Predicting plant extinction risk in a biodiversity hotspot: environmental and anthropogenic drivers in the Western Cape, South Africa

Despite the ecological and social importance of reef fishes, data on their populations, habitat use, and other drivers are often scarce, which creates challenges for effective management. These challenges are particularly acute for rare or at-risk species such as Acanthurus achilles, a reef fish with a documented population decline in recent years in Hawai‘i, USA. We used a data set of in situ fish surveys from across the main Hawaiian Islands combined from multiple survey programs to quantify A. achilles presence and absence and applied generalized linear mixed-effects models to examine the relationships between presence of (1) all individuals, (2) juveniles, and (3) adults with 27 spatially continuous environmental and anthropogenic drivers to understand the main drivers of presence. Using the modeled relationships between presence and all drivers, we predicted the probability of A. achilles presence at a 100 m scale within the 30 m depth contour of the main Hawaiian Islands. Environmental drivers, especially habitat drivers such as depth and rugosity, emerged as significant drivers of A. achilles presence, while anthropogenic drivers like land-based pollution and fishing had fewer significant relationships with A. achilles presence. The predicted probability of presence varied both between islands as well as within islands, with the highest probability of presence around Kaho‘olawe and Hawai‘i and the lowest around O‘ahu. Our modeling approach and high-resolution spatial predictions provide empirical evidence of the importance of environmental drivers in explaining A. achilles presence and identify preferred habitat at relevant scales for fisheries management.

The increasing frequency and intensity of wildfires necessitate effective risk management in biodiversity hotspots to mitigate the potential impacts of wildfire hazards. The study utilised a multi-criteria decision analysis-analytic hierarchy process (MCDA-AHP) model to analyse wildfire risk patterns in the Garden Route District (GRD), focusing on biodiversity hotspots in the Western Cape, South Africa. The study used weight assignment and overlay analysis to evaluate wildfire risk factors, including human, topographic, and climatic factors, using data from Landsat and WorldClim from 1991 to 2021. The wildfire risk model was validated using MODIS historical fire data from the Global Forest Watch database and Confusion Matrix, with the burned area extent identified using differenced Normalized Burn Ratio (dNBR). The results show that despite 53% of the most burned area, only 12% was burned, with the high-risk zone accounting for only 11%, indicating a higher likelihood of wildfires spreading and intensifying. The results reveal a weak positive correlation (r = 0.28) between historical fire occurrences and burned areas and a negative correlation (r = − 0.27) between historical fire occurrences and fire seasons. Human and climatic factors significantly impact wildfire propagation in high-risk zones, while topographic factors have less influence, indicating a lower risk of ignition. The findings show that 26% of high-risk zones in the southwestern region dominated GRD biodiversity hotspots, while 27% were in the low-moderate-risk zone in the northwestern parts. The results of this study can aid in assigning fire risk-based criterion weights to support decision-makers in regional and global wildfire prevention and management.

The number of African penguins Spheniscus demersus breeding in South Africa collapsed from about 56 000 pairs in 2001 to some 21 000 pairs in 2009, a loss of 35 000 pairs (>60%) in eight years. This reduced the global population to 26 000 pairs, when including Namibian breeders, and led to classification of the species as Endangered. In South Africa, penguins breed in two regions, the Western Cape and Algoa Bay (Eastern Cape), their breeding localities in these regions being separated by c. 600 km. Their main food is anchovy Engraulis encrasicolus and sardine Sardinops sagax, which are also the target of purse-seine fisheries. In Algoa Bay, numbers of African penguins halved from 21 000 pairs in 2001 to 10 000 pairs in 2003. In the Western Cape, numbers decreased from a mean of 35 000 pairs in 2001–2005 to 11 000 pairs in 2009. At Dassen Island, the annual survival rate of adult penguins decreased from 0.70 in 2002/2003 to 0.46 in 2006/2007; at Robben Island it decreased from 0.77 to 0.55 in the same period. In both the Western and Eastern Cape provinces, long-term trends in numbers of penguins breeding were significantly related to the combined biomass of anchovy and sardine off South Africa. However, recent decreases in the Western Cape were greater than expected given a continuing high abundance of anchovy. In this province, there was a south-east displacement of prey around 2000, which led to a mismatch in the distributions of prey and the western breeding localities of penguins.

