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Research about South Africa

Source-linked reports with geographic coverage including South Africa.

At least 19 recordsLinked to original sources
USGS2026

Individual encounter data of six African carnivore species optimized for multi-species density estimation

The ability to estimate abundances of multiple wildlife species within an area is valuable for both conservation and ecological inquiry. Spatially explicit capture–recapture (SCR) methods are commonly used to obtain reliable population size estimates, particularly for low-density and individually identifiable carnivore species. However, estimating abundance within multi-species communities poses a methodological challenge as survey designs and analytical tools are primarily tailored for single target species. Here, we present a dataset of spatially referenced individual encounter histories of six carnivore species with varying space requirements (lion, Panthera leo ; leopard, Panthera pardus ; spotted hyena, Crocuta crocuta ; cheetah, Acinonyx jubatus ; serval, Leptailurus serval ; large-spotted genet, Genetta tigrina ). These data were collected in a South African game reserve using a camera trap array optimized for multi-species density estimation using SCR methods. This dataset will be a valuable resource for studying spatial processes among potentially interacting carnivores without the common pitfalls that come with by-catch data of non-target species, and will provide a much-needed case study for the further development of multi-species statistical method development.

Munywana Conservancy↗
USGS2026

Optimizing camera-trap survey designs for multi-species density estimation using spatial capture–recapture models

Conservation efforts are increasingly required to move beyond single-species perspectives and towards community-level inferences. Obtaining reliable multispecies population size estimates poses practical challenges as analytical tools and design recommendations are primarily focused on single species. Density estimation using spatial capture–recapture methods requires deploying detectors (e.g. camera-traps) with spacing proportional to the space use of the focal species. Given that the design itself is species-specific, sampling can be inefficient for species with larger ranges than the focal species due to restricted spatial coverage and insufficient for species with smaller ranges because fewer recaptures are generated. To address this practical issue, we developed a two-stage optimization approach to generate camera-trap survey designs that are appropriate for estimating density of a suite of individually identifiable species that vary in home range sizes. Our approach applies an algorithm to first optimize placement of a subset of detectors for large and vagile species based on maximizing spatial coverage, followed by a second optimization for the remaining cameras based on maximizing spatial recaptures for smaller and less mobile species. We empirically tested our approach using six individually identifiable carnivore species with varying home range sizes in the Munywana Conservancy, South Africa. Our design included 60 camera locations optimized for leopards ( Panthera pardus ) and 40 cameras optimized for small-bodied, less-mobile carnivores. Our design optimization procedure generated designs characterized by a distribution of inter-trap distances, based on ecological parameters, and resulted in plausible density estimates for all species. The two-stage approach resulted in moderate precision gains for larger ranging species and, importantly, substantial gains for smaller ranging species. Simulations demonstrated improved precision of spatially explicit capture–recapture (SCR) parameter estimates for all species compared to standard grid-based designs, driven not solely by increased sampling but also by the optimized spatial configuration. Synthesis and applications . We developed and tested a new camera-trap survey design method for estimating population densities for multiple co-occurring species with differing spatial ecologies. By streamlining multispecies population monitoring, our approach reduces costs associated with species-specific programmes and broadens opportunities for community ecology and conservation research based on explicit demographic parameters.

Munyawana Conservancy↗
USGS2025

Comparative genomics of Bacillus anthracis A and B-clades reveals genetic variation in genes responsible for spore germination

Bacillus anthracis , the causative agent of anthrax, is composed of three genetic clades (A, B, and C). Clade-A is the most common and distributed worldwide, B-clade has a narrow geographic distribution, and C-clade is rare. South Africa's Kruger National Park (KNP) has high diversity of B. anthracis , with strains from A and B clades described from its northernmost region, Pafuri. We employed whole genome sequencing to investigate the genomic diversity of B. anthracis strains isolated from animal carcasses ( n = 34) during the 2012–2015 outbreaks. Whole-genome single-nucleotide polymorphism (wgSNP) analysis assigned the 2012–2015 B. anthracis genomes to the A-clade branch, distributed across the branch's two minor sub-clades A.Br.005/006. Additionally, pan-genomic analysis distinguished the A- and B-clade genomes, identifying unique accessory genes. Notable genetic differences include the biosynthetic spore cell wall genes; long-chain fatty acid CoA ligases ( FaD13 ), Bacillus collagen-like protein of anthracis (BclA) involved in the exosporium germination, as well as a truncated murein DD-endopeptidase ( mepH ) found in the pXO2 plasmid of the B-clade strains. The tryptophan synthase subunit alpha gene ( trpA ), which results in a pseudogene in B-clade genomes separates the A- and B-clade genomes. These differences in biosynthetic cell wall genes suggest variation in adaptability or cell growth of the B-clade strains in the environment, further influenced by the truncation of the trpA gene involved in spore germination. The A.Br.005/006-clade strains in KNP exhibit higher genetic diversity, which may enhance their resilience to environmental stressors. In contrast, the KNP B-clade (B.Br.001/002) strains show limited genetic variation, potentially reducing their adaptability. This pattern is evident through whole-genome SNP analysis and pan-genomics investigating the evolution of B. anthracis .

