MSc., Faculty of Science, University of the Witwatersrand, 2011 / Riparian zones harbour different species pools from the surrounding landscape and are thus important to biodiversity conservation. However, riparian zones are highly variable. Network characteristics, morphology, flow-sediment interactions, biophysical connectivity and biological characteristics all vary along the length of a river. It could therefore be expected that the biodiversity characteristics of different riparian zones may also be variable. To investigate this, this study quantified compositional and structural diversity in 1st, 2nd, 4th, 5th, and 7th stream order rivers in south-western Kruger National Park (KNP). A suite of measures, chosen to encompass the variety, balance, and disparity properties of diversity, was used to quantify woody vegetation and bird compositional and structural diversity within each stream order. Woody plant species richness and species diversity was highest in the 7th order river and similar in the 1st through 5th order rivers. Likewise the woody vegetation community composition of the 7th order river was distinct from those in the other stream order rivers. Bird species diversity was similar in all five stream orders considered. Bird community composition of the 7th order river was distinct from the bird community composition of the 4th and 5th order rivers, which in turn was distinct from the bird community composition of the 2nd and 1st order rivers. Woody vegetation height, canopy width and diameter diversity tended to be highest in the 4th and 5th order rivers, while number of stem (NoS) diversity was generally highest in the 1st order rivers and decreased along the stream order sequence to the 7th order river. Bird body mass diversity was highest in the middle of the stream order sequence, while bird wing length/body length (WL/BL) and leg length diversity was similar along the entire stream order sequence. Overall, a variety of patterns of change in biodiversity along the stream order sequence were observed The lack of a consistent pattern along the stream order sequence among the different elements of compositional and structural diversity illustrates that no single measure can properly characterise the biodiversity of an area, and thus researchers and managers need to be explicit about which aspect of biodiversity they are aiming to study/conserve. Additionally, the unique combination of biodiversity found in each of the stream orders illustrates that each contributes importantly to overall regional biodiversity, and thus there is need to consider the role of entire drainage networks in the landscape, rather than simply focusing on perennial rivers. Finally, this study illustrates the need to consider the heterogeneous nature of biodiversity itself.

Subsistence fishing is impacting on freshwater and marine biodiversity to the extent of extinction of some fish species. These illegal subsistence fishermen have created a huge impact on marine biodiversity, irrespective of marine and riverine laws that are put in place and practiced. There have been attempt to provide subsistence fishing extension officer services to facilitate in bringing subsistence fishermen fully into the management system, in an orderly and equitable manner, by facilitating the granting of formal subsistence fishing right, providing permits via policy management and effective rules via permit applications. However the follow up process as to whether these policies and rules administered is effective or not has not been measured. This investigation attempts to identify potential fishing that should be considered as suitable for subsistence fisheries in selected highly exploitable areas. Though it cannot be confirmed from previous studies that some relevant organizations are not fully taking their responsibilities, the study will further enable exploration of options and challenges associated with future management of subsistence fisheries and provide recommendations to enable proper implementation of the policies and legislations. / Environmental Sciences / M. Env. Sc. (Agriculture and Environmental Affairs)

Subsistence fishing is impacting on freshwater and marine biodiversity to the extent of extinction of some fish species. These illegal subsistence fishermen have created a huge impact on marine biodiversity, irrespective of marine and riverine laws that are put in place and practiced. There have been attempt to provide subsistence fishing extension officer services to facilitate in bringing subsistence fishermen fully into the management system, in an orderly and equitable manner, by facilitating the granting of formal subsistence fishing right, providing permits via policy management and effective rules via permit applications. However the follow up process as to whether these policies and rules administered is effective or not has not been measured. This investigation attempts to identify potential fishing that should be considered as suitable for subsistence fisheries in selected highly exploitable areas. Though it cannot be confirmed from previous studies that some relevant organizations are not fully taking their responsibilities, the study will further enable exploration of options and challenges associated with future management of subsistence fisheries and provide recommendations to enable proper implementation of the policies and legislations. / Environmental Sciences / M. Env. Sc. (Agriculture and Environmental Affairs)

