The flightless Cape High-mountain stag beetle genus Colophon (Coleoptera: Lucanidae) is studied. Represented by 17 species, which are restricted to the highest mountain peaks of the Cape Floristic Region in the Western Cape, South Africa, and show a strict association with the fynbos biome. The study aimed to determine the specific and phylogenetic status of the described species of Colophon and to determine the main factors driving their evolution by testing hypotheses of relationship and of a lowland origin. This was achieved by analysing DNA sequence data from three gene regions, the mitochondrial COI and 16S rRNA and the nuclear CAD, using a Maximum Likelihood (ML) and Bayesian approach. Timing of key biogeographical events in the diversification of Colophon was estimated in BEAST. The study also undertook to determine diagnostic larval characters for Colophon species and also to determine their phylogenetic implications for the sub-familial placement of the genus. Lastly, the study aimed to collate biological information on Colophon species so as to make suggestions for their revised conservation status in terms of IUCN and ToPS criteria. Most species of Colophon showed an allopatric distribution, although contact zones between geographically adjacent species are likely. Climate seems to be the main driving factor behind Colophon evolution and the hypothesis of a lowland origin appears to be supported. Larvae are soil-living and feed on humus, a habit unique to the family. There are only small inter-specific differences between larvae, with larval characters contributed little equivocal information from which phylogenetic support for family placement of Colophon could be deduced. The main threats to Colophon survival include overexploitation by commercial collectors, decline in habitat quality and habitat loss due to projected changes in climate. It is suggested that out of the 17 currently described species, eight should be listed as Critically Endangered, seven as Endangered, two as Data Deficient. Lastly, in light of this project‟s findings, it is suggested that future considerations in terms of Colophon research should focus on obtaining more information on their biology, behaviour and population size and in so doing contribute knowledge for the effective conservation management of each species. A taxonomic revision of the species, focusing on the C. stokoei varieties and C. eastmani subspecies, should be done and a complete taxonomic key of all described species compiled. Future fieldwork should focus on sampling the five species that remained elusive during the project, to eventually be included in phylogenetic analyses. / Dissertation (MSc)--University of Pretoria, 2013. / gm2013 / Zoology and Entomology / unrestricted

Philosophiae Doctor - PhD / Diabetes mellitus (DM), being one of the most common metabolic disorders with an elevated morbidity and mortality rate around the world. It is characterised by deficiency in insulin secretion or degradation of secreted insulin. Many internal and external factors such as oxidative stress, obesity and sedentary lifestyle among others have been suggested as the major causes of these cell alterations. Diabetes I and II are the most common types of diabetes. Treatment of type I requires insulin injection, while type II can be managed using different synthetic antidiabetic agents. However, their effectiveness is limited as a result of low bioavailability, high cost of drug production, and unfavourable side effects. There is a great need to develop alternative and more active antidiabetic drugs from natural sources. Natural products are a well-known source for the discovery of new scaffold for drugs discovery, and South Africa is one of the most important megaflora with high percentage of endemism. / 2023-12-01

Groundwater Dependent Ecosystems (GDEs) concentrate high levels of biodiversity and several species not found anywhere else. They prevail in the landscape through the ecological contribution of groundwater. They, GDEs, are vulnerable to drastic changes in groundwater depth. If, for example, bulk groundwater pumping drastically increases the groundwater depth and GDEs can no longer access it, they would die out. In the Cape Floristic Region (CFR), South Africa, there is limited information about the spatial distribution of groundwater dependent ecosystems. With the CFR having multiple locations with current and subsequent bulk groundwater pumping, identifying the spatial distribution of GDEs is a prerequisite for establishing their groundwater requirements. This dissertation presents a proposed novel method to identify rapid recovering wetlands predicted to be GDEs and uses Random Forest (RF) to predict their spatial distribution. The proposed novel approach leveraged the periodic fire disturbances in the CFR and applied the remote sensing index; Normalised Difference Vegetation Index (NDVI) extracted from high spatial resolution (1 m) aerial orthoimages. The proposed novel approach involves three levels of analysis. The first two levels used a one-way Analysis of Variance (ANOVA) to analyse the sensitivity of mean NDVI to discriminate wetland and non-wetland classes in burned and unburned study sites, and a post-hoc test: Tukey's Honest Significant Differences (HSD) pair-wise comparison to detect differences between the wetland and non-wetland mean NDVI and infer an NDVI threshold of wetland classes. In unburned sites, ANOVAshowed no statistical significance between wetland and non-wetland classes, F (2,15) = 3.53, p = 0.055. In burned sites, however, ANOVA showed there was a significant difference between wetland and non-wetland classes, F (2,15) = 9.66, p = 0.002. ANOVA and Tukey showed there were significant differences betweenwetland and non-wetland classes, with wetlands having between 0.22 and 0.37 greater NDVI than non-wetlands. The last level of analysis