Masters Degrees (Botany and Zoology)

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The abundance and diversity of meso- and macrofauna in vineyard soils under different management practices
(Stellenbosch : Stellenbosch University, 2005-03) Nel, Werner; Reinecke, A. J.; Reinecke, S. A.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: The agricultural sector in South Africa relies heavily on the use of pesticides to protect crops against pest organisms. Pesticides can affect non-target organisms such as the meso- and macrofauna in the soil detrimentally. Since these organisms play an important role in the processes of mineralization and decomposition in the soil and contribute to soil fertility, it is important that they are protected. A large amount of published literature exists on the biological importance of soil meso- and macrofauna and the effects that various agricultural practices have on them. The main aim of this study was to investigate the influence of agricultural practices on the abundance and diversity of meso- and macrofauna in different vineyard soils. A comparative study was conducted of an organically managed, conventionally managed and an uncultivated control soil. A secondary aim was to determine the effect of these agricultural management practices on the biological activity of these animals. Soil samples were taken, from which mesofauna (Collembola and Acari) were extracted with a modified Tullgren extractor, identified and counted. Earthworms were extracted from the soil using hand sorting methods. Soil parameters such as pH, water holding capacity, organic matter content, soil texture and soil respiration were determined. Bait lamina and litter-bags were also used to help determine the biological activity within the soil. The mesofauna diversity was quantified using the Shannon Weiner diversity index, as well as a diversity index described by Cancela da Fonseca and Sarkar (1996). Differences in abundance of both the meso-and macrofauna were statistically measured using ANOVA's. Biological activity results were also interpreted using ANOV A's. Results indicate that the abundance of the meso fauna was the highest at the organically treated vineyard soil and lowest in the conventionally managed soil where pesticide application took place. The earthworms also showed the same trend as the mesofauna, but were much more influenced by seasonal changes. Biological activity, according to the bait lamina and the litter-bag results, was higher in both the conventionally and organically managed soils than in the control, but no statistical significant differences were found between the two experimental soils. The soil respiration (C02-flux), also indicating biological activity, was highest in the organically treated soil and lowest in the conventionally treated soil. The different sampling techniques used gave variable results and although the organically managed soil proved to have higher abundances of both meso- and macrofauna, the biological activity did not show the same trends. In conclusion the data did not give enough evidence as to whether organic management practices were more beneficial than conventional management practices for the maintenance of soil biodiversity.
Acclimation effects on thermal tolerance in ameronothrid mites at sub-Antarctic Marion Island
(Stellenbosch : Stellenbosch University, 2005-12) Deere, Jacques Andries; Chown, S. L.; Marshall, D. J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Evidence for widespread ecological impacts due to rapid climate change is on the increase, with further warming predicted over the next century. This increase in warming has lead to organisms adjusting their distribution range and where this is not possible organisms must cope with the stressful environments in a different way. One potential way to handle environmental stress is via a mechanism known as phenotypic plasticity, which allows an organism to express different phenotypes depending on the biotic or abiotic environment in a way that may alter that organism's fitness. Acclimation temperatures can potentially cause plastic (reversible and irreversible) changes in the response of individuals to stressful experimental conditions that could increase their survival. The issue of whether this acclimation will be beneficial to the organism or not remains contentious, with support offered both for and against the idea of beneficial acclimation. The aims of the investigation were to determine the thermal limits of five ameronothrid mite species (Halozetes marinus, H marionensis, H belgicae, H. fulvus and Podacarus auberti) from varying terrestrial habitats and to test whether there is beneficial acclimation on the thermal traits. Along with the beneficial acclimation hypothesis several alternative hypotheses were also tested. In addition, locomotor performance was determined as it has been suggested that locomotion performance is a reliable and practical measure of potential fitness of animals. The same hypotheses testing the effects of acclimation temperature on the thermal limits were tested on three performance traits; performance breadth, optimum speed and optimum temperature. Support for beneficial acclimation was found in the performance breadth and optimum speed traits for all species except for Halozetes marinus. For the optimum temperature trait the prediction for the compensation hypothesis was met and that of the beneficial acclimation hypothesis rejected, with the only exception again being that of H marinus. In the case of the locomotor performance traits the prediction for the beneficial acclimation hypothesis in the performance breadth and optimum speed traits are the same for that of the compensation hypothesis, therefore the overall response of the more terrestrial mite species is one of compensation. However, support for beneficial acclimation was not found in the thermal limit traits of all five species, with the higher acclimation temperatures (specifically 150 C) resulting in negative responses in LLT in H. marinus and H. belgicae, and in ULT in H. fulvus. Phenotypic flexibility varied between marine and terrestrial species. The less variable marine environment showed lower flexibility than that of terrestrial species in the performance breadth trait and optimum temperature trait, but there was a lack of variation between the marine and terrestrial species in the temperature tolerance traits. These results show that the effects of acclimation on various traits, especially fitness related traits, are complex and require more attention if the consequences are to be fully explained. This study therefore provides insight into the effects of acclimation on performance traits and thermal limit traits and has implications for the evolution of plastic responses in terrestrial arthropods.
Acoustic Spatial Capture-Recapture (aSCR) and the Cryptic Cape Peninsula Moss Frog Arthroleptella lightfooti
(Stellenbosch : Stellenbosch University, 2018-12) Louw, Marike; Measey, John; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Quantitative measurements of wildlife populations, such as population density, are quintessential for management and conservation. Acoustic Spatial Capture-recapture (aSCR) is a technique that is used to estimate the densities of acoustically active animals. It is advantageous to use when animals defy the use of traditional methods of population estimation by being very visually cryptic, but remaining acoustically active. Arthroleptella lightfooti is a visually cryptic moss frog with an average snout to vent length of 14.5 mm. The males call during the austral winter from seepages within a restricted range across the Cape Peninsula. The species has an IUCN status of Near Threatened. Here, the population densities of the endemic A. lightfooti are estimated across their range on the Cape Peninsula for the first time using aSCR. Multiple microphones, termed “acoustic arrays”, are deployed in the field to record the calls of the frogs. I assess the use of aSCR in terms of reliability of the density estimates by examining the standard errors as coefficients of variation (CVs) of the density estimates. A density estimate with a CV above 30% was considered unreliable. Recording calls for the aSCR analyses involved visiting more than 200 sites during 2016 and 2017, and deploying acoustic arrays at a total of 149 sites, of which a subset of 85 sampling sites was used. I examined the influence of different variables on the size of the CV, namely: the average number of calls received by the acoustic array per minute, the array formation, and the detector frequencies (the combination of different numbers of microphones across which calls were heard). In addition, I made use of an output from aSCR that is an aerial view of the estimated calling locations of frogs relative to the acoustic arrays. I overlaid this output with aerial images taken at three different sites using a drone, and I examined the microhabitat features that relate most significantly to the presence of calling A. lightfooti. When there were less than 111call.min-1 received by the array, density estimates had CVs that exceeded 30% and were therefore considered unreliable. Above this threshold, 91% of density estimates were acceptable. When calls were heard on mostly one microphone, and decreasingly heard across two, three, four, five and six microphones, the density estimates were more reliable. However, when calls were mostly picked up across a combination of one and six microphones, density estimates became less reliable. This suggests that array formations should have the microphones spaced in such a way that not all calls are detected across all the microphones or only one microphone. The presence of calling frogs was significantly related to the presence of wet, seepy patches in the microhabitat and to the absence of standing water. This is consistent with observations in the field and reflects the biological needs of the species: it has no life stages in water but needs moist areas for eggs and tadpoles to develop. The successful application of aSCR to A. lightfooti is promising in the field of population studies on cryptic species, as it can be used to evaluate the populations of other calling taxa, which holds important implications for conservation and management.