Considering the challenges faced by the City of Cape Town such as loss of biodiversity, limited supply of energy and unsustainable land use, it is argued that it is imperative for the construction industry to promote sustainable development. The objective of the research was to understand the contributions of the construction industry to over exploitation of resources such as biodiversity, energy and land. Secondly, the study considers initiatives to be undertaken by the construction industry to enhance the environment so as to promote sustainable development. The research mixed methods was used as the form of collecting required data. The collection of data comprised of the design and administration of open-ended and closed-ended questionnaires among a non-random selected population of building contractor, public works officials and practising Architectural firms within the City of Cape Town. The data obtained from open-ended questionnaire on building contractors and public works officials was analysed qualitatively and data from the closed-ended questionnaires through practising Architectural firms was analysed quantitatively. Research results showed that biodiversity in the City of Cape Town is under threat. Passive design has a significant role in protecting the biodiversity and should be encouraged by the construction industry and the City of Cape Town. The City of Cape Town should strongly enforce polices that support the conservation of biodiversity. This will have a positive impact through encouraging the construction industry to adhere to these polices. The City of Cape Town is faced with energy shortage. The construction industry needs to reduce its energy usage as a dominant energy user. This will be achieved through energy efficient designs and retrofitting the existing buildings. The City of Cape Town has a responsibility to promote sustainable land use. Land prices are highly priced in the City of Cape Town as a result the poor cannot enter the market without external assistance. The construction industry has a role to encourage sustainable land use in the city.

Health condition of a river is a necessity for the sustainability of aquatic ecosystems. River health status of the Nzhelele River was assessed through the use of water quality, macroinvertebrate taxa composition and aquatic habitat conditions. The study was conducted along the Nzhelele River in Limpopo Province of South Africa where the river transcends six tribal villages. The objectives were to assess water quality conditions in order to determine the magnitude of pollution impact, to correlate species diversity and water quality parameters, to measure the size of degraded areas with respect to species richness and to develop a model for managing river health condition of the Nzhelele River. Data were collected monthly between February and December 2016 (early autumn to mid-summer). Macroinvertebrates were sampled where water samples were collected to ensure that the relationship between water quality and macroinvertebrates was adequately correlated. Water quality parameters that were analysed were pH, stream temperature, river velocity, conductivity, Dissolved Oxygen, Total Dissolved Solids, nitrates, nitrites and chlorine. Assessment of habitat conditions was done through the assessment of habitat and riparian zone integrity. One-way ANOVA was used to determine if there were significant differences between the six sampling areas in terms of water quality and aquatic species composition. Principal Correspondence Analysis (PCA) was used to correlate water quality and macroinvertebrate data. The results indicated that water quality parameters significantly differed among the six sampling sites and that also explained the variations in diversity of macroinvertebrates that were sampled from the six sampling sites. Pollution tolerant organisms constituted a total of 46.7% and the remaining 53.3% represented pollution sensitive organisms. PCA results showed positive and negative correlations between macroinvertebrates and water quality parameters to indicate variations in the levels of pollution along the Nzhelele River. Habitat integrity results indicated that the Musekwa sampling site was the most degraded and had lower species diversity. The Ratio of Ephemeroptera, Plecoptera and Trichoptera (EPT) and Chironomidae Abundances should be reviewed to read as Ratio of EPT and Chironomidae-Thiaridae Abundances in order to strengthen the study of the relationship between pollution tolerant and pollution sensitive organisms. / Environmental Sciences / Environmental Science