employed a kernel density estimator function to assess the recovery rate post-burn and use it to detect faster recovery as potential of wetlands to be GDEs; results showed that potential wetland GDEs experience rapid NDVI recovery > 236 days post-fire. In the fire prone CFR, leveraging fire data to detect GDEs provides a potentially simple and efficient way of building a local database for GDEs. The proposed novel approach showed leveraging fire data is a simple alternative to laborious field data to identify and map GDEs in the CFR. But because of the finite spectral bands in aerial orthoimages, Sentinel-2A multi-epochs dataset was utilised to carry out random forest for predicting the spatial distribution of potential wetland GDEs in the Kogelberg Nature Reserve. Sentinel-2A bands: Short-Wave Infrared (SWIR), NearInfrared (NIR), Red-edge, Red, Green, NDVI and Normalised Difference Wetness Index (NDWI) predictors and the potential wetland GDEs/non-wetland classes as the response. I tuned RF using five-fold repeated spatial cross-validation instead of the typical cross-validation tuning to account for the spatial structure of the data. The overall predictive accuracy of RF was between 59%-71%. This predictive accuracy may have been reduced by the application of spatial cross-validation that accounted for the spatial autocorrelation in the multi-date data. The dissertation showed that Sentinel-2A multi-date data applies in predicting the distribution of potential wetland GDEs but might not be effective for smaller (< 100 m2) wetlands. These small wetlands showed rapid post-fire recovery (less than a year post-fire) and were effectively detected with high resolution aerial orthoimages (1 m) spatial resolution.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: The Cape Floristic Region (CFR) of South Africa is well-recognised for exceptionally high plant species diversity and endemism. However, little attention has been bestowed on the pests and pathogens in this region, even though these may greatly influence plant distribution and evolution. In this study we identify various arthropods and fungi as pests and diseasecausing organisms of the ecologically and economically important CFR-endemic tree taxa of Virgilia. We isolated, identified and determined the pathogenicity of key fungal taxa from diseased Virgilia trees throughout the CFR. In addition we evaluated the role of possible pest arthropod taxa, including bark beetles, phoretic mites, larvae of a cerambycid beetle and larvae of the endemic Leto venus (ghost moth), in the death of Virgilia trees. Key fungal taxa were identified by comparisons of the internal transcribed spacer rDNA regions of the isolated taxa with those available on GenBank. Pathogenicity of the most commonly encountered fungal taxa was determined both in the field and under greenhouse conditions. Five different disease symptoms were observed on Virgilia trees throughout the CFR. At Table Mountain, Virgilia oroboides subsp. oroboides showed symptoms of: (1) several small cankers on stems, seemingly caused by a Fusarium acuminatum-like fungus, (2) a root rot disease caused by Armillaria mellea and (3) small bracket fungi on stems associated with Schizophyllum commune. Virgilia oroboides from the Harold Porter National Botanical Garden was diagnosed with a root disease consistently associated with an un-described Phomopsis species. Virgilia oroboides subsp. ferruginea and V. divaricata from Knysna and the Tsitsikamma area often showed symptoms of rapid wilting and death. The Virgilia stems were damaged by the tunnelling larvae of the ghost moth and those of an unidentified cerambycid beetle. Galleries and the surrounding wood tissues often housed the ophiostomatoid fungi Ceratocystis tsitsikammensis and Ophiostoma plurianulatum. These seem to originate from nitidulid beetles found feeding on gum exudate. Pathogenicity trials confirmed the virulence of the undescribed Phomopsis species, the F. acuminatum-like fungus, S. commune and C. tsitsikammensis to Virgilia. All four morpho-species of bark beetles found in this study, together with phoretic mites on two of the beetle morphospecies, were only collected from dead and dying Virgilia hosts and were classified as secondary pests. Both beetle taxa and mites commonly carried spores of various Geosmithia spp. These are not pathogenic to Virgilia trees, but may be an important food source for the bark beetles, as it dominated the fungal community in galleries. The phoretic mites were unable to feed on their Geosmithia associates, but have been observed to feed on dead bark beetle larvae within galleries. This suggests that the relationship of bark beetles, mites and their associated Geosmithia species in this system is complex and in need of further study. Our results show that natural populations of Virgilia play host to numerous destructive pathogens, some of which are non-native (e.g. A. mellea) and a cause for special concern. Additionally, the isolation of the undescribed Phomopsis species and A. mellea from botanical gardens, with A. mellea now spreading to natural areas, calls for stricter control over the movement of organic material from these areas. / AFRIKAANSE OPSOMMING: Die Kaapse Floristiese Streek (KFS) van Suid-Afrika is bekend vir buitengewoon hoë plantspesie-diversiteit en endemisme. Min aandag is egter tot dusver geskenk aan die peste en patogene in hierdie streek, al mag hulle plantverspreiding en evolusie dramaties beinvloed. In hierdie studie identifiseer ons verskeie geleedpotige diere en fungi as peste en organismes wat siektes veroorsaak in die ekologies en ekonomies belangrike, KFS-endemiese boom genus Virgilia. Ons het die sleutel fungi vanaf Virgilia oor die hele KFS geisoleer, geidentifiseer en hulle patogeniteit bepaal. Addisioneel het ons ook die rol van moontlike pes geleedpotiges, insluitende baskewers, cerambycid