School of Botany - Theses
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ItemDissecting antibiotic targeting in the malaria parasite Plasmodium falciparum(University of Melbourne, 2008)
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ItemThe saltmarshes of the southern coast of Victoria : floristic composition, variation and distribution(University of Melbourne, 2005)Although there has been some ecological analysis of Victoria�s saltmarshes, it has been predominantly based on observations and descriptive analyses. As Victorian saltmarshes face the continuing risk of destruction and degradation due to the effects of increasing urbanisation and global climate change, it is imperative that their composition and variation are quantified in order to develop appropriate conservation and management strategies. The past distribution of saltmarshes on the southern coast of Victoria was calculated using geographic and environmental data. Past distribution was compared to present distributions provided by the FIS database form the Department of Sustainability and Environment. The results indicate that only 45% of the saltmarsh that once covered this region remain intact. Many losses occurred prior to the legal protection of the coast from 1978 and are the result of land clearance for industrial uses such as salt production and waste treatment as well as agriculture the subsequent grazing of the region. Saltmarsh vegetation in Port Phillip and Western Port Bays was classified using the Department of Sustainability and Environment�s Flora Information Systems (FIS) database and compared with a 2003 field survey using a systematic, random sampling method. The non-metric multidimensional scaling (NMDS) ordination of the sites identified from the FIS database showed a distinct separation of samples from each of the saltmarsh communities sampled along the coast. In comparison, the 2003 survey results showed relatively little if any separation based on site location indicating that the sites all had similar vegetation composition. The exclusion of the non-indigenous species from both data sets indicated that non-indigenous species contribute to the convergence in the floristic composition between sites, but do not greatly effect the grouping of the sites. The differences between the two data sets were attributed to sampling methods and a number of limitations involved in using FIS data were identified. The usefulness of the FIS database for classifying saltmarsh vegetation would be improved with the inclusion of more information, such as quadrat size and placement details, when entering records. The results of the 2003 field survey were used to compare the floristic composition of Victorian saltmarsh vegetation along the southern coast of Victoria ranging from Portland to Shallow Inlet. A non-metric multidimensional scaling (NMDS) ordination and analysis of community similarity (ANOSIM) showed the floristics of each site to be very similar. The two most dominant species recorded were Sarcocomia quinqueflora and Sclerostegia arbuscula. Although the different communities from along the coast share similar floristic composition the presence of a number of less common species, which do not occur at all sites, contribute to the overall diversity of Victoria�s coastal saltmarshes. The lack of non-indigenous species in the vegetation indicates that they are not currently subject to exotic species invasion. This is most likely due to the harsh growing conditions that are typical of saltmarsh communities. However, the threat of invasion is always present due to surrounding areas of high weed cover. Environmental variables were correlated to the ordination of the sites indicating that although electrical conductivity is a factor in determining species composition it explains less than one third of the variation between sites
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ItemDetermining the optimal captive management of the helmeted honeyeater (Lichenostomus melanops cassidix) using stochastic dynamic programming(University of Melbourne, 2005)This thesis investigates the use of stochastic dynamic programming (SDP) in assisting managers of the helmeted honeyeater with decisions relating to the movement of birds in and out of captivity. SDP is a state dependent decision-making tool that requires a model to explain how the population responds to different management actions in different circumstances, or states. This model is then used to determine what strategy is best to meet a specified management objective. Three models were constructed, two addressing the optimal number of helmeted honeyeaters to move into or out of captivity and one addressing optimal resource allocation between two release methods. Optimal solutions produced from the SDP that used a general model of helmeted honeyeater dynamics were robust to moderate changes in most parameter values and performed better than strategies that moved a certain proportion of individuals into a population that fell below a given threshold. Results were similar to a investigation by Tenhumberg et al (2004), which also used SDP to determine the optimal number of individuals to move between wild and captive populations. The second and more complex model of helmeted honeyeater dynamics addressed most of the limitations of the previous model and incorporated a decision set that is more applicable to the helmeted honeyeater. Model structure and SDP parameters, such as timeframe and objective, could have very large effects on the optimal solution. Results suggest that more captures than have typically occurred at relatively large Yellingbo population sizes is the best option in most scenarios. To increase certainty in decisions at lower Yellingbo population size, more precise estimates of the cost of taking eggs from the wild and the benefit of bringing them into captivity are needed. When the captive population is full, and the target population is not, releases were optimal in almost every case. Recommendations for the current population sizes are releases in groups as large as possible from captivity and no captures from Yellingbo. The allocation of resources between two release methods was strongly influenced by the number of success previously achieved with the cheap method and the relative cost. For the levels of relative cost investigated, a very low level of cheap method success was necessary to allocate resources to the expensive strategy. If the range for the possible success rate for an expensive strategy is not substantially larger than that obtained with the cheap method resources should continue to be allocated to the cheap method. In the case of the helmeted honeyeater, optimistic estimates of expensive method success are large enough and cheap method success rate low enough to justify allocating resources to the more expensive strategy if it is three times the cost of the cheap strategy or less. This SDP provides an effective way of incorporating learning into a variety of decisions, and could be applied to any choice between methods that have individual trials, which can be classified as successes or failures.