Thesis (MSc (Microbiology))--Stellenbosch University, 2008. / Penicillium is a well‐known cosmopolitan genus with more than 225 accepted species. Species from this diverse genus, in general, are considered to primarily be soil fungi, with decomposition as its main function. Therefore, together with its ubiquitous nature, these species are of great importance in ecosystems, agriculture and biotechnology. However, in South Africa, very little research has been done on this complex genus, as species identification were often found to be problematic, even for experienced taxonomists. This lead to a number of South African studies only mentioning that a Penicillium spp. were isolated, without making any attempt of showing the extent of diversity within the genus from the unique habitats. The present study set out to explore the extent of the species diversity in Penicillium isolated from the Cape Floristic Region, specifically focusing on coastal fynbos soil. Soil samples were collected from this region, at sites situated outside Malmesbury. Four hundred and thirty four Penicillium strains were isolated from soil‐dilutions. The strains were characterized using morphological characters and subsequently placed into 24 morphological groups. There were, also, more or less 40 strains that could not be grouped with any other isolates. Groupings were made according to conidiophore branching patterns which divided the strains into their respective subgenera. Eight species from subgenus Aspergilloides, seven from subgenus Furcatum, eight from subgenus Biverticillium and one from subgenus Penicillium were isolated. The species were further characterized in subsequent chapters. In the second chapter of this thesis, one of the taxonomic groups in subgenus Biverticillium, isolated from coastal fynbos soil, Protea infructescences and on moth‐damaged Riesling grapes in Canada, was examined. This species was characterized using morphology and were found to have several unique characters, such as the very short synnema produced after prolonged incubation. These characters did not conform to descriptions of previously described species. Its novelty was confirmed by an ITS phylogeny and the strains were subsequently described as Penicillium ramulosum prov. nom. with P. cecidicola and P. dendriticumas its sister taxa. In chapter three, a further seven groups belonging to Penicillium subgenus Biverticillium were characterized. These strains were identified as P. minioluteum, P. verruculosum and P. rugulosum‐like, respectively. Four of the groups showed unique morphological characters, with the ITS phylogeny resolving the fynbos strains separate from all previously described species. The strains were, therefore, considered to be new to science and described as P. solicola prov. nom., P. ptychoconidium prov. nom., P. occultum prov. nom. and P. chloroloma prov. nom., respectively. A key to species from subgenus Biverticilliumcluded. is also inPenicillium subgenus Furcatum was the subject of the fourth chapter of this thesis. Our survey found that although the species diversity in this group was not as high as for the other subgenera, it was the group most often isolated in this study. Species were identified as P. janczewskii, P. canescens, P. melinii, P. corylophilum and P. citrinum using morphological characters. One species belonging to subgenus Penicillium, P. expansum, was also isolated and compared to species recorded during a previous survey. Amongst the identified species, were two groups that could not be identified using published keys, with their novelty confirmed by an ITS phylogeny. They are, therefore, described here as P. subturcoseum prov. nom. and P. hemitrachum prov. nom. A key to species in this subgenus is also provided. In Chapter 5 the presence of Penicillium subgenus Aspergilloides, which is characterized by monoverticillate conidiophores, were investigated. Species were identified as P. roseopurpureum, P. restrictum, P. hirayamae and P. toxicarium. Amongst the identified species, were four groups that did not conform to previously described species and are described here as P. brachycaulon prov. nom., P. malacosphaerula prov. nom., P. cumulacinatum prov. nom. and P. vulgaris prov. nom., respectively. The newly described species have been included in a key, together with closely related species and the other species of subgenus Aspergilloides from the fynbos soil. Species identifications in Penicillium is often problematic and South African taxonomists have often not attempt to identify strains down to species level. During this study, Penicillium was found to be well represented in the soil, with a large proportion being previously undescribed. For this reason, a dichotomous and synoptic key to species isolated during this study are provided in the final chapter. This study should thus serve as a basis for further explorations into the diversity and ecological role of this group of organisms in this ecologically mportant biome.

Thesis (MScConEcol)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: The role of mites as primary vectors of various fungi within Protea infructescences was recently confirmed and raised questions about their general diversity and their role within this unique niche. Although mites evidently form an integral part of Fynbos ecosystems and probably play a significant role in Protea population dynamics, there is a general void in our knowledge of mite diversity within the Cape Floristic Region. These organisms do not only affect ecological processes within the CFR, but also the economic value of Protea exports. This study sets out to describe mite communities within the infructescences of a variety Protea species. In the process, the role of various environmental variables and differences in host characteristics affecting these communities are also explored. A total of 24281 mite individuals, comprising of 36 morphospecies in 23 families, were collected from 16 surveyed Protea spp. Mite community structure and composition were significantly influenced by plant taxonomy, phenology and infructescence architecture in different Protea spp. At a temporal scale, infructescence age and season were influential factors on mite community structure. Collection locality significantly influenced mite communities within the infructescences of a single Protea sp. Host architecture had no influence on mite communities within a single host species. Geographic distance had no significant influence on mite community structure within Protea infructescences. This implies that factors particular to particular host species determine mite communities. These include factors such as the mode of pollination of the host plant, level of serotiny and plant life form. Numerous newly recorded mite species collected from Protea infructescences are also described in this study. An identification key to the Tydeidoidae of South Africa is provided here for the first time. This study forms a baseline dataset for future studies on the biodiversity of mites in this extremely diverse eco-region. / AFRIKAANSE OPSOMMING: Die rol van myte as primêre vektore van verskeie funguses binne Protea vrugtekoppe is onlangs bevestig, en het vrae laat ontstaan oor hulle algemene diversiteit en rol binne hierdie unieke nis. Alhoewel myte duidelik ‘n integrale deel vorm van Fynbos ekosisteme en waarskynlik ‘n belangrike rol speel in Protea populasie-dinamika, is daar ‘n algemene leemte in ons kennis van mytdiversiteit binne die Kaapse Floristiese Ryk (KFR). Hierdie organismes affekteer nie slegs ekologiese prosesse binne die KFR nie, maar ook die ekonomiese waarde van Protea-uitvoere. Hierdie studie mik as vertrekpunt om die verkillende myt-gemeenskappe binne die vrugtekoppe van verskeie Protea spesies te beskryf. In die proses is die rol van verskillende omgewingsveranderlikes en verskille in gasheer kenmerke wat hierdie gemeenskappe affekteer, ook ondersoek. ‘n Totaal van 24281 myt individue, saamgestel uit 36 morfspesies in 23 families, mytgemeenskappe is beduidende beinvloed deur die taksonomie van die plant, die fenologie en die vrugtekop-argitektuur van verskillende Protea spesies. Op ‘n temporale skaal is gevind dat vrugtekop-ouderdom en seisoen beduidende faktore is in die samestelling van mytgemeenskapstruktuur. Versamel-lokaliteit het verder mytgemeenskappe binne die vrugtekoppe mytgemeenskappe binne ‘n enkele gasheerspesie getoon nie. Geografiese afstand het geen beduidende invloed op mytgemeenskapstruktuur binne Protea vrugtekoppe getoon nie. Dit faktore in soos die metode van bestuiwing van die gasheer plant, die vlak van saadhoudendheid van die Protea koppe en plant-lewensvorm. Verskeie nuwe myt spesies wat uit Protea vrugtekoppe versamel is, word ook in hierdie studie beskryf. ‘n Identifikasie-sleutel vir die Tydeidoidae van Suid-Afrika word verder vir die eerste keer hier verskaf. Hierdie studie vorm die basis datastel vir toekomstige studies van die biodiversiteit van myte in hierdie besonder diverse eko-omgewing.

