The fluvio-lacustrine rocks of the Beaufort Group, South Africa have long been known for their tetrapod fossil record, which is the richest and most complete Middle Permian to Middle Triassic record for any terrestrial sequence in the world. The abundance of fossil material has enabled the Beaufort Group to be biostratigraphically subdivided into between 8 and 10 tetrapod assemblage zones, of which the lowest three (Eodicynodon, Tapinocephalus and Pristerognathus) are attributed to the Middle Permian. These lower assemblage zones record the earliest therapsiddominated faunas and, because they were recorded during a largely uninterrupted period of deposition, make the Beaufort Group the only place in the world where biodiversity change through the terrestrial Middle Permian can be effectively studied. In the last two decades, much interest has focused on an extinction of marine invertebrates at or close to the end of the Middle Permian (Guadalupian epoch), but the existence of a concurrent extinction in the terrestrial realm is contentious. The Beaufort Group is already well known to record the Permo-Triassic Mass Extinction but it also records an earlier extinction at the top of the Tapinocephalus Assemblage Zone (AZ). This extinction is very poorly understood but recent radiometric dates for many Permian assemblage zones of the Beaufort Group have confirmed a Middle Permian age for Eodicynodon, Tapinocephalus and Pristerognathus assemblage zones and suggest that the end-Tapinocephalus AZ extinction may coincide with the marine extinctions. A recently produced GIS database that accommodates all Beaufort Group fossil material curated in South Africa formed the basis on which the stratigraphic range of individual specimens was calculated. To put the fossil localities in a stratigraphic context, lithostratigraphic information was retrieved from the literature and extensive fieldwork was conducted, which measured stratigraphic sections in key areas and traced the surface outcrop of lithostratigraphic units. In order to compensate for lateral variations in lithostratigraphy, the basin was split into sectors, each represented by a stratigraphic section. The stratigraphic ranges of fossil specimens and, subsequently, of genera and families could then be calculated and a workable biostratigraphic subdivision of the Middle Permian Beaufort Group proposed. The Abrahamskraal Formation, which forms the majority of the Middle Permian Beaufort sequence, can be divided into six lithostratigraphic members based on the occurrence of sandstone ‘packages’. These members were traced laterally across the Basin and their correspondence with fining-upwards cycles was refined and correlated with the newly defined biostratigraphic units. This refined two-pronged stratigraphic subdivision allowed the recognition of a waning period of subsidence in the proximal sector of the Karoo Basin during the Middle Permian. Stratigraphic ranges of individual genera were found to be far more heterogeneous than previously recognised. Dicynodont genera are useful biostratigraphic indicators due to their relative abundance and well-defined stratigraphic ranges, while dinocephalians and pareiasaurs are clustered in the upper part of the Abrahamskraal Formation. The stratigraphic range of Eodicynodon extends further up in the Abrahamskraal Formation than was previously recognised. The Tapinocephalus AZ is restricted to approximately the upper fifth of the Abrahamskraal Formation and is characterised by advanced tapinocephalid dinocephalians and the pareiasaur Bradysaurus. Between these two biozones is a stratigraphic interval dubbed the mid- Abrahamskraal Formation Transition Zone, where both Eodicynodon and advanced tapinocephalids coexisted. A 75 % loss of generic diversity occurred between the upper Tapinocephalus AZ and the base of the Pristerognathus AZ, which corresponds to a stratigraphic interval between the mid-Karelskraal Member of the Abrahamskraal Formation and the mid- Poortjie Member of the Teekloof Formation. Several taxa that survive the end- Tapinocephalus AZ extinction, and are relatively common in the overlying Pristerognathus AZ (scylacosaurid therocephalians, the dicynodont genus Eosimops and the parareptile Eunotosaurus), all became extinct in the upper Poortjie Member at a time when generic originations are increasing. This suggests a second wave of extinctions in a similar fashion to that recorded at the Permo-Triassic boundary.

