Doctoral Degrees (Botany and Zoology)
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- ItemThe ability of terrestrial Oligochaeta to survive in ultramafic soils and the assessment of toxicity at different levels of organisation(Stellenbosch : University of Stellenbosch, 2006-12) Maleri, Rudolf A.; Reinecke, A. J.; Reinecke, S. A.; Mesjasz-Przybylowicz, J.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.Metals are natural elements of the earth crust usually present at low concentrations in all soils. Although many metals such as cobalt, copper, iron and zinc are essential to living organisms, at elevated concentrations most metals are toxic to organisms living in and on soils. Elevated concentrations of metals are caused either by anthropogenic deposition following remobilisation from the earth crust or are of natural origin. Ultramafic soils do not only pose unfavourable living conditions such as drought and poor organic content, these soils are also characterized by extremely high concentrations of a range of metals known to be toxic under normal circumstances. Ultramafic soils are of high ecological importance as a high proportion of endemic organisms, especially plants, live on these soils. As it is known that earthworms do occur in ultramafic soils, the aims of the present study were to investigate the abilities of earthworms to survive in these soils and the influences of elevated chromium, cobalt, copper, manganese and nickel levels. For the evaluation of the metal background conditions, soils originating from ultramafic rocks of the Barberton Greenstone Belt, Mpumalanga, South Africa were collected and different fractions representing different levels of bioavailability were analyzed for arsenic, chromium, cobalt, copper, manganese and nickel. To assess the mobile, readily available metal fraction, i.e. Ca2+- exchangeable metal cations, a 0.01 mol/L CaCl2 extraction was performed. To investigate the mobilisable metal fraction, representing the amount of easily remobilisable complexed and carbonated metal ions, a DTPA (di-ethylene-triamine-pentaacetic acid) extraction was conducted. In relation to non-ultramafic or anthropogenic contaminated soils, a far lower proportion of metals were extractable by the above mentioned extraction methods. To investigate the availability and effects of these metals on earthworms, two ecophysiologically different species were employed. Aporrectodea caliginosa and Eisenia fetida were long-term exposed to the ultramafic soils collected at the Barberton region and a control soil from a location at Stellenbosch with a known history of no anthropogenic metal contamination. The responses to the ecological stress originating in the ultramafic soils were measured on different levels of earthworm organisation. As endpoints affecting population development, cocoon production, fecundity and viability were evaluated. On individual level, growth, metal body burden and tissue distribution were investigated. As endpoints on subcellular level, the membrane integrity was assessed by the neutral red retention assay, the mitochondrial activity was measured by the MTT colorimetric assay and as a biomarker for the DNA integrity, the comet assay was performed. Focussing on manganese and nickel, the uptake by E. fetida of these metals was investigated with the exclusion of soil related properties using an artificial aqueous medium to draw comparisons to the uptake of these metals in natural soils. The possible development of resistance towards nickel was tested by exposing pre-exposed (for more than 10 generations) E. fetida specimens to ultramafic soils with concentrations of more than 4000 mg/kg nickel. The results showed that, except on the endpoint survival, which was less sensitive than all other bioassays, significant responses to the ultramafic challenge were observed in all earthworm bioassays and on all levels of organisation. The sensitivity of the responses of the earthworms towards the ultramafic conditions was not predictable by the level of organisation. The two species showed different strategies of metal elimination. In A. caliginosa, metals such as nickel, manganese and chromium were transported to the posterior section and the posterior section was subsequently pushed off by autotomization. In E. fetida, metals such as chromium and nickel were sequestered in storage compartments in the coelomic cells or fluid. Other metals, such as cobalt, were not taken up at elevated concentrations. Although an increased accumulation of nickel was observed in E. fetida specimens pre-exposed to nickel, development of resistance or cross resistance was not observed in this species. In contrast, pre-exposed specimen exposed to elevated concentrations of nickel showed a higher sensitivity in terms of survival, indicating the absence of acclimatisation or even genetic adaptation. A comparison of the two species employed indicated that A. caliginosa was less suited for the assessment of the ultramafic soils due to the high individual variation in metal body burden, the mass loss observed and the slow reproduction rate even in the control soils. This happened despite the fact that A. caliginosa was a soil dwelling species supposed to be better adapted to the soil substrate than the litter dwelling E. fetida. The toxicity of the ultramafic soils was not necessarily related to total or environmentally available amounts of the selected metals. Thus, it can be speculated that either these soils contained unidentified toxicants with resulting interactions between toxicants playing an important role or earthworms were able to remobilize metals occurring in these soils. As the singular application of an ecotoxicological endpoint did not give reliable results, especially seen over the duration of the exposures, it can be concluded that, when studying soils with such a complex composition, the utilisation of endpoints addressing different levels of organisation is necessary for the assessment of toxic stress emerging from these ultramafic soils.
- ItemAlien species and propagules in the Antarctic : movements through space and time(Stellenbosch : University of Stellenbosch, 2009-03) Lee, Jennifer Elizabeth; Chown, Steven L.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Although the impacts of biological invasions are widely appreciated, a bias exists in research effort to post‐dispersal processes because of the difficulties of measuring propagule pressure and the detecting of newly established species. Here the Antarctic is used as a model system in which to quantify the initial dispersal of alien species and investigate the factors that contribute to the establishment and range dynamics of alien species once they have arrived in the region. Human movements are known to transport alien species into the Antarctic, some of which have successfully established and had wide ranging consequences in recipient ecosystems. Considering terrestrial flora, this research found that over 700 seeds from 99 taxa, including some species known to be invasive, are transported into the Antarctic each year in association with South African National Antarctic Programme (SANAP) passenger luggage and cargo. The first ever assessment of propagule drop‐off indicated that 30‐50% of these propagules will enter the recipient environment. Further results suggested that the construction of the British Antarctic Survey Halley VI station will facilitate the transport of over 5000 seeds from 34 taxa into the region, making this a significant pathway for introductions. Propagule pressure due to SANAP logistics is also considerable for marine species. Fouling assemblages on the external hull surfaces of the SANAP resupply vessel, the SA Agulhas, form only once the vessel’s anti‐fouling paint has been damaged by travel through sea ice and are characterised by low diversity. Ice scour prevents fouling assemblages from being transported to the Antarctic continent, but assemblages remain largely intact when travelling to sub‐Antarctic Islands. In the sea‐chests of the vessel populations of a known invasive, Mytilus galloprovincialis, were found with some individuals having survived transportation to the Antarctic region on multiple occasions. Once species have overcome initial dispersal barriers, they face further ecological and physiological challenges in order to establish in the recipient region. The parasitoid wasp Aphidius matricariae was first recorded on Marion Island in 2001. Surveys around the island show that adult abundance and the frequency of aphid parasitism are highest adjacent to a common anchor point of the SA Agulhas and decline away from this region. Genetic diversity was low, suggesting that the population was established from a single introduction. This highlights that high propagule pressure is not necessary for successful establishment of introduced invertebrates. Another species that has overcome the dispersal barrier is the terrestrial slug Deroceras panormitanum, which was introduced to Marion Island in the 1970’s and has since spread throughout much of the coastal habitat of the island. For this species range limits are set by intolerance of low temperature and salinity, and abundance structure is characterized by patches and gaps which are associated with this species inability to tolerate dry conditions. To prevent further alien introductions in the region, targeted management of high risk pathways is required. In addition, increased vigilance is needed to detect and manage newly established aliens before their ranges expand.
