School of Botany - Theses
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ItemNo Preview AvailableEvaluating the ecological and operational basis of vegetation condition assessments(University of Melbourne, 2011)Globally, market based policies for biodiversity conservation are emerging that aim to achieve better and more cost efficient biodiversity outcomes than traditional command and control mechanisms. Investment accounting, reverse auctions and biodiversity offsets aim to achieve No Net Loss or Net Gain of biodiversity by incorporating biodiversity into the financial decisions of landholders. Market based policies require a proxy commodity for biodiversity that numerically express the capacity of a given site to support biodiversity, and Australia has pioneered the development of vegetation condition indices for this purpose. For every market based decision, there is a chance that the actual biodiversity outcome will be better or worse than expected. Risks of worse than expected outcomes may have significant financial implications and irreversible repercussions for biodiversity. Uncertainty in estimates of current and future vegetation condition may increase these risks. Despite this, market based policies have not been developed within a risk management framework and no systematic analysis of factors that may contribute to uncertainty in biodiversity valuation has previously been conducted. This thesis evaluates the nature of uncertainties in the ecological and operational basis of vegetation condition assessments, and considers the potential effects of uncertainty on the biodiversity outcomes of market based policies. Chapter 2 proposes a framework for identifying epistemic and linguistic uncertainties in current and predicted future estimates of vegetation condition. It contends that uncertainty may arise due to: i) conceptual uncertainty about the factors and processes that are causally related to the definition of biodiversity value; ii) quantitative uncertainty concerning misrepresentation of causal factors and processes by the mathematical constructs of the index; and iii) data uncertainty arising from errors in the input data. Specific occurrences of these uncertainties are discussed for two Australian vegetation condition indices, BioMetric and Habitat Hectares. It is concluded that the nature of uncertainties in estimates of current and future vegetation condition may increase the risk that any given decision will fail to achieve No Net Loss of biodiversity. Chapters 3 to 5 evaluate sources of uncertainty in current estimates of vegetation condition. Chapter 3 uses empirical biodiversity data to evaluate whether, on average, sites with higher vegetation condition scores support a greater diversity of native species than sites with lower scores. The strength of relationships between species composition and condition scores was primarily driven by plant species, which is included as a predictor variable in both BioMetric and Habitat Hectares. Vegetation condition was very poorly correlated with the richness and diversity of native butterflies and native ants, with the possible exception of very low scoring sites for butterflies. The results suggest that patterns in species composition were driven by factors other than the predictor variables included in the indices, and therefore that conceptual uncertainty may be a substantial cause of poor performance of vegetation condition indices. Chapter 4 empirically investigates the magnitude of uncertainty in estimates of current vegetation condition due to observer error in field estimates of predictor variables. Average coefficients of variation in total vegetation condition scores amongst ten independent observers were 15-18%. All observers estimated vegetation condition scores that were substantially different from the group mean on at least some sites. The results indicate that measurement error in field estimates of site attributes may cause vegetation condition to be under- or over-estimated on all but highly degraded sites. Chapter 5 examines the sensitivity of vegetation condition indices to observer error via simulated scenarios. Larger observer errors caused less precision and greater bias in total scores, although compensatory errors generally led to smaller coefficients of variation in total scores than predictor variables. Unexpectedly, unbiased observer errors in the predictor variables underestimated the true vegetation condition of most sites. The underestimation effect was more significant for sites with intact woody or herbaceous features, depending on the index used. Chapters 4 and 5 highlight the fact that quantitative aspects of vegetation condition indices are as important as the spread and bias of raw observer estimates in determining accuracy of vegetation condition assessments. These operational limitations of vegetation condition indices may significantly increase the risk of worse than expected biodiversity outcomes. Chapter 6 examines the implications of uncertainty in estimates of predicted future vegetation condition for achieving No Net Loss in biodiversity offsets. Expert models of change in 12 vegetation attributes were used to simulate change over time for five states of a grassy woodland ecosystem under six (gain and loss) management scenarios. The quantity of gains that would be required to compensate for each loss scenario (i.e. the offset ratio) was calculated using one method that ignored uncertainty and another that accounted for it. Uncertainty increased the offset ratio up to 1400% where the magnitude of both gains and losses were uncertain, but increased the ratio only marginally where minimal losses were incurred on highly degraded site types and offset with maximal gains. Both vegetation condition indices predicted greatest gains in woody vegetation attributes, which may result in landscape wide decline in herbaceous components of vegetation and their associated biodiversity if policies aim to maximise gains in vegetation condition. The results of this research indicate that aspects of the conceptual, quantitative and data models that underpin biodiversity valuation indices are likely to cause estimates of current and future biodiversity value to be unreliable. Outcomes of market based biodiversity conservation policies would greatly benefit from more rigorous procedures for developing and evaluating biodiversity valuation indices, which systematically identify and minimise uncertainties in the underpinning models. Information about uncertainty should be used in a risk-based approach to decision making in market based policies, whereby only low risk decisions are approved. It will be a shame if the pioneering work Australia has conducted in developing market based instruments for biodiversity conservation, and associated vegetation condition indices, is not used to fully evaluate the potential for overcoming market externalities and achieving optimal biodiversity outcomes for society.