White-breasted cormorants Phalacrocorax [carbo] lucidus breed around South Africa's coast and at inland localities. Along the coasts of the Northern, Western and Eastern Cape provinces, numbers breeding were similar during the periods 1977–1981 (1 116 pairs at 41 localities) and 2008–2012 (1 280 pairs at 41 localities). Along the coast of KwaZulu-Natal (not counted in 1977–1981), 197 pairs bred at nine localities in 2008–2012, when the overall number breeding around South Africa's coastline was about 1 477 pairs. Between the two study periods, numbers decreased in the Northern and Western Cape provinces following the loss of several breeding localities, but they increased in the Eastern Cape. In the Western Cape, however, numbers were stable east of Cape Agulhas and at nine well-monitored West Coast localities that were surveyed from 1978 to 2012. White-breasted cormorants breed throughout the year, with breeding at some localities more seasonal than at others and the timing of peaks in breeding varying at and between localities. In the vicinity of Saldanha Bay/Langebaan Lagoon (Western Cape), in Algoa Bay (Eastern Cape) and in northern KwaZulu-Natal, it is likely that birds moved between breeding localities in different years, although breeding often occurred at the same locality over several years. Human disturbance, presence of predators, competition for breeding space and occurrence of breeding by other waterbirds may influence movements between colonies. Securing sufficient good habitat at which white-breasted cormorants may breed will be important for conservation of the species. The species may breed at an age of 4 years, possibly younger. The bulk of their diet around South Africa's coast consists of inshore marine and estuarine fish species that are not intensively exploited by humans.

The Republic of South Africa, known as South Africa, occupies the most southern tip of Africa with a coastline stretching from the border of Namibia on the Atlantic Ocean (south-west coast) of Africa, down to the tip of Africa and then north along the south-east coast to the border of Mozambique on the Indian Ocean. South Africa is bordered by Namibia, Botswana, Zimbabwe, Eswatini (formerly Swaziland), and Mozambique and surrounds the small landlocked Kingdom of Lesotho in the east-central region of South Africa. The total area of South Africa is approximately 1.22 million square kilometres (km), with a population of an estimated 58.78 million (2019). The country is divided into nine provinces, Western Cape, Eastern Cape, Northern Cape, Free State, Kwa-Zulu Natal, Northwest, Gauteng, Mpumalanga, and Limpopo. Gauteng Province is the most densely populated province with approximately 809.6 people per square kilometre, Kwa-Zulu Natal being the second most densely populated at 120.7 people per square kilometre, with Western and Eastern Cape following substantially behind at 59.1 and 51.1 people per kilometres respectively. There are three capitals in South Africa: Pretoria in the Gauteng province (administrative), Cape Town in the Western Cape (Legislative), and Bloemfontein in the Free State (Judicial). The

Decision letter: COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron)

A major challenge for coral reef conservation and management is understanding how a wide range of interacting human and natural drivers cumulatively impact and shape these ecosystems. Despite the importance of understanding these interactions, a methodological framework to synthesize spatially explicit data of such drivers is lacking. To fill this gap, we established a transferable data synthesis methodology to integrate spatial data on environmental and anthropogenic drivers of coral reefs, and applied this methodology to a case study location–the Main Hawaiian Islands (MHI). Environmental drivers were derived from time series (2002–2013) of climatological ranges and anomalies of remotely sensed sea surface temperature, chlorophyll-a, irradiance, and wave power. Anthropogenic drivers were characterized using empirically derived and modeled datasets of spatial fisheries catch, sedimentation, nutrient input, new development, habitat modification, and invasive species. Within our case study system, resulting driver maps showed high spatial heterogeneity across the MHI, with anthropogenic drivers generally greatest and most widespread on O‘ahu, where 70% of the state’s population resides, while sedimentation and nutrients were dominant in less populated islands. Together, the spatial integration of environmental and anthropogenic driver data described here provides a first-ever synthetic approach to visualize how the drivers of coral reef state vary in space and demonstrates a methodological framework for implementation of this approach in other regions of the world. By quantifying and synthesizing spatial drivers of change on coral reefs, we provide an avenue for further research to understand how drivers determine reef diversity and resilience, which can ultimately inform policies to protect coral reefs.