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ItemEffective survey methods for detecting plants(University of Melbourne, 2001)Plant survey methods widely used in Australia to compile species lists and conduct baseline surveys are evaluated. In general flora surveys use one of two methods, a fixed- area quadrat or a wandering search. An untested assertion exists in the literature that suggests search sampling is better than quadrat sampling for detecting species. In order to test this claim empirically, an area of sclerophyll forest in southern Australia was sampled intensively using systematic quadrat sampling and search sampling. The number of species detected within quadrat samples was compared to the number detected in search samples. The pattern of species accumulation with time is modeled according to three types of botanical experience: the novice, average and expert searcher. The models are then used to predict the number of species gained with further sampling time. The likelihood of quadrat sampling to detect the same species within search samples is investigated. The expectation of life-form bias in the collections of individual searchers is also analysed. The results suggest that the number of samples taken should be guided by a consideration of how confidently the survey should detect the presence of relatively scarce species. A survey of botanists and biologists confirmed that individuals are poor judges of sample size and subjective estimates should be avoided. The results also suggest that in many circumstances, fixed-area quadrat sampling is preferable to search sampling. Measures of the adequacy of vegetation surveys are suggested.
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ItemEstablishing and elucidating conditional genetic manipulation of the malaria parasite, Plasmodium falciparum( 2013)Methods to alter gene function in Plasmodium are barely out of infancy, with much growth occurring within the past five years via adaptation of protocols established in other species. In this thesis, a method where the parasite’s innate ability to control gene expression in response to environmental stimuli, and a synthetic small molecule regulated protein stability system were applied to change the phenotypic expression of introduced transgenes. In chapter 2, we aim to control activity of a temperature sensitive mutant FLP recombinase protein. Our goal was to induce FLP activity and thus change the open reading frame of a GFP expressing plasmid to mCherry using single site recombination. Dual transgenic parasites were placed in a variety of conditions to favour FLP activity and to prevent negative selection. No evidence of conditional genetic recombination or phenotypic change from green to cherry was observed. Direct expression of FLP during a short period of drug selection produced a mixed population of GFP and mCherry genotypes. The activity of FLP is inefficient and was deemed unsuccessful for our goal of raising transgenic parasites poised for conditional genetic recombination. A homogenic population of mCherry genotypes by successful recombination of the GFP ORF was achieved after drug-cycled expression of evolved FLP (FLPe). Chapter 3 focuses on turning the Plasmodium specific phenomenon of altering rRNA expression profiles in response to fluctuations of temperature and glucose concentration into a tool suitable for conditional gene expression. We copied the promoter region of the S2-Type rRNA gene and measured its ability to express luciferase in altered environmental conditions. A low level of basal activity was observed during the intra-erythrocytic developmental cycle, with expression peaking at levels similar to the weak chloroquine transporter (CRT) promoter during the trophozoite stage. The S2-Type rRNA promoter region did not produce a notable increase of luciferase transcription or activity in response to environmental change. Use of the S2-Type rRNA promoter to express FLP at the enzymatic favourable temperature of 26°C did not result in genetic recombination. The tools developed are capable of expressing transgenes, however their ability to conditionally alter the gene product is limited.