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ItemThe sanitisation of urban ecosystems: simplification of the ground layer in eucalypt woodlands and the effects on arthropod communities( 2011)Green spaces in urban environments can provide valuable habitat for maintaining local and regional biodiversity. Many urban green spaces are, however, managed for human recreation, where the vegetation structure is reduced, and critical resources such as leaf litter and woody debris are removed. Reductions in ground layer resources have been implicated in the decline of urban vertebrate biodiversity, but the effects of this process on arthropod communities is poorly understood. The response of the ground-active arthropod community to differences in ground layer resources was studied in green spaces managed for human recreation compared to areas maintained in a ‘natural’ state, at 21 field sites in Melbourne, Australia. Sites were separated into two categories: 1) areas with high leaf litter levels (remnant woodland patches) and 2) areas with reduced leaf litter layers, which were regularly mown (public parks). All sites had overstoreys of Eucalyptus camaldulensis. Site assessments confirmed litter layers were greatly reduced in abundance and extent in public parks, and also showed that these sites had less vegetation in the mid- and over-storey, and fewer dead wood resources. The arthropod communities at the sites were examined at order level, and millipede (Diplopoda), slater (Isopoda: Oniscidea), ant (Hymenoptera: Formicidae) and beetle (Coleoptera) communities were examined at species-level. The millipede and slater (macrodetritivores) communities were made up almost exclusively of introduced species from Europe. Although they were able to persist in both Parks and Remnants, their abundance was greatest where there was more leaf litter and shrub cover. In contrast, the ant fauna was diverse, abundant and native at all sites, but had a different community composition at Parks compared to Remnants. These differences were associated with both local- and landscape-scale features of the sites. The beetle community showed strong changes in composition and diversity in response to differences in the leaf litter layer as well as to the composition of the ground layer species. The response of the invertebrate fauna to small-scale manipulations of common urban ground covers – bare ground, leaf litter, woodchips and grass – was investigated experimentally at a semi-field site. Diverse arthropods rapidly colonised previously cleared plots under all four ground covers and were most abundant in grass plots. This is likely to be related to the landscape context of the experiment and has important implications for small-scale landscape management for biodiversity conservation. This thesis provides information on the role of urban, managed green spaces for arthropod biodiversity conservation, and contributes to our understanding of the effects of management practices that influence the arthropod community composition and diversity in these areas. Green open spaces (parks) were not found to provide the same resources for ground-dwelling arthropods as woodland remnants, and this was associated with marked changes in their community composition. The findings have important implications for biodiversity conservation in an urbanising world.
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ItemThe intersection of ecology and evolution: a case study of Eucalyptus in the Grampians Ranges, Australia( 2011)This thesis explores the ecology and evolution of Eucalyptus species in the Grampians ranges, Australia. The Grampians ranges are an ancient isolated collection of three ranges with steep habitat gradients relative to the surrounding homogeneous landscape. This region is a local centre of species diversity and endemism, in which many closely related species interact. I use a range of approaches to understand the ecological and evolutionary history of contemporary patterns of species distribution, traits, and co-occurrence. First, I investigate speciation and gene flow for a clade of Eucalyptus endemic to high elevation rocky outcrops in the Grampians. I document chloroplast DNA structure for the three high elevation species (E. serraensis, E. verrucata, and E. victoriana) and a neighbouring species E. baxteri, which surrounds endemic populations. I found generally high chloroplast diversity, local genetic structuring, and local interspecific gene-sharing. Second, I broaden the scope to include all 20 Eucalyptus species in the region. I am generally interested in relations between species, functional traits, and environments. I model the distribution of species across environmental gradients using a modern niche modelling technique. I incorporate species interaction terms and model groups of species across a taxonomic hierarchy to explore species and clade interactions. Using a subset of variables found to be important in niche models, I then used a hierarchical modelling approach that describes how species responses to environmental variables change as a function of their traits. I used traits from the leaf-height-seed strategy scheme (specific leaf area (SLA), maximum height and seed mass). I found a range of important trait-habitat associations. For example, SLA modified species responses to rock cover such that thicker, denser leaves were found on rocky areas with less soil. Seed mass was associated with edaphic variables such as valley bottom flatness and soil texture. Maximum height of species increased with solar radiation and rainfall. Third, I explored the evolutionary history of these trait-habitat associations with phylogenetically independent contrasts using a phylogeny and niche model estimates. I found a general progression from early divergence of seed mass-edaphic associations to late divergence of height-climatic associations. SLA diverged early with edaphic associations and later with climatic associations. I interpret the early edaphic- late climatic- associations divergences with the paleoclimatic and geologic processes of the Grampians region. Finally, I again explore trait, niches, and phylogenetic relationship, this time in the context of local species assemblages. I address the longstanding observation that within large genera, closely related species do not co-occur in local neighborhoods. I find that habitat drives species assemblages except when species interbreed. I attribute the lack of co-occurrence of reproductively compatible species to reproductive interference via hybridization and introgression. Results from the initial genetics study confirm the importance of geneflow for these species. This approach describes a genetic mechanism underlying an ecological pattern and provides a cohesive story of the ecology and evolution of Eucalyptus in this region.