kewerlarwes en die endemiese Leto venus (spookmot) in die dood van Virgilia bome geevalueer. Sleutel fungi taksa is geidentifiseer deur die interne getranskribeerde spasieerder rDNS streke van die geisoleerde taksa met die wat op GenBank beskikbaar was te vergelyk. Patogenisiteit van die mees algemeen geisoleerde fungi taxa is beide in die veld en onder glashuis-toestande bepaal. Vyf verskillende siekte simptome is by Virgilia bome regdeur die KFS waargeneem. By Tafelberg het Virgilia oroboides subsp. oroboides simptome getoon van: (1) verskeie klein kankers op stamme, blykbaar veroorsaak deur ‘n Fusarium acuminatum-agtige fungus, (2) ‘n wortelvrot siekte veroorsaak deur Armillaria mellea en (3) klein rakswamme op stamme geassosieer met Schizophyllum commune. Virgilia oroboides in die Harold Porter Nationale Botaniese Tuin is gediagnoseer met ‘n wortelvrot siekte wat altyd met ‘n onbeskryfde Phomopsis spesie geassosieer is. Virgilia oroboides subsp. ferruginea and V. divaricata van Knysna en die Tsitsikamma area het dikwels simptome getoon van vinnige verwelking en dood. Die Virgilia stamme is deur die tonnelende larwes van die spookmot en dié van ‘n ongeidentifiseerde cerambycid kewer beskadig. Galerye en die omringende houtweefsel het dikwels die ophiostomatoid fungi Ceratocystis tsitsikammensis en Ophiostoma plurianulatum gehuisves. Dit lyk asof hierdie fungi van nitidulid kewers afkomstig is wat op die gomuitskeidings gevoed het. Patogeniteitsproewe het die kwaadaardigheid van die onbeskryfde Phomopsis spesie, die F. acuminatum-agtige fungus, S. commune en C. tsitsikammensis teenoor Virgilia bevestig. Al vier morfo-spesies baskewer wat in hierdie studie gevind is, sowel as die foretiese myte op twee van die kewer morfo-spesies, is slegs van dooie of sterwende Virgilia gashere versamel, en is as sekondêre peste geklassifiseer. Beide kewerspesies en myt taksa het algemeen spore van verskeie Geosmithia spesies (Geosmithia pallida, G. flava, G. microcorthyli, G. sp. 1 en G. sp. 2) gedra. Die Geosmithia spesies is nie patogenies teenoor Virgilia bome nie, maar mag ‘n belangrike voedselbron vir die baskewers wees, aangesien dit die fungus-gemeenskap in die galarye gedomineer het. Die foretiese myte was nie instaat om op Geosmithia-assosiate te voed nie, maar is waargeneem om op dooie baskewer larwes te voed binne die galerye. Dit stel voor dat die verhouding van die baskewers, myte en hulle geassosieerde Geosmithia spesies in die sisteem kompleks is, en verdere studie benodig. Ons resultate dui aan dat natuurlike populasies van Virgilia gashere is vir verskeie destruktiewe patogene, sommige waarvan nieinheems (bv. A. mellea) wat ‘n bron van groot kommer is. Verder noodsaak die isolasie van die Phomopsis spesie en A. mellea, wat beide wortelvrot siektes in botaniese tuine veroorsaak, strenger kontrole oor die verskuiwing van organiese materiaal uit hierdie areas, veral gegewe dat A. mellea reeds na natuurlike areas versprei het. / The Centre of Excellence In Tree Health Biotechnology for a bursary and funding the research conducted in this study

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Soil is one of the most complex and understudied terrestrial habitats, and it comprises a wide range of organisms that affect the functioning of terrestrial ecosystems. Despite the importance of these below-ground fauna, our understanding of this diversity remains limited, especially in the Cape Floristic Region (CFR), where higher plants and other more conspicuous invertebrates have been better represented in the literatures. The main aim of this thesis is to provide the first insights into the taxonomic, cryptic and spatial diversity of one of the more diverse Collembola genera, Seira (Collembola: Entomobryidae: Seirinae), in the Fynbos and Southern Afrotemperate forest habitats of the CFR. Collembola constitute an important component of terrestrial biodiversity and are essential for ecosystem functioning. The thesis is divided into two data chapters. The first data chapter examines the mitochondrial barcoding COI (Cytochrome-c oxidase subunit I) gene of 496 Seira specimens from 41 Fynbos and forest sites. Discrete Molecular Operational Taxonomic Units (MOTUs) are identified within Seira. Furthermore, divergence times are estimated and tentatively used to propose historical triggers for the diversification of Seira. Habitat specificity of Seira is assessed through phylogenetic reconstruction using Parsimony and Bayesian analyses based on the nucleotide and amino acid sequences. Genetic divergence indicates that Seira is composed of at least 91 MOTUs, suggesting that morphological taxonomy has vastly under-estimated the richness of this genus by at least four folds. Most of the MOTUs are highly habitat specific and geographically localised. The reconstruction of an evolutionary time frame of these lineages reveals several deep diversifications in the Miocene and a spate of more recent radiations in the Pleistocene and Holocene. Palaeo-environmental fluctuations and vegetation composition shifts are hypothesised as having increased the environmental complexity of the region and this may have influenced the diversification patterns of Seira. In the second data chapter, the spatial variation of Seira diversity is examined and compared between and within two major habitat types, Fynbos and forest, across nine study sites. Abiotic variables were recorded and compared for the investigation of environmental differences among habitat types. The habitat specificity of Seira is assessed, as well as the relative effects of habitat types and study sites on assemblage structure. Species richness of Seira is higher in Fynbos than in forest, and this could be due to the high heterogeneity of niches and resources created by the steep environmental and floristic gradients in the Fynbos habitats. Perhaps one of the most striking results is the high