Ailanthus altissima : an assessment of its distribution at different spatial scales and options for management in South Africa
(Stellenbosch : Stellenbosch University, 2017-03) Walker, Gareth Alexander; Richardson, D. M.; Robertson, M. P.; Gaertner, Mirijam; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: The constant flow of goods into and out of cities has resulted in the proliferation of invasive species in urban areas and, because of this, cities are viewed as ‘hotspots’ for invasive species. The rise of global trade and long distance transportation will ensure that further introductions will take place in urban ecosystems. Conditions that have been altered due to human activities enable some alien species to proliferate rapidly throughout urban centres, often also spreading into natural and semi-natural areas at the urban/wildland interface. Evaluating the current distribution of an invader by analysing potential patterns in its distribution, as well as determining the potential distribution of a species over multiple landscapes and identifying factors that promote its spread, is essential for determining the full extent of an invader. Understanding 1) where a species is; 2) where a species may spread to; and 3) the factors that promote the spread of a species are all needed to gain an understanding of the biological and biogeographical preferences that facilitate the spread of the species. This is best achieved by using a multi-scale analysis that studies all aspects of an invasive species over a variety of spatial scales. This study focusses on a notorious northern hemisphere invader - Ailanthus altissima – that, although having been introduced into South Africa in 1834, is yet to replicate similar levels of invasion success. I adopted for a multi-scale analysis of the species evaluating the current and potential distribution of the species at a global scale (Chapter 1), national scale (Chapter 2) and local scale (Chapter 3). Each chapter addresses a central aim in which a number of research questions are evaluated. In Chapter 1 I assess the biogeography, distribution, and habitat suitability of A. altissima by evaluating the current and potential distribution of the species (based on climatic suitability) at both a global scale and a national scale (in South Africa). The main conclusions of this chapter are that 1) online databases (although outdated at times) provide an accurate representation of the distribution of invasive species and should therefore be accessed. This was ascertained by cross referencing a number of online databases to evaluate whether they were largely in agreement with one another in terms of the distribution of an invader; and 2) modelling the potential distribution of an invasive species based on climatic suitability serves as a good first approximation of potential species spread. Although this may be true, it was also suggested in this chapter that to accurately quantify the potential distribution of an invasive species, other distribution drivers (such as land use and human mediated disturbances) need to be incorporated into the design of a species distribution model. Chapter 2 evaluates the degree of range filling exhibited by A. altissima in South Africa and identifies areas at risk of future invasion. This chapter also identifies specific factors that promote the spread of the species at a global and national scale. I determined that at the global scale, climate had the highest influence on the distribution of A. altissima whereas at the national scale, human mediated disturbances exerted a higher influence on the distribution of the species. This chapter builds on the concepts proposed in Chapter 1 by highlighting the importance of incorporating different environmental variables at various spatial scales to identify potential invasion ‘hotspots’. I conclude that the multi-scale approach presented in this chapter enables the early detection of invasive species, preventing damage associate with their potential spread. Also, the novelty of this approach is particularly effective when it comes to analysing urban invaders. The third chapter evaluates the distribution pattern of A. altissima within the City of Cape Town by using the suburb of Newlands as a case study. In addition, it determines potential options for management at a city scale. It can be concluded that fine-scale analysis of invasive species distributions is best achieved using Geographic Information System (GIS) techniques and that such these ultimately help to identify potential areas susceptible to future invasion while delimiting unsuitable areas. I determined that A. altissima has a preference for affluent urban areas with podzolic soils that are exposed to high levels of rainfall within the City of Cape Town. Using this information, I determined that there is a large capacity for further spread by the species throughout the city. The systematic approach that we used in Newlands is an effective way of gauging the full extent of an invader and is especially effective for evaluating the population structure of a particular invasive species. Future studies should adopt this approach in conjunction with remote sensing techniques to achieve the best possible results. The final chapter of this thesis provides the overall conclusions in which all the main findings are highlighted. Altogether, the approach presented in this thesis is an effective method that could be used on other emerging, urban invaders globally. The systematic, multi-scale analysis proposed in this project showed high levels of success and it is my belief that this project achieved its desired aims.
The alarm vocalizations of Brants' whistling rat, Parotomys Brantsii
(Stellenbosch : Stellenbosch University, 2001-12) Le Roux, Aliza; Cherry, M. I.; Jackson, T. P.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: The alarm calls of a colonial rodent, Brants' whistling rat (Parotomys brantsii), were investigated at Goegap Nature Reserve in the Northern Cape, South Africa. At this site P. brantsii occurs in sympatry with the congeneric P. littledalei, and the alarm calls in response to humans was compared between the two species. Parotomys brantsii's typical call in reaction to a human is a simple whistle, characterized by an initial upward frequency sweep and high frequency plateau, whereas the alarm whistle of P. littledalei has three overlapping components. Parotomys littledalei's calls are significantly shorter and lower in dominant frequency than those of P. brantsii, and have a significantly wider frequency bandwidth. These distinctions were attributed to species discrimination and habitat preferences. The acoustic adaptation hypothesis is supported in part, as P. littledalei, which inhabits a closed habitat in comparison with P. brantsii, has calls which are lower in frequency than P. brantsii calls, but contrary to the hypothesis, P. brantsii calls show less frequency modulation than those of P. littledalei. The high pitch of both species' vocalizations may be a convergent feature making the callers difficult for predators to locate. The alarm call repertoire of P. brantsii was investigated by presenting members of the P. brantsii colony with models of some typical predators, a raptor and puff adder, as well as a human observer. Virtually no variation was detected in the structure of alarm whistles elicited by different predators, indicating that P. brantsii did not identify different predator types by means of vocalizations, even though behavioural responses showed that P. brantsii do distinguish between different predators and non-predators. Note duration varied in conjunction with the physical reaction of the caller. When the caller bolted towards safety, the whistle was significantly shorter than when it remained aboveground. During an encounter with a snake or far-off human the caller would utter relatively long duration calls, signifying a low-risk situation, while highrisk situations such as a nearby human or raptor provoked short calls, emitted just before the whistling rat bolted underground. I regard P. brantsii's alarm call repertoire as a graded "urgency-based" system, indicating threat level perceived rather than predator type. This system is widespread among ground squirrels and is usually associated with animals inhabiting a two-dimensional environment. Playback experiments were conducted to determine the meaning of alarm calls to conspecifics, focusing specifically on the effect of variation in single call duration and function of alarm-calling bouts. All alarm calls induced heightened vigilance in receivers, but the behavioural response did not differ between short and long single calls. Multiple calls lead to significantly longer periods of high vigilance than single calls even after calling bouts have ended, showing that one of the functions of multiple calls is to maintain high vigilance in conspecifics for relatively long periods. The non-iconic nature of their alarm calls and the undiscriminating response of receivers to different calls emphasizes the importance of contextual clues in the communication system of animals living in an open habitat like that of P. brantsii.