Chromolaena odorata (L.) King and Robinson is an alien invasive weed to most of the Old World tropical regions of the earth, including South Africa where it is morphologically distinct from most other C. odorata plants examined from both its native and invasive range. It is thought that these morphological differences are related to difficulties encountered in successful establishment of biological control agents on the South African population of C. odorata. It has been postulated that the source population of the South African population will harbour potential biocontrol agents that will be suited to successful establishment on the South African plants. Several morphological, cytological and isozyme studies have been attempted to identify the source population of the South African population, but these have failed to identify the origin of the South African population. In this dissertation two PCR-based methods were attempted, in an investigation into whether the morphological differences and difficulties in establishment of biocontrol agents have a genetic basis. The two techniques attempted were: Inter Simple Sequence Repeat (ISSR) amplification, and DNA sequencing. Results could not be obtained using the ISSR method, and the reason for this was not discovered despite extensive trials. The internal transcribed spacer region and the external transcribed spacer region sequences were obtained from five samples, and compared. It was found that the ETS region gave more phylogenetic signal at the intraspecific level than the ITS region. However, due to difficulties in amplification of the external transcribed spacer region, work here focussed on obtaining Internal Transcribed Spacer sequences for 61 samples. Each of the samples sequenced had a unique ITS sequence, displaying a high level of intraspecific genetic diversity. The degree of this diversity is discussed with reference to the possible influences of polyploidy and concerted evolution on genetic structure. The ITS data indicated that some of the physical traits used to define ‘morphotypes’ of C. odorata were not correlated to genotype. From discussion and comparison of morphological character distributions and the ITS-based phylogeography it is suggested that the geographical origin of the South African population is Greater Antilelan, rather than from the continents of North and South America, which is where the Australasian, West African and Mauritian infestations are suggested to have originated.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. Johannesburg, 14 December 2016. / The interaction between business and biodiversity has seen growing importance in corporate management; impacting policy, practices and strategy. This study examines South African companies’ assimilation of recommended biodiversity management practices, as communicated through their annual reporting and official websites. A selection of nine South African companies in the forestry, sugar and mining sectors were studied with regards to their reporting on biodiversity management practices. The research aimed to understand the extent of structured approach to biodiversity management, and explore potential sectorial differences. The study found a wide acceptance of the UN Global Compact Principles, the GRI reporting guidelines and the King Code of good governance principles. However, the companies did not demonstrate a consistent governance structure for biodiversity management. The study revealed one mining company with a stronger biodiversity governance structure making the use of various dedicated policies and standards. Furthermore, the study identified few sector specific differences. Though the forestry sector demonstrated good practice with its emphasis on biodiversity in its supply chain management. The study did not reveal a particular uptake of emerging biodiversity concepts such as No Net Loss, payment for ecosystem services or agroforestry, however the companies had adopted several sustainability and governance recommendations and standards. The study did not identify the existence, nor the use, of dedicated biodiversity certification programmes or South African developed cross-sector biodiversity certification programmes. The finance sector is in a good position to positively influence corporate biodiversity management practices. However, the study results give an impression that there is untapped potential in the finance sector to further drive the biodiversity management agenda in South Africa. Keywords: Corporate Biodiversity Management, Biodiversity Management Framework, Biodiversity Best Practices, / LG2017