- ItemAn analysis of the Pseudocordylus melanotus complex (Sauria: Cordylidae)(Stellenbosch : Stellenbosch University, 2007-04) Bates, Michael Francis; Mouton, P. le F. N.; Branch, W. R.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: The taxonomic status of southern Africa’s rupicolous crag lizards (genus Pseudocordylus) was investigated. As considerable confusion exists in the literature regarding the type specimens and type localities of the various taxa, resolution of these problems were considered the starting point of the study. Examination of museum specimens allowed for the designation of lectotypes, alloparalectotypes and/or paralectotypes. Of particular relevance to this study was the rediscovery of Andrew Smith’s type specimens of P. m. melanotus and P. m. subviridis. Restriction of the type locality of P. m. subviridis, based on entries in Smith’s diary and journal, allowed for the confirmation of previous interpretations and definitions of the two taxa. The geographical distribution of the various taxa and populations was determined using an extensive locality database. Two kinds of molecular markers, namely allozymes and mitochondrial DNA, were used in an attempt to resolve taxon boundaries within the P. melanotus species complex. The allozyme analysis indicated that P. m. melanotus might be polyphyletic and comprised of two unrelated lineages. Furthermore, fixed allelic differences between parapatric populations of P. m. melanotus and P. m. subviridis, and between sympatric populations of P. m. subviridis and P. langi, suggested that all three forms might be considered full species, with the possibility of more cryptic species present in the complex. Pseudocordylus transvaalensis differed from most other populations by 1-3 fixed allelic differences, but was indistinguishable from the Nkandhla district (central KwaZulu-Natal) population of P. m. melanotus. There were no heterozygous individuals in a sample from Monontsha Pass (Qwa-Qwa), a population reportedly comprising P. m. melanotus and P. m. subviridis, as well as intermediates, and all specimens were assignable to P. m. subviridis. The allozyme study was, however, based on phenetic principles and for further taxonomic resolution a cladistic approach was required. An mtDNA analysis (16S rRNA gene) using Maximum Parsimony, Maximum Likelihood and Bayesian analyses was therefore conducted to determine phylogenetic relationships among species and subspecies and to re-assess the taxonomic status of forms in the P. melanotus species complex. The mtDNA analysis corroborated most of the results obtained in the allozyme analysis. Firstly, P. langi was again found to be basal. With the addition of P. microlepidotus and P. spinosus to the ingroup, it is now apparent that P. langi is the basal species in the genus. (Recent studies have indicated that P. capensis and P. nebulosus are not congeneric with Pseudocordylus.) Secondly, the 16S rRNA results confirm that P. m. melanotus, as presently construed, is comprised of two clades that are not sister groups. The northern populations of P. m. melanotus (Sabie and Lochiel) form a fairly deeply divergent clade that may represent a separate species. The Nkandla population was, however, found to cluster with the other southern P. m. melanotus populations and not with P. transvaalensis as was the case in the allozyme electrophoretic analysis. However, the most surprising result of the 16S rRNA analysis was the finding that both P. microlepidotus and P. spinosus are embedded within P. m. subviridis. This suggests that these two species evolved from within P. m. subviridis and may have been separated only recently, with rapid morphological divergence occurring, but with limited genetic differentiation. It is suggested that all of the above three taxa be provisionally treated as full species. There was also morphological support for the uniqueness of all groupings indicated by the mtDNA analysis. Pseudocordylus transvaalensis is characterized by its large size, unique dorsal and gular (black) colour patterns, as many as three horizontal rows of lateral temporal scales, a series of small scales posterior to the interparietal scale, and usually two subocular scales behind the median subocular on either side of the head. The various populations currently classified under the name P. melanotus are more difficult to separate, but P. m. melanotus and P. m. subviridis usually differ as follows: frontonasal divided in P. m. melanotus, undivided in P. m. subviridis (and most Northern melanotus); lateral temporals in two rows, upper more elongate versus single row of much elongated scales; longitudinal rows of dorsolaterals closely-set versus widely separated; femoral pores of females pit-like versus deep with secretory plug. Northern melanotus differs from Southern melanotus in usually having an undivided frontonasal scale and seldom having a small scale present behind the frontonasal. Pseudocordylus langi has unique dorsal and gular colour patterns (including a series of blue spots on the flanks), granular dorsals with 6-9 paravertebral rows of enlarged flat scales, high total numbers of femoral pores (25-34) and usually only five (smooth not keeled or ridged) infralabial scales on either side of the head. Pseudocordylus spinosus also has unique dorsal and gular colour patterns, spinose lateral scales, frontonasal longer than wide and excluded from the loreal scales, low total femoral pore counts (6-9), and females (not only males) have differentiated femoral scales. Both Principal Components Analysis (PCA) and Canonical Discriminant Analysis (CDA) distinguished four groups, namely P. transvaalensis, P. langi, P. spinosus and a P. melanotus/subviridis/microlepidotus cluster. A separate CDA of all P. melanotus populations partly distinguished between Southern melanotus and P. m. subviridis, and largely separated Northern melanotus; whereas a CDA of P. transvaalensis showed that all three allopatric populations are 100% distinguishable in morphological space. A Nested Clade Analysis indicated that fragmentation as well as range expansion played a role in the distribution of the P. melanotus species complex. This may be explained by climatic oscillations (high-low temperatures and wet-dry cycles) during the Cenozoic that caused habitat expansion and contraction. Based on the topology of the mtDNA phylogram it is apparent that the genus Pseudocordylus originated along the eastern escarpment. A P. langi-like ancestor may have had an extensive range along the eastern escarpment, with the Maloti-Drakensberg forming the southern limit of its range. During a subsequent rise in global temperatures, range contraction and fragmentation took place, leaving an isolated population in the south and one in the north. The southern population survived unchanged in the Maloti-Drakensberg refugium, but the northern population was forced to adapt to the warmer conditions. Thereafter, the northern form expanded its range again, but during a subsequent cooler period, range contraction occurred, resulting in an isolated north-eastern population in the Sabie-Lochiel area in Mpumulanga (Northern melanotus) and a western population. Relationships in the latter clade are not sufficiently resolved to allow further reconstruction of biogeographic history, but it is clear that a P. m. subviridis-like form became isolated in the south where it eventually came into contact with P. langi at high elevations. Pseudocordylus m. subviridis eventually extended its range southwestwards into the inland mountains of the Eastern Cape and Cape Fold Mountains to give rise to the P. microlepidotus complex. This cycle of range expansion and contraction may also account for the isolated populations at Suikerbosrand, Nkandhla district, and in the Amatole-Great Winterberg mountain region. Furthermore, it is suggested that P. spinosus originated from a P. m. subviridis-like ancestral population that became isolated on the lower slopes of the Drakensberg where terrestrial predation pressure resulted in a quick shift in morphology from fairly smooth body scales to a more spiny morphology.
- ItemAn anatomical and systematic study of the family Mesosauridae (reptilia : proganosauria) with special reference to its associated fauna and palaeoecological environment in the Whitehill Sea(Stellenbosch : Stellenbosch University, 1900) Oelofsen, B. W.(Burger Wilhelm); Stellenbosch University. Faculty of Science. Department of Botany & Zoology.ENGLISH ABSTRACT: The anatomy and taxonomy of the southern African fossil reptile Mesosaurus from the Whitehill Shale has shown that the Formation is a chronostratigraphic unit. It is postulated that the almost identical Whitehill and Iraty Formations were deposited in shallow contemporaneous embayments of a central sea arm that occupied a position between the two continents. The water body was stratefied with anoxic, toxic, bottom brines that prevented the establishment of a benthonic fauna. A Study of the newly collected fossil material led to a new interpretation of the cranial morphology of Mesosaurus and it was found to be anapsid and closely allied to Limnoscelis. If M.tenuidens is to be regarded as typical for the Mesosauridae, all the members of the order Proganosauria will have to be transferred to the order Cotylosauria. M. tenuids was found to differ from M.brasiliensis and is the only species of Mesosaurus in the southern African Permo-Carboniferous Whitehill Formation. Along with it two more forms, noteosaurus africanus Broom and a yet unidentified species, identical with or closely allied to Stereosternum tumidum occur.
- ItemAspects of ecosystem function in a woodland savanna in South West Africa(Stellenbosch : Stellenbosch University, 1975-12) Rutherford, Michael Charles; Smith, J. G.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: A study was made of certain relations operating within a South West African woodland savanna ecosystem which was characterised by simplification within most of its basic components. . Main attention was given to the relatively unexplored field of spatial and structural organisation of the primary producer component in relation to its quantified intra-seasonal functional changes including its phenology. Simple mathematical model descriptions of seasonal mass change of the herbaceous parts of the primary producer component were derived. Various parts of the primary producer component were also evaluated in terms of some of the main climatic driving forces of the ecosystem, decomposition relations in the form of disappearance rates, soil-vegetation mineral relations and consumer (mainly insect) relations. Gross effects of manipulation of the ecosystem type by fire and management is included.