The German immigrants who formed the three “waves” of Germans to settle at Philippi in the Western Cape (South Africa) in the 19th century, and their descendants, contributed not only to the agricultural well-being of the Western Cape by providing the growing population with fresh produce, but also to the diversity of the region with their German cultural heritage. The arrival in the Western Cape of specifically the last two “waves” of German immigrants was both the result of the Hermannsburg “Bauernmission” – “agricultural missionary society” – as well as a specifi c immigration drive by the British colonial government to recruit specifi cally Germans to populate various areas of the Western and Eastern Cape colonies, which coincided. This article discusses the history of the resultant Philippi German farming community – a typical “Bauernsiedlung” – and the irony of their religio-cultural legacy and a new generation of (im)migrants to the Western Cape. Translations of the German quotations are provided as footnotes. Key words: agri/culture, German immigrants, Hermannsburg Missionary Society, Philippi, religion, Western Cape.

BackgroundStudies have shown that drug-resistant tuberculosis (DR-TB) in South Africa (SA) is clonal and is caused mostly by transmission. Identifying transmission chains is important in controlling DR-TB. This study reports on the sentinel molecular surveillance data of Rifampicin-Resistant (RR) TB in SA, aiming to describe the RR-TB strain population and the estimated transmission of RR-TB cases.MethodRR-TB isolates collected between 2014 and 2018 from eight provinces were genotyped using combination of spoligotyping and 24-loci mycobacterial interspersed repetitive-units-variable-number tandem repeats (MIRU-VNTR) typing.ResultsOf the 3007 isolates genotyped, 301 clusters were identified. Cluster size ranged between 2 and 270 cases. Most of the clusters (247/301; 82.0%) were small in size (< 5 cases), 12.0% (37/301) were medium sized (5–10 cases), 3.3% (10/301) were large (11–25 cases) and 2.3% (7/301) were very large with 26–270 cases. The Beijing genotype was responsible for majority of RR-TB cases in Western and Eastern Cape, while the East-African-Indian-Somalian (EAI1_SOM) genotype accounted for a third of RR-TB cases in Mpumalanga. The overall proportion of RR-TB cases estimated to be due to transmission was 42%, with the highest transmission-rate in Western Cape (64%) and the lowest in Northern Cape (9%).ConclusionLarge clusters contribute to the burden of RR-TB in specific geographic areas such as Western Cape, Eastern Cape and Mpumalanga, highlighting the need for community-wide interventions. Most of the clusters identified in the study were small, suggesting close contact transmission events, emphasizing the importance of contact investigations and infection control as the primary interventions in SA.

Understanding the Implications of Mitochondrial DNA Variation in the Health of Black Southern African Populations: The 2014 Workshop.

South Africa's AIDS response: the next 5 years

Psidium cattleyanum (Myrtaceae) invasions in South Africa: Status and prognosis

Genotyping of multidrug-resistant (MDR) Mycobacterium tuberculosis strains isolated from tuberculosis (TB) patients in four South African provinces (Western Cape, Eastern Cape, KwaZulu-Natal, and Gauteng) revealed a distinct population structure of the MDR strains in all four regions, despite the evidence of substantial human migration between these settings. In all analyzed provinces, a negative correlation between strain diversity and an increasing level of drug resistance (from MDR-TB to extensively drug-resistant TB [XDR-TB]) was observed. Strains predominating in XDR-TB in the Western and Eastern Cape and KwaZulu-Natal Provinces were strongly associated with harboring an inhA promoter mutation, potentially suggesting a role of these mutations in XDR-TB development in South Africa. Approximately 50% of XDR-TB cases detected in the Western Cape were due to strains probably originating from the Eastern Cape. This situation may illustrate how failure of efficient health care delivery in one setting can burden health clinics in other areas.