Amphibian conservation in an urban park : a spatial approach to quantifying threats to Anura on the Cape peninsula
(Stellenbosch : Stellenbosch University, 2017-12) Ebrahim, Zishan Cassiem; Measey, G. J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Species’ threat assessments produce generalized threat impact scores, often by considering regional-scale representations of threats. Cities, on the other hand, produce municipal-scale, high resolution data that are proxies for threats; furthermore, cities in mega-diverse regions are home to a high number of threatened species. Prioritization of conservation action is biased for where more information is known (about the ecosystem), and where a positive outcome can be anticipated. Eight Cape peninsula amphibian species have a threatened conservation status. They are isolated on highlands or are restricted to remnant and suburban habitats, dependent on both urban and protected terrestrial and freshwater habitats found in the City of Cape Town and Table Mountain National Park. In Chapter Two, I used spatial data (shapefiles) to represent threats in a Geographic Information System to spatially define threats to eight amphibian species (five lowland, three upland). I used two approaches: weighted and un-weighted by a threat impact-score, to produce five indices of local threats. The Micro Frog (Microbatrachella capensis) is assessed as the most threatened peninsula frog species by three of the five indices considered. The results show that for lowland species, the threat-class of greatest extent is ‘Residential and commercial development’. The three lowland species most exposed to this threat are M. capensis (100% exposed to potential development), Breviceps gibbosus (55.6% of its 8.5 km2 putative peninsula distribution), and Sclerophrys pantherina (38.4% of its 199.7 km2 distribution). The Compounded and the General Threat Index correlate to the (global) Redlist Index (P < 0.05); but no correlation to the regional Red Listing, indicating congruency of threats and threat status. The Critically Endangered Table Mountain Ghost Frog (Heleophryne rosei) is torrent adapted, and found only on the Table Mountain massif. CapeNature monitors tadpoles, and SANParks monitors (selected) stream parameters. In Chapter Three, I analyse water-habitat monitoring data (controlled for altitude) to show where threats of habitat alteration, drought, or temperature extremes may affect the H. rosei metapopulation. Permanence of water-flow and water temperature are shown to be very highly significant predictors of tadpole presence (p = 0.0005, r = 0.78). The lower the water temperature, the more likely tadpoles are present. Streams with a mean summer temperature greater than 17.2°C (n=3) at 400 to 300 meters above sea level were found to have no tadpoles at this altitude. Permanence of water flow is significant, as tadpoles need more than one year to reach metamorphosis. Summer water temperatures over an average of 17.2°C should be a red-flag for management authorities responsible for bulk-water supply, threat mitigation efforts, and biodiversity conservation. Spatial indices of threat are useful to illustrate the relative exposure to threats at a local (city) scale. Threats to different lowland amphibians are similar (e.g. residential and commercial development), which varies from the mutual threats to different upland amphibians. Fundamental to stream species’ conservation is water supply and demand management, while upland terrestrial species are most affected by veld age and invasive alien flora. Some threats are common for both areas (e.g. invasive alien species). Key words: Threat impact score, threatened areas, GIS, habitat loss, amphibians, Table Mountain National Park, Cape Town, environmental water requirement, water temperature, habitat.
An analysis of the Cordylus Polyzonus complex (Reptilia : Cordylidae) in the South-Western Cape
(Stellenbosch : University of Stellenbosch, 1990-03) Badenhorst, N. C.; Mouton, P. le F. N.; Van Wyk, J. H.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.
Mouton and Oelofsen (1988) suggested that melanistic cordylid populations in the southwestern Cape represent relict, cold-adapted populations which evolved under adverse climatic conditions during the Last Glacial Period, 18000-16000 BP. The first section of this study was undertaken to test their model for the evolution of melanism in the cordylid species, Cordylus polyzonus. For this purpose, geographic character variation among populations of Cordylus polyzonus in the region south of 32°15' latitude and west of 19015' longitude was investigated. Variation in 122 external morphological characters was analysed in 306 specimens from 93 localities. Although no inter-locality variation was observed in most of the characters, a high degree of concordancy was observed in the geographical variation of three headshield characters. These three headshield characters are considered non-adaptive and can accordingly be regarded as good indicators of genealogical relationship. Since they varied together with other adaptive characters such as melanism and body size, it can be concluded that geographically isolated melanistic populations of Cordylus polyzonus represent relicts of a once larger melanistic population. The data underscore the Mouton-Oelofsen hypothesis for the evolution of melanistic cordylid taxa in the south-western Cape. A further corrolary of the Mouton-Oelofsen hypothesis, is that melanistic cordylids are presently restricted to cool enclaves. This assumption was evaluated in the second section of this study by analysing prevailing climatic conditions associated with the occurrence of extant melanistic populations of the genera Cordylus and Pseudocordylus in the southwestern Cape. Climatic data were obtained from 123 weather stations in the study-area. A close correspondence was found between the distribution of melanistic populations along the westcoast and the primary upwelling zones of the southern Benguela Current. Lower mean daily temperatures and a high incidence of advective sea fog on the adjacent coastal regions are direct effects of these cold upwelled waters. Likewise, montane melanistic populations, occurring at relatively high altitudes along the extreme western borders of the Cape Fold Mountains, also experience lower mean daily temperatures and a high incidence of orographic fog and cloud cover. Melanistic cordylid populations therefore generally have to 4. contend with relatively exposed environmental conditions of low temperature and limited solar radiation due to the filtering effect of fog and cloud cover. The fact that all the melanistic taxa in this region occur as small isolated populations limited to cool enclaves, suggests that they are presently in a contracted state under strong environmental pressure. It is postulated that palaeoclimatic conditions very similar to climatic conditions presently prevailing in these enclaves were experienced over the entire western coastal region, at least as far as the Orange River, during the Last Glacial Maximum when melanism probably evolved. Our results therefore corroborate the Mouton-Oelofsen hypothesis that isolated melanistic cordylid populations represent cold-adapted relicts. One would accordingly expect melanistic populations to posses some enhanced ability to absorb infrared radiant heat to cope with these conditions of limited sunshine and lower temperatures. In section three of this study, differences in dorsal skin reflectivity between melanistic and turquoise ~. polyzonus populations were quantified. Furthermore, the physiological ability of this species to change body colour was investigated, as well as ontogenetic colour change. Significant differences in dorsal skin reflectivity existed between melanistic and turquoise specimens in the 500-1300 mjl spectral range, demonstrating the greater heat-absorbing capacity of melanistic populations. The data underscore the MoutonOelofsen model that melanistic populations are "cold-adapted" relicts. Furthermore, ontogenetic colour change is a real phenomenon in the melanistic variation of C. polyzonus. In this respect it is unique among the melanistic cordylid taxa in that ontogenetic colour change seemingly does not occur in the other forms. Experiments to investigate short term colour change in response to different temperatures regimes, produced no conclusive results. On the other hand, seasonal colour changes could be demonstrated for both melanistic and turquoise specimens, indicating that this species has the physiological capacity to change colour. It is, however, believed that geographic colour variation in ~. polyzonus cannot be attributed to this capacity, but is rather the result of selection over time. This view is underscored by the results of section one demonstrating that, apart from colour and body size, melanistic and turquoise forms also differ in certain non-adaptive traits; suggesting that they do not belong to the same primary gene pool.
