School of Agriculture, Food and Ecosystem Sciences - Theses

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    Predicting redistribution of species and communities under environmental change: Improving the reliability of predictions across time
    Uribe Rivera, David Eduardo ( 2023-04)
    Ecological models used to forecast range change (range change models; RCM) have recently diversified to account for a greater number of ecological and observational processes in pursuit of more accurate and realistic predictions. Theory suggests that process-explicit RCMs should generate more robust forecasts, particularly under novel environmental conditions. RCMs accounting for processes are generally more complex and data-hungry, and so, require extra effort to build. Thus, it is necessary to understand when the effort of building a more realistic model is likely to generate more reliable forecasts. During my thesis, I investigated how explicitly accounting for processes improves the temporal predictive performance and transferability of RCMs. I first identified key knowledge gaps, and the challenges of evaluating temporal predictive performance and transferability. One of the main challenges is the lack of robust metrics to assess predictive performance and transferability. To address this I implemented and tested the use of new emerging tools to enable fair comparisons of predictive performance across samples with varying degrees of imbalance (e.g. species with low and high observed prevalence). I then tested a couple of hypotheses related to whether modelling observational processes explicitly results in better forecasts. In particular, I evaluated under what circumstances the benefits of explicitly accounting for imperfect detection and allowing information sharing across multiple species are retained when the models are extrapolated to generate predictions beyond the training temporal window. The findings should shed light on how to address remaining knowledge gaps, and how to generate more reliable forecasts on species’ responses to global change scenarios.
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    Trees Need Closure Too: Unveiling The Molecular Control Of Wound-Induced Secondary Vascular Tissue Regeneration In Trees
    Karunarathne, Sachinthani Isurika ( 2023-09)
    Trees play a pivotal role in terrestrial ecosystems and are an important natural resource. These attributes are primarily associated with the capacity of trees to continuously produce woody tissue from the vascular cambium, a ring of meristem cells located just beneath the bark between phloem and xylem tissue layers. Long-lived trees are exposed to a myriad of biological and environmental stresses that may result in wounding, leading to a loss of bark and the underlying vascular cambium. This affects both wood formation and the quality of timber arising from the tree. In addition, the exposed wound site is a potential entry point for pathogens that cause disease and may even lead to the death of the whole plant. In response to wounding, trees have the capacity to regenerate lost or damaged tissues at a wound site. Investigating gene expression changes associated with different stages of wound healing reveals complex and dynamic changes in the activity of transcription factors, signalling pathways and hormone responses. This thesis investigated molecular regulators of wound-induced secondary vascular tissue (SVT) regeneration. It summarises current literature on primary and secondary vascular tissues and bark wounds and related revascularisation processes, specifically on genes and hormones. Using this information, eight genes from Eucalyptus, including WUSCHEL RELATED HOMEOBOX 4 (EgrWOX4), Arabidopsis thaliana HOMEOBOX GENE 8 (EgrATHB8), CORONA (EgrCNA), PHABULOSA/PHAVOLUTA (EgrPHX), REVOLUTA (EgrREV), AUXIN RESPONSE FACTOR 5 (EgrARF5), PIN-FORMED 1 and 3 (EgrPIN1 and EgrPIN3) were chosen for subsequent experiments on wound-induced SVT regeneration. During these in-planta experiments, Induced Somatic Sector Analysis (ISSA) was used as a molecular tool to assess promoter activity and gene function of these candidate genes in wild-type stems and those where auxin transport was chemically inhibited. Endogenous auxin (IAA) concentrations were quantified using LC-MS to understand how varying auxin concentrations might be required for proper vascular tissue patterning during various stages of regeneration. Results show that the remaining xylem tissues on the wound surface regenerate all lost tissues in a four-step process. EgrPIN1/3 are expressed in all tissue types, EgrWOX4, EgrARF5 and EgrREV predominantly in cambium tissues and EgrATHB8, EgrCNA and EgrPHX in cambium and xylem tissues. Overexpressing micro-RNA-resistant REV leads to faster regeneration rates, while over-expressing miR166 and chemical inhibition of polar auxin transport leads to slower regeneration rates. Samples from overexpression experiments and auxin inhibition also lead to defects in cell anatomies, arrangement, and organisation. Quantification of IAA levels suggests alternating high and low auxin signalling during different stages of regeneration. Together, this thesis provides novel insights into spatial-temporal expression patterns of the selected molecular regulators and discusses how they relate to our current understanding of vascular cambium formation and xylem differentiation during secondary growth. Based on the findings, I propose a model for wound healing that provides the conceptual foundations for future studies aiming at understanding this intriguing process.