Kruger National Park↗
USGS2024

Roles of host and environment in shift of primary anthrax host species in Kruger National Park

Environmental and climatic factors, as well as host demographics and behaviour, significantly influence the exposure of herbivorous mammalian hosts to pathogens such as Bacillus anthracis , the causative agent of anthrax. Until the early 1990s in Kruger National Park (KNP), kudu ( Tragelaphus strepsiceros ) was the host species most affected by anthrax, with outbreaks occurring predominantly in the dry season, particularly during drought cycles. However, the most affected host species has shifted to impala ( Aepyceros melampus ), with more frequent anthrax outbreaks during the wet season. This study investigates the roles of environmental variation and other host species in this shift. Temporal trends in environmental variables such as precipitation, soil moisture, temperature, and normalised difference vegetation index (NDVI) were analyzed in relation to anthrax occurrence (presence/ absence and counts). Additionally, correlations between host species’ densities and anthrax mortalities over time were examined. Anthrax cases in 1990 were concentrated in the central and northern regions of KNP(excluding Pafuri), primarily affected kudus; while subsequent mortalities affected mostly impala and were restricted to the far north, in Pafuri. Significant correlations were found between kudu anthrax mortality and a decrease in NDVI, average temperature, SPI-6 and SPI-12 (Standardised Precipitation Index in various time intervals. Conversely, anthrax occurrence in impalas was associated with a decline in SPI-3, and temperature rise, with increased mortality during the rainy season. Elephant density correlated negatively with kudu mortality, but a positive correlation with both impala mortality and impala density. The study concludes that environmental variables and species’ densities may alter the diversity and frequency of hosts exposed to B . anthracis . Climate extremes and alterations therein may exacerbate anthrax severity by modifying species susceptibility and their probability of exposure over time.

Kruger National Park↗
USGS2024

Carbon isotope trends across a century of herbarium specimens suggest CO2 fertilization of C4 grasses.

Increasing atmospheric CO 2 is changing the dynamics of tropical savanna vegetation. C 3 trees and grasses are known to experience CO 2 fertilization, whereas responses to CO 2 by C 4 grasses are more ambiguous. Here, we sample stable carbon isotope trends in herbarium collections of South African C 4 and C 3 grasses to reconstruct 13 C discrimination. We found that C 3 grasses showed no trends in 13 C discrimination over the past century but that C 4 grasses increased their 13 C discrimination through time, especially since 1950. These changes were most strongly linked to changes in atmospheric CO 2 rather than to trends in rainfall climatology or temperature. Combined with previously published evidence that grass biomass has increased in C 4 -dominated savannas, these trends suggest that increasing water-use efficiency due to CO 2 fertilization may be changing C 4 plant–water relations. CO 2 fertilization of C 4 grasses may thus be a neglected pathway for anthropogenic global change in tropical savanna ecosystems.