Anatomical survey of the formation of primary xylem and nutrients supply to the reproductive apple bud
(Stellenbosch : Stellebosch University, 2017-03) Frazenburg, Madelaine; Dreyer, L. L.; Lotze, Elmi; Turketti, S. S.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Apple (Malus domestica Borkh.) is a deciduous fruit species, which is subject to dormancy before bud break occurs in spring. Although not noticed externally, anatomical changes occur in the reproductive bud during this dormant period, including formation of the carpels, enlargement of the petals and carpel and anther elongation. In this study, we determined i) the time of primary xylem formation as influenced by cultivar, month and/or climate (expressed by winter chilling) and ii) the distribution and quantification of a selected nutrient calcium (Ca) in, (a) the primary xylem tissue as well as (b) in reserve tissues (spur, leaf and apical meristem). Four different commercial apple cultivars were selected for this investigation. Golden Delicious and Braeburn represented cultivars with typical Ca deficiency symptoms in the fruit if additional Ca is not applied, whereas Royal Gala and Cripps Pink represented cultivars in which Ca related problems occur less frequently. Golden Delicious and Royal Gala are cultivars associated with high chilling requirements, and Braeburn and Cripps Pink, with medium chilling requirements. Sampling of dormant buds occurred during June, July, August and September in 2012, 2014 and 2015. The different cultivars used for this investigation were cultivated in Stellenbosch and Elgin. Although these regions are both in the Western Cape Province, the Elgin region is an area with a higher chill unit accumulation than Stellenbosch. Light, fluorescence and scanning electron microscopy imaging techniques were used to study the anatomy of primary xylem development. To differentiate the degree of lignification in primary xylem from secondary xylem, samples were imaged with a Zeiss LSM880 confocal microscope equipped with ZEN 2 software. Scanning electron microscopy images were acquired using a Zeiss Merlin FEG Scanning Electron Microscope (SEM). After the time (month) of primary xylem establishment in the bud was identified, Ca concentration (%) was quantified in reproductive apple bud tissues of all four cultivars during three seasons (2012, 2014 and 2015). Ca concentration was quantified with Wavelength Dispersive Spectrometer (Oxford Instrument® Wave Dispersive X-ray Spectrometer). Ca was simultaneously quantified with Electron Dispersive X-ray (Oxford Instrument ® Energy Dispersive X-ray). In Golden Delicious and Braeburn, the process of secondary xylem development commenced earlier than in Cripps Pink and Royal Gala. While this process is slow in Cripps Pink, xylem development proceeds much faster in Royal Gala and changes from having only primary xylem in July to having secondary xylem a month later. The timing and duration of xylem development in Cripps Pink and Royal Gala were similar in the Stellenbosch and Elgin regions in June, but differed in July and August in all three seasons. Results clearly show differences in Ca distribution and Ca concentration in the tissues of dormant reproductive apple buds of the four cultivars studied. High Ca levels were noted in the spur transport tissue of Royal Gala, Cripps Pink and Braeburn during June, with considerably lower levels of Ca in the same region in Golden Delicious. Cripps Pink and Royal Gala have a higher Ca concentration in the xylem in June, followed by an increase in Ca concentration towards September. The reduction in Ca concentration in the spur during the same period may indicate that reserve Ca from the spur is allocated towards the xylem. This needs further investigation. Although trends were not as clear in Golden Delicious and Braeburn and did not always follow the same pattern, observations in these cultivars differed from those in Cripps Pink and Royal Gala, confirming the higher presence of primary xylem reported previously. Thus, later formation or presence of primary xylem in the dormant bud of these cultivars may partly explain the lower Ca concentrations and difference in Ca distribution between tissues compared to Cripps Pink and Braeburn.
n Anatomiese studie van Vitis-wortels, gesond en beskadig deur Filloksera
(Stellenbosch : Stellenbosch University, 1968-03) Britz, C. J.; De Vos, M. P.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
Please refer to full text for abstract
Androgen controlled secondary sexual characters in the male African clawed frog, Xenopus laevis, as potential biomarkers for endocrine disruptor contaminants (with special reference to fungicides) in aquatic systems
(Stellenbosch : Stellenbosch University, 2014-04) Archer, Edward; van Wyk, Johannes, Hendrik; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Endocrine disrupting contaminants (EDCs) coming from households, industrial parks, wastewater (sewage) treatment and agricultural areas have been shown to pollute our freshwater systems. These contaminants may disrupt early development and reproductive systems in freshwater organisms (fish, frogs and crocodile species) as well as humans. Agricultural pesticides are shown as a large contributor to endocrine disruption activity in water catchment areas through spray drift, runoff, and/or groundwater leeching. Although South Africa is recognized as the largest consumer of agricultural pesticides in Africa, few studies have been undertaken to assess the prevalence and impact of endocrine disorders activities of pesticides in local freshwater systems. Recent studies have suggested that various agricultural pesticides, especially fungicides, might have adverse effects on the male endocrine system. There is therefore a need to test for a wider range of endocrine disrupting activities (mechanisms) in environmental waters other than conventional estrogenic (feminising) activities. Furthermore, there is a need to establish biomarkers in endemic species (bio-indicators) to show endocrine disruption in vertebrates (therefore also apply to humans). The specific objectives of the study were to: (1) describe and confirm the use of androgen-controlled breeding glands in male African clawed frogs (Xenopus laevis) as a biomarker for (anti)androgenic endocrine disruption activity (Chapter 2), (2) to investigate the premature development of breeding glands in X. laevis tadpoles (pre-metamorphic) and young froglets (post-metamorphic) (Chapter 2), (3) to investigate the disruption of male reproductive traits in adult X. laevis frogs by exposure to substances disrupting two different anti-androgenic endocrine disruption pathways (Chapter 3), (4) screen for (anti)androgenic activity of individual and binary mixtures of pesticides, which are regularly used in agricultural areas in the Western Cape Province of South Africa (Chapter 4), and (5) to test for (anti)androgenic and estrogenic endocrine disrupting activities by making use of in vitro assays as well as adult male X. laevis frogs collected from selected ponds surrounded by vineyards and fruit orchards in the Stellenbosch Winelands. The present study confirmed that male breeding glands can serve as biomarkers for (anti)androgenic endocrine disruption and that male reproductive and secondary sexual characteristics can be disrupted through two different biochemical control pathways. The study also confirmed that the expression of androgen-regulated breeding glands can be stimulated in pre-metamorphic tadpoles and immature, post-metamorphic frogs, and can thus be used for (anti)androgenic testing. The rapid testing and predictive value of an in vitro recombinant yeast screen for androgen receptor binding inhibition of selected individual or binary mixtures of pesticides was also confirmed. However, the current study showed that the predicted in vitro (anti)androgenic activity did not always correspond with in vivo (anti)androgenic biomarker outcomes. This It also confirmed that single-cell in vitro assays can be used as a first-level prediction for (anti)androgenic activities of individual or mixtures of agricultural pesticides. This study provides a better understanding for potential mixture interactions of commonly used agricultural pesticides, the hormonal control of secondary sexual characteristics in male frogs and the use of reproduction biomarkers to study long-term effects of endocrine disruptors in local water supplies.