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ItemThe ecology and ecophysiology of Caulerpa in Port Phillip Bay( 2012)While recognized as a key ecosystem component since at least the 1960s, Caulerpa has not received the attention that Port Phillip Bay (PPB) sediment, pelagic, reef and seagrass ecosystems have. Contemporary data on native PPB Caulerpa populations are a notable omission from the global literature on the genus. The genus Caulerpa has been heavily researched on a global scale for at least the past two decades, mostly due to the introduction of two species to several ecosystems overseas and in Australia. Here current Caulerpa species distributions were documented and modeling used to elucidate correlations with environmental variables. The ecophysiology of Caulerpa remotifolia was investigated using PAM fluorometry due to its broad environmental distribution. Current Caulerpa species distributions and abundance in western Port Phillip Bay were found to be consistent with historical records. Cross-validated Boosted Regression Tree models applied to data on three Caulerpa species distributions were able to model strong relationships between distributions and predictor variables (giving high correlations (0.66-0.80) and ROC scores (0.86-0.97)). Environmental variables describing substrate availability were consistently the most influential predictors of distributions while light and nutrient availability were also important. Caulerpa longifolia was mostly confined to the area adjacent to the Western Treatment Plant wastewater discharges; an area also having high Caulerpa species richness. Caulerpa remotifolia was the most widely distributed in both environmental and physical space; over most of its range it appears to be epizoic on the benthic ascidian Pyura dalbyi. Caulerpa sedoides was mostly confined to the deeper areas; their fine organically rich sediments indicating a role for it in sediment biogeochemistry. Caulerpa remotifolia was found to have substantial physiological plasticity over daily and seasonal variations in light availability. Despite low light availability and temperature in winter this species was able to achieve photosynthetic rates only slightly lower than in summer. Nutrient status appears to reflect C. remotifolia light harvesting efficiency suggesting a role for nutrients in its acclimation to light availability. Physiological plasticity of C. remotifolia’s photosynthetic apparatus explains some of its success in Port Phillip Bay. The prevalence of Caulerpa in the PPB ecosystem warrants substantial further investigation, especially regarding its role or services to the ecosystem, temporal dynamics and ecophysiology. This study provides suggestions of avenues for such investigation.
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ItemBayesian modelling of tree mortality( 2012)In this work I aimed to relate two topics of importance in applied ecology and the statistical analysis of ecological data: the challenge of analysing tree mortality data and the use of informative priors in Bayesian ecological models. To achieve these aims I conducted analyses on two separate case studies of tree mortality. The first study concerned the mortality of transplanted eucalypt tree seedlings during an experiment carried out in Southeastern Australia. For the second case study I used data collected over 20 years in a 50 ha tropical forest dynamics plot located in Northern Thailand. A key challenge when modelling death data is how to account for a hazard that varies through time. Ignoring a variable hazard leads to biased estimates of mortality rate. I identified evidence of a declining hazard rate in the eucalypt seedling data. To account for a potential source of bias in estimating the mortality rate of the seedlings I introduced a novel method whereby the expected mortality is a function of the sum of mortality experienced in the past. Bayesian methods have become common in the ecological research literature. Yet ecologists rarely use informative priors in their Bayesian models—a feature which has been shown to increase the precision of model predictions. This reluctance may in part stem from a perception that informative priors could introduce bias and lead to less accurate models, compared with those that use uninformative priors or fit with non-Bayesian methods. To date there have been no comprehensive tests of the effect of informative priors on the accuracy of Bayesian ecological models. Using the eucalypt seedling dataset I demonstrate that incorporating an informative prior based on the results of a pilot study does not negatively affect the accuracy of the model, while increasing the precision and making cost-effective use of the available information. With the tropical forest dataset I tested the effect on model accuracy of informative priors. In the first comprehensive test of this kind, I demonstrate that a properly specified informative prior, in this case based on the correlation between tree growth and mortality, will on average have no effect on the accuracy of models of mortality rate.
