Dirk Cilliers

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.

Environmental management frameworks: results and inferences of report quality performance in South Africa

Environmental management frameworks (EMFs) were developed in South Africa as strategic environmental management instruments to map environmental sensitivity in order to aid the screening out of undesired developments and to minimise unnecessary project level environmental impact assessment (EIA) in preferred development areas. This article reports on the quality performance of a sample of seven EMFs conducted in South Africa, in terms of document and procedural quality. To this end, 13 measures (sub-criteria) were developed and classified into five thematic areas (review criteria), against which the EMF documents were appraised using a six-level rating. The review criteria were developed around the validity of sensitivity mapping methodology; the extent to which potential developments were identified as either desired or unfavourable; the effectiveness of EMF outcomes in relation to the broader decision making context; integration of stakeholder engagement inputs into EMF outcomes and the sufficiency of provisions spelling out the implementation of EMF outcomes. Public participation emerged as the weakest component of EMF practice, while certain aspects of sensitivity analysis also performed weaker than other review areas. More focus is required on aligning scales and resolutions of map inputs, mapping methods and general integration of spatial data. The practice of conducting EMF is well established, and can make a valuable contribution to inform strategic planning and to improve the effectiveness of EIA screening in South Africa, provided that appropriate improvements in quality are made, along with proper implementation of the instrument by the authorities, including their formal adoption.

Developing a site selection tool to assist reintroduction efforts for the Southern Ground– Hornbill Bucorvus leadbeateri

The Southern Ground-Hornbill Bucorvus leadbeateri (SGH) is regarded as Vulnerable globally and Endangered in South Africa as a result of losing close to 70% of its range and 50% of its historic population in the country. One of the conservation tools being used to address this issue and restore the population to its historic range is reintroductions. The aim of this study was to identify and prioritise probable reintroduction sites in the Mopane Bioregion and the Limpopo and Mpumalanga sections of the Lowveld Bioregion of South Africa (all in the Savanna Biome), by using a niche-based modelling technique (Maxent) combined with GIS analyses. Suitable SGH habitat was determined for farms in the study area and evaluated for the absence of mappable threats. Three priority areas were identified for reintroductions. These areas are in a near-natural state, offer sufficient habitat, are free of mappable threats and are close to formally protected areas. Field surveys of these three priority areas are needed next to validate their suitability for reintroduction purposes. This is the first spatially explicit reintroduction plan for the SGH that has been developed and will contribute to conservationists’ efforts to conserve the SGH.

Reflecting on GIS-related research in South Africa: 1980–2012

Since the early 1980s, geographic information systems (GIS) have increasingly been applied in research or used to support research in South Africa. The nature and extent of such research has not been investigated, and this paper seeks to address this hiatus. A number of academic databases were consulted to identify South African authored peer-reviewed academic papers and postgraduate dissertations referring to GIS in the title, keywords or abstract. A total of 468 papers and 238 dissertations were identified and analysed for temporal and spatial trends, fields of application and methods and techniques in GIS-related research. This paper shows that the use of GIS as a research technique in South African has increased considerably since the mid-1990s, reflected by continuing growth in peer-reviewed articles, but a decrease in postgraduate writings since 2005. Possible reasons for the observed trends are suggested.

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.

The extent and status of environmental management frameworks (EMFs) in South Africa, 2006–2015

Abstract An environmental management framework (EMF) is a uniquely South African environmental management tool legislated since 2006. Although the tool has been widely applied there has been no empirical research on the overall extent and status of EMF practice. The aim of this paper is to describe the extent and status of EMF practice between 2006 and 2015 through a combination of survey methods. The ‘extent’ of practice is described against the number of EMFs, the lead agents, spatial distribution, scale, time frames and accessibility of information, while the ‘status’ is discussed in relation to the legal mandate of EMF and the number of adopted and gazetted EMFs. The research results show that 53 EMF projects were initiated between 2006 and 2015 and that practice varies significantly in terms of lead agents, spatial distribution, scale and time frames. Moreover the research shows that just over half of the EMFs have been gazetted and that access to information in the public domain is limited. Finally, recommendations are made for future research around the quality and effectiveness of EMF.

Current distribution and population size of the Blue Swallow Hirundo atrocaerulea in the southern Tanzanian highlands

Two surveys of Blue Swallows were conducted in the southern Tanzanian highland grasslands in order to determine the habitat preferences and estimate the size of this subpopulation. During the 2008/09 and 2012 surveys, a total distance of 3 635 km was travelled in search of Blue Swallows (at an altitude of above 1 400 m above sea level). Blue Swallows showed no preference for any altitude range above 1 400 m. The Blue Swallows showed a preference for natural pastures and for rural villages interspersed with crops and natural pasture. The buildings in the rural villages provide the nesting sites and, in close proximity, the crops, natural pastures, livestock and their dung possibly provide the food source for the aerial arthropods on which the Blue Swallows feed. In total, 151 Blue Swallows were recorded consisting of 62 males, 68 females and 21 unsexed individuals at 62 localities. These data along with environmental variables were used to construct an ecological niche model for the Blue Swallow. It was estimated that a mean of 12 791 km2 of suitable habitat was available for Blue Swallows. The 151 Blue Swallows recorded within the maximum perpendicular distance of 262 m on either side of the survey route resulted in a subpopulation estimate of 1 014 (338 to 507 pairs) Blue Swallows in the southern Tanzanian highland grasslands (12 791 km2). Mean densities were 0.023 to 0.035 pairs km − 2. A density of 0.13 pairs km − 2 recorded on a cattle farm consisting primarily of grasslands and wetlands was similar to the density of pairs found on sites in South Africa and Swaziland of compara- ble size and with matching characteristics to this site in Tanzania. Based on this new information the global Blue Swallow population estimate is updated to between 1 169 and 1 338 pairs.