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ItemThe epidemiology and control of spot form of net blotch of barley in Victoria, Australia( 2011)Spot form of net blotch (SFNB) caused by the fungus Pyrenophora teres f. maculata is a relatively new foliar disease of barley in Victoria. It was first detected during the 1990s and has since become common throughout, due to widespread adoption of stubble retention practices and the cultivation of susceptible varieties. Due to the relatively recent establishment of SFNB, current importance and management strategies have not been investigated. This thesis describes the prevalence of SFNB in Victoria, the associated production loss, effectiveness of chemical fungicides and host plant resistances for future management of this disease. Additionally the genetic and pathogenic diversity of the pathogen population and its ability to develop new virulent pathotypes is reported. The importance of SFNB was investigated during surveys of foliar diseases in barley crops throughout Victoria during 2007, 2008 and 2009. Pyrenophora teres f. maculata was present in more than 90% of crops with severity of up-to 56% on the top three leaves. Severity was typically less than 1% and as a result approximately 25-51% of barley crops grown in Victoria would have experienced grain yield loss, of which the majority was less than 6%. Spot form of net blotch caused significant reductions to grain quality in the Wimmera region of Victoria, with measurements of screenings and retention significantly reduced at two and four out of five trial sites, respectively. This indicates that while SFNB infection was common in barley crops of Victoria, significant production loss was restricted to a low percentage of crops where disease pressure was high. To manage SFNB, a single application of chemical foliar fungicide (propiconazole) was applied at different growth stages of crop development where disease pressure was high. A single application of foliar fungicide at stem elongation (Z31) or flag leaf emergence (Z39) consistently provided the best suppression of SFNB infection, however, these applications did not always maximise grain quality. A range of different fungicides applied to the seed were ineffective in controlling SFNB in the field. Cultivation of barley varieties with host resistance is the best strategy for managing SFNB in Victoria. However, this is reliant on the identification of suitable resistance sources for inclusion into breeding programs. The resistance response of ninety-three barley lines with diverse genetic background was tested toward Australian and North American isolates of P. teres f. maculata as seedlings and as adults. In general, seedling and adult plant resistance was not related with two and fifteen resistant lines identified, respectively. These lines require further investigation to determine the resistance genes involved and to identify suitable molecular markers for their identification in breeding programs. The effectiveness of seedling, adult and complete host resistances in four barley lines was tested. The var. Barque, which possessed complete resistance to SFNB, provided the best control. Varieties with resistance effective at the seedling and adult stages provided control of SFNB in most cases but were generally less effective than Barque, indicating that multiple partial resistances may be required to provide adequate resistance. The population of P. teres f. maculata is genetically and pathogenically diverse and potentially able to overcome host resistances. Analysis of P. teres f. maculata isolates from Victorian barley crops using sequence tagged microsatellite (STMs) primers and mating type primers revealed high genetic diversity and the presence of two-mating types necessary for sexual reproduction. This indicates that the Victorian population of P. teres f. maculata frequently undergoes its sexual cycle and is therefore able to develop new virulent pathotypes. This study has identified several areas of research that can be undertaken in order to better manage this important disease in the future. Further research to determine which of the barley lines identified in this study are suitable for inclusion into barley breeding programs and to monitor the virulences in the P. teres f. maculata population is required. A differential set of barley lines has been proposed for discriminating the effectiveness of resistance sources to P. teres f. maculata.
