Environment predicts Batrachochytrium dendrobatidis lineage distribution and zones of recombination in South Africa.

The amphibian-infecting chytrid fungus, Batrachochytrium dendrobatidis (Bd), is widespread throughout Africa and is linked to declines of populations and species across the continent. While it is well established that the lineage of Bd encodes traits which determine disease severity, knowledge around how lineages are distributed according to environmental envelope is unclear. We here studied the distribution of Bd in South Africa based on the two lineages found, BdGPL and BdCAPE, in terms of their genome and environmental envelope statistically associated with their distribution. We used Bd surveillance data from published studies, as well as data collected during fieldwork from across South Africa, Lesotho, and eSwatini with samples collected along a transect spanning most of South Africa from Lesotho to the west coast. We utilized lineage-typing qPCR to resolve the spatial distribution of BdGPL and BdCAPE across South Africa and used the resulting surveillance data to create a predictive ecological niche model for Bd lineages in South Africa. Phylogenomic analyses were performed on isolates sourced from across the transect. We show that BdGPL demonstrates a strong isolation by distance suggestive of stepping-stone dispersal, while BdCAPE showed two distinct clusters within their genomic structure that appear geographically and temporally clustered, indicating two separate invasions. Our predictive niche model revealed that the two lineages tended to occur in different ecotypes; BdGPL was associated with lower altitude, arid regions while BdCAPE occurred across cooler, higher altitude environs. Niche predictions identified a zone of lineage contact, where genomics identified inter-lineage recombinants. We argue that this zone of recombination should be prioritized for disease surveillance as it is a potential hotspot for the evolution of variants of amphibian chytrid with novel traits that may be epidemiologically relevant.

Modelling the historical distribution of schistosomiasis-transmitting snails in South Africa using ecological niche models.

Schistosomiasis is a vector-borne disease transmitted by freshwater snails and is prevalent in rural areas with poor sanitation and no access to tap water. Three snail species are known to transmit schistosomiasis in South Africa (SA), namely Biomphalaria pfeifferi, Bulinus globosus and Bulinus africanus. In 2003, a predicted prevalence of 70% was reported in tropical climates in SA. Temperature and rainfall variability can alter schistosomiasis-transmitting snails' development by increasing or decreasing their abundance and geographical distribution. This study aimed to map the historical distribution of schistosomiasis from 1950 to 2006 in SA. The snail sampling data were obtained from the historical National Snail Freshwater Collection (NFSC). Bioclimatic variables were extracted using ERA 5 reanalysis data provided by the Copernicus Climate Change Service. In this study, we used 19 bioclimatic and four soil variables. The temporal aggregation was the mean climatological period pre-calculated over the 40-year reference period with a spatial resolution of 0.5° x 0.5°. Multicollinearity was reduced by calculating the Variance Inflation Factor Core (VIF), and highly correlated variables (> 0.85) were excluded. To obtain an "ensemble" and avoid the integration of weak models, we averaged predictions using the True Skill Statistical (TSS) method. Results showed that the ensemble model achieved the highest Area Under the Curve (AUC) scores (0.99). For B. africanus, precipitation-related variables contributed to determining the suitability for schistosomiasis. Temperature and precipitation-related variables influenced the distribution of B. globosus in all three models. Biomphalaria pfeifferi showed that Temperature Seasonality (bio4) contributed the most (47%) in all three models. According to the models, suitable areas for transmitting schistosomiasis were in the eastern regions of South Africa. Temperature and rainfall can impact the transmission and distribution of schistosomiasis in SA. The results will enable us to develop future projections for Schistosoma in SA based on climate scenarios.

A Critical Evaluation of International Agreements Towards a Revised Categorization for Transfrontier Conservation Areas (TFCAs).

Transfrontier Conservation Areas (TFCAs) are widely promoted as an international instrument to achieve certain conservation, cooperation and developmental goals, especially within the Southern African Development Community (SADC). In the SADC context, the status of TFCAs is categorized based on the extent to which international agreements have been signed. These agreements take different forms such as treaties, memorandums of understanding (MoUs), protocols and bilateral agreements. However, the efficacy of agreement-based approaches towards the categorization of TFCAs has been questioned because it does not acknowledge the implementation complexities of TFCAs and lacks a sound conceptual basis. This research evaluates the international TFCA agreements in SADC with a view to recommending a revised categorization. This is achieved by applying Theory of Change (ToC) to a sample of ten signed TFCAs agreements. The results show a lack of enforcement mechanisms, weak provision for implementation and poorly defined objectives. These weaknesses of agreement-based approaches can best be addressed by expanding the categorization of TFCAs to also include the extent of legislative and operational alignment. The revised categorization supports a more complete understanding of TFCA implementation.

Identifying key risks to the performance of privately protected areas (PPAs) through theory of change (ToC).