The antimicrobial interactions of Agathosma crenulata, Dodonaea viscosa and Eucalyptus globulus combination and their chemical profiling
(Stellenbosch : Stellenbosch University, 2013-12) Zonyane, Samkele; Makunga, N. P.; Van Vuuren, S. F.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: In traditional medicine, there is a long-standing culture of combining herbal drugs to increase the therapeutic efficacy. The improved medical action is thought to be due to synergistic interactions between different plant bioactive components. The aim of this study was to test the pharmacological interactions in a medicinal plant combination which consisted of Agathosma crenulata, Dodonaea viscosa and Eucalyptus globulus. The rationale for the analysis of this particular mixture is that it had noteworthy antibacterial activity and exhibited the highest activity out of seven medicinal plant mixtures previously investigated. Using chromatographic analysis, the phytochemistry of the plants was also assessed. The chloroform: methanol (1:1; v/v) extracts or hydo-distilled essential oils (A. crenulata and E. globulus) were screened individually and in combinations (double and triple plant combination) for activity against five respiratory pathogens using a microdilution assay. The antimicrobial interactions in combinations were assessed with the fractional inhibitory concentration (FIC) and the isobolograms. The organic extracts generally showed the highest antimicrobial activity with E. globulus having the highest activity with MIC values below 1 mg ml-1 representing noteworthy activity. The overall activity of the aqueous extracts was poor. The essential oil activity of E. globulus was mostly noteworthy (0.5 to 2 mg ml-1) while A. crenulata essential oil displayed moderate activity (1 to 4 mg ml-1). The ΣFIC values for double combinations (1:1) of A. crenulata with D. viscosa, A. crenulata with E. globulus and D. viscosa with E. globulus were calculated from the minimum inhibitory concentration (MIC) data and the interactions were classified as synergistic, additive, indifferent and antagonistic. The highest synergistic interactions observed were for a 1:1 combination of A. crenulata with E. globulus against K. pneumoniae, S. aureus and B. subtilis with ΣFIC values of 0.07. There was only one incident of antagonism noted in the study for D. viscosa with E. globulus (1:1) against C. neoformans with ΣFIC value of 4.25. The double combinations against selective pathogens (K. pneumoniae, S. aureus and E. coli) were further analysed for interactions using isobolograms. Mostly, the antimicrobial interactions as presented by the isobolograms were congruent with FIC results which further validated the occurrence of relevant antimicrobial interactions in those combinations. The ΣFIC values for triple combinations (1:1:1) revealed mostly synergistic interactions. When the triple combinations were analysed further against certain pathogens based on the predictions of the Design of Experiments software program (MODDE 9.1®), the MIC values remained the same despite the different combinations that were tested Thin layer chromatography (TLC) was used for a quick chemical fingerprinting of the plant extracts. This was followed by a bio-autographic assay. The chemical profiles of the organic extracts and essential oils from two of the study aromatic plants (A. crenulata and E. globulus) were further analysed with liquid chromatography mass spectrometry (LC-MS) and gas chromatography mass spectrometry (GC-MS) respectively. For combined plant extracts, a multivariate data analysis using principal component analysis (PCA) and hierarchical clustering analysis (HCA) was used to determine the relationship of the chemical make-up of combinations with that of individual plant extracts. According to the TLC analysis, E. globulus extracts had more compounds than the other two plants in the study. For the bio-autographic assay, E. globulus and combinations that included this plant showed greater inhibition zones than A. crenulata and D. viscosa. For the LC-MS analysis, PCA and HCA showed a close relationship between A. crenulata with D. viscosa, D. viscosa with E. globulus and the triple combination. Twenty one components were identified in the essential oil of A. crenulata representing 88.83% of the total oil composition. The oil was dominated by oxygen-containing monoterpenes (46.25%). In the essential oil of E. globulus, twenty six compounds were identified making up to 95.62% of the oil composition. Oxygen-containing monoterpenes (32.98%) also dominated the E. globulus essential oil. There was no great variation in essential oil metabolites of the individual plants and their combination as shown by both PCA and HCA. The enhanced in vitro antimicrobial activity and pharmacological interactions (synergy and additivity) in some of the combinations (double and triple) that were tested in this study adds scientific support to the use of medicinal plant combinations in Western Cape traditional medicine. The metabolic profiles of plants in combination might be unique due to interaction of the different plant bioactive molecules and thus result into defined antimicrobial activity.
The applicability of radiocarbon dating to understanding lifespan and mortality patterns in the quiver tree, Aloidendron dichotomum (Masson) Klopper & Gideon F.Sm.
(Stellenbosch : Stellenbosch University, 2024-03) Murray, Kayleigh; Midgley, Guy F. ; Foden, Wendy Bernardina; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: This thesis investigates the use of accelerator mass spectrometry (AMS) radiocarbon dating as a means of estimating the maximum longevity and time-of-death across the range of the quiver tree (Aloidendron dichotomum (Masson) Klopper & Gideon F.Sm.). The quiver tree was identified as an indicator species for climate change impacts due to measured increases in population mortality and decreased juvenile recruitment in regions of its range that have experienced warming and drying over the past century. Dead quiver trees persist in situ due to slow decay rates meaning a metric of mortality rate can be estimated as a proportion of the number of live to dead individuals in the population. The use of this metric was subsequently challenged due to doubt over the true time-of-death of trees in situ. The attribution of mortality to climate change was disputed citing instead centennial and millennial-scale population extinction debt as the cause for increased mortality and adult-heavy population structure. Discerning historical and contemporary causes of population mortality is, thus, of great importance for understanding and mapping climate change impacts on the quiver tree and co-occurring species. Doing so requires population demographic modelling which depends on metrics for the age of maximum longevity of the tree and verified time-of-death of the mortality class. In this thesis I aimed to develop radiocarbon dating methods for accurate estimation of these two metrics. After a first chapter reviewing the literature relevant to the quiver tree as an indicator species, my second chapter estimated the maximum age for four trees from the arid north of the species’ range in Namibia by analysing the radiocarbon ages of samples collected across the radius of the tree base. The oldest sample originated between 1277 - 1452 (95% CI) placing the maximum age of this tree at more than double that of the previous maximum estimates (350 years old). I discovered that the core tissue of the trees was consistently contemporaneous with the date-of-death, and that other samples along the radius deviated from the expected linear model of growth. This suggests material turnover and potential mixing of old and new carbon - a process which needs further investigation to understand how this impacts interpretation of results. As the core material is not present, Bayesian age-depth modelling should be used to estimate the true maximum age of the trees, and this can be supported by increasing the number of samples analysed. The third chapter of my thesis aimed to test whether trees in the mortality class died before or after 1950 using the presence or absence of a specific radiocarbon signal known as “bomb carbon”. This would test a hypothesis that the mortality is a relict of an early 1900’s drought. The majority of samples from the core and all of the samples from the edge of the tree post-date 1950, but five trees analysed only at the core pre-date 1950. I have deemed these results inconclusive considering material turnover at the core, and thus the inference which can be drawn from this chapter is incomplete. Despite this, radiocarbon dating shows promise as a forensic method for estimating an accurate year of death of the quiver tree if sampling is expanded to two proximal samples from the edge of the tree.
Aspects of the thermal ecology of the group-living lizard, Cordylus cataphractus : a spatial and temporal analysis
(Stellenbosch : University of Stellenbosch, 2011-03) Truter, Johannes Christoff; Van Wyk, Johannes H.; Mouton, P. le Fras N.; University of Stellenbosch. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Thermal ecology is a central theme in reptilian biology because of the thermodynamic rate dependence of virtually all biological processes in these ectothermic animals. Thermoregulation includes active processes (with associated energetic costs related to altered behaviour and physiology) functioning to maintain body temperatures within a preferred temperature range, so that the majority of physiological functions occurs optimally, despite natural variation in the animal’s thermal habitat. The recent development of quantitative thermal indices now allows researchers to describe the thermal habitat and thermoregulatory functioning of an ectotherm within its environment from a cost-benefit perspective. The use of such quantitative biophysical approaches to reptile thermal ecology studies is however limited in the African context. Cordylus cataphractus is one of the best studied cordylids, and exhibits various characteristics atypical for the family, such as permanent group-living, seasonally lowered surface activity, a low resting metabolic rate and large fat bodies. These characteristics are generally thought to be associated with groupliving in a semi-arid habitat, yet, the possible links to thermal ecology remains unexplored. The objectives of the current study was: firstly, to characterize the preferred temperature range (Tp) of C. cataphractus through the use of ecologically realistic laboratory thermal gradients; secondly, to explore seasonal and geographical variation in thermal preference, by comparing Tp among individuals captured from a coastal and inland population and during different seasons (autumn and spring); thirdly, to describe the thermal habitat of a C. cataphractus population during summer, autumn, winter and spring and to then relate these findings to the seasonal activity patterns reported in literature for the species; fourthly, to describe the seasonal patterns of thermoregulation (during summer, autumn, winter and spring) in a C. cataphractus population through quantitative thermoregulatory indices; fifthly, to assess geographic variation in the thermal habitat and IV associated patterns of thermoregulation in C. cataphractus among a coastal population (western range limit) and an inland population (eastern range limit). The thermal habitat of C. cataphractus was described by measuring operative environmental temperatures (Te) with hollow copper lizard models placed around rocks according to the natural surface movement patterns of the species. Variation in thermal habitat quality was subsequently calculated (de = |Te – Tp|) and averaged. Field body temperatures (Tb) of lizards were measured with dorsally attached miniature temperature loggers. Thermoregulatory indices were calculated from Te, Tb and Tp, describing: thermoregulatory accuracy, the effectiveness of thermoregulation and thermal exploitation for each population (coastal and inland) for the respective sampling periods. The preferred body temperature range of C. cataphractus is the lowest recorded among cordylids to date (mean Tp = 29.8oC) and was conserved among different populations and within these populations among seasons, despite the fact that environmental temperatures are known to vary geographically and seasonally. Thermal habitat quality varied significantly at micro spatial scale around rocks in the coastal population. Since C. cataphractus males are territorial, competition for thermal habitat quality around rocks may therefore occur. Such effects will be a function of the time of year since the variability in thermal habitat quality among rock aspects (around rocks) varied seasonally. Thermal habitat quality of crevices varied among seasons and was typically higher in the open, outside rock crevices, during the cooler winter and spring periods, whereas in summer and autumn the crevice environments were more favourable. Thermal habitat quality was high in crevices during autumn, suggesting that the observed repressed surface activity of C. cataphractus described for the time is not necessarily, as previously thought, only due to food constraints. Moreover, in contrast to earlier reports, the current results (Tb versus Te) indicate that individuals emerged from crevices in summer. The geographical assessment indicated that lizards from the coastal population, with generally larger groups, thermoregulated more successfully than those from the inland population. The higher thermoregulatory success in the coastal population occurred in spite of the fact that thermal habitat quality was significantly lower at the coastal locality. The higher thermoregulatory success in the coastal population was likely due to reduced predation risk associated with increased group-size. The seasonal trends in thermoregulation at the coastal and inland population corresponded to the patterns predicted by the cost-benefit model of thermoregulation, accuracy of thermoregulation and the effectiveness of thermal exploitation being higher during the thermally more favourable autumn.