New Phytologist↗
USGS2024

Deep magmatic staging chambers for crustal layered mafic intrusions: An example from the Bushveld Complex of southern Africa

The deep mafic magmatic staging chambers of layered mafic intrusions have been conjectured but not imaged. Their existence has long been postulated from geochemical models which require multiple magma injections from staging chambers to account for their multi-scale igneous layering and variations in sources and degrees of crustal contamination. For the Bushveld Complex of southern Africa, the world’s largest layered mafic intrusion, seismic receiver functions identify a diffuse crust-mantle transition beneath the Complex that suggests high velocity lower crust and/or uppermost lithospheric mantle. Here we present 3D gravity modelling of the Bushveld Complex that includes dense material at the crust-mantle boundary, imaging for the first time, remnants of magma staging chambers. They underlie the whole Bushveld Complex and extend westwards to the Molopo Farms Complex in Botswana. Feeders to the Bushveld Complex coincide with intersections of major faults like the Thabazimbi-Murchison Lineament and Sugarbush Fault with the staging chamber. This identification of magmatic staging chambers beneath the Bushveld relates to similar geophysically imaged lower crustal features beneath the Duluth and Stillwater Complexes. Comparison of seismic and gravity data with geochemical models from other complexes aid in development of models for the magmatic architecture of layered mafic intrusions in general.

Precambrian Research↗
USGS2022

How lions move at night when they hunt?

Movement patterns of lions ( Panthera leo ) reveal how they hunt large herbivores in heterogeneous landscapes such as the Kruger National Park in South Africa. Large herbivores are distributed differently on the landscape and therefore have different vulnerabilities as prey for lions. For instance, blue wildebeest ( Connochaetes taurinus ) occupy small grazing lawns at night but are difficult for lions to capture because open areas lack cover for stalking. African buffalo ( Syncerus caffer ) aggregate in large herds but are less available because these herds only intermittently enter the home ranges of individual lion prides. Unlike large herds of wildebeest and buffalo, plains zebra ( Equus quagga ) move widely in small herds while browsing greater kudus ( Tragelaphus strepsiceros ) and giraffes ( Giraffa camelopardalis giraffa ) generally occur in lower densities. We used spatial data derived from GPS collars to investigate several hypotheses regarding the movements of three lion prides in response to their prey. We found that lions were most active and moved longer distances during nighttime than during daytime. Lions remained within their core home ranges on 87% of nights and wandered to the outlying areas of the home ranges every second night. Lions visited grazing lawns, that is, area of short grass, where wildebeest herds resided every second night, and moved toward the direction of buffalo herds within 2 km of vicinity. Lions spent more time near riverbanks that provided dense woody cover at night than expected but concentrated only weakly near sites with surface water where herbivores drank in the dry season. Our study contributes to understanding how lions vary their movements in response to the spatial and temporal heterogeneity in the relative availability and vulnerability of multiple prey species.

Kruger National Park↗
USGS2021

South Africa's experimental fisheries closures and recovery of the endangered African penguin

In a scientifically-transformative project, South Africa implemented a decade-long field experiment to understand how fisheries may be affecting its most iconic seabird, the African penguin Spheniscus demersus. This unique effort prohibits the take of anchovy and sardine within relatively small areas around four African penguin breeding colonies, two in the Benguela upwelling ecosystem and two in the adjacent Agulhas region. For the Benguela, fisheries closures within the birds’ primary foraging range increased their breeding productivity and perhaps reduced parental foraging efforts, indicating that the fisheries are competing with the birds for food. Results were less clear for foraging behaviour in the Agulhas, but no data on breeding success were collected there. The African penguin is endangered, its population continues to decline, and fisheries closures have been demonstrated to improve demographic traits that contribute to population growth. Therefore, given the critical status of the species, fisheries closures should be maintained, at least at Dassen Island where the population has great capacity to expand and support other nearby colonies. Continuing or implementing corresponding fisheries closures in the Agulhas region is also warranted, as well as creating and testing the value of pelagic closed areas during the non-breeding season when the penguins disperse widely across these ecosystems. These management actions would increase penguin food supplies and may help to meet societal goals of halting the decline of the penguin population, as well as maintaining the economic and cultural services provided by fisheries and ecotourism.

Agulhas, Benguela, Dassen Island↗
USGS2021

Flight altitudes of raptors in southern Africa highlight vulnerability of threatened species to wind turbines

Energy infrastructure, particularly for wind power, is rapidly expanding in Africa, creating the potential for conflict with at-risk wildlife populations. Raptor populations are especially susceptible to negative impacts of fatalities from wind energy because individuals tend to be long-lived and reproduce slowly. A major determinant of risk of collision between flying birds and wind turbines is the altitude above ground at which a bird flies. We examine 18,710 observations of flying raptors recorded in southern Africa and we evaluate, for 49 species, the frequency with which they were observed to fly at the general height of a wind turbine rotor-swept zone (50–150 m). Threatened species, especially vultures, were more likely to be observed at turbine height than were other species, suggesting that these raptors are most likely to be affected by wind power development across southern Africa. Our results highlight that threatened raptor species, particularly vultures, might be especially impacted by expanded wind energy infrastructure across southern Africa.