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. Johannesburg, 2014. / The persistence of rare plants is an important dimension in the conservation of biodiversity. Consequently an improved understanding of the nature and determinants of plant rarity and its relation with vulnerability to extinction could provide a basis for “proactive conservation” instead of the present day tendency for conservation actions to be “reactive”. In this dissertation I explore the relation between plant rarity and anthropogenic pressures (land transformation and use), biophysical factors, and plant traits in KwaZulu-Natal Province. Rarity was defined as the product of plant species abundance (population size) and its distribution (extent of occurrence). A number of a priori hypotheses regarding plant rarity were developed from the literature and these were then tested on a sample of plant species from KwaZulu-Natal. Species were selected in a stratified random manner to include species from different levels of threat and rarity or commonness. As the interest of this study was KwaZulu-Natal, only KwaZulu-Natal records were used for the analysis. Although the study suffered from a paucity of data particularly on the biological traits and behaviour of each species I was able to explore rarity in terms of seed dispersal distance, stress tolerance, habitat specificity and ecological niche width. I also explored potential island effects based on a species affinity to isolated erosional land surfaces and the anthropogenic effects of utilization and land transformation. To get an initial insight into relations, rarity was compared with each explanatory variable independently prior to using a multiple regression analysis approach aimed at understanding the potential interactive effects of suitable variables on rarity. Three different analytical techniques were used to provide a more robust understanding of the variable associations. These included Regression tree analysis (CART Salford Systems Inc., USA) and two generalized linear regression approaches; Generalized Linear Modelling (GLM) and Generalized Additive Modelling (GAM). All three multiple regression methods indicated that niche width had the strongest influence on rarity. Although Land Surface was shown to be the second strongest variable this, according to the GLM and GAM analyses, was due to a positive correlation between species with no affinity to land surface and species commonness. Visual representation of the regression tree analysis showed inconsistent partitioning of this variable throughout the tree indicating that land surfaces are not good predictors of rarity. Although the relation between Rarity Index and Habitat Transformation is not linear it was shown to be significant (p <0.1(p=0.0549)) after “smoothing” in GAM analysis. A smoothing curve on the bivariate analysis and the regression tree analysis indicated that species start to become rare after approximately 36% of their habitat is transformed. While GLM and GAM showed little or no relation between life history, dispersal distance, habitat specificity and rarity, the regression tree selected habitat specificity as the third most important splitter in the tree and dispersal distance was selected as a primary splitter for species with a niche width of greater than four. These differences observed in the three multiple regression analyses highlight the value of using more than one method to explore relations in ecological data. Considering all three analyses Niche Width is the strongest determinant of Rarity in KwaZulu-Natal, followed by Habitat Transformation and then Habitat Specificity. This improved understanding of the determinants of rarity will enhance our ability to prioritise plant species for conservation action. Key Words: ecological niche width, habitat specificity, habitat transformation, rarity, seed dispersal distance, stress tolerance, human use.

In this study, the diversity of forty Salmonella isolates from selected drinking water and wastewater sources in the Eastern Cape Province of South Africa was assessed using parameters such as protein and lipopolysaccharide profile analysis, DNA fingerprinting and antibiotic susceptibility profile as test indices. Wastewater samples from Amalinda, Shornville and Fort Hare wastewater plants, and water samples from Gogogo and Tyume rivers were collected on ice and transported to the laboratory of the department of Microbiology and Biochemistry, University of Fort Hare for processing. The DNA dendograms of Salmonella and the applied UPGMA revealed 4 similarity groups of the strains. Most of the strains recovered from Amalinda, Shornville, Fort Hare wastewater plants, Gogogo and Tyume rivers show a high percentage of genetic similarity. On the other hand, protein dendograms of Salmonella isolates revealed 2 similarity groups which varied widely. Also, the lipopolysaccharide dendograms revealed three similarity groups with the first similarity groups showing a very high relatedness between strains from different water sources. The second similarity group included 16 strains which formed a rather homogenous group, and the third similarity group formed a distinct group. Of the seven antibiotics and sulfonamides tested against the Salmonella species, five namely, neomycin, chloramphenicol, kanamycin, streptomycin and cotrimoxazole were significantly inhibitory, while the bacteria showed considerable resistance to doxycycline and sulphamethoxazole. Our results based on restriction digestion, SDS/PAGE and dendogram construction show that there is a high similarity between the forty Salmonella strains studied, and that these methods are valuable tools for evaluating the relatedness ofSalmonella species. Our observations have proffered a veritable reference point on the diversity of Salmonella strains in the studied area.