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    Epidemiology of mint rust and variation in the Pathogen, Puccinia menthae Pers
    Edwards, Jacqueline. (University of Melbourne, 1998)
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    A genetic evaluation of dystocia in Australian Holstein-friesian cattle
    McClintock, Sara Elizabeth Juliette (University of Melbourne, 2004)
    This thesis presents the first large-scale study of the genetic and non-genetic influences on dystocia (calving difficulty) for dairy cows in Australia, and their costs, focusing especially on the Holstein-Friesian breed, but also with some analyses of frequently occurring crossbreeds. Analyses used data collected since 1986, collected by the Holstein-Friesian Association of Australian and the Australian Dairy Herd Improvement Scheme. The calving traits examined were gestation length, calf size, dystocia (measured as any or none, severe or none, and none, slight and severe). I investigated the influence on calving ease of non-genetic variables such as month of calving, cow age or parity, calf sex, and breed of cow and bull. The genetic parameters were estimated: the heritabilities and genetic correlations between traits calculated, separately for primiparous and multiparous, and for sires, maternal grandsires and the maternal effects. Costs associated with dystocia (such as labour costs, loss or fertility, veterinary costs and deaths of cow and or calf) are estimated, and a cost model for dystocia under Australian conditions is proposed. The influence of crossbreeding on calving was investigated, especially with respect to dystocia and calf mortality. Recommendations are made for improving the recording system and the evaluation of bulls, as the sire of calf and as the sire of cow.
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    Genetic variation in Eucalyptus regnans F. Muell
    Nevill, Paul (University of Melbourne, 2010)
    Past climate changes and associated range contraction, expansion and introgression events are regarded as major forces shaping the evolution of the genus Eucalyptus. Previous investigations in south-eastern Australia have identified some putative refugia and recolonised areas for tall eucalypt forests during the last glacial cycle but the response of individual species are very little understood and in some regions, the evidence for migration or persistence is completely absent. Here I uncover the response of Eucalyptus regnans and two species (E. delegatensis and E. obliqua) which often occur with it and among all of which there is likely to be introgression. These results have important implications for understanding forest responses to climate change and for current gene pool management. Chloroplast variation in Eucalyptus regnans suggests that in spite of the narrow ecological tolerances of the species and the harsh environmental conditions of the Last Glacial Maximum (LGM), E. regnans was able to persist locally, in or near its current range, often in what would have been unfavourable conditions. Therefore, rather than the waves of recolonisation or long distance dispersal experienced by tree species in much of Europe or North America, E. regnans, with the exception of the Central Highlands region of Victoria in mainland Australia and the central region of Tasmania, does not appear to have migrated great distances. A comparative phylogeographic study of three south-east Australian Eucalyptus species (E. delegatensis, E. obliqua, and E. regnans) with different tolerances, in terms of cold, drought and soils revealed that, despite ecological differences, the three species have responded to past climatic changes in a similar way, by persisting in multiple refugia in similar locations. Inter-specific sharing of haplotypes was extensive, and fixation of shared, regional haplotypes, was more likely in areas postulated as treeless at the LGM. It seems likely that the process of recolonisation, in particular, results in loss of chloroplast diversity within species and interspecific haplotype sharing. A nuclear microsatellite study of range wide variation in E. regnans found a high level of diversity, and, in contrast to the findings from the study on chloroplast variation, a generally low level of geographic differentiation. The findings do not support the hypothesis of a high level of genetic differentiation in the species that was suggested by the chloroplast data and its disjunct distribution. No loss of nuclear diversity was found at locations fixed or nearly fixed for the hypothesised recolonising chloroplast haplotypes. I argue that a loss of diversity at recolonised locations has been offset by hybridisation with, and genetic displacement of a pre existing (species was already present at site), compatible species. Extensive pollen mediated gene flow both during and after recolonisation from E. regnans in refugia may have led to the displacement of a pre-existing species and the homogenisation of nuclear microsatellite allele frequencies but retained the pattern of chloroplast variation from the displaced species. This scenario would explain the maintenance of high nuclear and low chloroplast variation at recolonised locations and the low level of genetic differentiation between recolonised locations and adjacent refugia. These results suggest that E. regnans