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ItemAustralasian Huperzia as potential sources of Huperzine alkaloids( 2010)The Lycopodiaceae is an ancient and cosmopolitan family of fern allies that include an estimated 35 Huperzia species occurring throughout the South-East Asian and Australian region. Thirteen species naturally occur in Australia and are found mainly in the tropical rainforests of far north Queensland. Over the past decade, there has been renewed interest in Huperzia and their respective Huperzine alkaloid concentrations following the discovery of Huperzine A (HupA) and Huperzine B (HupB) alkaloids in H. serrata (Thunb. ex Murray) Trevis. Both alkaloids are of pharmaceutical interest since they are highly selective and potent reversible inhibitors of acetylcholine esterase. Huperzine alkaloid concentrations of Australasian Huperzia have not been well documented, and no prior studies have been undertaken to investigate the amenability of Australasian Huperzia to alternative propagation techniques such as axenic culture. This research presents an extensive screen of 16 Australasian Huperzia species to investigate their Huperzine alkaloid concentrations. HupA (0.032 to 1.012 mg g-1 DW) was detected in ten out of the sixteen Huperzia species examined, while HupB (0.008 to 0.339 mg g-1 DW) was detected in eight. From this extensive study, H. elmeri (Herter) Holub was observed as the species with the greatest potential to yield high Huperzine-containing individuals. In addition, the screen established that Australasian Huperzia generally contain higher HupA levels than H. serrata, the main source of commercial HupA, which on average only contains 0.082 mg g-1 DW HupA. The fractionation and spectrometric analysis of alkaloids as part of the screen led to the discovery of three Huperzine alkaloids co-occurring within the same plant: HupA, HupB and Huperzine C, isolated from an individual of an Australian H. carinata (Desv. Ex Poir.) Trevis. The potential of establishing axenic cultures of Australasian Huperzia was also investigated in this research. Actively growing axenic cultures of H. carinata, H. squarrosa (C.Forster) Trevisan, H. phlegmaria (L.) Rothm. and H. phlegmarioidies (Gaudich.) Rothm., together with callus and cell suspension cultures of H. carinata and H. phlegmaria, were successfully established. The results suggest that culturing in total darkness is essential to allow for optimal callus and cell suspension growth. In addition, this study also investigated the possibilities of germinating various Huperzia spores, by both symbiotic and asymbiotic means. Germination of H. squarrosa spores was achieved by both symbiotic and asymbiotic means, and was only observed in cultures which were kept in the dark, implying that there is a form of photo-inhibition mechanism preventing spores from germinating when they are exposed to light. Beneficial effects of various types of spore treatments prior to sowing, in terms of increased spore germination was also observed. In conclusion, the results presented suggest that Australasian Huperzia are indeed a potentially valuable resource for Huperzine alkaloids. The investigations into the conditions required for the successful introduction and maintenance of Australasian Huperzia in axenic culture has also further extended our understanding of these plants, and their amenability towards axenic culture conditions as a means of alternative propagation.
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ItemIncorporating uncertainty into expert models for management of box-ironbark forests and woodlands in Victoria, Australia( 2009)Anthropogenic utilization of forest and woodland ecosystems can cause declines in flora and fauna species. It is imperative to restore these ecosystems to mitigate further declines. In this thesis, I focused on a highly degraded region, the Box-Ironbark forests and woodlands of Victoria, Australia. Rather than mature stands with large trees, stands are currently dominated by high densities of small stems. This change has resulted in reduced populations of many flora and fauna species dependent on older-growth forests and woodlands. Managers are interested in restoring mature Box-Ironbark forests and woodlands through three alternative management strategies: allocating land to National Parks and allowing stands to develop naturally without harvesting, modifying timber harvesting regimes to retain more medium and large trees, or a new ecological thinning technique that retains target habitat trees and removes competing trees to encourage growth of retained stems. The effects of each management strategy are not easy to predict due to complex interactions between intervention and stochastic natural processes. Forest simulation models are often employed to overcome this problem. I constructed state-and-transition simulation models (STSMs) to predict the effects of alternative management actions and natural disturbances on vegetation structure. Due to a lack of empirical data, I relied on the knowledge of experts in Box-Ironbark ecology and management to construct STSMs. Models predicted that the development of mature woodlands under all strategies was minimal over the next 150 years, and neither current harvesting nor ecological thinning is likely to expedite the development of mature stands relative to growth and natural disturbances. However, differences in experts’ opinions led to widely diverging model predictions. Uncertainty must be acknowledged in model construction because it can affect model predictions. I quantified uncertainty due to four sources – between-expert variation, imperfect expert knowledge, natural stochasticity, and model parameterization – to determine which source caused the most variance in model predictions. I found that models were very uncertain and between-expert uncertainty contributed the majority of variance in model predictions. This brings into question the use of consensus methods in forest management where differences between experts are ignored. Using uncertain model predictions to make management decisions is problematic because any given action can have many plausible outcomes. I applied several decision criteria to uncertain STSM predictions using a formal decision-making framework to determine the optimal management action in Box-Ironbark forests and woodlands. I found that natural development is the most risk-averse option, while ecological thinning is the most risky option because there is a small likelihood that it will greatly expedite the development of mature woodlands. Rather than selecting one option, managers could rely on a risk-spreading approach where the majority of land is allocated to no-cutting National Parks and a small amount of land is allocated to the other two harvesting strategies. This would allow managers to collect monitoring data for all management strategies in order to learn about effects of harvesting and update model predictions through time using adaptive management.