- ItemAssembly and disassembly of bird pollination communities at the Cape of Africa(Stellenbosch : Stellenbosch University, 2011-03) Geerts, Sjirk; Pauw, A.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: With the current global decline in pollinators, and the concurrent decline in plant species, pollination research is becoming increasingly important. However, studies outside Europe and North-America and on groups other than insects are needed to make generalisations possible. In this thesis I study how pollination structures plant and bird communities in a biodiversity hotspot, the Cape Floristic Region of South Africa. I show that bird-plant pollination mutualisms are an important ecological factor structuring ornithophilous Proteaceae and nectar-feeding bird communities. This close association between plant and bird communities suggests an important role for community wide pollination mutualisms. How these mutualisms disassemble in reaction to a range of anthropogenic impacts is determined. Firstly, I use experimental manipulation of honeybee density to test whether honeybee farming affects nectar-feeding birds. Hive addition increased honeybee abundance far above natural levels but nectar-feeding bird pollinators were not consistently affected. Secondly, I document the impact of a two lane tar road on the bird pollination community. The two-fold decline found in pollination along roadsides, should have important implications for the way we view and manage road verges for ecological processes. Thirdly, I investigated how fragmentation affects bird-pollination communities by assessing an endangered, bird-pollinated plant, Brunsvigia litoralis. The only flower visitor at the urban sites, the shorter billed Greater Double-collared Sunbird is unable to access the nectar due to a long perianth tube. The longer billed Malachite Sunbird was the sole pollinator of B. litoralis at the rural site, significantly increased seed set. The lack of ecological analogs in these urban fragments might place pollinator specialist plants, such as B. litoralis, at risk. Fourthly, fire is a frequent disturbance in communities of bird-pollinated plants. In a before/after fire observation study and a burnt/unburnt transplant study, birds visited flowers in the “before fire” and “unburnt” areas only. The results are surprising given the large number of bird-pollinated plants flowering in the early post-fire vegetation. Lastly, I find that alien invasive plant species are incorporated into the native pollination community in a spectacular way; sunbirds adapt to a hummingbird-like, hovering lifestyle to obtain nectar. Alien invasive plants greatly increase nectar-feeding bird abundance; in turn, birds enhance seed set in these alien plants. I conclude by asking whether the disassembling of bird pollination communities really matters. To answer this question I report on a decade of demographic data on the geophytic bird-pollinated Brunsvigia orientalis. In the demographic analysis, the elasticity component for reproduction was more important than expected for a long lived plant. Reduced population growth in the shade and a large investment in a winged inflorescence, suggest B. orientalis is a light demanding, well dispersed, gap colonising species. The link between pollination and seed has been made before, but I take this one step further and show that pollination intensity predicts population growth rate. By linking plant demography and pollination, I was able to predict the future of plant populations under variable pollination conditions. The disassembly of bird pollination communities only becomes important for population persistence once the mutualism has almost entirely broken down.
- ItemAssessing the evolutionary and physiological resilience of southern African marine species(Stellenbosch : Stellenbosch University, 2021-04) Mertens, Lisa; Measey, John; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Assessing the genomic basis of local adaptation and critical thermal limits is essential for anticipating species persistence and distribution under climate change. Environmental gradients are associated with genomic and physiological differences between populations. South Africa's two ocean regime creates a thermal gradient, which delimits distinct bioregions between its cold-temperate west coast, warm-temperate south coast and warmsubtropical east coast. Three co-distributed key rocky shore invertebrate species representing different phyla were selected for a multi-species approach. The objectives of this dissertation were to 1) identify selectively neutral genomic loci and neutral population structure, 2) determine putatively adaptive loci and adaptive population structure, 3) explore functional annotations and 4) measure critical thermal limits (CTmin, CTmax). Pooled RAD-Seq (ezRAD) was utilised to identify selectively neutral shared and populationspecific single nucleotide polymorphisms (SNPs) in six populations of shore crab Cyclograpsus punctatus (CP), granular limpet Scutellastra granularis (SG), and Cape sea urchin Parechinus angulosus (PA). Population-specific SNPs were detected in all populations. Nucleotide diversity indices (Tajima.s pi, Watterson.s theta)) appear heightened in PA's northern west coast population compared to the remaining sites. Estimated pairwise FST values range from 0.043-0.055 (CP), 0.044-0.066 (SG) to 0.039-0.089 (PA). Selectively neutral genomic population structure indicates instances of intraspecific subdivisions present in all populations. All species populations harbour unique SNPs, yet increased nucleotide diversity is only detected in PA. The empirical FST-method, BayeScan and BayeScEnv identified overall 1102 outliers under positive selection, of which 69 (CP), 11 (SG) and 27 (PA) could be functionally annotated. Candidate loci are involved in various cellular functions including membrane transport, vesicle signalling, protein folding/modification and cytoskeleton function. Identified loci related to energy cycling might point to selection on metabolic capacity to counter environmental stressors. Environmental differentiation of sea surface temperature (SST), salinity and air temperature could be associated with several putative outliers. There is no isolation-by-distance (IBD), but isolation-by-environment (IBE) suggests salinity variation to account for 48% of genomic variation in P. angulosus and SST and air temperature for 45% in S. granularis. Outlier-based population structure indicates possible intraspecific subdivision in some species. Critical thermal limits (CTmin, CTmax) were investigated with thermal tolerance trials and compared to local min/max environmental temperature for warming and cooling tolerance. Across populations, mean CTmin ranges from -1.5-0.6°C (CP), -0.4-3.2°C (SG) to 5-10.9°C (PA). Mean CTmax ranges from 43.8-46.1°C (CP), 34.4-35.7°C (SG) to 28.9-32.4°C (PA). West coast crabs have significantly higher CTmax than east coast crabs. CTmin is negatively and thermal breadth positively correlated with body mass (CP, PA). Significant regional differences in mass were detected (SG, PA). Warming and cooling tolerance appears sufficient, requiring further investigation within situ microhabitat data. East coast rocky shore populations likely face future warm-edge range contractions, whereas the south coast might experience distributional shifts depending on local thermal conditions. The west coast is an anchor for rocky shore species in South Africa and represents a possible climate change refugium. Strategic recognition in regional marine conservation management is warranted.
- ItemAssessing the impacts of invasive alien plants on urban ecosystem services(Stellenbosch : Stellenbosch University, 2019-04) Potgieter, Luke; Richardson, David M.; O'Farrell, Patrick J.; Gaertner, Mirijam; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: The sustainable provision of ecosystem services (ES) is a critical issue in the ongoing and evolving urbanization process that is placing enormous pressures on natural resources within and around urban landscapes. Urban ecosystems provide multiple ES for human well-being, but they can also generate functions, processes and attributes that result in perceived or actual negative impacts on human well-being, termed ecosystem disservices (EDS). Understanding the ES-EDS dichotomy within the context of the urban landscape is important for promoting the development of resilient and sustainable cities. Many alien plants introduced to urban areas around the world specifically to create, augment or restore key ES, are now firmly embedded in urban landscapes and have complex social and economic ties. Urban areas are particularly susceptible to invasion by alien plant species and some have subsequently spread beyond original plantings and have become invasive, causing negative effects on existing ES or creating novel ES or EDS. Complex interactions between humans and alien plants allow these impacts to manifest in many ways. Managing urban plant invasions is particularly challenging given the complex interactions between ecological, economic and social elements that exist in the urban milieu. Management decisions need to give explicit and transparent consideration to divergent stakeholder perceptions to mitigate potential conflicts of interest around alien and invasive plants and their management. Additionally, practical approaches for integrating ES and EDS in the decision-making process are needed to guide urban managers and planners. Given the limited resources available for managing invasive alien plants (IAPs), efficient prioritization of areas for IAP control is crucial for effective land management and ecological restoration. A literature review was conducted to determine the role of alien plants in providing urban ES and EDS globally (Chapter 2). The city of Cape Town was then used as a study system to elucidate the complex interactions between urban residents and managers, and alien and invasive plants in a unique ecological, political and social setting. Questionnaire-based surveys were conducted across the city to determine the perceptions of urban residents regarding IAPs and the capacity of IAPs to provide ES and EDS (Chapter 3). A multi-criterion decision-making analysis (using the Analytic Hierarchy Process approach) was then performed for the city to develop a prioritisation framework for managing areas invaded by alien plants at the city/landscape and at local scales (Chapter 4). The impact of IAPs on safety and security was assessed by exploring the link between urban vegetation and criminal activity through questionnaire-based surveys, analysing criminal court cases, and searching the grey literature (Chapter 5). Finally, an approach, merging several available tools and techniques (such as remote sensing), was developed to assess the role of urban vegetation (including alien and invasive plants) in providing ES and EDS at a local-scale urban context (Chapter 6). A small number of alien plant taxa were recorded as providing multiple ES in many urban ecosystems around the world. Some of these species also generate significant EDS (Chapter 2). IAPs and their management are perceived both negatively and positively by urban residents - these perceptions were shaped by socio-demographic characteristics of individuals (Chapter 3). Factors related to safety and security (such as fire risk to infrastructure) emerged as key features for setting spatially-explicit priorities for IAP management (Chapter 4). The association between vegetation and criminal activity may not always be determined by the biogeographical status of dominant plants (i.e. whether vegetation is dominated by native, alien, or invasive alien species), but rather on the structure they provide. A stronger link between crime and vegetation is likely to occur in areas where plant invasions have drastically altered vegetation structure, as is the case in the Cape Floristic Region (Chapter 5). At the local scale, nodes of high ES provision such as residential gardens and urban green spaces are characterized by the presence of large trees. However, many of these areas also experience numerous EDS due to invasions of alien trees and shrubs – particularly along rivers, in wetlands, and along the urban edge where tall alien trees have established and spread into natural vegetation. This suggests significant trade-offs regarding the management of species and the ES and EDS they provide (Chapter 6). Using and developing new approaches across disciplines and spatial scales, this thesis provides new insights on the role of alien and invasive plants in providing ES and EDS in urban areas. It highlights the need to integrate public perceptions into the planning and management of IAPs in urban areas to alleviate potential conflicts of interest; it also emphasises the importance of including ES assessments in the decision-making process. The findings will be useful for managers in all urban settings to guide the selection and prioritization of land parcels for IAP management at multiple spatial scales to maximise the provision of ES.