levels of beta diversity exhibited by Seira. The spatial turnover of the Seira assemblage is complete or nearly complete among and within habitat types across study sites within the CFR. Low dispersal abilities and consequently isolated evolutionary histories may account for the strong assemblage differences within the same habitat type of different study sites. However, the substantial differences in assemblage composition between adjacent habitat types in the same site are likely to be the result of the contrasting abiotic conditions exhibited by the Fynbos and forest habitats, as found by this study. Overall, the results of this thesis suggest that Seira species richness is much greater than previously thought. It follows similar diversity patterns to the well-described and hyper-diverse plant communities of the CFR. Here, for both CFR plants and Seira, the spectacular regional diversity displayed is not the result of high alpha diversity, but rather of substantial beta diversity. Because of the high beta diversity and the fact that only two CFR vegetation types were sampled from a limited number of study sites, I predict that the Seira species richness presented here is but the tip of the iceberg. / AFRIKAANSE OPSOMMING: Geen opsomming beskikbaar

Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Understanding how divergent selection results in the evolution of reproductive isolation (i.e. speciation) is an important goal in evolutionary biology. Populations of herbivorous insects using different host plant species can experience divergent selection from multiple selective pressures which can rapidly lead to speciation. Restio leafhoppers are a group of herbivorous insect species occurring within the Cape Floristic Region (CFR) of South Africa. They are specialised on different plant species in the Restionaceae family. Throughout my thesis I investigated how bottom-up (i.e. plant chemistry/morphology of host plant species) and top-down (i.e. predation and competition) factors drive specialisation and divergence in restio leafhoppers. I also investigated interspecific competition as an important determinant of restio leafhopper community structure. In chapter 2 I quantified host specificity of restio leafhopper species within a local community for 24 months. I found that restio leafhopper species are highly host specific and potentially synchronised with the growth phases of their host plants. In chapter 3 I used a network metric, modularity, to determine whether host plant partitioning in a restio leafhopper community is non-random (i.e. driven by a deterministic process). This metric allows the identification of the components underlying host plant partitioning (modules). I then performed experiments to show that modules, and therefore host plant partitioning, can mostly be explained by preference and performance relationships (i.e. bottom-up factors). In chapter 4 I used null models to test whether niche partitioning in restio leafhopper communities is a general pattern across the landscape. I found non-random niche partitioning, which results from strong host specificity, in all investigated restio leafhopper communities. In addition, I performed binary host choice experiments in the presence and absence of interspecific competition, but found no evidence that interspecific competition narrows host preferences. These findings suggest that host specificity, the cause of niche partitioning, is likely shaped over evolutionary time. Sampling multiple interaction networks across the CFR, in chapter 5, I tested whether restio leafhopper populations are more host specific in species rich communities and regions in the CFR than in species poor communities and regions. I found no positive relationship between restio leafhopper species richness and host specificity at any scale. These findings suggest that specialisation is not driven by interspecific competition. In chapter 6 I investigated host shifts in Cephalelus uncinatus. C. uncinatus has a broader distribution than any single restio species that it can use; suggesting that host plant related divergence may result from geographic range expansion. I found that allopatric and parapatric populations, but not sympatric individuals, using different host plants have divergent host preferences. I also found evidence for morphological divergence in traits related to predator avoidance in population pairs that exhibit divergent host preferences. My findings emphasise the importance of both bottom-up and top-down factors, with the exception of interspecific competition, as determinants of specialisation and divergence in restio leafhoppers. I find no evidence that interspecific competition is an important force structuring restio leafhopper communities. Instead, strongly niche partitioned community structure appears to emerge from the speciation process. / AFRIKAANSE OPSOMMING: Die wyse waarop uiteenlopende seleksie lei tot die evolusie van seksuele isolasie (n.l. spesiasie) is ‘n belangrike vraag in evolutionêre biologie. Plantetende insekpopulasieses wat verskillende gasheerplante gebruik kan onder uinteenlopende veelvoudige seleksie wees en vinnig spesiasie ondergaan. Restio-blaarspringers is ‘n groep plantetende insekspesies wat gespesialiseerd is op verskillende plantspesies in die restio familie. In my tesis ondersoek ek die onder-op (n.l. plantchemie en morfologie) en bo-af seleksiekragte (n.l. predasie en kompetisie) wat lei tot gasheerspesialisasie en -spesiasie in restio-blaarspringers. Ek ondersoek ook die belangrikheid van tussen-spesieskompetisie in gemeenskapsorganisasie. In hoofstuk 2 het ek gasheerspesialisasie gekwantifiseer in ‘n klein restio-blaarspringergemeenskap oor 24 maande. Ek het gevind dat restio-blaarspringers hoogs gasheerspesifiek is en moontlik met die groeifase van hul hoofgasheerplante gesinchroniseerd is. Ek het in hoofstuk 3 ‘n