With current biota under constant threat of extinction, it is important to ascertain where and how biological diversity is generated and partitioned. Phylogeographic studies can assist in the identification of places and processes that indicate the origin and maintenance of biodiversity. Forest fragmentation has a big effect on local extinction and loss of genetic diversity of forest-restricted taxa, along with divergence and speciation of forest biota. This study aims to understand the effects of these processes on a number of forest-dwelling butterflies using a comparative phylogeographic approach. Mitochondrial DNA of five different Papilio species with different degrees of forest specificity was analysed using phylogenetic methods. In addition, the subspecific taxonomy of P. ophidicephalus was investigated using morphometrics of discal spots on the wings and nuclear DNA analysis along with mitochondrial DNA analysis. The results show that the forest-restricted species (P. ophidicephalus and P. echerioides) have more genetic structure and less genetic diversity than the more generalist species (P. dardanus, P. demodocus and P. nireus). This could be due to inbreeding depression and bottlenecks caused by forest fragmentation. As forest patches become smaller, the population size is affected and that causes a loss in genetic diversity, and increasing habitat fragmentation disrupts gene flow. The intraspecific taxonomy of P. ophidicephalus is far from revealed. However, this study shows there is evidence for the different subspecies when comparing morphological results and genetic results. From the evidence provided here it is suggested that P. ophidicephalus should be divided into two separate species rather than five subspecies.

The study focused on the development of an environmental education (EE) strategy framework in the Endangered Wildlife Trust (EWT) of South Africa. Evidence shows that the roles of conservation and biodiversity education could potentially be merged towards producing a practical strategy, beneficial to the organisation and its individual staff members. Questionnaires, interviews and the individual perceptions of staff members, as well as the analysis of relevant documents, suggested that the potential for the practice of EE towards the development of an EE strategy within the organisation is substantial. EWT staff members can contribute towards a change in the way that South Africans think about conservation and nature. Environmental ethics need to be promoted and understood by all. Within the EWT, environmental education activities are in place and diverse, yet they lack any form of monitoring and evaluation. The Trust is already practicing a form of EE but the potential to do more and the opportunities for expansion are unlimited.

The decrease of biological diversity from low latitudes near the equator towards high latitudes is one of the most fundamental patterns noted in ecology. These trends have been the subject of numerous terrestrial and marine studies and have caused the proposal of several explanatory hypotheses. No single hypothesis has adequately accounted for these observed trends. Furthermore, large-scale patterns are frequently modified by processes acting at meso- to small-scales. It is imperative to understand the interaction of these processes to elucidate the mechanisms controlling the structure of intertidal assemblages. The main aim of this thesis was to test the influence of multiple processes at a range of spatial scales on biogenic engineers. Biogenic engineers, such as macroalgae, have been reported to be strongly influenced by processes such as grazing, biogeography and upwelling and subsequent effects are expected to be linked to their associated assemblages. I used infaunal assemblages associated with macroalgae as a model system to understand the interactive effects of meso-scale upwelling in conjunction with large-scale factors (regional and biogeographic). Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis, inhabiting different but overlapping home ranges were used in this study. Smaller scale, physical attributes and the associated fauna of these algal species were compared. The effects of meso- to large-scale physical gradients on marine organisms have been investigated in many instances and resultant gradients in physical variables observed. This study was undertaken to investigate morphological trends exhibited by Hypnea spicifera and Champia lumbricalis to compare possible similarities between coastlines and to determine if inferred meso- to large-scale processes influence physical trends in a similar manner despite the coastlines being affected by different hydrodynamic processes. The macroalgae were located in two distinctly different upwelling regimes, Hypnea spicifera on the east and south coasts and Champia lumbricalis on the west coast. Upwelling (delivery of nutrients and primary production) was not found to be an important factor in determining the physical characteristics of macroalgae but there were clear patterns linked to latitude. Mean