is a species with a strong phylogeographic structure but a low level of nuclear differentiation. Across the species range there is a complex mosaic of populations with different histories of colonisation, persistence and introgression. Phylogeographic patterns in this study indicate that the major biotic responses of tall eucalypt forest to climatic changes were persistence and resilience. The implications of these findings are discussed in the context of defining gene pool management strategies for E. regnans. They generally support the conservative management objectives of the current seed transfer guidelines for commercial forestry operations in both Victoria and Tasmania: seed should be sourced from the harvested coupe if possible or from nearby stands matched for environment. In the central highlands of Victoria and central Tasmania where there is low between stand differentiation longer distance transfers may be more acceptable provided the environment is matched. In other regions such as East Gippsland where long-term, in situ persistence has resulted in strong differentiation between stands, then transfer of seed over relatively small geographic distances will disrupt the established patterns of evolutionary lineages. Given the evidence of the importance of introgression in E. regnans and its relatives, the current policy of maintaining the pre-existing species mix on regeneration should also assist in preserving the collective adaptive potential of the species at a site.
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    Community dynamics in natural resource governance : building adaptive management capacity towards ecological sustainability
    Meilasari-Sugiana, Astrid (University of Melbourne, 2010)
    The aim of the research was to analyze community dynamics and collective action for sustainable natural resource governance in decentralized Indonesia. The research was an ethno-methodology research in which in-depth interview and participant observation were used for data collection. Data analysis was carried out by examining the distribution of narratives provided by the respondents, and by carrying out a thematic analysis in which emerging themes were used to produce a complex and coherent narrative of the discourse found within the case study site. The research aims to explore the various practices of natural resource governance and the complex social relations which influence collective action for the sustainable governance of natural resources. Natural resource governance in modem Indonesia is marked by the tension between the centralized policy strategy of the Suharto period and the reactive strategy of Post-Suharto decentralization. To some extent, decentralization led to devolution of power and opportunities for local resource users to make consequential decisions over the natural resources upon which they depend. However, this approach rested upon the capacity of communities to reach a consensus untainted by local politics, commercial imperatives and traditional power stmctures. Moreover, decentralization had not given the majority access to strategic and structural decision making power. Empirical findings from Tongke Tongke�s mangroves in Sinjai, South Sulawesi, suggest that social institutions and local mles came into play and the people felt honored to protect the resource on behalf of the community. These social institutions took the form of neighborly ties, collective identity, reciprocity and social and ecological responsibilities. Access to Tongke Tongke�s mangroves was not free but governed by local and informal mles to maintain its benefits for the good of the community. The community, through the elders, was determining access and making decisions about management on behalf of them all. Community members acted in a way that benefited the overall good even when they were avowing individual rights. The thesis argued that individuals evolved behavior which was commensurate with their responsibilities, leading to innovative power stmctures which were more locally sensitive and environmentally appropriate. The case study in the village of Tongke Tongke within the Regency of Sinjai suggested a rebuttal of Hardin�s Tragedy of the Commons. In line with Ostrom�s theory, the commons is governed by local and often informal mles which induce behavior that are in line with a collaborative mentality to maintain its benefits for the good of the community. Nonetheless, as suggested by Bookchin and argued in the thesis, collective natural resource governance is also about individuals who resist and accept the shaping of civic collaboration and ecological sustainability. In addition, barriers and enablers for sustainable natural resource governance need to emerge from local contexts; they could not emerge as a consequence of top down devolution alone. Moreover, no preparation of local communities could be made to assume the unintentional consequences of complex power relations. In line with Etzioni�s theory, empirical findings suggest that real power relationships in real resource management contexts can undermine the possibility of democratic and equitable consensus making. The thesis argued that social reciprocity, identity validation and symbolic capital can motivate resource users to behave in line with a collaborative mentality for mangrove protection.
