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(2020)ThesisClassification methods capable of identifying signals or groups of samples, whose geochemical composition is affected by dispersion from mineralisation, are critical in regional and local scale mineral exploration projects. This study compares various population and spatial fractal classification models with several new models to identify populations associated with VMS-style mineralisation in regional till geochemical data from Sweden and both Cyprus-style VMS deposits and anthropogenic contamination in soil data from Cyprus. The new models include concentration-distance from centroids (C-DC), concentration-concentration (C-C), and simulated-based and category-based fractal models applied to representative and simulated samples (CF-R and CF-S). The precision (stability) of the models and spatial uncertainty were tested using Monte Carlo and sequential Gaussian simulations, as well as the effects of pre-processing of the geochemical data. In the Sweden till data, CF-R, spectrum-area (S-A) and the related simulated (SS-A) approach proved more effective in delineating known VMS mineralisation in some regions than single element patterns for mineralisation-related metals such as Cu. In Cyprus, both established and new fractal approaches were marginally more effective at separating areas of known mineralisation (including the major deposits) against a backdrop of generally elevated levels of VMS-related elements in the pillow basalts and underlying sheeted dyke complex. The C-C and C-DC approaches define a contiguous zone whose multivariate patterns are closely linked to either geogenic dispersion or anthropogenic contamination including historical contamination that cuts across current land use zoning. Population or spatial features in geochemical data delineated by different fractal approaches are dependent on the mathematical basis of specific fractal models. Application of a wide range of fractal methods, along with assessment of uncertainty in sample classification and stability of spatial patterns, provides a firmer basis for quantifying the processes and features that control element distributions in regional geochemical data. It also provides criteria for selection of the most effective combination of data pre-processing and fractal modelling to extract desired features or signals in the data.
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(2023)ThesisPlant introductions to novel environments, whether intentional or accidental, have occurred for centuries and are the precursor to the thousands of invasions that are currently threatening ecosystems across the globe. One of the common, well-studied mechanisms that is thought to aid in successful introduction is known as the enemy release hypothesis, which explains that organisms may thrive in their new environments as they have escaped their co-evolved natural enemies. While enemy release may facilitate introduction in some species or situations, half of the time it does not, and we did not understand the circumstances that lead to its occurrence. Using a robust, biogeographical approach, I quantified herbivore damage across 16 plant species at varying sites across their native and introduced ranges and found that neither time, space, climate, or leaf palatability explained patterns of enemy release. Most research on invasion ecology tends to focus on the negative interactions that are missed in the introduced range and fails to consider how positive interactions are affected. Here, I provide the first broad test of the missed mutualist hypothesis across ten plant species in their native and introduced ranges, that accounts for variation between locations. Following over 120 hours of in-situ observations I found plants to be visited 2.6 times less frequently and with 1.8 times lower richness of pollinators in their introduced range in comparison to their native range. I also introduce the ZAX Herbivory Trainer, a globally accessible software that can reduce researchers’ inaccuracy of herbivory estimates by 7% in less than 10 minutes, which can be retained for up to 3 months. My thesis deepens our understanding of the mechanisms that facilitate and hinder successful introduction and provides an effective tool scientists can use to further this area of research at even larger scales.
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(2022)ThesisDissolved organic carbon is stored and processed in groundwater in three ways. It is stored on minerals by adsorption, it is biologically processed through biodegradation, and it also undergoes a process to return to groundwater called desorption. This biophysiochemical research shows that the groundwater system is therefore a vital part of the global carbon cycle and carbon sink. This research fills a gap in the existing understanding of how to calculate the global carbon budget, as does not yet include the dissolved organic carbon that is stored in groundwater. This thesis exclusively explores processes determining dissolved organic carbon character and concentration in groundwater in different geological environments. This is new, useful knowledge to describe the biophysiochemical process. This research did not examine human interference in adding carbon to groundwater. This research found how dissolved organic carbon is stored and processed in groundwater due to biodegradation and desorption, and how it is adsorbed onto sediment surface. This research explored the characteristics and concentration of Dissolved organic carbon in groundwater by using Liquid Chromatography-Organic Carbon Detection, and other techniques, to examine dissolved organic carbon in terms of its fractions: humic substances, hydrophobic organic carbon, biopolymers, building blocks (BB), low molecular weight neutrals and low molecular weight acids. There were several key findings. First, the results showed that both semi-arid inland low sedimentary organic carbon environments – i.e., Maules Creek and Wellington – were a carbon source; while the high rainfall temperate coastal peatland environment of Anna Bay was a carbon sink. Secondly, another key finding was that dissolved organic carbon was not processed as a whole chemical compound, but it was processed by its fractions where each fraction was processed distinctly. For example, humic substances were only adsorbed/desorbed in groundwater; while low molecular weight neutrals were only consumed by microbes in the biodegradation process in groundwater.
