An assessment of different methods for measuring mammal diversity in two Southern African arid ecosystems.
- Authors: Burt, Chloe
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Biodiversity -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52338 , vital:43591
- Description: A current critical environmental problem is the loss of biodiversity. To allow for adaptive management and effective conservation interventions, reliable data needs to be readily available and effectively collected. To gather reliable data, the most appropriate method must be used. The aim of this thesis was to compare the effectiveness and efficiency of different mammal diversity sampling techniques, including discussing specificities and complementarity of each. I also assessed the limitation of methods in terms of the influence of species traits on detectability. I used standard mammal field methods such as block transects, camera traps, track plates, spotlight surveys, mist nets, acoustic surveys, and live traps for a wide range of mammal taxa, and also included the use of local knowledge in the comparison. I assessed the cost-efficiency of each method by determining the cost per species. The efficiency of each method was assessed by observing when the species accumulation curve reached an asymptote. The effectiveness was determined by the species richness and the taxonomic groups the method detected. My results indicated that block transects were the most efficient and effective method to assess species richness. However, a combination of methods allowed for a more comprehensive survey and my results indicate that block transects and live traps were the best combination. It is important to note, not only the effectiveness and efficiency of methods be assessed, but also their limitations. I therefore also assessed the influence of species traits on the detectability of five methods. The species traits that I tested were body size, diet, activity, and if they lived in groups. On both study areas, body size was the main trait that influenced detectability with most field methods. Diet and activity had varying influence on detectability depending on the method. Group living did not significantly influence detectability. Based on my results, I provide guidelines for choosing the most appropriate survey method for targeted studies on mammals in arid ecosystems as well as guidelines for choosing the most appropriate methods for a terrestrial mammal inventory. Survey methods selection and guidelines provided here can allow for effective monitoring and therefore effective and adaptive management and having reliable and repeatable outcomes from surveys. , Thesis (MSc) -- Faculty of Science, School of Natural Resource Management, 2021
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- Date Issued: 2021-04
Variation in forage quality in subtropical thicket
- Authors: Nyembe, Khulisile Jacqueline
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Biodiversity -- South Africa
- Language: English
- Type: Master's theses , text
- Identifier: http://hdl.handle.net/10948/52088 , vital:43440
- Description: Several studies have assumed that the plant communities of the Subtropical Thicket biome are nutritious throughout the year. This is based on the observation that they are evergreen, palatable and grow on fertile soils; however this assumption has not been tested. Therefore the aim of this study was to assess forage quality variation in the Subtropical Thicket. This was done at three levels; first we measured the plant quality of dominant plant species in the diets of Thicket herbivores. Secondly, we measured the realised diet quality of Thicket herbivores through the analysis of faecal samples. Lastly we assessed the body condition of Thicket herbivores. The study was conducted at the Colchester (plant quality and diet quality) and Addo Main Camp (body condition assessment) sections of Addo Elephant National Park. To measure the food quality of Thicket plants we analysed 10 plants that are dominant in the diets of Thicket herbivores. To measure diet quality we collected faecal samples from ten herbivores with body mass ranging from 25 kg to 6000 kg. Plant quality results showed that only 30% of the sampled plants met the high energy goat diet protein requirements and that all the sampled plants did not meet the high energy goat diet fibre requirements. This indicates that Thicket plants are not as highly nutritious as they were thought to be. The principle components analysis together with overlapping confidence intervals showed that there was no significant difference between the summer plant samples and the winter plant samples. The faecal quality results showed that there was significant seasonal difference and that faecal diet quality was a function of body size. The body condition results showed that all the sampled herbivores lost condition in the cold dry months. The evidence from faecal diet quality and body condition assessment is sufficient for us to reject the assumption that Thicket forage is consistently nutritious throughout the year. , Thesis (MSc) -- Faculty of Science, School of Environmental Sciences, 2021
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- Date Issued: 2021-04
Terrestrial alien ferns (Polypodiophyta): a global assessment of traits associated with invasiveness and their distribution and status in South Africa
- Authors: Jones, Emily Joy
- Date: 2019
- Subjects: Biodiversity -- South Africa , Alien plants -- South Africa , Botany -- South Africa , Plant ecology -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10948/39995 , vital:35643