netwerkmetriek, modulariteit, gebruik om te bepaal of restio-blaarspringers se gasheerverdeling nie-stokasties is (n.l. deur deterministiese prosesse veroorsaak is). Hierdie metriek laat ‘n mens toe om die komponente van gasheerverdeling (modules) te identifiseer. Deur middel van eksperimente het ek bepaal dat modules, en dus gasheerverdeling, deur gasheervoorkeur en prestasie (onder-op prossesse) verduidelik kan word. In hoofstuk 4 het ek ondersoek of gasheerverdeling algemeen is. Ek het deur middel van nulmodelle gewys dat gasheerverdeling algemeen is en veroorsaak is deur sterk gasheerspesifiekheid. Ek het ook voorkeureksperimente uitgevoer in die teenwoordigheid en afwesigheid van tussen-spesies kompetisie. Hier het ek geen teken gevind dat huidige tussen-spesies kompetisie gasheervoorkeur beïnvloed nie. My bevindinge in hierdie hoofstuk stel dus voor dat spesialisasie, die oorsaak van gasheerverdeling, oor evolutionêre tyd gevorm word. In hoofstuk 5 het ek ondersoek of populasies van restio-blaarspringers meer gasheerspesifiek is in restio-blaarspringerspesies ryke gemeenskappe en streke as populasies in spesies-arm gemeenskappe en streke. Ek het geen positiewe korrelasie tussen spesiesrykheid en gasheerspesialisasie gevind nie. Dit dui daarop aan dat gasheerspesialisasie, en dus gasheerverdeling, nie deur tussen-spesies kompetisie veroorsaak word nie. In hoofstuk 6 het ek gasheerplantgekoppelde divergensie ondersoek in Cephalelus uncinatus. C. uncinatus se verspreiding is breër as enige restio-spesies wat dit kan gebruik. Dit stel voor dat verspreidingvergroting gasheerverskuiwing mag veroorsaak. Ek het gevind dat populasies wat verskillende plante in allopatrie en parapatrie gebruik uiteenlopende gasheerkeuses maak, maar insekte wat verskillende plante in sympatrie gebruik wys nie ontwrigtende gasheerkeuses nie. Die populasies wat uiteenlopende gasheerkeuses getoon het, het ook verskillende morfologiese teen-predasie eienskappe getoon. Dit dui daarop aan dat predasie belangrik mag wees vir spesiasie in restio-blaarspringers. Die bevindinge van my tesis dui daarop aan dat beide onder-op en bo-af seleksie belangrik is vir gasheer-spesialisasie in divergensie. Nietemin, tussen-spesies kompetisie is nie ‘n belangrike bron vir spesialisasie, divergensie of gemeenskapsorganisasie nie. Gemeenskapsorganisasie is klaarblyklik slegs ‘n gevolg van die spesiasie proses.

Magister Artium (Development Studies) - MA(DVS) / It is well established that the modern global food system is highly unsustainable, distorted by industrialisation and corporate consolidation, with negative repercussions on the environment and biodiversity as well as human health. Innovative approaches are necessary to push food systems to be more sustainable, equitable, and healthy for all people regardless of income and wealth. In the Cape Town area, the food system is failing to adequately nourish the poor, while climate change poses increasing challenges to the region’s agricultural system. Conceptualising food systems as complex adaptive social ecological systems and utilising the Multilevel Perspective (MLP) framework, this thesis looks at the burgeoning economy in neglected and underutilised species (NUS) in the Cape Town area as a potential innovation that could make the local food system more socially and ecologically resilient. Though at present NUS are only marginally included in the local food system and policy debates, they are increasingly appearing in the food service industry, driven by international gastronomic trends. They hold potential as climate resilient, nutritionally dense, and socially and culturally significant foods in the region, but also carry ecological and social risks. This thesis critically examines the fledgling NUS economy in the Cape Town area, using participant observation and semistructured interviews to unpack its primary motivations and challenges, and ultimately contributes towards a better understanding of the NUS economy as it develops locally. This research shows that the main risks associated with NUS are negative ecological repercussions, privatisation of the NUS economy, and the reproduction and further entrenchment of unequal power dynamics in the region. In order to mitigate these risks and actualise the related benefits associated with NUS, engagement with the ecological, social, and political context of NUS needs to be significantly deepened. This is particularly true for those working in food service, who appear to be driving the NUS economy, and will require education around sustainability and TEK as well as a foregrounding of power-awareness.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Only a limited number of systems involving anther-smut fungi have been studied, usually due to the economic significance of their crop plant hosts. A smut fungus of the genus Thecaphora has been discovered infecting Oxalis hosts in South Africa. This pathogenic fungus, Thecaphora capensis, produces dark-coloured spores in the anthers of host flowers, rendering it an anther-smut fungus. The host genus is the seventh largest plant genus in the Cape Floristic Region (CFR) and the largest geophytic genus of this region. Nine Oxalis species that host T. capensis have been identified across a wide distribution in the CFR of South Africa. A preliminary assessment of T. capensis infections of Oxalis was conducted in 2009, which provided a foundation for further research into the ecological and evolutionary consequences of hosting this fungus. In this study, a comprehensive host diversity assessment was conducted to determine the extent of infected Oxalis individuals within the CFR. Three new Oxalis host species for Thecaphora capensis were discovered. This brings the total number of known hosts to twelve. The morphological and reproductive effects of the fungus were assessed on two host species (O. incarnata and O. lanata) by comparing