Research examining hormonal injectable contraceptive continuation has focused on clients' intentional discontinuation. Little attention, however, has been paid to unintentional discontinuation due to providers' management of clients who would like to continue use but arrive late for their scheduled reinjections. A cross-sectional survey of 1,042 continuing injectable clients at 10 public clinics was conducted in South Africa's Western and Eastern Cape provinces. Bivariate logistic regression analyses were used to identify associations between specific variables and the likelihood of receiving a reinjection, among clients who returned to clinics late but within the two-week grace period for reinjection. Of 626 continuing clients in the Western Cape, 29% were up to two weeks late and 25% were 2-12 weeks late for their scheduled reinjection; these proportions among 416 continuing clients in the Eastern Cape were 42% and 16%, respectively. Only 1% of continuing clients in the Western Cape who arrived during the two-week grace period did not receive a reinjection; however, 36% of similar clients in the Eastern Cape did not receive a reinjection. Among late clients in the Eastern Cape who did not receive a reinjection, 64% did not receive any other method. Few variables were significant in bivariate analyses; however, certain characteristics were associated with receiving reinjections among late clients in the Eastern Cape. It is common for clients to arrive late for reinjections in this setting. Providers should adhere to protocols for the reinjection grace period and have a contraceptive coverage plan for clients arriving past the grace period to reduce clients' risk of unintentional discontinuation and unintended pregnancy.

Honeybush (Cyclopia spp.) is an indigenous, leguminous member of the Cape fynbos biome growing in the coastal winter rainfall districts of the Western and Eastern Cape Provinces of South Africa (Joubert et al. 2011). Honeybush is used for the production of herbal teas and is harvested from wild-growing and cultivated plantations (du Toit et al. 1998). Very little is known regarding diseases caused by pathogens on this indigenous plant. Only one report of twig dieback on honeybush caused by several Diaporthe Nitschke species have been reported in South Africa (Smit et al. 2021). Several honeybush producers reported poor growth and dieback in their C. subternata plantations in the Western Cape Province, South Africa. Symptoms included twig dieback, branch dieback, death of branches as well as death of entire plants. In April 2008, branches from 8-year-old cultivated plants with dieback symptoms were collected in Stellenbosch. Fungal isolations were carried out from affected material as described by Van Niekerk et al. (2004) which consistently revealed the presence of a Botryosphaeriaceae species. Two isolates were grown on water agar with sterile pine needles and incubated at 25˚C using a 12-hour day/night cycle and near-ultraviolet light. Pycnidia formed after two weeks. Morphological characteristics similar to Neofusicoccum australe (Slippers, Crous & Wingfield) Crous, Slippers & Phillips were observed (Phillips et al. 2013). Conidia were hyaline, aseptate, fusiform with subtruncate bases (16.8-)18.8-22.1(-24.6) × (4.8-)5.3-6.1(-6.4) µm (n=50). Conidiogenous cells were holoblastic, hyaline and subcylindrical to flask-shaped tapering to the apex (11-15 × 2 µm) (n=10). Colonies on potato dextrose agar were light primrose turning olivaceous grey after 7 days with a light-yellow pigment diffusing into the medium. Mycelia was moderately dense with an appressed centre mat. The identity of the isolates was further confirmed by sequencing the ribosomal RNA Internal Transcribed Spacer (ITS) and the elongation factor 1-alpha (EF-1α) gene regions using primer pairs ITS4-ITS5 (White et al. 1990) and EF1-728F-EF1-986R (Alves et al. 2008), respectively. Sequences had a 100% similarity to N. australe ex-type CMW6837 isolate (accessions AY339262 and AY339270) (Slippers et al. 2004). Two isolates (STEU6554 and STEU6557) were deposited in the culture collection at the Department of Plant Pathology at Stellenbosch University and the sequences were submitted to GenBank with accession numbers ON745603, ON745604, ON746573 and ON746574. Pathogenicity tests using the two N. australe isolates were conducted by inoculating two shoots each of three field-grown C. subternata plants with a 4mm colonised potato dextrose agar (PDA) mycelium plug of each isolate on wounds made by a 4mm cork borer (Van Niekerk et al. 2004). A third shoot was inoculated with a uncolonized PDA plug as the negative control. After 12 weeks, brown-black lesions that were significantly longer (average 55.2 mm) than the uncolonized agar plug control (16.1 mm) were observed. Lesions were observed in all three plants. Neofusicoccum australe was re-isolated (van Niekerk et al. 2004) from all inoculated shoots confirming Koch's postulates. The economic impact and damages caused by N. australe as well as its incidence and severity on honeybush in South Africa is unknown. However, the pathogen caused dieback of entire branches and death of plants indicating that it could be an important pathogen of honeybush. Additionally, N. australe is one of the most important disease-causing Botryosphaeriaceae pathogens on a wide range of economical fruit and vine crops globally (Mojeremane et al. 2020). This is the first report of N. australe as a known pathogen causing decline and dieback of C. subternata in South Africa.