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ItemHighly modified mitochondrial genomes: the case of the dinoflagellates( 2011)The mitochondrion is an indispensable organelle present in all eukaryotes, and is vital for energy metabolism as well as being implicated in iron homeostasis, fatty acid and lipid biosynthesis. All mitochondria are derived from one endosymbiotic event, involving uptake of an α-proteobacterium, and with the exception of a few groups of anaerobic eukaryotes all mitochondria retain vestiges of their original bacterial genome. In comparison to the genomes of free-living bacteria, which are generally > 1 Mb and encode several thousand genes, mitochondrial genomes (mtDNAs) are highly reduced in both size and gene content. Moreover, some mtDNAs have evolved elaborate genome structures, sometimes involving multiple chromosomes, as well as complex gene organisations and gene expression processes. Hence, they have deviated significantly from the original endosymbiont bacterial genome. Dinoflagellates are a large group of flagellated protists, and include both heterotrophic and autotrophic members. The closest relatives of the dinoflagellates are the apicomplexans, which are all obligate intracellular parasites, and the ciliates, a common protist group that is basal to the dinoflagellate and apicomplexan sister group. Together, the dinoflagellates, ciliates and apicomplexans form the group Alveolata. The mitochondrial genome of ciliates is relatively ‘normal’ in comparison to the majority of known mtDNAs, comprising a single linear chromosome ~40-50 kb in length, and encoding ~30 common mtDNA genes. Conversely, the apicomplexan genome (best known from the parasite Plasmodium, which causes malaria), is one of the most reduced mtDNAs known, comprising a tiny 6 kb chromosome that occurs as tandem repeats, and it encodes only three protein-coding genes (cox1, cox3 and cob) and two highly fragmented ribosomal RNAs (rRNAs). The alveolates therefore provide an excellent opportunity to investigate the evolution of highly divergent mitochondrial genomes. However, prior to this PhD little was known about the dinoflagellate mitochondrial genome. To compare the mtDNA states between dinoflagellates and other alveolates, and also within dinoflagellates, I have investigated the mtDNA gene content and gene organisation of two dinoflagellate species, Karlodinium micrum (synonyms: Karlodinium venificum, Ballantine) and Hematodinium sp. Hematodinium sp. is a basal dinoflagellate, whereas K. micrum branches higher within the majority of dinoflagellate diversity. I have shown that the dinoflagellate mtDNA is one of the most complex known. My data strongly supports that, like in apicomplexans, the dinoflagellate mtDNA contains only cox1, cox3 and cob as well as two highly fragmented rRNAs. Unlike the apicomplexan mtDNA, all genes occur as multiple copies that occur in many genomic contexts. There is considerable predicted secondary structure present in intergenic regions. Further, in addition to full-length copies (with the exception of cox3 in K. micrum, which apparently lacks a full-length cox3 gene), all genes are found in a variety of fragmented forms. Both the K. micrum and Hematodinium sp. mtDNAs exhibit a very similar, and equally complex, mtDNA arrangement. In addition to mtDNA gene content and gene arrangement, I have also investigated the transcription of mtDNA genes, and uncovered further novel features. Standard start codons are missing from cox1, cox3 and cob mRNAs. More unusually, cox1 and cob mRNAs are oligoadenylated upstream of standard stop codons or any apparent alternative stop codon. K. micrum cox3 mRNAs contain an in-frame standard UAA stop codon, apparently generated by oligoadenylation of cox3 transcripts immediately following a U nucleotide. Hematodinium cox3 mRNAs, on the other hand, contain a UAA stop codon that is encoded in the mtDNA, and this is the only known example of a dinoflagellate mtDNA transcript with an encoded stop codon. In both K. micrum and Hematodinium all three protein-coding transcripts undergo substitutional RNA editing, as do the fragmented rRNA transcripts. Preliminary data presented in this PhD indicate that transcripts from the K. micrum plastid genome also undergo substitutional RNA editing. In the K. micrum mtDNA, a number of additional transcripts of unknown identity were detected, and polycistronic transcription has been detected from both the K. micrum and Hematodinium mtDNAs. Finally, in K. micrum and the dinoflagellates Alexandrium catenella and Symbiodinium sp., the cox3 gene appears to be split into two main fragments in the genome. Unlike gene fragments for cox1 and cob (and also additional cox3 fragments), these two fragment types appear to directly contribute to protein expression. Both are individually transcribed, and transcripts are subsequently trans-spliced to generate a full-length cox3 mRNA. The trans-splicing mechanism appears to differ from splicing mechanisms identified in other mitochondrial systems. Analysis of cox3 sequences from additional species suggests that cox3 trans-splicing is widespread throughout later-branching dinoflagellates. Overall, my studies show that the dinoflagellate mtDNA shares some of the highly derived features of the apicomplexan mtDNA, as well as exhibiting a suite of additional novel features. Therefore, within the alveolates the dinoflagellate mtDNA is arguably the most highly derived, with the apicomplexan mtDNA representing an intermediate stage between the ciliate and apicomplexan mtDNAs. Moreover, the presence of many dinoflagellate-specific mtDNA innovations in the basal species Hematodinium suggests that these evolved early during dinoflagellate evolution, and have been retained during the diversification of the group.