In partial fulfilment of the requirements for the degree of Master of Commerce University of the Witwatersrand, October 2017 / Biodiversity is a serious concern for companies using natural resources in their operations and should be examined closely in order to assess how these companies are reporting their biodiversity related impacts. This thesis evaluates the biodiversity disclosures reported by companies in the South African fishing industry. The integrated and sustainability reports of these companies were examined over a three year period for the quantity and quality of their biodiversity related disclosures. This involved the examination of the extent, location, and quality of such disclosures by South African fishing companies. The thesis finds that there is a distinct lack of biodiversity-related disclosures in the South African fishing industry. This thesis highlights the operation of organised hypocrisy in an industry which relies on the availability of natural resources and the state of biodiversity in order to continue its operations. It was found that a possible reason for limited biodiversity disclosures by South African fishing companies was to avoid public scrutiny of their biodiversity impact. The thesis contributes to the evaluation of a country, and more specifically an industry, that is heavily reliant on the state of biodiversity. / GR2018

Land use and land transformation are major threats to biodiversity. Only a small percentage of land and thus biodiversity is protected within reserves. The majority of biodiversity lies in the hands of private and communal farmers and in order to protect biodiversity they must perceive it as having some value and have the means and incentive to conserve it. This study examined two things: (i) the relationship between biodiversity and measures of ecosystem health, range condition, primary production and presence of useful plants that would be expected to be of relevant use to land users, (ii) the perceptions of farmers of vegetation states that differ in the abovementioned attributes. Within the Eastern Province Thornveld of the Smaldeel area, four different vegetation states were selected for the study, namely park-like grassland with scattered Acacia karroo (“savanna”), heavily infested Acacia karroo grassland (“acacia”), thicket-grassland mosaic (“thicket”) and heavily utilised thicketgrassland in communal lands (“communal”). The four states are a consequence of different patterns of browsing and fire, in both pre-colonial and recent times. Different ecological attributes were assessed and compared for each state and the relationships between the different attributes determined. Ecosystem health, in terms of stability or resistance to erosion, infiltration/water-holding capacity, and nutrient cycling were compared using Landscape Function Analysis. The agricultural value of the different landscapes was measured using range condition assessment techniques. Plant species richness and other measures of diversity, along with their conservation and usefulness values, were compared between states. Plant productivity and biomass were compared using satellite data. The thicket state was found to be the most functional due to the added habitat complexity provided by the vegetation. It was the most biodiverse, the most useful and contained many, but not all of the important conservation species. The communal state had high biodiversity and was be fairly resilient to heavy usage, not showing the expected signs of land degradation. The savanna state, although thought of as the optimum state for cattle production, was not significantly different from the other states in terms of agricultural potential, but had the lowest values for plant diversity, browse potential, abundance of useful plant species and biomass. The acacia state had the highest and least stable values in terms of biomass production, however it was found to contain species of conservation importance. The preference that four groups of land users, namely men and women from commercial and communal farming areas, expressed for the four vegetation states was assessed using semi-structured interviews in conjunction with A3 colour photographs. The men and women from the communal areas and the men from the commercial areas valued the thicket state highly for its farming potential. The male commercial farmers also valued the savanna state highly as they perceived it as being most productive for cattle farming. Both the thicket state and the savanna state were found aesthetically pleasing by all the user groups, in line with theories of preference for modified savannas and for familiar environments. There appears to be potential for preserving biodiversity on farmland. The farmers in this study, with their very utilitarian perspective, were found to intuitively gauge the health of the landscape and recognise biodiversity as indicating good farming land. The commercial farmers were strongly influenced by economic motives and thus attracted to the savanna state, but also recognised the opportunity for a wider variety of farming activities in the thicket state. The communal farmers have a high dependence on the land for their livelihoods and preferred the thicket state for its overall usefulness. The views of the farmers indicate that the opportunity for conservation is good, however much of the thicket state lies in the communal land, where the openaccess land use system makes managing for biodiversity difficult.