healthy and infected individuals of these species. Infection by Thecaphora capensis had a significantly negative effect on both of these factors. Host resources appear to be co-opted for fungal spore production, since floral morphological characters of infected individuals were reduced in size. Furthermore, infection by T. capensis ensured near-universal sterility in both hosts. Differences in floral characters and pollinator preferences for healthy Oxalis incarnata and O. lanata individuals from disease-free and diseased populations were compared to determine the evolutionary influence of Thecaphora capensis infections. It was shown that this pathogen can have a significant evolutionary influence on its hosts, showing its ability to shape flower size and pollinator activity in O. lanata, but not in O. incarnata. A need has therefore been identified to assess these evolutionary forces independently for each host and its pathogen before making erroneous assumptions for conservation practices. Plant pollinators play an integral role in plant fitness. Pollinator movements within a population are important when between-flower spore transfer by pollinators increases the likelihood of new infections. Pollinator movements may be influenced by host density and the frequency of diseased individuals, amongst other factors. Pollinators were found to mediate Thecaphora capensis spore transfers within diseased Oxalis populations. Host density and disease frequency affected the number of spores transferred under field and standardized conditions. More research is required to investigate confounding factors in these complex systems. This study highlighted the complexities of a fungal-plant-insect relationship, the evolutionary consequences of such fungal infections and the various factors influencing the likelihood of new infections. This research adds to the limited body of knowledge on multi-organismal interactions in the CFR and provides a base for more detailed future studies on this intriguing system. / AFRIKAANSE OPSOMMING: 'n Brandswam, wat deel is van die Thecaphora genus,is ontdek in 'n Oxalis blom waar dit die gasheer plant se blom gebruik om spore in te produseer. Die swam, Thecaphora capensis, produseer donker gekleurde spore in die helmknoppe van die blomme van gasheer plante, daarom word dit geklasifiseer as 'n brandswam van die helmknop. Die gasheer plante van die swam is deel van die genus Oxalis, die sewende grootste plant genus in die Kaapse Floristiese Streek (KFS) en die grootste geofitiese genus in die streek. Nege Oxalis species is al klaar identifiseer as gasheer plante van T. capensis. Hulle is versprei oor 'n groot area van die KFS van Suid Afrika. 'n Primêre ondersoek van T. capensis infeksies op Oxalis is in 2009 onderneem. Hierdie ondersoek het gelei tot meer vrae oor die sisteem en het 'n goeie fondasie geskep vir verdere navorsing rakende die ekologiese koste verbonde daaraan om as gasheer plant vir 'n swam op te tree. 'n Deeglike ondersoek is in die KFS aangepak om die Oxalis gasheer plante van die brand swam te identifiseer en om voort te bou op die basiskennis wat in die primêre ondersoek daargestel is. Drie nuwe Oxalis gasheer plante van Thecaphora capensis is ontdek. Die totale aantal gasheer plante staan nou op twaalf. Gesonde en geinfekteerde individuele gasheer plante is gebruik om die morfologiese en reproduktiewe effekte van die swam te toets in twee Oxalis spesies (O. incarnata en O. lanata). Die negatiewe gevolge om 'n gasheer plant van die brand swam te wees was duidelik toe gesonde en geinfekteerde individuele met mekaar vergelyk is. Dit kom voor asof gasheer plante se hulpbronne vir spoor produksie gebruik word, want hulle is morfologies kleiner en meestal steriel. Die evolusionêre effek van Thecaphora capensis op 'n populasie is getoets met gesonde individuele in populasies van twee Oxalis spesies. Blomkenmerke en insek bestuiwers van gesonde individue in gesonde en geinfekteerde populasies is ondersoek om die effekte van T. capensis op populasies te toets. Daar is suksesvol gedemonstreer dat swamme sterk evolusionêre kragte uitoefen, en die vermoë het om plantpopulasies te vorm en te verander, ofskoon nie in alle gevalle ewe sterk nie. Daarom is dit belangrik om die evolusionêre kragte vir elke gasheer plant en sy patogeen onafhanklik te assesseer, sonder om algemene aannames te maak in bewaringspraktyke. Plantbestuiwers speel 'n belangrike rol in die fiksheid van plante. Hulle kan hul fiksheid verbeter deur bestuiwers te lok met blomme en deur aspekte geassosieer met blomme. Die bewegingspatrone van plantbestuiwers is baie belangrik indien hulle helmknop-geproduseerde spore van brandswamme vervoer instede van stuifmeel, want dit vergroot die kanse vir nuwe infeksies. Die bewegingspatrone van plantbestuiwers word, onder andere, beinvloed deur die digtheid en frekwensie van geinfekteerde individue. Plantbestuiwers speel 'n belangrike rol in die vervoer van Thecaphora capensis spore in geinfekteerde Oxalis populasies. Die digtheid en frekwensie van geinfekteerde blomme het die vervoer van spore geaffekteer onder veld en gestandardiseerde kondisies, alhoewel baie veranderlikes so 'n komplekse natuurlike sisteem beinvloed. Hierdie studie beklemtoon die kompleksiteit van 'n fungus-plant-insek verhouding, die gevolge van so 'n interaksie en die verskeie faktore wat die waarskynlikheid van nuwe infeksies beinvloed. Tot dusver is daar 'n beperkte aantal sisteme soos hierdie bestudeer waarin 'n brandswam van die helmknop betrokke is, en die enkele beskikbare studies is onderneem meestal as gevolg van hulle ekonomiese effekte op landboukundig belangrike gasheer plante. Hierdie studie verteenwoordig 'n belangrike byvoeging tot die inter-organismiese studies in die KFS. 'n Holistiese ekologiese oorsig soos hierdie verskaf 'n belangrike basis vir toekomstige studies en bewarings- en bestuurspraktyke.