- ItemAssessing the interaction between history of usage and plant invasions : Bamboo as a case study(Stellenbosch : Stellenbosch University, 2018-12) Canavan, Susan; Wilson, John R.; Le Roux, Johannes J.; Richardson, David Mark; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Studies in invasion science often focus on the biological or environmental implications of invasive alien species. However, biological invasions are inherently due to the humanmediated dispersal of species; this means that there needs to be a greater focus on the socioeconomic context of why species have been introduced by humans, and how humans have created environments or situations to foster the success of alien taxa. This dissertation explores the interaction of human usage and plant invasions using bamboos as a case study, with the intention of answering the following questions: Why are some species selected by humans over others? How does this influence invasion success, impacts, and the cultural role of alien species in receiving environments? I found that, like many other alien taxa, the transfer of bamboos globally has been nonrandom. Large-statured Asiatic species and those with a greater number of cultivars are more likely to have been introduced outside of their native ranges. The species with high introduction rates are the bamboos that are found to be invasive; this supports the notion that propagule pressure is a universally important factor in facilitating invasions. However, in contrast to many other studies, biogeographic status (the native status) of bamboo was not a strong predictor of the type and magnitude of impacts. Impacts are rather explained by certain human activities (disturbance such as logging and clearing, increasing temperatures related to climate change, and the promotion of bamboo monocultures in mixed forests for commercial purposes). As such, the management of highly competitive native species should be considered in conjunction with the management of invasive alien species in forest ecosystems where bamboos are present. The competitive nature of bamboos that leads to impacts can be applied to other tall-statured grasses. Specifically, rapid growth rate and the capacity to accumulate biomass (a function of height) allow many tall grasses to form monospecific stands, accumulate dense and deep litter mats, reduce light availability and alter fire and nutrient-cycling regime. Naturalisation rates are greater in tall-statured grasses compared to other grasses, and the pathways of introduction are generalizable (e.g. for addressing environmental problems). Tall-statured grasses are a useful functional group for predicting high-risk taxa and for making generalised management plans. iv Looking at South Africa as a case-study, I found 26 alien species of bamboo recorded as introduced, with populations of several species widely naturalised around the country. I also found bamboos to be an inherently difficult group to identify to the species level, emphasizing the caution that must be taken with regard to future introductions. Amongst the public there is a complex tapestry of perceptions towards bamboos related to (1) a long history of introduction, and multiple introduction events, where bamboos have become culturally significant for some groups of people, and (2) the realisation that they can cause problems. In conclusion, many bamboos can be classified as synanthropic species in that they have benefited from human activity or the habitats that humans create around them. Studying bamboos has provided further insights into how social and economic imperatives are shaping a new biota at a global level.
- ItemAssessing vegetation dynamics in response to climate variability and change across sub-Saharan Africa(Stellenbosch : Stellenbosch University, 2018-03) Davis-Reddy, Claire; Midgley, Guy F.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Understanding and predicting how anthropogenic climate change is likely to impact terrestrial ecosystems across sub-Saharan Africa is a key question for both ecology and for regional and global climate policy development. This predictive understanding hinges on a far better ability to detect, interpret, and attribute changes in vegetation cover and productivity, which is the basis for ecosystem response and resilience to anthropogenic climate change. Monitoring and modelling of vegetation dynamics in the context of climate change requires long-term datasets of key ecosystem indicators such as vegetation productivity and phenology. The use of remotely sensed vegetation indices to detect vegetation change related to climate has become an important application of remotely sensed imagery. The third generation Normalized Difference Vegetation Index (NDVI3g) time series from the Global Inventory Modeling and Mapping Studies (GIMMS) has a 34-year long history (1982-2015) and provides unprecedented opportunity to examine vegetation dynamics in response to changes in temperature, rainfall, and increases in atmospheric carbon dioxide (CO2). This thesis makes use of the NDVI3g time-series to examine the influence of climate on vegetation productivity and phenology in order to (i) assess recent shifts in vegetation across sub-Saharan Africa (SSA) and (ii) facilitate improved simulations of vegetation by Dynamic Global Vegetation Models (DGVMs). The NDVI3g information was integrated with climate data and large-scale climate fluctuations and oscillations in sea surface temperature and atmospheric pressure to test hypotheses on the role of both climate variability and change on vegetation activity. Seasonal and long-term patterns of change were compared with projections of a dynamic global vegetation model, the "adaptive Dynamic Global Vegetation Model" (aDGVM) that was initially developed for application in sub-Saharan Africa. In the first component of the thesis results show that the vegetation of SSA is driven by rainfall and associated fluctuations and oscillations in sea surface temperature (SST) and atmospheric pressure, with the El Niño-Southern Oscillation (ENSO) being the most dominant driver of variability in both vegetation productivity and phenology over eastern and southern Africa. Vegetation tends to show a stronger positive response to rainfall in the 3 months preceding vegetation growth suggesting that time-lag effects are significant when assessing the influence of climate. In the second component, trend analyses provide evidence for a number of important spatial and temporal patterns of change in vegetation productivity and phenology over SSA, which are generally consistent with independently reported long-term trends. Significant added value was provided to previous studies through the use of productivity and phenology metrics, which facilitated an assessment of vegetation dynamics at both the seasonal and inter-annual scale. A clear latitudinal pattern of change was detected where significant increases in both productivity and the length of the growing season were observed over the northern hemisphere tropics (0-10°N) and sub-tropics of southern hemisphere (20-35°S) and significant decreases observed over the southern hemisphere tropics (0-20°S). The greening trends account for approximately 50% of the observed changes over SSA. Over West Africa and parts of central Africa the greening trends are linked to increases in rainfall and possibly atmospheric CO2 concentration as well as reforestation efforts in some countries. Over the south-western Cape, eastern coastline, and northeast extent of South Africa the greening trends are consistent with the observed patterns of bush encroachment and expansion of alien invasive species in these regions. The trends in many of these regions have been attributed at least partly to increased atmospheric CO2. Over southern Africa, simulations of vegetation productivity derived from the adaptive DGVM indicate that vegetation should have been increasing across southern Africa over the last 30 years. This finding combined with the lack of evidence of substantial changes in rainfall over the region suggests the role of land-use in limiting the increase in vegetation as observed in the aDGVM simulations. Lastly, the comparison between observed remotely sensed vegetation indices and historical simulated values of vegetation productivity from the aDGVM over SSA provided valuable insight into the utility of remotely sensed vegetation indices to assist in the validation, refinement and overall improvement of simulation of vegetation by DGVMs. While the model performs well over grassland and savanna regions of southern Africa it tends to underestimate grass productivity in East Africa and over the Sahel, overestimate tree cover in tropical humid forests of central and West Africa. The model also fails to capture the unique seasonal pattern of the Mediterranean-type vegetation of south-west cape of South Africa and the inter-annual pattern of variability in vegetation over SSA. These biases and limits of the model are likely to have implications for the performance of model in projecting future vegetation cover over these regions. This research contributes to the understanding of landscape-scale vegetation response patterns that will provide an important benchmark against which future vegetation change can be assessed. Importantly, it highlights that testing the performance of dynamic vegetation models in the context of regional climate models is a research imperative.