Prestonella bowkeri and Prestonella nuptialis are montane specialists endemic to the southern Great Escarpment of South Africa. Phylogeographic analyses of these species based on mitochondrial markers CO1 and 16S reveal extremely high levels of divergence between populations indicating a lack of gene flow between populations. This is not surprising, because P. nuptialis and P. bowkeri have limited dispersal capacity, low vagility, a highly fragmented distribution and are habitat specialists that are restricted to isolated mesic refugia associated with waterfalls and montane seepages. A relaxed Bayesian clock estimate suggests that populations diverged from one another during the mid-late Miocene (12.5-7 MYA) which coincides with the modern trends of seasonal aridity which began during the Miocene. This result should be viewed with caution because the rates used are at best imprecise estimates of mutation rates in snails. There is no clear dichotomy between the two species and P. bowkeri is paraphyletic with respect to P. nuptialis, as a consequence the taxonomy is unclear. Due to the high levels of sequence divergence between populations they may be considered as evolutionary significant units (ESU’s). An assessment of haplotype diversity (h) and nucleotide diversity (π) reveals that populations in the western part of the Great Escarpment are more genetically depauperate than populations in the east. Correlations between genetic diversity and climatic variables show that genetically depauperate populations are found in areas that have lower annual rainfall, less reliable rainfall and higher potential evaporation, all factors associated with a drier, less mesic environment that increases the chances of a population bottleneck. This indicates that a shift towards a more arid environment may be a driver of genetic erosion. Historical climate change may thus have affected the amount and distribution of genetic diversity across the Great Escarpment since the Miocene. This has serious future implications for the survival of Prestonella. With predicted increase in global temperatures, climate change in South Africa is likely to result in range contraction and an eastward range shift for many species in the drier central and western areas (Erasmus et al. 2002) and regions along the Great Escarpment are likely to become more arid. Prestonella populations found living on inselbergs along the Great Escarpment are already restricted to site specific watercourses and seepages. An increase in the periods between stream flow, and increasing rainfall variability and mean annual potential evaporation are likely to have an adverse affect on species living in these habitats, resulting in further bottlenecks and possibly local extinction. An IUCN assessment of P. nuptialis and P. bowkeri suggests that these two species are probably endangered. The issue surrounding the conservation of Prestonella species is that they are threatened by global climate change, which cannot be simply restricted or prevented, which makes dealing with the threat of climate change difficult. Assisted migration (MA) may be considered as a method to prevent possible future extinctions of Prestonella populations, but will only be considered as a last resort. The thermal tolerance (Arrhenius breaking temperature and flat-line temperature) of individual snails from three Prestonella populations (one forest population and two thicket populations) were assessed using infrared sensors that detected changes in heart rate with increasing temperature. The forest population had a significantly lower Arrhenius breaking temperature (ABT) and flat-line temperature (FLT) than the two thicket population (p<0.05). Our results do not show a correlation between upper thermal limits and maximum habitat temperatures or other climatic variables in Prestonella populations. Although no correlation is found between ABT and maximum habitat temperature, it is likely that the differences seen between these populations are due to local micro-climate adaptation. The climatic variables used in this experiment are coarse estimates from GIS data and do not reflect actual microhabitat conditions. Forest environments are less heat stressed than thicket environments due to the forest canopy which may explain the lower ABT and FLT of the forest population.