- Description: Globally, invasive alien plants (IAPs) are one of the greatest threats to biodiversity, ecosystems and ecosystem services. The threats posed by IAPs have prompted inventory compilations and screening exercises which aim to understand why some taxa become invasive and others do not. Ferns are a diverse taxon that appear to have a high invasive potential, however ferns have been vastly understudied in the field of invasion biology. This study aimed to establish a basic understanding of terrestrial alien true ferns (Polypodiophyta, hereafter ‘alien ferns’) at both global and national (South African) scales. We developed a global inventory of alien ferns comprising 157 species using published literature and online inventories. Our global inventory indicated that there are significantly more alien fern species than previously estimated (60 species). We used generalised linear models with binomial response variables to determine which traits influenced the probability that an alien fern would become naturalised or invasive. Our models explained 30-40 % of the variance associated with invasiveness and showed that ground-dwelling life forms, reproductive plasticity, tolerance to disturbances and varied light conditions, and a broad introduced range (interpreted as high environmental tolerance and popularity in horticulture) were important determinants of invasiveness in alien ferns. Ultimately, we found that the probability of alien ferns becoming naturalised or invasive is more than 50 %. We further established which geographic regions and fern families had the highest incidences of alien ferns and identified species that were invasive over extensive introduced ranges. For the national scale study, we aimed to assess the distribution, abundance, invasion status, and habitat associations of terrestrial alien fern species present outside of cultivation in South Africa. Field surveys were conducted across the country in habitats suitable for ferns, guided by pre-existing records of alien fern occurrences. Thirteen species occurred outside of cultivation, all of which were classified as invasive, and among these, approximately 5000 plants were recorded across 300 localities. Species richness and abundance peaked along the Indian Ocean Coastal Belt and the Afro-montane phytogeographical regions. A multiple correspondence analysis revealed that alien ferns in South Africa were most strongly associated with indigenous forest habitats and the majority of species selected for shaded conditions, close to water. Only two species were closely associated with open habitats under high light conditions, with plantations also infrequently selected by alien ferns. Habitat generalists were closely associated with disturbance, but avoided open habitats, far from water. Compared to the most prominent angiosperm invaders in South Africa, alien ferns have a lower potential for widespread ii invasion and range expansion, probably due to their habitat specificity. We identified four species as potential targets for eradication and which should be listed as Category 1a under the Alien and Invasive Species regulations of the National Environmental Management: Biodiversity Act of South Africa. The remaining species should be listed as Category 1b since they occupied an extensive geographic range. The most prominent ferns included Adiantum raddianum, Sphaeropteris cooperi, Deparia japonica and Cyrtomium falcatum. Our study informed appropriate regulation for several species of alien ferns that were deemed to be data deficient and in need of assessment by a recent report on the status of biological invasions in South Africa. A risk analysis completed for S. cooperi confirmed that the species has a high invasion risk in South Africa and should be listed as Category 1b. Given that the outcomes of the risk analysis completed for S. cooperi matched the findings from our field surveys, this study supported risk analysis as a reliable (literature-based) method to evaluate IAPs. The findings of our assessments at the global and national scale corresponded in that various traits that promoted invasiveness in alien ferns globally were also facilitating invasion in South Africa. Additionally, of the eleven species found to be invasive over extensive introduced ranges at global scale, only two (Lygodium microphyllum and Angiopteris evecta) were not yet recorded in South Africa. Since horticulture was established as the primary pathway for the introduction of alien ferns, the management of alien ferns (globally and in South Africa) should focus on regulating trade. The sources of cultivation and the pathways of dissemination across the globe also need consideration. Basic environmental and biological associations of alien ferns were evident in this study, but to fully understand their invasive potential further research should focus on niche-based modelling to predict potential invasion ranges, the effects of biological traits on invasiveness, and the potential ecological impacts of these species.
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- Date Issued: 2019
Comparative phylogeography of five swallowtail butterfly species (Lepidoptera: Papilionidae) in South Africa : ecological and taxonomic implications.
- Authors: Neef, Götz-Georg
- Date: 2014
- Subjects: Swallowtail butterflies , Papilionidae -- South Africa , Phylogeography -- South Africa , Swallowtail butterflies -- Effect of habitat modification on , Biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4266 , http://hdl.handle.net/10962/d1013574
- Description: With current biota under constant threat of extinction, it is important to ascertain where and how biological diversity is generated and partitioned. Phylogeographic studies can assist in the identification of places and processes that indicate the origin and maintenance of biodiversity. Forest fragmentation has a big effect on local extinction and loss of genetic diversity of forest-restricted taxa, along with divergence and speciation of forest biota. This study aims to understand the effects of these processes on a number of forest-dwelling butterflies using a comparative phylogeographic approach. Mitochondrial DNA of five different Papilio species with different degrees of forest specificity was analysed using phylogenetic methods. In addition, the subspecific taxonomy of P. ophidicephalus was investigated using morphometrics of discal spots on the wings and nuclear DNA analysis along with mitochondrial DNA analysis. The results show that the forest-restricted species (P. ophidicephalus and P. echerioides) have more genetic structure and less genetic diversity than the more generalist species (P. dardanus, P. demodocus and P. nireus). This could be due to inbreeding depression and bottlenecks caused by forest fragmentation. As forest patches become smaller, the population size is affected and that causes a loss in genetic diversity, and increasing habitat fragmentation disrupts gene flow. The intraspecific taxonomy of P. ophidicephalus is far from revealed. However, this study shows there is evidence for the different subspecies when comparing morphological results and genetic results. From the evidence provided here it is suggested that P. ophidicephalus should be divided into two separate species rather than five subspecies.