percentage cover of Hypnea spicifera was positively correlated with distance along the east and south coasts. Mean mass and mean surface area of H. spicifera were, however, negatively correlated with distance from Port St Johns. Mean frond length showed a negative trend but this relationship was not statistically significant. On the west coast, there was a significant increase in mean frond length from north to south for Champia lumbricalis. Mean surface area and mean mass of C. lumbricalis exhibited non-significant negative trends from north to south while there was a non-significant positive trend for mean percentage cover. Following the “Productivity Hypothesis”, these patterns from north to south along the coastlines of South Africa could have important implications for biodiversity associated with these algae. Many previous studies have focussed on the effects of upwelling on species (i.e. effects of nutrients and temperature) but have failed to separate this effect from large scale effects such as biogeography and latitudinal gradients. I tested the influence meso-scale upwelling, large-scale biogeographic processes and latitudinal gradients with two different species of macroalgae one on the east and south coasts of South Africa and the other on the west coast. Hypnea spicifera inhabits the east and south coasts of South Africa spanning two biogeographic provinces and is generally affected by relatively weak upwelling, whereas Champia lumbricalis inhabits the west coast spanning one biogeographic province which is subjected to intense persistent upwelling year round. Within the east and west coast biogeographic provinces there are, however, regions with both upwelling and non-upwelling. On the east and south coasts, entire assemblages differed significantly among the three Regions (St Lucia, Port Alfred and Knysna, while assemblages between upwelling/non-upwelling areas were not different. Assemblages on the different shores differed significantly from each other. There were no significant effects of region or upwelling for the number of individuals of Crustacea or Polychaeta, while Mollusca showed a significant effect of region. The number of individuals of other taxa showed a significant interaction of region and upwelling. Region had a significant effect on number of species of molluscs and other taxa, while there was no effect for either region or upwelling for the Crustacea or Polychaeta. In general different factors were shown to be important (region and shore) while upwelling was rarely important. On the west coast assemblages associated with C. lumbricalis were not influenced by region or upwelling but there were significant differences between shores. Region, upwelling ad shore did not affect number of individuals. There was a significant interaction of region and upwelling for the number of species of crustaceans, while numbers of species of Mollusca, Polychaeta and other taxa showed no effects. In general, regional factors strongly influenced most organisms, while upwelling played a minor role. Hypotheses about differences between upwelling and non-upwelling regions in terms of species abundances and composition due to the input of cold nutrient rich water were not supported. A link between the effects of larger-scale biogeographic factors and their influence on habitat forming taxa and the resultant effects on associated infauna would be a likely explanation for the patterns observed in this study. Diversity of assemblages is known to be influenced by the structural complexity of a habitat, increasing complexity increases the amount of available niches therefore potentially increasing the number of species found within that habitat. Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis were selected on the basis of being structurally similar and having their distributional ranges overlap in order to elucidate the effects of structure and macroalgal species on associated assemblages. Hypnea spicifera is different in terms of surface area and biomass from Champia lumbricalis and Bifurcaria brassicaeformis. Assemblages of species found on the three rhodophytes showed both shore and the species of alga had significant effects on composition. Only numbers of individuals of molluscs were affected by the species of alga. Crustacea and Polychaeta showed an interaction of the species of alga with shore. In the case of this study, it is likely that the three species of macroalgae mitigate biological stressors such as predation and physical stressors such as wave exposure and desiccation. In general, meso-scale upwelling is suggested to be marginalised when considering the structuring of assemblages associated with macroalgae, while large scale biogeography has more of an influence. Within shores, assemblages were also strongly influenced by smaller-scale factors such as differences in the structure and species of alga. This study indicates the importance of investigating patterns across a range of spatial scales to gain a comprehensive understanding of factors influencing intertidal organisms.

