing including a reduction in smoothhound (Mustelus mustelus) and soupfin (Galeorhinus galeus) sharks; and novel predation on white sharks are discussed as possible causative factors for this decline in white shark sightings.SIGNIFICANCE: • The results of this paper highlight the need to reassess the impact of marine conservation initiatives and fishing practices. Failure to do so could seriously affect ecologically and economically important marine species. This paper reveals a potentially serious decline to the South African white shark population, characterised by a substantial decline in white shark sightings. This decline correlates with the overfishing of prey species, bycatch, the use of lethal gill nets and ecological changes such as the novel presence of orca. Better marine management is required if South Africa wishes to keep a healthy white shark population.