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(2023)ThesisEvolutionary biology literature often suggests that the sexes express reproductive behaviours completely differently from one another, with stereotypical representations such as choosy females and competitive males. This thesis explores this concept at multiple levels from examining whether this is the actual perception of the research community to investigating overlooked behaviours like male mate choice and female-female competition. In chapter 2, I conducted a survey in which I asked participants about their perceptions on sex differences in reproductive behaviours in non-human animals. I found that although people agree with the stereotypical roles proposed in the literature, they understand variation exists around these stereotypes. More importantly, I found that personal and research experiences from participants were associated with their perception about sex differences, revealing potential sources of biases about this topic. In chapter 3, I assessed whether male mate choice occurs in the praying mantis Miomantis caffra, in which females often cannibalize males before copula. I found evidence that males express mate preferences in that species and that males’ personality (activity) was associated with differences in approaching behaviour to females, showing that the common stereotype of males always being eager to mate is not true. In chapter 4, I conducted a meta-analysis across all animals to evaluate whether male mate choice varies among individuals. I found that, on average, higher quality males (e.g. larger and in better body condition) are choosier than their counterparts. Finally, in chapter 5, I explored whether mate competition in humans impacts their same-gender friendships. More specifically, I hypothesized that physical similarity in same-gender friendships would be more prominent for women than for men. This is because physical traits are often mentioned by men to determine mates’ attractiveness and thus could be a potential source of rivalry in friendships between women. I found no support that men and women choose friends differently. Altogether, I show that the simplifications of sex differences that stereotypes convey can conceal complexities found in nature.
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(2023)ThesisMethane (CH4) is the second most abundant anthropogenic greenhouse gas (GHG) (after carbon dioxide), accounting for around 20 per cent of global emissions. At the global scale, the primary driver for the increasing CH4 mixing ratio in the atmosphere remains under debate. Resolving the debate is challenging because many CH4 sources are co-located resulting in source attribution errors. This thesis demonstrates that CH4 stable isotope analysis can be used to constrain source attribution in rural, industrial and urban settings. There is a paucity of isotopic measurements for all CH4 sources in Australia. CH4 plumes were mapped using laser-based CH4 analysers transported in a car or aircraft. Discrete air samples were collected as part of these surveys and analysed for both their CH4 mole fraction and stable isotopes composition. This enabled the characterisation of the isotopic signatures of major sources of CH4. Two settings of high CH4 emissions in Australia were studied: the coal seam gas (CSG) fields and adjacent agricultural districts in the Surat Basin, Queensland, and the city of Melbourne. The Surat Basin is a major CSG producing basin where numerous CH4 sources are co-located and poorly characterised. The results presented in this thesis (Chapters 2 and 3) demonstrate that CSG sources and ruminants can be distinguished by using dual isotope tracers (carbon and hydrogen) and that the isotopic insights can be used to verify the regional bottom-up emission inventory. A vehicle-mounted GHG analyser was used to map the CH4 mole fraction in the ground-level atmosphere throughout Melbourne. Major CH4 sources detected included plumes from natural gas distribution network leaks, landfills, wastewater treatment plants and domestic fires. The isotopic signatures of these plumes were characterised and used to interpret a one-year time series dataset of CH4, and stable isotope composition collected at the Commonwealth Scientific and Industrial Research Organisation (CSIRO) Aspendale monitoring site. The seasonal and diel trends of the observed CH4 mole fraction and stable isotope composition coupled with meteorology data show that CH4 mole fraction enhancements were observed under low wind speed conditions when there was limited mixing and dilution of each plume, suggesting the measurements captured were recording emissions from local sources. Isotopic evidence demonstrated that microbial sources such as landfills and wastewater treatment plants are major contributors to the elevated CH4 recorded at the monitoring site.