Frontiers in Ecology and Evolution↗
USGS2021

Geometry of the Bushveld Complex from 3D potential field modelling

A full three-dimensional (3D) potential field model of the central and southern Bushveld Complex reveals information about the Complex in areas obscured by younger geological cover. Previously, two-dimensional gravity models and a few magnetic models limited to certain sections of the Bushveld Complex have been used to propose geometries for the Rustenburg Layered Suite, especially in the western and eastern lobes. These models were often used to support different emplacement models. Although these models provided valuable information, two-and-a-half-dimensional (2.5D) potential field modelling is not well suited to modelling complex 3D geology. Also, in most cases, only the magnetic or gravity data were modelled, but jointly modelling both data sets better constrains the results, as was shown recently for a 3D model of the northern lobe. Joint 3D modelling of regional gravity and magnetic data combined with published crustal thickness models derived from broadband seismic tomography studies and constrained by density and susceptibility data, geologic mapping, boreholes and seismic reflection data were used to create a 3D model of the central and southeastern sections of the Bushveld Complex, as well as the southern part of the northern lobe. The model shows a complex geometry with thick continuous Rustenburg Layered Suite S in most of the western and southeastern lobes, but less continuous Rustenburg Layered Suite in the eastern lobe. Large domes or thick granites and granophyre in the latter interrupt the continuity of the Rustenburg Layered Suite and the western and eastern lobes are strictly speaking only partially connected in places. However, they are not separate intrusions, but one disconnected by pre-existing and synmagmatic updoming. Three possible feeders were modelled in the northern, western, and south-eastern lobes.

Precambrian Research↗
USGS2017

Mercury and trace element distribution in density separates of a South African Highveld (#4) coal: Implications for mercury reduction and preparation of export coal

Eight density separates of Permian Highveld (#4) coal were investigated for partitioning of Hg and trace elements. The separates include float fractions obtained in heavy media having densities of 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, and 2.0 g/cm 3 , and the sink fraction for 2.0 g/cm 3 . Bulk analysis of the separates shows strong (R 2 ≥ 0.80) positive correlations between pyritic sulfur and mercury, and between ash yield and both pyritic sulfur and mercury. Laser ablation (LA) ICP-MS analysis of individual pyrite grains in the separates confirms association of Hg and As with pyrite as indicated by bulk analysis. Other elements detected in pyrite by LA-ICP-MS include Mn, Co, Ni, Tl, and Pb. Results for the separates allow prediction of Hg, trace elements, and ash yields expected in specific South African coal products. These range from 0.06 ppm Hg and an ash yield of 11.5% ash for the export fraction to 0.47 ppm Hg and an ash yield of 60.9% for the discard (stone) fraction (dry basis). Results show pronounced differences expected between coal used for domestic power generation and coal which is exported.

International Journal of Coal Geology↗
USGS2015

Moment tensors and other source parameters of mining‐induced earthquakes in TauTona Mine, South Africa

Induced seismicity exhibits diverse source mechanisms that are often difficult to constrain for small events. Here, we use data from the in‐mine seismic network, the Natural Earthquake Laboratory in South African Mines network, and a temporary Program for the Array Seismic Studies of the Continental Lithosphere deployment in TauTona Mine, South Africa, to determine full moment tensors of 100 mining‐induced earthquakes in the magnitude range −2.7< M w <2.5. Ground displacement derived from velocity and acceleration data show clear near‐field effects, indicating that the lowest frequencies are well resolved. Phase amplitudes of between 11 and 77 picks per event were inverted to obtain the six independent moment tensor components. The quality of each moment tensor solution is quantified using (1) the misfit between observed and synthetic waveforms, (2) bootstrap resampling to estimate uncertainties, and (3) the F ‐test to determine the need for including an isotropic component with an extra degree of freedom in the solution. The results indicate 82% of the events have well‐constrained solutions, and 45% of the well‐constrained events require an isotropic source term. Throughout the magnitude range, both deviatoric and implosive mechanisms are observed, with implosive ratios of volume change to shear deformation (ΔV/Σ τ ) of −1.03 to −0.15. Two explosive events are observed at M w −0.5 and −0.2, withΔV/Σ τ =0.15 and 0.51, respectively. For the largest events, we determine maximum slip and apparent stress ( τ a ) and find values consistent with those of natural tectonic earthquakes, with 0.1≤ τ a ≤9.2 MPa. Our results support previous speculation on the nature of isotropic components of mining‐induced earthquakes, in which events of all sizes begin as shear failure that may intersect a void (tunnel or stope) and cause collapse, whereas only small events result in explosive sources.