Thesis (PhD (Zoology))--University of Stellenbosch, 2009. / ENGLISH ABSTRACT: The Cape Floristic Region (CFR) is a biodiversity hotspot in South Africa, threatened by climate change and various other processes. The Greater Cederberg Biodiversity Corridor (GCBC) is a conservation area incorporating both public and private land, providing a practical and effective solution to conserve biodiversity in the CFR. This area is also home to two of the eight melanistic cordylid lizard species found in south-western South Africa. One of the herpetological conservation targets identified for the GCBC was an understanding of the ecology of melanistic cordylid populations with particular reference to global environmental change. Most melanistic cordylids occur in cool coastal and montane localities, and it was suggested that melanism has a thermoregulatory function in these species. The first aim of this study was to determine the climatic conditions with which melanistic cordylids are currently associated. Several melanistic cordylid populations showed a distinct association with a high incidence of fog and cloud cover, underscoring the thermal melanism hypothesis, which predicts that melanistic lizards should occur in cool environments. Several other populations, however, did not show such an association. The next aim was thus to compare habitat use and morphology among 10 melanistic cordylid populations. Individuals of the northern population of Pseudocordylus capensis and the Cordylus peersi population occurred in the warmest environments, used significantly higher rock formations, and had relatively longer limbs than those of other melanistic populations. Having a morphology that allows for flexibility in habitat use, may enable species such as P. capensis to overcome the constraints of melanism in warm environments. Being melanistic may result in decreased activity times in warm environments. The variation in habitat thermal quality and daily activity patterns of two melanistic cordylid species with different morphologies and habitat preferences, occurring sympatrically, was investigated. During summer, high rocks provided a better thermal quality habitat to P. capensis than small rocks, and P. capensis had a longer activity period than C. oelofseni. This suggests that the thermal opportunities provided by high rock enables P. capensis to increase its activity time. The impact of terrestrial and aerial predators can help shape body armour in lizards, with those species more exposed to aerial predators being faster and less armoured, and those more exposed to terrestrial predators being more heavily armoured. The degree of body armour in melanistic cordylids and their non-melanistic relatives was investigated. Melanistic members of the cordylus-niger-oelofseni and C. polyzonus clades had less armour than their non-melanistic relatives, supporting the prediction that melanistic cordylids basked more and were more exposed to aerial predators than non-melanistic lizards. An increase in body armour in C. peersi indicated exposure to terrestrial predators, whereas P. capensis had a reduction in body armour, indicating exposure to aerial predators. Little body armour, together with a slender morphology and long limbs, may thus enable this species to move with ease on large boulders and scale vertical surfaces to successfully avoid predators. Pseudocordylus capensis displayed much greater movement rates during activity than other cordylids. A less sedentary foraging strategy may be a prerequisite for life on large, barren rock surfaces where food availability may be low or not uniformly distributed. Both males and females of this species also had large home ranges, a unique phenomenon for cordylids. Space use of males only overlapped marginally, but extensive overlap among males and females and among females, respectively, was observed. Due to the constraining effect of climate on the distribution of most melanistic populations, melanistic cordylids should be considered as priority species for conservation. While P. capensis is pre-adapted for survival in warm climates, it is dependent on the availability of suitable habitats. The GCBC would thus play an important role in the conservation of this species’ habitat. / AFRIKAANSE OPSOMMING: Die Kaapse Blommeryk (KBR) is ‘n “biodiversity hotspot” in Suid-Afrika wat deur klimaatsverandering en verskeie ander prosesse bedreig word. Die Groter Cederberg Biodiversiteitskorridor (GCBK) is ’n bewaringsarea wat beide openbare en privaatgrond inkorporeer, en ’n praktiese en effektiewe oplossing tot die bewaring van biodiversiteit in die KBR bied. Twee van die ag melanistiese gordelakkedisse wat in suidwestelike Suid-Afrika aangetref word, kom ook hier voor. Een van die herpetologiese bewaringsdoelwitte vir die GCBK was om insig oor die ekologie van melanistiese gordelakkedis populasies met verwysing na globale omgewingsveranderinge in te win. Die meeste melanistiese gordelakkedisse kom in koel kus- en berggebiede voor, en daar is voorgestel dat melanisme ‘n termoregulerende funksie by hierdie spesies het. Die eerste doel van die studie was om die huidige klimaatstoestande waarmee melanistiese gordelakkedisse geassosieer word, te bepaal. Verskeie melanistiese gordelakkedis-populasies het ‘n duidelike assosiasie met mis en wolkdekking getoon, wat die termiese