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- Date Issued: 2014
Responses of intertidal macroalgae and associated fauna to interactive processes acting over multiple spatial scales
- Authors: Mostert, Bruce Petrus
- Date: 2011 , 2010-12-01
- Subjects: Biodiversity -- South Africa , Spatial ecology , Marine algae -- South Africa , Marine organisms -- Effect of water pollution on
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5890 , http://hdl.handle.net/10962/d1013370
- Description: The decrease of biological diversity from low latitudes near the equator towards high latitudes is one of the most fundamental patterns noted in ecology. These trends have been the subject of numerous terrestrial and marine studies and have caused the proposal of several explanatory hypotheses. No single hypothesis has adequately accounted for these observed trends. Furthermore, large-scale patterns are frequently modified by processes acting at meso- to small-scales. It is imperative to understand the interaction of these processes to elucidate the mechanisms controlling the structure of intertidal assemblages. The main aim of this thesis was to test the influence of multiple processes at a range of spatial scales on biogenic engineers. Biogenic engineers, such as macroalgae, have been reported to be strongly influenced by processes such as grazing, biogeography and upwelling and subsequent effects are expected to be linked to their associated assemblages. I used infaunal assemblages associated with macroalgae as a model system to understand the interactive effects of meso-scale upwelling in conjunction with large-scale factors (regional and biogeographic). Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis, inhabiting different but overlapping home ranges were used in this study. Smaller scale, physical attributes and the associated fauna of these algal species were compared. The effects of meso- to large-scale physical gradients on marine organisms have been investigated in many instances and resultant gradients in physical variables observed. This study was undertaken to investigate morphological trends exhibited by Hypnea spicifera and Champia lumbricalis to compare possible similarities between coastlines and to determine if inferred meso- to large-scale processes influence physical trends in a similar manner despite the coastlines being affected by different hydrodynamic processes. The macroalgae were located in two distinctly different upwelling regimes, Hypnea spicifera on the east and south coasts and Champia lumbricalis on the west coast. Upwelling (delivery of nutrients and primary production) was not found to be an important factor in determining the physical characteristics of macroalgae but there were clear patterns linked to latitude. Mean percentage cover of Hypnea spicifera was positively correlated with distance along the east and south coasts. Mean mass and mean surface area of H. spicifera were, however, negatively correlated with distance from Port St Johns. Mean frond length showed a negative trend but this relationship was not statistically significant. On the west coast, there was a significant increase in mean frond length from north to south for Champia lumbricalis. Mean surface area and mean mass of C. lumbricalis exhibited non-significant negative trends from north to south while there was a non-significant positive trend for mean percentage cover. Following the “Productivity Hypothesis”, these patterns from north to south along the coastlines of South Africa could have important implications for biodiversity associated with these algae. Many previous studies have focussed on the effects of upwelling on species (i.e. effects of nutrients and temperature) but have failed to separate this effect from large scale effects such as biogeography and latitudinal gradients. I tested the influence meso-scale upwelling, large-scale biogeographic processes and latitudinal gradients with two different species of macroalgae one on the east and south coasts of South Africa and the other on the west coast. Hypnea spicifera inhabits the east and south coasts of South Africa spanning two biogeographic provinces and is generally affected by relatively weak upwelling, whereas Champia lumbricalis inhabits the west coast spanning one biogeographic province which is subjected to intense persistent upwelling year round. Within the east and west coast biogeographic provinces there are, however, regions with both upwelling and non-upwelling. On the east and south coasts, entire assemblages differed significantly among the three Regions (St Lucia, Port Alfred and Knysna, while assemblages between upwelling/non-upwelling areas were not different. Assemblages on the different shores differed significantly from each other. There were no significant effects of region or upwelling for the number of individuals of Crustacea or Polychaeta, while Mollusca showed a significant effect of region. The number of individuals of other taxa showed a significant interaction of region and upwelling. Region had a significant effect on number of species of molluscs and other taxa, while there was no effect for either region or upwelling for the Crustacea or Polychaeta. In general different factors were shown to be important (region and shore) while upwelling was rarely important. On the west coast assemblages associated with C. lumbricalis were not influenced by region or upwelling but there were significant differences between shores. Region, upwelling ad shore did not affect number of individuals. There was a significant interaction of region and upwelling for the number of species of crustaceans, while numbers of species of Mollusca, Polychaeta and other taxa showed no effects. In general, regional factors strongly influenced most