- ItemAn assessment of the potential biodiversity impacts from biofuel production in South Africa(Stellenbosch : Stellenbosch University, 2014-12) Blanchard, Ryan; Richardson, David M.; O'Farrell, Patrick J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Biofuels are being promoted as a global necessity to meet climate change targets through the replacement of fossil fuels. Many countries have identified biofuels as a potential mechanism to meet these challenges, with policy directives driving biofuel production. The South African government has proposed that biofuels form part of the country’s future renewable energy and has proposed a draft biofuel strategy. This study aims to investigate appropriate approaches to determine potential biodiversity impacts from biofuel production. Since biofuels are not currently grown to any large extent in South Africa, impact was modelled using future scenarios of converting available land within the Eastern Cape Province of South Africa. Suitable species were identified using the species distribution modelling programme MaxEnt. Some of the proposed biofuel crops were considered as invasive (i.e. they spread from sites where they are cultivated) or are very likely to be invasive in South Africa. This study also highlighted the considerable overlap between suitable growing areas and areas considered important for future biodiversity conservation. The biodiversity intactness index (BII), a broad based biodiversity indicator, was used to assess the biodiversity implications of transforming available land to biofuels. The BII indicates losses of biodiversity between 17.6% and 42.1% for the land use scenarios identified. An important finding was that excluding important biodiversity areas that occur outside of protected areas can reduce biodiversity losses by as much as 13% and maintain an overall intactness of ~70%. Currently the BII does not account for fragmentation or landscape configuration. This was addressed by developing a revised biodiversity intactness index (R-BII) which included the effect of patch-size and habitat fragmentation on biodiversity intactness. This study found that although the original BII reported on the biodiversity trends of large-scale shifts in land-use across multiple scales it could not detect changes in landscape configuration which was reflected by the R-BII. Land-use change can impact on ecosystem processes that underpin the provisioning of ecosystem services by changing the combinations of species and the plant functional traits within communities. The impacts of cultivating potential biofuel species (Acacia mearnsii, Sorghum halepense and Eucalyptus species) were investigated using a plant functional traits approach. These species were shown to affect the leaf nitrogen content, leaf phosphorous content and leaf dry matter content associated with important ecosystem functions within an ecosystem service hotspot in the Eastern Cape. A decline in functional diversity was reported for all transformed land-uses by as much as ~40%. These shifts may be used to identify potential changes to ecosystem services associated with natural vegetation. The methods used in this thesis highlight the overall relevance of this work and its importance to minimising biodiversity resulting from biofuel production. Some of the key findings address resolving spatial conflict, using biodiversity indicators, assessing impacts of potential invasive species and planning for ecosystem services. New drivers of change to land-use, such as biofuel production, are a major challenge to conservation biologists and planners and the insights derived in from this study can be successfully applied to guide biofuel production.
- ItemBacterial biological control of toxic cyanobacteria and the resulting eco-toxicity(Stellenbosch : Stellenbosch University, 2019-12) Ndlela, Luyanda Lindelwa; Oberholster, Paul Johannes; Van Wyk, Johannes Hendrik; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: The increased frequency and toxicity of freshwater cyanobacterial blooms is a cause for concern globally. Not only do these blooms result in reduced levels of oxygen in the water column and unpleasant odour, they also produce cyanotoxins as secondary metabolites. These toxins have resulted in the death of humans, aquatic organisms and wildlife. Bloom occurrences have been mapped globally and pose a challenge to water quality management due to toxin release, oxygen depletion, unpleasant water taste and odour. Biological control as a mitigation measure of these blooms has been explored using microorganisms and higher order grazers. A need exists for low cost, passive treatments through environmentally favourable control agents. In this dissertation, the biological control of filamentous Oscillatoria and unicellular Microcystis was investigated using predatory bacteria. Bacterial isolates from the phylum Proteobacteria were isolated and found to be effective in the reduction of microcystins released by both cyanobacteria. These were compared to a Lysinibacillus related isolate, which is from the phylum Firmicutes. The research conducted indicated a need for more molecular identification of wild strains of cyanobacteria, especially the less studied filamentous isolates to expand the database of sequences deposited for identification to be more conclusive through 16srRNA gene sequencing. Microcystis was positively identified through 16srRNA identification and showed similarity to a species collected from another province in the same country. The exposure of cyanobacteria to bacterial numbers at lower ratios (2:1 ratios of cyanobacteria to bacteria) indicated a stress response from cyanobacterial cell morphology and a reduction in toxicity. The research found that Pseudomonas rhodesiae (isolate 3w) and the Lysinibacillus fusiformis related isolate (isolate B) resulted in a greater reduction of toxins (microcystins) in both the filamentous and unicellular isolates. Measurement of toxicity was through the ELISA (enzyme linked immunosorbent assay) and confirmed through HPLC (high performance liquid chromatography), which indicated the presence of two microcystin variants, microcystin -LR and -RR. The bacterial isolates readily reduced the more toxic microcystin -LR as opposed to microcystin R-R, indicating that there may be microcystin degrading capacity in the isolates. Screening of eco-toxicity from the resultant bacterial treatment in the water indicated that reduced toxicity resulted in higher survival from the bio-indicator organisms overall. Thamnocephalus platyurus, a freshwater crustacean, was the most sensitive to changes in toxicity, proving to be a more suitable confirmation method of microcystin reducing treatment interventions. Isolate B was the best isolate from both a toxin reducing and eco-toxicity response perspective. This study also compiled all the findings from cyanobacterial bloom research in the African context as well as gaps in the area of bacterial biological control globally. In summary, the present study confirmed the potential to optimize passive bacterial control of cyanobacterial blooms on a larger scale, within a mixed bloom population.
- ItemBarriers to ecosystem restoration after clearing invasive Acacia species in the South African fynbos : soil legacy effects, secondary invaders and weedy native species(Stellenbosch : Stellenbosch University, 2018-12) Nsikani, Mlungele Mlungisi; Esler, Karen J.; Gaertner, Mirijam; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: A significant proportion of the world’s ecosystems are invaded by alien N2-fixing woody species such as Australian acacias. Invasive alien N2-fixing woody species often transform ecosystems through their negative impacts on soil chemistry, seed banks and microbial communities, and native plant diversity. Management interventions such as clearing are necessary to reduce these negative impacts. It is often assumed that clearing the invasive species will lead to a dissipation of their impacts and native plant diversity recovery. However, this is often not the case because the invasive species’ negative impacts can become persistent soil legacy effects and present barriers to restoration of viable native plant communities. Understanding barriers to restoration can lead to improved restoration outcomes. Using Acacia saligna invasions in the South African fynbos as case study, this thesis explored soil legacy effects, secondary invasion and weedy native species dominance after clearing invasive acacias. In chapter one, I reviewed global literature to understand how soil legacy effects of invasive alien N2-fixing woody species present barriers to restoration, and identify management actions that could potentially be used to address them. In chapter two, I investigated how long soil legacy effects of invasive A. saligna persist after clearing using soil sample analyses. In chapter three, I explored the effect of invasive A. saligna’s soil chemical and biotic legacies, and weedy native species on native species re-establishment using a greenhouse experiment. In chapter four, I identified species that are secondary invaders after clearing invasive A. saligna across several sites and investigated the effects of vegetation type and fire application on their establishment over three years after clearing using vegetation monitoring. In chapter five, I investigated interactions between secondary invaders and the extent to which soil nitrate levels, apparent after clearing invasive A. saligna, influence secondary invasion and weedy native species dominance using growth chamber and greenhouse experiments. I found that altered soil microbial communities, depleted native soil seed banks, elevated N status, secondary invasion and weedy native species dominance, and reinvasion can be barriers to restoration. Furthermore, management actions such as carbon addition, soil microbial treatments, herbicide or graminicide application and native species reintroduction can be used to address these barriers to restoration. Acacia saligna’s soil chemical legacies persisted up to ten years after clearing. However, they did not have direct negative consequences on the re-establishment of native proteoid shrubs but soil biotic legacies and presence of weedy native species reduced their growth. Secondary invasion was not habitat specific, was promoted by fire application and persisted up to three years after clearing at levels similar to or higher than the first year. Lastly, growth of secondary invaders and weedy native species increased with an increase in soil nitrate levels. I conclude that practicing restoration ecologists should manage soil legacy effects, secondary invaders and weedy native species after clearing invasive A. saligna to improve restoration outcomes.