Aspekte van die ekofisiologie van die halofiet Triglochin bulbosa L.
(Stellenbosch : Stellenbosch University, 1990-03) Becker, Theresa; Jooste, J. H.; Stellenbosch University. Faculty of Science. Department of Botany and Zoology.
ENGLISH ABSTRACT: The adaptibility of the halophytic plant Triglochin bulbosa to pollution of the Berg River estuary and high concentrations of sodium chloride was investigated. The relation of plant to environment was determined by means of comparative analysis of plant and substrate, an anatomical study and cultivation of plants in culture solutions of various concentrations and osmotic potentials. Knowledge of the mechanism of ion absorption was obtained by short-term studies of the absorption of cations by excised roots.
Assessing the feasibility of assisted colonisation to reduce climate change extinction risk for Western Cape proteaceae
(Stellenbosch : Stellenbosch University, 2021-12) Vanmali, Namita Madhu; Midgley, Guy F.; Foden, Wendy
ENGLISH ABSTRACT: Anthropogenic climate change may be testing certain species’ abilities to adapt via range migration, or natural selection in situ. Particularly vulnerable species have restricted ranges and limited dispersal capabilities – characteristics of many endemic species found in the Cape Floristic Region (CFR). Many have evolved anti-telechory, including several Proteaceae species, and may thus require active conservation interventions to ensure their future persistence in the wild. Assisted Colonisation (AC) is a conservation strategy aimed at reducing species’ climate change-induced extinction risk, but no detailed assessments exist of the feasibility of assisted colonisation in the CFR context. By combining Species Distribution Modelling (SDM) outputs for 191 Proteaceae species under future climate scenarios, with selected species traits and land-use maps, this study developed a hierarchical screening approach to identify potential assisted colonisation candidates in the CFR. Using projections over shorter time periods allowed for more potential assisted colonisation candidates to be identified and using life-history traits in conjunction with spatial projections shifted the prioritisation of some assisted colonisation candidates. Thirty-one potential assisted colonisation candidates were identified and subset into three types: Sustained intervention, Short-term intervention, and Mitigation dependent candidates, indicating different degrees of active intervention. The Mitigation dependent candidate group highlighted the potential for future global emissions reductions to reduce extinction risk for several assisted colonisation candidate species projected to become highly vulnerable after 2040. Vulnerable species not suitable for assisted colonisation were also identified. Some implicit assumptions behind assisted colonisation implementation were explored using field measurements on selected populations of Protea compacta, a species historically planted and harvested for the cut flower industry. P. compacta allowed exploration of ecological performance differences across a range of environmental suitability levels. P. compacta populations were targeted in sites defined by species distribution models (SDMs) as having high bioclimatic suitability in ‘core’ range sites, supporting naturally established populations, and sites of ‘marginal’ bioclimatic suitability, occupied by artificially introduced populations. The latter represents a pragmatic assisted colonisation approach – establishing populations in marginal sites that are projected to become more suitable with progressive climate change. Microhabitat buffering against low suitability in a marginal site was also explored. Measurements unexpectedly showed individuals in marginal sites had higher growth and flowering rates, but higher disease susceptibility. Additionally, the densely populated core sites showed significantly more monopodial branching, and sympodial branching in marginal sites, suggesting that the relaxation of strong intraspecific competition in marginal sites may compensate for lower population densities, supporting population establishment, and thus favouring the practical implementation of assisted colonisation. This pattern was confirmed by a finer-scale study at a marginal site, where high population densities found in wetter microhabitats showed growth and flowering responses similar to those in core populations. This supports the idea that purposeful microhabitat choices may buffer marginal unsuitability and increase likelihood of successful assisted colonisation implementation. This work has allowed for a novel assessment of the feasibility of assisted colonisation in the CFR, but assessment of unintended consequences and generalising to more species and systems is necessary to further establish a basis for considering assisted colonisation implementation.
Assessing the invasiveness of Acacia stricta and Acacia implexa : is eradication an option?
(Stellenbosch : Stellenbosch University, 2012-03) Kaplan, Haylee; Wilson, John R.; Richardson, David M.; Le Roux, Jaco J.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: This thesis investigates the invasiveness and current status of two Acacia species recently identified as invaders in South Africa in order to determine the feasibility of their eradication. Australian acacias are among South Africa’s worst invasive species and many have had widespread damaging impacts on native ecosystems. In addition, several Acacia species still exist as small isolated populations in the country and have been targeted for eradication in order to prevent potential widespread impacts. This work assesses Acacia implexa (Chapter 2) and Acacia stricta (Chapter 3) as potential eradication targets by quantifying the extent of their invasion in South Africa, assessing the risk they pose to the country and evaluating the feasibility of their eradication based on estimated costs of clearing. Results of formal risk assessments show that both A. implexa and A. stricta should be considered high risk species, and bioclimatic model predictions indicate that both species have large potential ranges in South Africa. Detailed population surveys found that A. implexa and A. stricta each occur at several distinct localities all in the Western Cape Province. Acacia implexa populations were found at three sites (Tokai, Wolseley and Stellenbosch) where they have densified by means of vegetative suckering allowing A. implexa to outcompete native vegetation. No evidence of large seed banks of A. implexa were found, however vigorous resprouting following damage makes the control of A. implexa difficult. Acacia stricta was found at nine localities all in the Knysna area of the Garden Route, where populations are spreading along disturbed roadsides in plantations. Acacia stricta produces large amounts of seeds and can accumulate large seed banks. Seed spread is most likely due to large-scale soil movement by road maintenance vehicles which can easily lead to the establishment of new populations. We therefore used a predictive risk mapping approach based on the association of A. stricta to roadsides and disturbed plantations to enable effective searching to detect all infestations of A. stricta. Based on the high risk of both species and the limited range sizes of the currently known populations, we recommend that A. implexa and A. stricta remain targets for eradication. Management strategies proposed for these species (Chapter 4) include clearing on an annual (in the case of A. stricta) or biannual (for A. implexa) basis to prevent seed production, and targeted awareness campaigns at a national scale to determine whether our current knowledge of the extents of A. implexa and A. stricta are accurate. This work has shown that detailed assessments of species at intermediate stages of invasion is an important initial step in an eradication attempt, and better understanding of species specific invasion characteristics can help to improve management and potentially increase the probability of success of eradication.