Privately protected areas (PPAs) are internationally considered to be important policy implementation instruments to augment and strengthen protected area networks. However, there has been limited reflection on the performance of PPAs over time. This paper aims to identify key risks to the performance of PPAs as policy implementation instruments through the application of Theory of Change (ToC). Identifying and understanding these risks are important to allow for the evaluation and monitoring of PPA performance. The ToC method was applied to a specific PPA policy instrument namely, private nature reserves (PNRs) in the South African context. The research results produced 29 key assumptions translated into 29 key risks. These risk are critically discussed against existing South African and international literature. To test and refine the risks further it is recommended that they be applied to PPA case studies in different contexts.

Considering flood risk in spatial development planning: A land use conflict analysis approach.

Flooding is the predominant natural hazard observed in Africa, and it often leads to damage to property and losses in human lives. To ensure that the detrimental effects of flooding are kept to a minimum, flood-prone areas should best be left undeveloped. Spatial development planning is a tool that can assist disaster risk managers in ensuring the aforementioned. This article proposes the use of a land use conflict analysis approach through which flood risk can be considered in spatial development planning in a proactive manner, specifically contributing to the flood risk management effort. A land use conflict analysis approach, relying on a variety of spatial analysis techniques, was used to identify areas that were both suitable for residential development and free from flood risk in the Batlhaping Ba-Ga-Phuduhucwana tribal area in South Africa. It was found that only 8% of the study area met these criteria. A comparison between the identified 8% and the existing spatial development plan for the study area revealed that some of the areas portrayed as suitable for development in the current spatial development plan are in fact flood risk areas. The article illustrates the value that a land use conflict analysis approach might have for flood risk management when integrated with spatial development planning. Keywords: flooding; land use conflict analysis; suitability analysis; flood-prone area; disaster management; spatial development planning; South Africa.

Assessing the Likelihood of Gene Flow From Sugarcane (Saccharum Hybrids) to Wild Relatives in South Africa.

Pre-commercialization studies on environmental biosafety of genetically modified (GM) crops are necessary to evaluate the potential for sexual hybridization with related plant species that occur in the release area. The aim of the study was a preliminary assessment of factors that may contribute to gene flow from sugarcane (Saccharum hybrids) to indigenous relatives in the sugarcane production regions of Mpumalanga and KwaZulu-Natal provinces, South Africa. In the first instance, an assessment of Saccharum wild relatives was conducted based on existing phylogenies and literature surveys. The prevalence, spatial overlap, proximity, distribution potential, and flowering times of wild relatives in sugarcane production regions based on the above, and on herbaria records and field surveys were conducted for Imperata, Sorghum, Cleistachne, and Miscanthidium species. Eleven species were selected for spatial analyses based on their presence within the sugarcane cultivation region: four species in the Saccharinae and seven in the Sorghinae. Secondly, fragments of the nuclear internal transcribed spacer (ITS) regions of the 5.8s ribosomal gene and two chloroplast genes, ribulose-bisphosphate carboxylase (rbcL), and maturase K (matK) were sequenced or assembled from short read data to confirm relatedness between Saccharum hybrids and its wild relatives. Phylogenetic analyses of the ITS cassette showed that the closest wild relative species to commercial sugarcane were Miscanthidium capense, Miscanthidium junceum, and Narenga porphyrocoma. Sorghum was found to be more distantly related to Saccharum than previously described. Based on the phylogeny described in our study, the only species to highlight in terms of evolutionary divergence times from Saccharum are those within the genus Miscanthidium, most especially M. capense, and M. junceum which are only 3 million years divergent from Saccharum. Field assessment of pollen viability of 13 commercial sugarcane cultivars using two stains, iodine potassium iodide (IKI) and triphenyl tetrazolium chloride, showed decreasing pollen viability (from 85 to 0%) from the north to the south eastern regions of the study area. Future work will include other aspects influencing gene flow such as cytological compatibility and introgression between sugarcane and Miscanthidium species.

Spatial assessment of amphibian chytrid fungus (Batrachochytrium dendrobatidis) in South Africa confirms endemic and widespread infection.

Chytridiomycosis has been identified as a major cause of global amphibian declines. Despite widespread evidence of Batrachochytrium dendrobatidis infection in South African frogs, sampling for this disease has not focused on threatened species, or whether this pathogen poses a disease risk to these species. This study assessed the occurrence of Bd-infection in South African Red List species. In addition, all known records of infection from South Africa were used to model the ecological niche of Bd to provide a better understanding of spatial patterns and associated disease risk. Presence and prevalence of Bd was determined through quantitative real-time PCR of 360 skin swab samples from 17 threatened species from 38 sites across the country. Average prevalence was 14.8% for threatened species, with pathogen load varying considerably between species. MaxEnt was used to model the predicted distribution of Bd based on 683 positive records for South Africa. The resultant probability threshold map indicated that Bd is largely restricted to the wet eastern and coastal regions of South Africa. A lack of observed adverse impacts on wild threatened populations supports the endemic pathogen hypothesis for southern Africa. However, all threatened species occur within the limits of the predicted distribution for Bd, exposing them to potential Bd-associated risk factors. Predicting pathogen distribution patterns and potential impact is increasingly important for prioritising research and guiding management decisions.