- ItemBiochemical and physiological changes associated with estrogenic activity in Xenopus laevis : a model for the detection of endocrine disruption(Stellenbosch : Stellenbosch University, 2003-03) Hurter, Etienne; Van Wyk, J. H.; Pool, E. J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Concern has increased that widespread adverse effects are occurring in humans and wildlife populations as a result of exposure to environmental chemicals (mostly man-made) that disrupt the normal functioning of the endocrine system. Many pharmaceutical, agricultural and industrial chemicals, acting as endocrine modulating compounds (EDCs), have been detected in an accumulated form in food, in drinking water and in the environment. Although the levels of these chemicals can be measured analytically, it is important to evaluate biological activity. For this, animal models are used and relevant bioassays developed. These assays are based on biological markers, which are specific xenobiotically-induced physiological responses and are usually deviations in cellular or biochemical components, processes or structures. Vitellogenin is a large protein complex, produced in the liver under estrogen control and circulates in the plasma, destined for incorporation into the developing oocyte in female oviparous vertebrates. Since vitellogenin production is low or nonexistent in males, its presence may therefore be interpreted as evidence of exposure to estrogenic environmental contaminants. In this study the African Clawed Frog, Xenopus laevis was used as model to study the effects of estrogens on biochemical and physiological parameters associated with vitellogenesis. As a starting point the seasonal female reproductive cycle in a natural Xenopus laevis population in terms of ovarian state, plasma vitellogenin and plasma estrogen levels was studied. It was shown that plasma vitellogenin and estrogen levels were seasonal and correlated to a seasonal ovarian cycle, which peaked during spring. However, although seasonality existed, there were reproductively active individuals at any time during the year. Increases in plasma estrogen levels predated increases in plasma vitellogenin levels and ovarian maturation. Lipoprotein profiles, as well as plasma cholesterol, triglyceride and phospholipid concentrations were determined and it was shown that estrogen affected these in such a way that these parameters could be used as additional markers in estrogen contamination studies. In order to develop an in vitro bioassay to screen for estrogenic activity, the use of hepatic tissue cultures was investigated. Optimal culture conditions were established and increased sensitivity in the estrogenic response was obtained by using liver slices from male frogs that were pre-treated with estrogen. Validation studies proved that this bioassay could be employed for routine screening of water and chemical samples. In order to refine the Xenopus laevis vitellogenin ELISA and liver slice bioassay, existing polyclonal anti-vitellogenin antibodies were replaced by culturing monoclonal antibodies. Selected antibodies were characterised and ELISAs developed and validated. This study showed that the newly developed Xenopus laevis vitellogenin ELISA and liver slice bioassay have the potential to be employed in environmental monitoring programmes.
- ItemBiodiversity and ecology of ophiostomatoid fungi associated with trees in the Cape floristic region of South Africa(Stellenbosch : Stellenbosch University, 2014-04) Musvuugwa, Tendai; Dreyer, L. L.; Roets, Francois; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Very little is known about the diversity of fungi associated with Afromontane forests of the Cape Floristic Region (CFR) of South Africa. The ophiostomatoid fungi include many species, some known as pathogens in the CFR, while others are well-known saprophytes important in wood degradation. This study focused on the biodiversity and ecology of tree-associated ophiostomatoid fungi (Ophiostomatales) in the CFR. In addition to this, mites and subcortical beetles associated with the CFR trees were collected, regardless of whether they were associated with ophiostomatoid fungi or not. A relatively high diversity of ophiostomatoid fungi were collected from native trees, ten of which were newly described here. Three further fungal species, two of which are probably new to science, were also collected from exotic Pinus species growing in these forests. Four Ophiostomatales species (including three newly described species) were associated with subcortical beetles on Rapanea melanophloeos and Olea capensis ssp. macrocarpa. These were Sporothrix pallida, Sporothrix aemuluphilus, Raffaelea scabbardiae and Raffaelea rapaneae, associated with the beetles Lanurgus sp. 1, Ctonoxylon sp. 1, Xyleborinus aemuluphilus and a Platypodinae species. This represents a first study to explore the associations between subcortical beetles and ophiostomatoid fungi on native trees in the CFR. In addition to fungi associated with subcortical beetles, several members of the Ophiostomatales associated with wounds on Rapanea melanophloes trees were also collected. These included Ophiostoma stenoceras, Sporothrix reniformis, S. rapaneae, S. lunateae and S. noisomeae. All but O. stenoceras were new to science, and were formally described here. All of these wound-associated species from R. melanophloeos belong to the Sporothrix schenckii – O. stenoceras complex, except for S. noisomeae that was provisionally placed in the S. lignivora complex. Besides fungal taxa collected from wounds on Rapanea melanophloeos, other fungi were also collected from wounds on other host trees species. Three more previously undescribed ophiostomatoid fungal species were collected from this niche. They included Sporothix capensis collected from O. capensis ssp. macrocarpa, Graphilbum roseus collected from many different, unrelated host trees and Graphium ilexiense (Microascales), isolated from wounds on Ilex mitis. The latter represented the first isolation of an ophiostomatoid fungus from this host tree species. Two possibly new fungal species (Sporothrix sp. 1, Ceratocystiopsis sp. 1) and Ophiostoma ips, associated with three bark beetles (Orthotomicus erosus, Hylurgus ligniperda and Hylastes angustatus), were collected from Pinus. Several fungal species were collected from both native trees and non-native trees. These included Sporothrix fusiforme from Brabejum stellatifolium and Acacia mearnsii, O. quercus and O. pluriannulatum-like fungus from several native trees and from A. mearnsii. This suggests a possibility for host shifting of some of these fungi between native and non-native hosts or even between different native hosts. Eight non-ophiostomatoid fungi associated subcortical beetles taxa were found also to infest native trees in the Afromontane forests and in total more than 4500 beetle individuals were collected. Some species of ophiostomatoid fungi collected in this study were found to be associated with other arthropods such as mites. Four phoretic mites species associated with ophiostomatoid fungi (Dendrolaelaps quadrisetus, Histiogaster sp. 3, Elattoma sp. 1 & 2) were collected. In addition, sixteen species of tree wound-associated mites were collected from 12 native trees. Of these, nine were associated with several ophiostomatoid fungi (Graphilbum roseus, O. pluriannulatum-like, O. quercus) that were isolated from several different host trees. This suggests that they may aid in the transport of these fungi from one host species to another. The possible consequences of transfers of Ophiostomatales species between hosts were tested using pathogenicity tests, which highlighted that some fungi are pathogenic on several different trees. Transfers seemed most likely in fungal species isolated from wounds, especially those associated with mites, because the mites may aid in the vectoring of these. When phoretic mites were tested for their specificity to their vector beetles, they proved to be highly specific. Although some of the fungi associated with these mites and their sub-cortical beetles were also pathogenic, it is less likely for these fungi to be transferred to other host tree species due to the high specificity of their arthropod associates. This study represents one of a few studies that focused on ophiostomatoid fungi, subcortical beetles and mites associated with trees in the Afromontane forests of South Africa. Although we collected a high diversity of Ophiostomatales members, many more still await discovery. It is recommended that future studies focus on the complex inter-organismal interactions in many of the systems uncovered in this study.