A significant proportion of the South African coastline is composed of both soft (mostly sand) and hard (mostly bedrock) substrata, i.e. “mixed”. This study described and classified macrobenthic assemblages of 20 Eastern Cape mixed substrate shores that differed in shore topography and the extent and position of intertidal rock and sand. A stratified random approach was used. Species richness, composition, abundance and environmental variables were determined. Commonly used beach indices were calculated. A total of 78 macrofaunal and 172 macroalgal species from rock substrate assemblages and 205 macrofauna species from sediment were recorded. Total species richness and richness per substratum exceeded that of sandy beaches devoid of rock and rocky shores with no sand. Rhodophyta were the most diverse and abundant algae, dominating all low-elevation rock surfaces as midlittoral and infralittoral turfs. Chlorophyta diversity was higher than at rocky shores, contributing more to cover-abundance at study sites and in microhabitats with an increased sand load. Sessile macrofauna species richness and abundance was lower than that of rocky shores. Polychaetes and crustaceans were the most diverse and abundant beach infauna. Species richness of both substrates declined from the low shore towards the high shore, but abundance trends varied substantially. The presence and extent of an intertidal biotope/subzone at either substrate depended on substrate availability.The supralittoral fringe in both substrate types was most often affected. Zonal overlap was evident on rock substrate: assemblages of raised midlittoral rock surfaces were enriched by species from lower surfaces sometimes leading to elimination of character taxa. Classification and ordination identified three potential mixed substrate shore biotic types: Biotic type A (Jania-Corallina- Polysiphonia turf) was characterised by robustly-textured algal turfs, a lowered predominance and diversity of polychaetes and an increase in crustacean abundance and diversity in sediment. Biotic type B (Polysiphonia-Tayloriella-Caulacanthus turf) had intermediately and biotic type C (Arthrocardia-Laurencia turf) the most sheltered eulittoral zones and beaches. DCCA identified the major environmental parameters affecting the macrobiota as: the level of wave energy, geological control of waves by hard substrate, sediment grain size and sediment inundation. A strong cross-shore wave attenuation results in sheltered sediments and midshore rock surfaces. Beach macrofauna were highly variable and diverse, which directly opposes previous perceptions about the sediment-bound biota of mixed substrate shores. The hierarchical cluster analysis produced a biotic classification of mixed substrate shores that was indicative of a biotic response to the total effects of leading environmental parameters. Macrobenthos of rock surfaces and sediment therefore showed potential to be used as an alternative or complementary to physical characteristics in classifying mixed substrate shores.

It is well known that invasive alien plants (IAPs) pose a significant threat to natural biodiversity and human well-being. Through various pressures exerted on natural ecosystems, IAPs decrease and alter natural processes that provide important ecosystems services and livelihoods to human communities. These plants also displace and out-compete natural plant communities in the areas in which they invade. Management of IAPs is a complex issue with social, environmental and financial challenges. The long-term sustainable management of IAPs requires a management approach that monitors and measures the outcomes of current management practices, and considers the lessons learnt in future decision making. Adaptive management is such an approach and is characterised by monitoring, assessment, reflection and adaptation. In this dissertation I explore IAP management within the South African National Parks (SANParks) organisation. I focus on the quality of the available IAP clearing data for monitoring and environmental decision-making and explore how strategic adaptive management (SAM) is being applied to IAP management. Strategic adaptive management is a form of adaptive management that SANParks adopted to deal with the inherent unpredictability of the social ecological systems they manage, and is primarily a learning-by-doing approach. In chapter one I describe the various impacts that IAPs have on natural environments. I also discuss management of IAPs, the national Working for Water (WfW) programme and how SANParks control IAPs in partnership with WfW. Clearing of IAPs within the borders of SANParks is funded by the Department of Environmental Affairs‘ (DEA) Natural Resource Management programmes and carried out through the Working for Water programme, under SANParks‘ Biodiversity Social Projects programme and is done on a contract basis. Contract data are stored in the Working for Water Information Management System (WIMS) database. Although IAP clearing is well established, the efficiency of overall clearing operations within the parks, and quality and reliability of the data available in the WIMS, needs to be examined. In Chapter two, I (i) assess the status of IAP clearing and the direct clearing costs in each of the five national parks (costs are inflated to 2012 equivalents using the consumer price index), (ii) assess the accuracy of workload estimations for WfW IAP clearing, and (iii) discuss the utility of WIMS as a system to collate and store accurate data for monitoring purposes, focusing on the integrity and reliability of the data, the accuracy of density estimations and whether it can inform sound decision making. The planning of future clearing contracts lacks efficiency due to inaccuracies and unreliability of input data, specifically estimates of invasive alien plant density. The accuracy of density estimation and cost of clearing varies greatly between parks and does not appear to reflect the reality on the ground. In Chapter 3, through an interview process with IAP managers, I 1) unpack the steps in the SAM ‗cycle‘ and investigate the effectiveness of implementation of each step according to respondents; 2) assess the barriers that are currently keeping managers from implementing effective IAP management; 3) discuss whether learning and adaptation is taking place, and 4) discuss how the SAM process can be modified to promote its effectiveness.