melanisme hipotese se voorspelling dat melanistiese akkedisse in koue omgewings moet voorkom, ondersteun. Verskeie ander populasies, het egter nie so ‘n assosiasie getoon nie. Die volgende doel was om habitatgebruik en morfologie tussen 10 melanistiese gordelakkedispopulasies vergelyk. Individue van die noordelike populasie van Pseudocordylus capensis en Cordylus peersi het in die warmste omgewings voorgekom, het relatief langer ledemate gehad en beduidend hoër rotsformasies as ander melanistiese populasies benut. ’n Morfologie wat buigsame gebruik van die habitat toelaat, kan sommige spesies soos P. capensis in staat stel om die beperkinge van melanisme in ‘n warm omgewing te oorkom. In warm omgewings mag melanisme tot ’n afname in aktiwiteitstye lei. Variasie in termiese kwaliteit van die habitat en daaglikse aktiwiteitspatrone van twee melanistiese spesies, met verskillende morfologieë en habitatvoorkeure, wat simpatries voorkom is bestudeer. Gedurende somer het hoë rotse ‘n beter termiese kwaliteit habitat aan P. capensis verskaf as die klein rotse, en P. capensis het ‘n langer aktiwiteitsperiode as C. oelofseni gehad. Dit stel voor dat die termiese geleenthede wat deur hoë rotse verskaf word, P. capensis in staat stel om sy aktiwiteitsperiode te verleng. Die invloed van terrestriële en lugpredatore kan help om liggaamspantser in akkedisse te vorm. Spesies wat hoofsaaklik aan lugpredatore blootgestel is, is vinniger en het minder pantser, terwyl spesies wat hoofsaaklik aan terrestriële predatore blootgestel is, meer pantser het. Die graad van pantser in melanistiese gordelakkedisse en hulle nie-melanistiese naasverwantes is ondersoek. Melanistiese lede van die cordylus-niger-oelofseni en C. polyzonus klades het minder pantser as hulle nie-melanisties naasverwantes gehad, en ondersteun die voorspelling dat melanistiese gordelakkedisse meer in die son gebak het en meer aan lupredatore blootgestel was. ’n Toename in pantser by C. peersi dui op blootstelling aan terrestriële predatore, terwyl P. capensis die minste pantser van alle melanistiese gordelakkedisse het, wat dui op blootstelling aan lugpredatore. Min beskerming, tesame met ‘n lenige morfologie en lang ledemate, mag dus hierdie spesie toelaat om gemaklik oor groot rotse en vertikale oppervlaktes te beweeg en roofdiere suksesvol te vermy. Pseudocordylus capensis het groter bewegingstempo’s tydens aktiwiteit as ander gordelakkedisse getoon. ‘n Meer beweeglike voedingstrategie mag ook ‘n voorvereiste wees vir ‘n lewe op groot, leë klipoppervlaktes waar voedselbeskikbaarheid dalk laag kan wees en nie eweredig versprei is nie. Beide mannetjies en wyfies het ook groot tuisgebiede gehad, ’n unieke verskynsel by gordelakkedisse. Mannetjies se ruimtes het slegs marginaal oorvleuel, terwyl daar heelwat oorvleueling tussen mannetjies en wyfies se ruimtes was. As gevolg van die beperkende invloed van klimaat op die verspreiding van die meeste melanistiese populasies, moet melanistiese gordelakkedisse as prioriteitspesies vir bewaring beskou word. Terwyl P. capensis pre-aangepas is vir oorlewing in warm klimate, is hierdie spesie afhanklik van die beskikbaarheid van gepaste habitatte. Die GCBK sal dus ’n belangrike rol vervul in die bewaring van die habitat van hierdie spesie.

Biodiversity considerations form an essential component of Environmental Impact Assessment (EIA), especially in areas with both a high biodiversity value and development pressure such as the Cape Floristic Region (CFR) in South Africa. Limited research has been conducted within the South African context on the quality of biodiversity inputs to EIA. The aim of this research was to evaluate the quality of biodiversity input to EIA in the CFR. To address this aim, a customised review package was generated to evaluate the quality of 26 Biodiversity Impact Assessment (BIA) reports in the CFR. The results were then compared with international trends of biodiversity input to EIA in order to show how prevalent such trends are within an area with high biodiversity value. This comparison showed that the quality of biodiversity input to EIA in the CFR generally concur with inadequacies identified in international EIA literature. Typically, significant weaknesses identified during the review were the lack of public participation and an insufficient evaluation of alternatives. Specialists also failed to develop adequate monitoring programmes. Furthermore, a very pertinent limitation was that, in general, assessments are conducted during inappropriate seasons and over insufficient time periods. However, some variations to the international trends are also present within the Region. For example, a particular strength was that a precautionary approach was adopted by most of the specialists to avoid negative impacts on biodiversity. In addition, specialists did not merely focus on lower levels (species and habitats) of biodiversity, but incorporated ecological processes in assessment techniques. The inadequacies identified in this dissertation pose particular challenges for biodiversity management and conservation practices. The development and implementation of mechanisms such as Best Practice Guidelines and improved biodiversity related legislation is proposed to improve biodiversity input to EIA. / M Environmental Management, North-West University, Potchefstroom Campus, 2014