- ItemThe biogeography, systematics and conservation of Phreatoicidean isopods in South Africa(Stellenbosch : University of Stellenbosch, 2004-12) Gouws, Gavin; Cook, B. A.; Matthee, C. A.; University of Stellenbosch. Faculty of Science. Dept. of Botany and ZoologyENGLISH ABSTRACT: Historically, isopods of the suborder Phreatoicidea were thought to be represented in southern Africa by four species belonging to the endemic genus Mesamphisopus. This taxonomy was based on poor collections and the extent of variation among and within populations were poorly understood. In the present study, intensive sampling was undertaken to determine the diversity, distribution and biogeography of phreatoicidean isopods within South Africa. Analyses of allozyme data and mitochondrial DNA sequences (from the 12S rRNA and protein-coding COI genes) were used to examine differentiation among populations, extricate species boundaries (in combination with morphometric and morphological data) and to elucidate the evolutionary relationships among taxa. Additionally, conservation units were identified among the sampled populations and conservation threats highlighted. First, genetic and morphometric differentiation was examined among populations identified morphologically as M. capensis. Collection localities spanned two mountainous regions in the Western Cape and these were separated by a coastal plain remnant. Five morphometrically and genetically distinct species were identified. These taxa are also geographically partitioned in two regions, which were regarded as Evolutionarily Significant Units. Differentiation among populations of the two regions, and similar patterns in other taxa, was attributed to Cenozoic sea-level fluctuations. Second, populations, variably assigned to M. abbreviatus or M. depressus, were examined to determine whether they were conspecific. A large geographic area was sampled to account for intraspecific differentiation. Limited morphometric discrepancies were observed, with individual populations being either similar to the M. abbreviatus or the M. depressus syntypes. Genetic support for the recognition of a cryptic species complex among the sampled populations was equivocal. Substantial genetic differentiation and a lack of gene flow were observed among all populations. Clear patterns of isolation by distance were not detected, and genetic structure appeared to be unrelated to geography or drainage systems. The mosaic pattern of relatedness among populations was best explained by stochastic demographic processes, such as extinction-recolonization events or population bottlenecks.Thirdly, detailed taxonomic descriptions and illustrations of six new species, identified genetically and morphometrically among the populations included in the above analyses, were provided. These species were largely distinguished from each other, and the four original species, using a combination of setation, mouthpart, pleopod and uropod features. Lastly, phylogenetic relationships among all ten recognized Mesamphisopus species, and an additional unresolved group of populations, were examined. MtDNA data partitions and a recoded allele frequency matrix were analysed independently and in combination. Topologies indicated unrecognized species-diversity within an unresolved group of populations. Evolutionary relationships, the identification of six biogeographic centres, and the dating of divergences using a relaxed Bayesian clock suggested that differentiation and speciation within Mesamphisopus was largely allopatric or vicariant and driven by Mesozoic sea-level and climate change. Chance long distance dispersal events would, in turn, explain spurious phylogenetic relationships and distributions. This study contributes significantly to the understanding of the diversity and the conservation of the little-studied southern African freshwater invertebrates. Moreover, this study is the first to investigate genetic and morphometric differentiation, and phylogenetic relationships, below the generic level within the Phreatoicidea; thus establishing a methodological and theoretical framework for species delineation and the accurate determination of biodiversity within individual phreatoicidean genera.
- ItemA biosytematic [i.e. biosystematic] study of the seven minor genera of the Hyacinthaceae(Stellenbosch : Stellenbosch University, 2002-03) Van der Merwe, Alison M. (Alison Mary); Marais, E. M.; Bellstedt, D. U.; Stellenbosch University. Faculty of Sciences. Dept. of Botany and Zoology.ENGLISH ABSTRACT: A biosytematic revision of the seven minor genera of the Hyacinthaceae, including twenty-two species, was undertaken. Muller-Doblies & Muller-Doblies (1997) considered these seven genera (Amphisiphon Barker, Androsiphon Schltr., Daubenya Lindl., Massonia Thunb. ex Houtt., Neobakeria SChItL, Polyxena Kunth and Whiteheadia Harv.) together with the genus Eucomis L'Herit. to form the subtribe Massoniinae of the tribe Massonieae. Previous revisions of the group were based only on morphological characters (Jessop 1976; Muller-Doblies & Muller-Doblies 1997). The subtribe Massoniinae is characterised by the large variety of floral forms exhibited by the different species in the group. In the past this has led to the establishment of many monotypic genera for species thought to have unique floral structures. Morphological, leaf anatomical, palynological, geographical and molecular data were studied in order to delimit the taxa and determine the phylogenetic relationships within the group. This showed that most of the unique floral structures are probably only adaptations to pollination strategies and all except one of the monotypic genera are now placed in the genus Daubenya. In the genus Massonia there is a great deal of variation in leaf morphology and this resulted in the establishment of many invalid species, now mostly reduced to synonymy. A new species was described, several name changes made and several species were reduced to synonymy.
- ItemThe botanical origin, physicochemical properties and antibacterial activity of selected West Coast honeys(Stellenbosch : Stellenbosch University, 2020-04) Esterhuizen, Nanike; Wossler, Theresa Clair; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Honey is a complex natural product made by honey bees. In recent years consumer preference in the market has shifted towards honeys with distinct characteristics such as unique floral origin (i.e. monoflorals) and potential health benefits. The specific physical and chemical properties that make every honey unique are primarily influenced by the distinct nectar composition of the plants that were visited by the bees. The Cape Floristic Region (CFR) is characterised by high plant species diversity and exceptionally high species endemism. With the close association between botanical origin and honey properties in mind, this study aimed to identify novel honeys produced from fynbos plants along the West Coast of South Africa that could be marketed as an exclusive, niche product to higher tier local and international consumers. The botanical composition of honeys was investigated by generating the first pollen library for the West Coast and using melissopalynology to identify honey floral components and monofloral varieties. Honey bees preferred and utilised similar floral sources across space and time, with differences in botanical origin between years ascribed to differences in floral availability, due to changes in rainfall. Sandbos (Aspalathus spinescens form A) was the most abundant monofloral honey produced. The physicochemical composition of honey also varied over space and time, as well as with honey age. However, the majority of honeys produced along the West Coast were of good quality and complied with local as well as international regulations – fresh and after 12-months in storage. Hydrogen peroxide was responsible for the antibacterial activity of the West Coast honeys, which was confirmed using a phenol equivalence agar well diffusion assay. Almost 70% of honeys were potentially therapeutically useful, although the variation in antibacterial activity of specific monofloral honey varieties was quite high. Unfortunately, the sample sizes of different honey varieties were limited due to the severe drought conditions experienced between 2015 and 2017, making it difficult to give definitive recommendations on honey properties to be used for value-added marketing. Climate change scenarios predict that the West Coast will become warmer and drier in the future and environmental fluctuations such as changes in rainfall and temperature that affect nectar availability will also greatly influence honey production. The beekeeping industry should focus on optimising the honey yield from drought-tolerant plant species such as sandbos, through the identification and preservation of sites where these plants occur, or through cultivation. This approach of botanical, physicochemical and antibacterial characterisation of honeys produced from indigenous flora could be extended over larger areas of the CFR with the help of beekeepers and citizen science initiatives. Research characterising the unique honeys produced from indigenous vegetation must continue, increasing honey’s value on local as well as international honey markets and in turn boosting the beekeeping industry of South Africa.