organisms, while upwelling played a minor role. Hypotheses about differences between upwelling and non-upwelling regions in terms of species abundances and composition due to the input of cold nutrient rich water were not supported. A link between the effects of larger-scale biogeographic factors and their influence on habitat forming taxa and the resultant effects on associated infauna would be a likely explanation for the patterns observed in this study. Diversity of assemblages is known to be influenced by the structural complexity of a habitat, increasing complexity increases the amount of available niches therefore potentially increasing the number of species found within that habitat. Three species of macroalgae, Hypnea spicifera, Champia lumbricalis and Bifurcaria brassicaeformis were selected on the basis of being structurally similar and having their distributional ranges overlap in order to elucidate the effects of structure and macroalgal species on associated assemblages. Hypnea spicifera is different in terms of surface area and biomass from Champia lumbricalis and Bifurcaria brassicaeformis. Assemblages of species found on the three rhodophytes showed both shore and the species of alga had significant effects on composition. Only numbers of individuals of molluscs were affected by the species of alga. Crustacea and Polychaeta showed an interaction of the species of alga with shore. In the case of this study, it is likely that the three species of macroalgae mitigate biological stressors such as predation and physical stressors such as wave exposure and desiccation. In general, meso-scale upwelling is suggested to be marginalised when considering the structuring of assemblages associated with macroalgae, while large scale biogeography has more of an influence. Within shores, assemblages were also strongly influenced by smaller-scale factors such as differences in the structure and species of alga. This study indicates the importance of investigating patterns across a range of spatial scales to gain a comprehensive understanding of factors influencing intertidal organisms.
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- Date Issued: 2011
The genetic diversity and conservation biology of the rare terrestrial snail genus Prestonella
- Authors: Fearon, Janine Lee
- Date: 2011
- Subjects: Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4191 , http://hdl.handle.net/10962/d1003760 , Snails -- South Africa , Snails -- Conservation -- South Africa , Snails -- Variation -- South Africa , Biodiversity -- South Africa , Snails -- Genetics -- South Africa , Snails -- Habitat -- South Africa
- Description: 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.
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- Date Issued: 2011
An assessment of the genetic diversity and origin of the invasive weed Chromolaena Odorata (L.) King and Robinson in South Africa
- Authors: Von Senger, Inge
- Date: 2002
- Subjects: Biodiversity -- South Africa , Chromolaena odorata -- Biological control -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4233 , http://hdl.handle.net/10962/d1003802 , Biodiversity -- South Africa , Chromolaena odorata -- Biological control -- South Africa
- Description: Chromolaena odorata (L.) King and Robinson is an alien invasive weed to most of the Old World tropical regions of the earth, including South Africa where it is morphologically distinct from most other C. odorata plants examined from both its native and invasive range. It is thought that these morphological differences are related to difficulties encountered in successful establishment of biological control agents on the South African population of C. odorata. It has been postulated that the source population of the South African population will harbour potential biocontrol agents that will be suited to successful establishment on the South African plants. Several morphological, cytological and isozyme studies have been attempted to identify the source population of the South African population, but these have failed to identify the origin of the South African population. In this dissertation two PCR-based methods were attempted, in an investigation into whether the morphological differences and difficulties in establishment of biocontrol agents have a genetic basis. The two techniques attempted were: Inter Simple Sequence Repeat (ISSR) amplification, and DNA sequencing. Results could not be obtained using the ISSR method, and the reason for this was not discovered despite extensive trials. The internal transcribed spacer region and the external transcribed spacer region sequences were obtained from five samples, and compared. It was found that the ETS region gave more phylogenetic signal at the intraspecific level than the ITS region. However, due to difficulties in amplification of the external transcribed spacer region, work here focussed on obtaining Internal Transcribed Spacer sequences for 61 samples. Each of the samples sequenced had a unique ITS sequence, displaying a high level of intraspecific genetic diversity. The degree of this diversity is discussed with reference to the possible influences of polyploidy and concerted evolution on genetic structure. The ITS data indicated that some of the physical traits used to define ‘morphotypes’ of C. odorata were not correlated to genotype. From discussion and comparison of morphological character distributions and the ITS-based phylogeography it is suggested that the geographical origin of the South African population is Greater Antilelan, rather than from the continents of North and South America, which is where the Australasian, West African and Mauritian infestations are suggested to have originated.
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- Date Issued: 2002