TauTona Mine↗
USGS2015

Context-dependent survival, fecundity and predicted population-level consequences of brucellosis in African buffalo

Chronic infections may have negative impacts on wildlife populations, yet their effects are difficult to detect in the absence of long-term population monitoring. Brucella abortus , the bacteria responsible for bovine brucellosis, causes chronic infections and abortions in wild and domestic ungulates, but its impact on population dynamics is not well understood. We report infection patterns and fitness correlates of bovine brucellosis in African buffalo based on (1) 7 years of cross-sectional disease surveys and (2) a 4-year longitudinal study in Kruger National Park (KNP), South Africa. We then used a matrix population model to translate these observed patterns into predicted population-level effects. Annual brucellosis seroprevalence ranged from 8&middot;7% (95% CI = 1&middot;8&ndash;15&middot;6) to 47&middot;6% (95% CI = 35&middot;1&ndash;60&middot;1) increased with age until adulthood (>6) and varied by location within KNP. Animals were on average in worse condition after testing positive for brucellosis ( F = &minus;5&middot;074, P < 0&middot;0001), and infection was associated with a 2&middot;0 (95% CI = 1&middot;1&ndash;3&middot;7) fold increase in mortality (&chi; 2 = 2&middot;039, P = 0&middot;036). Buffalo in low body condition were associated with lower reproductive success ( F = 2&middot;683, P = 0&middot;034), but there was no association between brucellosis and pregnancy or being observed with a calf. For the range of body condition scores observed in the population, the model-predicted growth rate was &lambda; = 1&middot;11 (95% CI = 1&middot;02&ndash;1&middot;21) in herds without brucellosis and &lambda; = 1&middot;00 (95% CI = 0&middot;85&ndash;1&middot;16) when brucellosis seroprevalence was 30%. Our results suggest that brucellosis infection can potentially result in reduced population growth rates, but because these effects varied with demographic and environmental conditions, they may remain unseen without intensive, longitudinal monitoring.

Kruger National Park↗
USGS2014

Collaborative Studies for Mercury Characterization in Coal and Coal Combustion Products, Republic of South Africa

Mercury (Hg) analyses were obtained for 42 samples of feed coal provided by Eskom, the national electric utility of South Africa, representing all 13 coal-fired power stations operated by Eskom in South Africa. This sampling includes results for three older power stations returned to service starting in the late 2000s. These stations were not sampled in the most recent previous study. Mercury concentrations determined in the present study are similar to or slightly lower than those previously reported, and input Hg for the three stations returned to service is comparable to that for the other 10 power stations. Determination of halogen contents of the 42 feed coals confirms that chlorine contents are generally low, and as such, the extent of Hg self-capture by particulate control devices (PCDs) is rather limited. Eight density separates of a South African Highveld (#4) coal were also provided by Eskom, and these show a strong mineralogical association of Hg (and arsenic) with pyrite. The density separates were used to predict Hg and ash contents of coal products used in South Africa or exported. A suite of 48 paired samples of pulverization-mill feed coal and fly ash collected in a previous (2010) United Nations Environment Programme-sponsored study of emissions from the Duvha and Kendal power stations was obtained for further investigation in the present study. These samples show that in each station, Hg capture varies by boiler unit and confirms that units equipped with fabric filters for air pollution control are much more effective in capturing Hg than those equipped with electrostatic precipitators. Apart from tracking the performance of PCDs individually, changes resulting in improved mercury capture of the Eskom fleet are discussed. These include Hg reduction through coal selection and washing, as well as through optimization of equipment and operational parameters. Operational changes leading to increased mercury capture include increasing mercury adsorption on unburned carbon and minimizing the concentration of sulfuric acid vapor in the flue gas. Equipment options for improving Hg capture include addition of fabric filters, use of halogenated sorbents, and addition of flue gas desulfurization (FGD) scrubbers, listed in order of increasing cost. The capital cost of adding FGD scrubbers to existing plants is probably too high to be justified on the grounds of Hg removal alone. However, if future regulations require reductions in sulfur dioxide emissions, and FGDs are installed to meet these standards, further reduction in Hg emissions will be a co-benefit of this installation. In this revised version, corrected results for the suite of 42 samples of feed coal and 8 density separates determined by inductively coupled plasma-mass spectrometry (ICP-MS) replace results originally reported in the 2014 version of this report. In many cases, especially for the transition metals, values reported here are lower than those originally reported, and in some cases, the corrected results are less than 50 percent of their original values. Note that results for mercury (Hg) and halogens contained in the original report are unaffected by revisions to ICP-MS data included here. This revised version also includes the following updates: (1) data for selenium, which were not available for inclusion in the original publication, are now provided; (2) results for ICP-MS trace element data are expressed here on a whole-coal dry basis to facilitate comparison with published results for coals elsewhere; and (3) the text has been updated to take into account the U.S. Supreme Court decision of June 29, 2015, which puts on hold implementation of U.S. Environmental Protection Agency Mercury and Air Toxics Standards in the United States.