- ItemCarcinus maenas in South Africa : status, impacts and management(Stellenbosch : Stellenbosch University, 2018-03) Mabin, Clova Airth; Robinson-Smythe, Tammy; Wilson, John; Le Roux, Jaco; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: The European shore crab, Carcinus maenas, has established invasive populations on four continents, with its congener, the Mediterranean shore crab, C. aestuarii, invading another. Carcinus maenas, in particular, has caused ecological and economic impacts in several regions which led to targeted management. This crab was first detected in Table Bay harbour, Cape Town, South Africa in 1983, with little research undertaken in this region until the current study. Research conducted two decades ago suggested the presence of interspecific Carcinus hybrids in South Africa and accordingly, unless specified otherwise, the crab will be referred to as Carcinus only from hereon. This thesis firstly conducted a detailed assessment of the current population status in South Africa, followed by the undertaking of an intensive management programme. This intervention offered a rare opportunity to experimentally assess the trophic impacts of this crab in the field and apply genetic techniques to reconstruct its invasion history in the South African context. To establish the current status of the species in South Africa, Chapter 2 assessed the distribution and abundance of Carcinus. This involved the first account of seasonal patterns in abundance and demographics for the crab. Six intertidal sites were visually surveyed during shore walks on a monthly basis for a year, with surveys extended quarterly at one site for another year. An additional four sites outside the known range of the species were surveyed quarterly, resulting in a total of 92 intertidal surveys through time over the ten sites. Subtidal surveys were conducted at three sites along the open coast. Baited traps were used to confirm the presence of the crab in two harbours (Hout Bay and Table Bay). Following this, Table Bay harbour was surveyed monthly for one year while targeting three life stages (postlarvae, juveniles and adults). The crab was only found at one intertidal site and no crabs were found during open coast subtidal surveys. Gravid females were recorded in all months except for February - May. Unexpectedly, no postlarvae were detected, suggesting that settlement collectors are ineffective in the South African context and should not be used for future monitoring. These results highlight a decline in open coast populations and substantial harbour populations. This suggests that management of harbour populations of Carcinus only, would be sufficient to remove the species from South Africa. Due to the ecological impacts of this genus elsewhere, the Carcinus population in Hout Bay was targeted for management, with the aim of assessing the feasibility of removing the crab from the two invaded South African harbours. This first attempt at managing a marine invasive species in Africa is documented in Chapter 3. Prior to management, four potential control methods (baited traps, crab condos, diver collections and sediment dredging) were trialled to establish their efficacy and suitability for use on a large scale in the South African context. Baited traps were selected as the most appropriate and cost-effective method. Management was conducted from June 2014 to June 2015. During this period, approximately 21,800 traps were deployed and a total of 18,450 person hours were spent in the field. This resulted in the removal of 36,244 crabs from the harbour, approximately six times the most recent population estimate. Despite this, extirpation was not achieved. The recovery of the population was then monitored for six months. A Bayesian depletion model was developed to simulate the response of the population under management scenarios of varying effort. This approach suggested that even if control effort had been doubled (i.e. to 8,000 hours per month) there would only have been an 86% probability of extirpation. If this effort were to be applied in both Hout Bay and Table Bay harbours, it would cost an estimated ZAR 60 million. This cost would need to be considered against the threat posed by the invasion and the likelihood of reintroduction. Despite the impacts reported from invasive populations elsewhere in the world, the trophic impacts of Carcinus remain unknown in South Africa, therefore, this was addressed in Chapter 4. The management of Carcinus provided an opportunity to experimentally assess the impact of the crab by comparing community structure in Hout Bay and Table Bay using benthic cores and vertical fouling scrapes collected prior to (2014), during (2015) and after (2016) management. A total of 78 tethering experiments were conducted to identify potential predators of the crab in Hout Bay harbour and a large public aquarium setting (as a proxy for natural habitats in the absence of Carcinus in such systems), resulting in 128 hours of underwater camera footage. Benthic communities were similar between harbours prior to management, but contrary to expectations, the community remained similar through time in the managed harbour, while changing in the control harbour. In contrast, fouling communities differed between harbours at the onset and changed at both locations through time. Thus, the crab appears to have no detectable impact on benthic communities while its impact on fouling communities remains uncertain. While, no tethered crabs were attacked in Hout Bay, under aquarium conditions all crabs were preyed upon by native fish, suggesting that predator-driven biotic resistance might constrain the spread of Carcinus in natural habitats. Thus, despite notable impacts elsewhere, impacts of Carcinus were not detected in this study, highlighting that alien species impacts can vary among regions and context-dependent risk analyses are needed to inform evidence-based management. In order to elucidate the historical and contemporary gene flow between selected international populations and South Africa, microsatellite DNA markers were used to assess the genetic diversity and structure of Carcinus populations across the native and invasive ranges in Chapter 5. To determine if the management action in Hout Bay had a detectable genetic impact on the demographics of the crab, Hout Bay and Table Bay were sampled prior to, during and after management. DNA was extracted from 898 samples, collected from eight international and the two South African populations (across three years) and amplified across eight microsatellite loci. Clustering analyses and approximate Bayesian computations (ABC) were performed to reconstruct the invasion history of the South African populations. South Africa had significantly higher genetic diversity than the other alien Carcinus populations, suggesting a lack of a founder effect. In the most supported ABC invasion scenario, the South African populations established following admixture between native and invasive C. maenas populations approximately 150 years ago. Evidence of interspecific hybridization between C. maenas and C. aestuarii was detected, with the presence of several hybrid genotypes (5% of all individuals sampled). The harbours had a similar genetic diversity and no structure, suggesting migration between the populations or the same founding populations. There was no effect of management on genetic diversity, its structure, or effective population size of Hout Bay. Migration from Table Bay is, however, unlikely to be the dominant explanation of such observations. Rather, the most likely explanations are that a cohort of crabs produced prior to management was detected during sampling and reflected the gene frequencies of the previous generation or management interventions did not reduce crab populations below levels required to observe changes in genetic diversity. Given the probability of migration between the South African populations and the potential for re-introduction from international populations, the probability of successful management is considered low. This thesis utilised approaches from several different disciplines, including ecology, population genetics and environmental management, to better understand Carcinus invasions in South Africa and to undertake the first management of a marine alien species on the continent. Despite the recent listing in national legislation that mandates the management of this crab, the results of this project suggest that (1) there is a lack of evidence of trophic impacts, (2) migration occurs between the harbours, (3) there is evidence for a complex introduction history to South Africa and appreciable levels hybridization between different crab species, and (4) there are administrative challenges to be addressed prior to management, including insufficient financing. It is thus recommended that a national eradication programme not currently be implemented. Importantly, while this project has provided responses to locally relevant questions, the scientific and administrative insights gained have broad applicability within the field of invasive alien species management. The scientific insights include the value of trialling methods used elsewhere, as well as the use of depletion models to estimate the effort required to increase the probability of management success. Often managers of invasive species rely on dated population estimates and impacts assessed elsewhere to inform management decisions. However, based on the outcomes of this study, management undertaken prior to the assessment of such factors can be unsuccessful and result in a sub-optimal use of limited resources. Overall, this work highlights the importance of context-specific field studies and molecular approaches to establish the need for and determine the feasibility of management.
- ItemCauses and consequences of body armour in the group-living lizard, Ouroborus cataphractus (Cordylidae)(Stellenbosch : Stellenbosch University, 2015-03) Broeckhoven, Chris; Mouton, P. le Fras N.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.ENGLISH ABSTRACT: Cordylidae is a family of predominantly rock-dwelling sit-and-wait foraging lizards endemic to southern Africa. The significant variation in spine length and extent of osteoderms among taxa makes the family an excellent model system for studying the evolution of body armour. Specifically, the Armadillo lizard (Ouroborus cataphractus) offers an ideal opportunity to investigate the causes and consequences of body armour. Previous studies have hypothesised that high terrestrial predation pressure, resulting from excursions to termite foraging ports away from the safety of the shelter, has led to the elaboration of body armour and a unique tail-biting behaviour. The reduction in running speed associated with heavy body armour, in turn, appears to have led to the evolution of group-living behaviour to lower the increased aerial predation risk. In this thesis, a comparative and integrative approach is used to provide more insight into the conditions under which body armour could have evolved in O. cataphractus and the consequences of body armour for life-history traits. Chapter 2 attempts to investigate how competitive and predatory pressures affect the activity patterns of O. cataphractus. Analysis of activity patterns, obtained via remote camera trapping techniques, show low levels of activity during summer in O. cataphractus, resulting from increased competition for food and high predation pressure. In contrast, a shift in activity to spring, when food availability is relatively high, appears to override the negative effects of body armour and group-living behaviour in O. cataphractus. Chapter 3 tests the hypothesis that body armour serves as protection against attacks from predators during foraging excursions away from the safety of the shelter. The relatively high skin toughness, due to the presence of thick osteoderms in the dermis, protects O. cataphractus against most terrestrial predators, while the skin toughness values for other cordylid lizards are well-below the bite forces of potential mammalian predators. The remaining chapters focus strongly on the feeding behaviour of O. cataphractus and how it is linked to body armour. Chapter 4 investigates the consequences of a reduction in running speed for the diet and tests for the presence of compensatory alternative performance capacities (i.e. increased bite force or jaw closing velocity). A comparative phylogenetic analysis shows that the possession of body armour affects the proportion of evasive prey items that can be included into the diet, thereby restricting the prey spectrum of heavily armoured taxa, such as O. cataphractus, to slow-moving prey (e.g. Coleoptera). Although the results indicate a relatively high bite force in O. cataphractus, the primary selection pressure seems to be tail-biting behaviour, rather than the consumption of hard-bodied Coleoptera (Chapter 5). Bite force, however, trades-off with jaw closing velocity in lizards. A novel lingual prehension mode, exclusive to O. cataphractus (Chapter 6) appears to have evolved in response to the force-velocity trade-off. Given the slow nature of lingual prehension, increased prey capture efficiency appears to be the main selection pressure (Chapter 7), rather than miminsing exposure to predators by reducing the time spent in the open.