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(2023)ThesisThere has been a recent explosion of genomic data facilitated by rapid technological advances in sequencing and bioinformatics coupled with decreasing cost. However, the distribution of species with sequenced genomes across the plant tree of life is highly uneven. The genomic era is an opportunity to accelerate our understanding of plant evolution and efforts in conservation in the face of the Anthropocene. The overarching aims of this PhD encompass the development and optimisation of genomic resources for plants. This thesis focuses on two groups of Australian native plants – Telopea (waratahs) and Myrtaceae. I assembled the first chromosome-level reference genome for Telopea speciosissima (New South Wales waratah) using Nanopore long-reads, 10x linked-reads, and Hi-C data (Chapter 2). I applied reduced representation sequencing (DArTseq; n = 244), whole-genome sequencing (n = 14), and chloroplast sequencing (n = 50) to reveal insights into the population structure and demographic history of the genus, demonstrating a downstream application of the reference genome (Chapter 3). There was a decline in effective population sizes in all lineages coinciding with the Last Glacial Maximum (LGA); the drop was especially apparent in the Monga and Victorian waratahs. I assembled reference genomes for four Myrtaceae species – Syzygium oleosum (blue lilly pilly), Rhodamnia argentea (malletwood), Rhodamnia rubescens (brush turpentine), and Rhodomyrtus psidioides (native guava) – that display varying degrees of resistance to myrtle rust (Chapter 4). The latter two species are native rainforest species in rapid decline due to the invasive fungal pathogen Austropuccinia psidii and are currently being conserved and protected in ex-situ collections. Here, I analysed DArTseq data to develop recommendations for the conservation management of these critically endangered species, and demonstrate the value of genomic resources in conservation (Chapter 5). Overall, this PhD thesis demonstrates how references genomes, complementary genomic data and bioinformatic tools are valuable resources that contribute to our understanding of the Australian flora and pave the way for the persistence of plant populations into the future.
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(2023)ThesisShifting patterns in consumption and the inadequate disposal of wastes has led to the escape of anthropogenic debris into the marine environment. The growing volume of debris, both within and entering coastal and marine areas, has prompted global concern over the risks they may pose to environmental and human health. Responses to curb further entry and address debris already within the environment include several management interventions, informed by policies and legislation. Effective debris management requires an understanding of potential sources, subsequent dispersion and an estimate of the risks posed to habitats and biological assemblages, which could be attained through environmental monitoring. Monitoring across relevant spatio-temporal scales, however, is often outside the reach of formal government and research programs and there is a growing recognition of the role citizen science data may play in debris management and decision making. This thesis aims to bridge environmental monitoring with policy and decision making, combining citizen science with other data into an evidence-base for management. The thesis assesses several citizen science datasets from a local to Federal scale to identify debris trends and their drivers (Local: four estuaries; State: Queensland; Federal: Australia). Further, I combine expert elicitation and empirical debris data to assess the risk posed by debris. I provide a framework for linking debris identified within the environment to economic sectors, as part of a formal accounting framework. The thesis also provides methodological guidance to refine citizen science sampling during monitoring programs, to improve the accuracy and reliability of resulting datasets. Through careful application and consideration of data quality, citizen science data could be used to supplement formal monitoring efforts to better understand and address the challenge of marine debris. This thesis advances the role of citizen science beyond environmental monitoring to inform management efforts at scale.
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(2023)ThesisThe transmission of dengue fever is already being impacted by the changing climate. This phenomenon poses a considerable public health challenge for countries like Bangladesh, where regular seasonal outbreaks of dengue fever are already prevalent. This thesis aims to investigate how changing climate will impact long-term dengue epidemiology in Bangladesh as a whole and more specifically in Dhaka, the capital city of the country over the 21st Century. Several statistical models have been developed to estimate the short-term risk of dengue outbreaks as a function of climate variables but the underlying causal relationships that contribute to dengue transmission and the observed patterns of dengue epidemiology are not accounted for in these models. Initially, we determined the suitability of using climate projections for 21st Century from Global Climate Models (GCM) to assess the impact of changing climate on future dengue risk in Bangladesh setting. We then used the GCM output to assess the impact of changing climate on one aspect of dengue transmission by calculating the change in vectorial capacity (VC) of Aedes aegypti mosquitoes at a seasonal level for all regions in Bangladesh under two future climate change scenarios. The analysis indicates that the annual VC in all divisions of Bangladesh is expected to consistently exceed the threshold for dengue transmission throughout the 21st Century, regardless of the climate change scenarios considered. However, during the latter half of the century, there is a projected decline in the annual VC compared to the period between 1986 and 2005. Despite this, monthly VC variations reveal that the winter/dry season could see an increase in VC, potentially leading to a longer dengue season with outbreaks occurring year-round. The application of the VC calculation is limited by the fact that it only accounts for temperature and does not consider the impact of other climate variables such as rainfall and humidity, as well as the role of host immunity. To incorporate these factors, we then developed a mechanistic dengue transmission model that considers the influence of temperature, rainfall, and humidity on the transmission of two different dengue serotypes among human hosts and mosquito vectors. We calibrated and validated the model against observed dengue epidemiology data from Dhaka for 1995-2014 using observed climate data as input. We then used GCM output for two future climate change scenarios to simulate the model for two future periods (2030-2049 and 2080-2099) to assess the potential changes in dengue epidemiology in Dhaka. When utilizing observed climate data and climate projections from GCMs specific to Dhaka, our mechanistic model reasonably reproduced the observed dengue epidemiology in Dhaka between 1995 and 2014 in terms of the recurring annual dengue outbreaks, the seasonal pattern of transmission, and the increase in seroprevalence. Simulations for 2030-2049 indicate that dengue transmission is likely to increase regardless of the combination of initial seroprevalence, GCM, and climate change scenario, when compared to the baseline period of 1995-2014. However, for the period 2080-2099, the projected changes in dengue transmission vary, with some combinations of initial seroprevalence, GCM, and climate change scenario predicting a slight increase and others indicating a decrease. The simulations also suggest the seasonal pattern of dengue infections is likely to change in future, with more pronounced change projected for the 2080-2099 period, resulting in a lengthening of the dengue season. The primary contribution of this thesis is to present a modelling framework that considers the anticipated changes in the future climate and immunological factors to project the long-term risk of dengue epidemics. The model is flexible enough to be adapted to other settings and other pathogens transmitted by the same mosquito vector.