Open-File Report↗
USGS2013

Overview of the magnetic signatures of the Palaeoproterozoic Rustenburg Layered Suite, Bushveld Complex, South Africa

Aeromagnetic data clearly delineate the mafic rocks of the economically significant Bushveld Igneous Complex. This is mainly due to the abundance of magnetite in the Upper Zone of the Rustenburg Layered Suite of the Bushveld, but strongly remanently magnetised rocks in the Main Zone also contribute significantly in places. In addition to delineating the extent of the magnetic rocks in the complex, the magnetic anomalies also provide information about the dip and depth of these units. The presence of varying degrees of remanent magnetisation in most of the magnetic lithologies of the Rustenburg Layered Suite complicates the interpretation of the data. The combination of available regional and high resolution airborne magnetic data with published palaeomagnetic data reveals characteristic magnetic signatures associated with the different magnetic lithologies in the Rustenburg Layered Suite. As expected, the ferrogabbros of the Upper Zone cause the highest amplitude magnetic anomalies, but in places subtle features within the Main Zone can also be detected. A marker with strong remanent magnetisation located in the Main Zone close to the contact with the Upper Zone is responsible for very high amplitude negative anomalies in the southern parts of both the eastern and western lobes of the Bushveld Complex. Prominent anomalies are not necessarily related to a specific lithology, but can result from the interaction between anomalies caused by differently magnetised bodies. The magnetic data provided substantial information at different levels of detail, ranging from contacts between zones, and layering within zones, to magnetite pipes dykes and faults that can have an impact on mine planning. Finally, simple modelling of the magnetic data supports the concept of continuous mafic rocks between the western and eastern lobes.

Bushveld Complex↗
USGS2012

An implosive component in the seismic moment tensor of a mining-Induced tremor

In early 1988, a special study in one of the major South African gold fields yielded seismograms that indicate seismic moment tensors having substantial implosive components. The moment tensor, resulting from the inversion of the ground motion data from the best-recorded event, was decomposed into isotropic and deviatoric components from which both the coseismic volumetric closure Δ V and the total shear deformation AD , where A is fault area and D is average slip, could be estimated. The finding here that Δ V ∼ AD is consistent with earlier analyses of how the tabular mine stopes interact with the surrounding rock mass to produce seismic deformation.

Geophysical Research Letters↗
USGS2012

Assessment of undiscovered oil and gas resources of the South Africa Coastal Province, Africa

The South Africa Coastal Province along the South Africa coast recently was assessed for undiscovered, technically recoverable oil, natural gas, and natural gas liquids resources as part of the U.S. Geological Survey's (USGS) World Oil and Gas Assessment. Using a geology-based assessment methodology, the USGS estimated mean volumes of 2.13 billion barrels of oil, 35.96 trillion cubic feet of natural gas, and 1,115 million barrels of natural gas liquids.

Fact Sheet↗