Assessing the phylogeography and metabolomic signatures of wild rooibos (Aspalathus linearis) ecological populations
(Stellenbosch : Stellenbosch University, 2021-04) Brooks, Jolene; Makunga, Nokwanda; Malgas, Rhoda R.; Roodt-Wilding, Rouvay; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Aspalathus linearis (Burm. F.) R. Dahlgren, Fabaceae, is an entirely endemic fynbos species, limited to the Cape Floristic Region of South Africa. It is commonly known as rooibos, and is enjoyed as a herbal tea by many South Africans. It is sought after for its health-promoting effects, particularly its antioxidant, antispasmodic and antiaging potential owing to its phytochemical profile. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics and is classified into ecological types (ecotypes). Ecotypes can broadly be distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. These ecotypes are perceived as being variable and distinct by local harvesters and land-user communities, who possess traditional ecological knowledge associated with its rooibos population. Scientific studies have complimented this traditional knowledge to characterise and create a detailed account of morphological, chemical and ecological differences between ecotypes, coupled to their geographical location. Variability among wild rooibos populations were investigated to determine the impact of environmental influences and biochemical differences on genetic variability. Few studies currently exist that address the genetic characterisation and diversity of wild rooibos. The study described here focuses on the metabolomic and genetic variation between six collected wild ecotypes, occurring in the Cederberg Mountains of the Western Cape and the Suid Bokkeveld and Nieuwoudtville area of the Northern Cape. Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) revealed three main metabolomic clusters, yet each population showed distinct chemical profiles. The principal component analysis (PCA) displayed unique chemical profiles between collected wild resprouter populations of the Northern Cape versus the reseeder populations of the Cederberg. The PCA analysis explained 36.79 % of the total variance. Metabolites were identified using a systematic semi-targeted approach and it is also in these plants that several unknown metabolites were detected in this rooibos populations. Overall, the Dobbelaarskop population appeared to have higher concentrations of the metabolites in comparison to the other populations. Dobbelaarskop had the highest relative concentration of aspalathin (165 mg/kg dry weight). Heuningvlei had a relative concentration of 50 mg/kg dry weight of nothofagin, while the rest of the populations contained less than 20 mg/kg dry weight. Overall, plants from the Jamaka region had consistently lower metabolite concentrations than the other populations. Phylogeographical analysis of both chloroplast and newly developed species-specific nuclear markers (microsatellites) was performed on the collected populations. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in Aspalathus linearis. From the diversity indices, it is evident that the wild rooibos populations have low-to- moderate genetic diversity. The Jamaka population had the lowest haplotype diversity (0.286), and the lowest nucleotide diversity (0.006) even though haplotype diversity generally varied considerably across the wild populations (h = 0.286 - 0.900). The data revealed large variations in haplotype diversity and nucleotide diversity between populations and between regions. Our data suggests that populations of rooibos become less diverse from the Melkkraal population down towards the Cederberg populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei and Jamaka (FST = 0.101), and Blomfontein and Jamaka (FST = 0.101). There was also a significant correlation between geographical distance and genetic distance (R2 = 0.296, P = 0.044). The presence of three main clusters are also clearly reflected in the discriminant analysis of principal components (DAPC) based on the newly developed set of microsatellite markers. This study has successfully established a best practice protocol and provided a highly regenerative plant growth regulator (PGR) regime for shoot multiplication and in vitro seed (cultivated type) germination of Aspalathus linearis. A combination of smoke and sulphuric acid scarification of 20-30 minutes yielded the highest germination rate of cultivated seeds. The PGR ratios, 1:0 and 3:0 [benzyladenine (BA): 1-naphthaleneacetic acid (NAA)], resulted in micropropagules with longer stems and an increase in number of leaves. A phytohormone combination of 5 BA: 3 NAA resulted in callus formation and root growth. The chemical profiles provided by this study are complementary to the novel contribution of genetic characterisation of wild rooibos. These findings may be useful in identifying unique populations for agricultural, phytopharmaceutical or industrial purposes without overlooking conservation and sustainable harvesting priorities.
Assessment of genomic diversity and population sub-structuring of kingklip (Genypterus capensis) off Southern Africa
(Stellenbosch : Stellenbosch University, 2019-03) Schulze, Melissa Jane; Von der Heyden, Sophie; Henriques, Romina; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Kingklip (Genypterus capensis) represents a valuable marine resource for both South Africa and Namibia. Historical exploitation levels led to substantial declines in abundance, resulting in the species being considered over-exploited in the past. Currently, there is a lack of consensus regarding kingklip stock structure, with previous studies providing evidence for both multiple and single stocks. Understanding stock structure is vital for the appropriate assessment and management of marine resources. Taking into account both the commercial importance and trans-boundary nature of this species, it is therefore evident that a consensus regarding the fine-scale genetic structure is needed in order to best inform future management decisions. Next Generation Sequencing (NGS) has revolutionised population genetics allowing for the sequencing and identification of thousands of loci at reduced costs, thereby helping to identify weak genetic differentiation and adaptive divergence even in species with high gene flow levels. By employing a pooled ezRAD sequencing technique, the first chapter of this thesis isolated and identified a novel set of genome-wide molecular markers (Single Nucleotide Polymorphisms – SNPs). Over 40 000 SNP loci were identified in chapter 1, both neutral as well as putative outlier loci, potentially under selection. The second chapter of this thesis subsequently employed the SNP database developed in chapter 1 to investigate i) the relation of previous genetic versus genomic divergence levels and patterns of sub-structuring along the South African coastline, as well as ii) genome-wide patterns of fine-scale sub-structuring along Kingklip’s southern African distribution, thereby providing novel insight into the genetic relation of Namibian and South African Kingklip. Overall, the results of chapter 2 provided evidence for a three-stock hypothesis with signficant levels of adaptive divergence identified between “Northern Benguela” (North of Lüdertiz), “Southern Benguela” (South of Lüderitz to Cape Agulhas) and “Eastern Cape (Cape Agulhas to Algoa Bay) populations. However, adaptive divergence appears to be occuring in the face of high levels of gene flow, thereby creating a dynamic system across the southern African distribution. Based on the findings of chapter 2, the third chapter addresses management recommendations and the potential for the use of the newly developed marker panel for future Kingklip fisheries management.