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    Making sense of social research in forestry : an exploration of interactions in an interdisciplinary research process
    Dunn, Caroline Jane (University of Melbourne, 2010)
    Many social scientists believe their disciplines bring a critically important perspective to environmental problems (Ewert, Baker, & Bissix, 2004; Lockie, Higgins, & Lawrence, 2001; Reser & Bentrupperbaumer, 2001; Roughley & Salt, 2005). Problems involving natural resource management, particularly competing land uses, are often thought to inherently be social problems. Despite this, social researchers have faced challenges in contributing to solving these problems. A critical challenge is lack of understanding of social science by natural scientists, policymakers and non-academic research partners, such as industry. The complex nature of these problems requires coordination between these stakeholders. Gibbons et al. (1994) have described the trend towards collaborations which involve a broader range of academic and societal stakeholders as a new �mode� of knowledge production. Inroads have been made to understanding how knowledge production occurs in the new �mode�, especially in the area of study focused on interdisciplinary collaboration. Some of this work has specifically focused on collaboration across the �great divide� of natural-social sciences in natural resource management and environmental problem settings (e.g. L�l� & Norgaard, 2005), yet it is still unclear how social scientists can, and do, contribute alongside others. The aim of this study is to understand and conceptualise the processes in which social scientists and others engage to make social research usable. This study uses a narrative ethnographic approach (B. Tedlock, 1991), taking advantage of my position as a collaborator studying collaboration between social researchers and foresters in the Cooperative Research Centre Forestry (CRC) Communities Project based in Australia. Principal methods involved participant-observation over 21 months, detailed field note-taking, interviewing members of the Communities Project, and analysis by renarrating field experiences. Studies of natural-social scientific interdisciplinarity provided the expectation that there would likely be miscommunication, misunderstandings and missed opportunities. Instead, social researchers and industry partners managed to make connections. Social researchers were able to communicate the messages they saw as important (even when these had negative implications for industry partners) while industry partners increased their understanding of the methods, findings and implications of social research. I found that this was facilitated by two interactive processes. The first, I labeled �reframing�. This involved participants engaging in questioning and clarification as well as mutually learning each others� vocabularies and concepts. I labeled a second process �stretchy narratives�, referring to participants� stretching, or expansion of their original narrative to incorporate critical features of others� narratives. These interactive processes constituted integrative practice in this interdisciplinary collaboration, adding to previously abstract conceptualization of integration (e.g. Klein, 2001b; Newell, 2001). Working with industry partners, I redefined the nature of our differences, finding that they were focused on practical measures such as clear project explanations and valuable research outcomes. This, and the lack of obvious �disciplinary� struggle, suggests that in some �interdisciplinary� collaborations, particularly those with non-academic stakeholders, philosophical differences may be less relevant than social scientists have argued (e.g. Eigenbrode et al., 2007). Given the notion that disciplinarians have somewhat fixed epistemological positions, project partners� perspectives were more fluid than anticipated. My research suggests that those working in natural-social science collaborations in environment and natural resource management problem settings can make social research usable by adopting a gradual and incremental approach to educating and learning from others, engaging opportunistically in teaching moments.