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(2023)ThesisBlue whales, like many other baleen whale species, are threatened by anthropogenic activities and climate change. In the previous century, blue whales were hunted to the brink of extinction and their numbers remain at a fraction of their original population. Studying blue whales can be difficult due to their low numbers and often remote habitat where they are found. To identify how climate change is affecting blue whales, long term data is needed. However long-term studies can be logistically difficult and financially costly. Passive acoustic monitoring (PAM) provides a cost-effective and non-invasive way for collecting long-term data on vocal species. PAM is a suitable tool for studying blue whales as they produce highly stereotypical songs. In this thesis, I examined the acoustic presence of several blue whale populations across the Southern Hemisphere. I examined the degree of overlap between Antarctic blue whales and subantarctic blue whales in the Southeast Pacific Ocean and the Southeast Indian Ocean. I found that Antarctic blue whales were sympatric with both the Chilean blue whale and the Southeast Indian Ocean blue whale during the austral autumn/winter. However, the peak in acoustic detection occurred later for the Antarctic blue whales. I modelled the interannual variability of the SEIO pygmy blue whale with environmental data and found a strong correlation with El Niño Southern Oscillation (ENSO) and the number of whale call detections. I also modelled the Antarctic blue whale presence across four sites in the Southern Hemisphere and found that ENSO, the Southern Annular Mode, Antarctic sea-ice extent, and Antarctic krill abundance were correlated with the acoustic detections of Antarctic blue whales. These results show that blue whale migration is influenced by environmental conditions likely due to changing availability of their prey such as krill. This highlights that climate change will impact blue whales in the future by altering productivity in their primary feeding areas with the potential to impact their reproductive success.
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(2024)ThesisLengthy motorised public transport travel times can decrease opportunities for physical activity. However, public transport use includes incidental exercise to, from and between stops, forming an important component of meeting physical activity recommendations. The aims of this thesis are therefore to estimate public transport commuter travel time and physical activity in Sydney, Australia. Chrono-urbanism targets, measuring time travelled from home to destinations, like the 30-minute city promise average commuting times of one hour per day. However, existing 30-minute city calculations either do not include first- and/or last- public transport segments or transfers. Most research examining public transport-related physical activity relies on expensive travel survey data. Studies using GPS or accelerometers have higher accuracy but typically smaller sample sizes. Smart card data provide a cost-effective approach to modelling door-to-door travel times for the 30-minute city and public transport-related physical activity. Travel times and physical activity were modelled using GIS and Python scripting. This involved generating and matching a synthetic population to smart card data, using a trip planning API to estimate motorised public transport times, conducting network analyses, and distance conversions to steps and/or MET minutes. The 30-minute city goal for public transport commutes in Sydney is yet to be realised when a door-to-door approach is used. For public transport commuters, while the median commute time for the analysis without the first- and last-segment was 25 minutes, the door-to-door median was 44 minutes. Such varying estimates could influence different infrastructure policies. A mean of 2400 steps per day weighted across modes was modelled for public transport commuters. A mean of 89.1 MET minutes per day from walking and/or cycling components was modelled. An additional 36.5 and 116.3 MET minutes per day could be gained by commuters with a potential mode shift from private transport as the feeder mode to walking and cycling respectively. Novel ways for measuring public transport-related travel times and physical activity for the 30-minute city have been demonstrated. This research can assist policy-makers to understand where public transport commutes exceed 30 minutes so that interventions may be targeted in these areas to encourage public transport-related walking and cycling. Novel ways for measuring public transport-related travel times and physical activity for the 30-minute city have been demonstrated. This research can assist policy-makers to understand where public transport commutes exceed 30 minutes so that interventions may be targeted in these areas to encourage public transport-related walking and cycling.