An assessment of invasive predatory marine crabs and the threat they pose along the South African coastline
(Stellenbosch : Stellenbosch University, 2017-12) Swart, Cheruscha; Robinson-Smythe, Tammy; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Invasions by marine alien species are occurring at an unprecedented rate and are known to negatively impact upon society and biodiversity. Due to the weak regulatory forces exerted by native predators, South African intertidal systems could be considered vulnerable to the invasion by predatory crabs. As this group has been suggested as one of the most successful marine invasive taxa and can have negative ecological impacts in recipient regions, mitigating their potential establishment is important. As such the main aim of this study was to review global invasions by predatory crabs, assess their ecological impacts and finally create a watch-list of species that could establish along the South African coastline under both current and predicted future temperature regimes. As part of the review, a list was developed of all predatory crab species reported as alien. Additionally, their global occurrence, vectors and potential traits associated with their successful establishment were documented. In total, 56 alien crab species were recorded with more than half these being documented in the last two decades. The majority of species originated from the North West Pacific, while the Mediterranean received more alien crabs (33 species) than any other bioregion. Shipping, specifically ballast water, has been responsible for the majority of introductions. Unexpectedly, no biological or ecological traits could be identified as good predictors of establishment success in crabs. While this work identified the most important vectors and most invasive crab families, it emphasises the need for more studies considering the basic biology of these crabs so as to improve our understanding of the traits governing their invasion. The Environmental Impact Classification for Alien Taxa (EICAT) was used to assess the impacts of the species identified in the review. It was found that impacts had been quantified for only 9% of the 56 alien crab species. Thus, only five species could be allocated EICAT ratings due to the data deficiency of the remaining 51 species. The Japanese shore crab Hemigrapsus sanguineus was rated as having Major impacts, while impacts of the remaining four species, the Chinese mitten crab Eriocheir sinensis, European shore crab Carcinus maenas, Indo-Pacific swimming crab Charybdis hellerii and brush-clawed shore crab Hemigrapsus takanoi were rated as Moderate. To create an ordered watch-list for South Africa, species that could be expected to reach the region, on account of the pathways they are associated with, were identified. Their realised temperature ranges were compared to that of each of the four South African marine ecoregions and finally they were ranked based on their EICAT rating. In total, 28 alien crab species had pathways to reach South Africa, with shipping highlighted as the most important pathway. At least 26 species could survive along the South African coast under both present and predicted future temperatures, with warm water species being excluded from the cool west coast and temperate species excluded from the warm east coast. Three species, H. sanguineus, E. sinensis and H. takanoi were placed on the top of the watch-list due to their negative ecological impacts identified by the EICAT scheme. This study provides the first South African horizon scanning assessment to identify and prioritise potential marine alien species. This watch-list can be used to support at-border management enabling the fast response to new arrivals, ultimately minimising chances of establishment of these alien crabs along South African shores. This thesis has provided a detailed global review of predatory marine crab invasions. It has highlighted that despite few studies quantifying impacts of these invaders, it is clear that they can have notable ecological impacts in recipient regions. Nonetheless, there is a dire need for more research into their impacts so as to support evidence based management. Until such evidence becomes available it is suggested that a precautionary approach be applied when managing alien crabs.
An assessment of Melaleuca (Myrtaceae) as invasive species in South Africa
(Stellenbosch : Stellenbosch University, 2017-03) Jacobs, Llewellyn E. O.; Wilson, John R.; Richardson, David M.; Stellenbosch University. Faculty of Science. Dept. of Botany and Zoology.
ENGLISH ABSTRACT: Evaluating potentially invasive plants is an important part of invasive species management. Reports of several naturalized and invasive Melaleuca species in South Africa prompted an investigation into which species are in the country and of these which pose a risk. I evaluated two Melaleuca species in South Africa, differing in initial invasive risk profile (Chapters 2 and 3); assess the invasion status of Melaleuca species introduced to South Africa, while identifying errors in taxonomic identification (Chapter 4); and explored how some traits influence invasiveness in this group (Chapter 5). In Chapter 2 I document and assess management options for the first reported invasion of Melaleuca parvistaminea Byrnes (initially identified as M. ericifolia) in the world, in the context of a South African wetland ecosystem. Delimitation surveys indicate that the entire invasion is restricted to three sites between Tulbagh and Wolseley in the Western Cape province and that populations are confined to areas that were currently or previously covered by pine plantations (primarily Pinus radiata). To estimate levels of abundance I surveyed 42 % of the three identified areas and found ~26 000 plants over 1800 ha (condensed canopy area of 1.15 ha). At least 63 % of recorded plants were seedlings or juveniles, mostly < 4yrs old, and most occurred in seasonally inundated (but not waterlogged) habitats. Melaleuca parvistaminea creates monospecific stands that overtop the native shrubland vegetation (Breede Shale Renosterveld) and is thus considered a potential transformer species. Species distribution modelling identified large areas of climatically suitable habitat in the Western Cape, pointing to substantial invasion debt for the species in South Africa. Felling triggers seed release from serotinous capsules, resulting in prolific seedling recruitment after winter rains (up to ~18 000 seedlings/m2). No evidence of a soil-stored seed bank was found, and when plants are cut at ground level or treated with herbicide after cutting, plants do not resprout. The invasive populations of this water-dispersed species are close to major rivers (the Berg and Breede), but the intervening countryside is largely transformed and is unfavourable for establishment. Much of the area downstream from the invaded area is open vegetation that is unsuitable for major recruitment; this area would be easy to survey and detect small plants. Consequently, although the extent of invasion is large (potentially 9185 ha), the invasion can be delimited with some confidence, and eradication is considered achievable since seeds only survive for about a year, seedlings achieve maturity after 4 years, and the species is an obligate reseeder. Given the threats posed, eradication is desirable and M. parvistaminea should be listed as a category-1a invader (requiring compulsory control) under the Alien and Invasive Species Regulations of South Africa's National Environmental Management: Biodiversity Act (10/2004). I estimate that search-and-destroy operations could eradicate the species by 2021 at a cost of ZAR 3 475 000 (US$ 355400). Chapter 3. The discovery of a naturalised population of Melaleuca quinquenervia in South Africa in 2009 prompted an evaluation of the species’ distribution across South Africa. I found records at seven localities in two of the nine provinces of South Africa, with naturalized populations at two sites—~300 plants were discovered over 0.3ha in a confined-seep on a mountain slope, while at an old arboretum 12 large, planted trees and 9 naturalised trees were found. An additional herbarium record from Mozambique suggests that this global invader is present at other sites within the sub-region. This means that although the extirpation of populations in South Africa is recommended (and seems feasible), further work is required to determine the status and evaluate whether eradication from the sub-region is possible. Chapter 4. Lists of introduced species provide essential background information to inform management of, and research on, biological invasions. The compilation of these lists is, however, prone to a variety of errors. I highlight the frequency and consequences of such errors using introduced Melaleuca (sensu lato, including Callistemon) species in South Africa as a case study. I examined 111 herbarium specimens from South Africa and noted the classes and types of errors that occurred in identification. I also used information from herbarium specimens and distribution data collected in the field to determine whether a species was introduced, naturalized and invasive. I found that 72% of the specimens were not named correctly. The inaccuracies were due to human error (70%) (misidentification, and improved identifications) and species identification problems, (30%) (synonyms arising from inclusion of Callistemon and unresolved taxonomy). At least 36 Melaleuca species have been introduced to South Africa, and field observations indicate that ten of these have naturalized, including five that are invasive. While most of the errors likely have negligible impact on management, I highlight one case (M. parvistaminea) where incorrect identification led to an initially inappropriate management approach and the initial error was propagated in later lists of invasive species. Invasive species lists need to be carefully reviewed to minimise errors, and herbarium specimens supported by DNA identification are required where identification using morphological features is particularly challenging. Chapter 5. To improve prediction of which Melaleuca species could become naturalized or invasive I assessed a variety of traits for 36 Melaleuca species in South Africa. I collected information on traits that reflect species characteristics, biogeographic and human-usage patterns, and looked for predictors of invasiveness and naturalisation using generalised linear models. Residence time for Melaleuca species in South Africa is strongly positively correlated with naturalization, indicating that an invasion debt for the 27 non-naturalized species might exist. Native range size (using the convex-hull methodology) is not an important correlate for ability to naturalise or invasiveness. This indicates that stochastic factors like fire and finer scale habitat requirements may play a bigger role in invasion. The thesis is a contribution to the study of model groups in invasion biology (Kueffer et al., 2013). The case studies for M. parvistaminea and M. quinquenervia highlighted the need for early detection and provided practical management guidelines and recommendations for the entire group. Chapter 4 contributed a specimen-based list of Melaleuca species present in South Africa that included information on the introduction status for each species. The need for accuracy in invasive species lists was also highlighted with recommendations as to how this could be addressed. The prediction of risk was informed by the traits analysis, emphasizing residence time as a key predictor, while also comparing and contrasting findings in previous studies. Thus this study combines elements informing the management of biological invasions while furthering current knowledge in the field.

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