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  • (2021) Byrnes, Juliet
    Thesis
    This PhD thesis moves beyond conservation genetics/molecular ecology’s traditional consideration of genetic loci acting in isolation from other genetic loci, in a species that is acting in isolation from other species. I use modelling to explore these interactions, and produce some surprising results with implications for evolutionary biology and for conservation management. The first chapter presents a meta-analysis and simulations of recombination with epistatic selection – where a combination of alleles at different loci produces a fitness effect neither could produce alone. Epistasis is ubiquitous in nature, but difficult to detect. Additionally, mathematical models of recombination and epistatic interactions are typically intractable or contradictory. Consequently, epistatic interactions are often ignored. The main conclusion of the first chapter is that in Drosophila melanogaster, and in some models, lethal combinations of alleles at different loci tend to have a low recombination rate and thus break up less easily, though beneficial combinations show a different pattern. The second and third chapters use modelling to study correlations between species diversity and genetic diversity (SGDCs). If strong positive SGDCs are common, it may be possible to use one diversity measure in the place of another. Conversely, if strong negative SGDCs are common, conservation measures which target one diversity will negatively impact the other. There are theoretical arguments in support of positive and negative SGDCs, but little formal algebraic theory. Moreover, despite many SGDC studies, the results are equivocal. The second chapter shows that SGDCs which measure diversity using richness tend to be positive due to the construction of the SGDC as well as sampling bias but that assemblages with the same SGDCs can evolve very differently. Therefore, SGDCs may not be meaningful. However, many SGDC researchers use measures other than richness which weight rare variants differently from common ones. Therefore, the third chapter shows that the choice of weighting can seriously bias the interpretation of SGDC studies. In summary, this thesis lays the groundwork for a version of molecular ecology based upon a more thorough and accurate assessment of interactions of genes with one another, and with other species.

  • (2020) Sadeghi, Behnam
    Thesis
    Classification 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.

  • (2021) Webb, David
    Thesis
    Planetary waves play a role in a large variety of oceanic and climate dynamics. In particular, Kelvin waves can provide rapid teleconnections from large-scale climate and weather events to remote regions of the globe. Kelvin waves may be partially responsible for linking climatic changes in Southern Ocean winds to increases in subsurface warming around Antarctica that can lead to glacial ice-melt and increases in global sea level rise. Kelvin waves may also link changes in Southern Ocean winds to increases in North Atlantic Deep Water (NADW) formation and an enhancement of the Atlantic Meridional Overturning Circulation (AMOC), which is responsible for circulating a vast amount of the ocean’s heat and nutrient content. However, the exact role of Kelvin waves in these processes is unclear. This thesis aims to further clarify the role that Kelvin waves play in these high-latitude climate processes. First, we use a suite of idealized models in order to better understand the dynamics of barotropic Kelvin waves around Antarctica. We find that super-inertial (high frequency) barotropic Kelvin waves are nearly completely scattered away from the Antarctic coastline due to a combination of coastal geometry and bathymetry. Sub-inertial (low frequency) barotropic Kelvin waves are mostly scattered away from the Antarctic coastline due to bathymetry, however a significant amount of barotropic Kelvin wave energy remains at the Antarctic coastline after one circumnavigation of the continent, enabling a gradual build-up of energy along the coast and the ability to sustain a barotropic Kelvin wave signal around Antarctica over time. Secondly, we perform a diagnostic study using theory and a range of varying resolution model simulations to quantify the amount of subsurface warming along the West Antarctic Peninsula caused by barotropic Kelvin waves via an induced bottom Ekman flow that advects warm Circumpolar Deep Water onto the Antarctic continental shelf. We find that barotropic Kelvin waves can account for a substantial amount of warming within one year, depending on the background temperature gradients and thickness of the bottom Ekman layer. Lastly, we explore the role of Kelvin waves in linking Southern Ocean wind-stress to NADW formation and the AMOC by analysing ensemble simulations from a fully-coupled ocean-sea-ice model at 1/4 degree horizontal resolution (50 vertical levels). We find first mode baroclinic Kelvin waves to propagate along a global coastal and equatorial waveguide from the Southern Ocean forcing region to the North Atlantic, where downwelling waves initiate an enhancement of the AMOC by making surface waters denser.

  • (2023) Xirocostas, Zoe
    Thesis
    Plant 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.

  • (2022) Higgins, Philippa
    Thesis
    Increasing population and resource demands, a changing hydroclimate, and increasing risks of extreme events means that sustainable water management is more important now than ever before. Water planners are increasingly recognising that short instrumental records are insufficient to understand fully natural trends and variability in climate. High resolution paleoclimate proxies, like tree rings, can provide long time series of observations prior to the instrumental period, to better understand instrumental and pre-instrumental variability, the occurrence, trends, and drivers of extreme events, and provide insights into possible future hydroclimatic scenarios. However, tree-ring proxies are not evenly distributed in the landscape, and the South Pacific has very few high-resolution paleoclimate proxies to develop detailed reconstructions of climate variability. This thesis explores whether the relationships between tree-ring proxies in regions with strong teleconnections to the Pacific (i.e., ‘remote’ tree rings) can be exploited to reconstruct hydroclimatic indices across eastern Australia and the South Pacific Islands. Methods for hydroclimatic reconstruction are investigated, considering the unique challenges of the region: strong inter-annual and inter-decadal variability, very short data records, data gaps, and potential non-stationarities in climate teleconnections. Existing methods for tree-ring reconstructions have been successfully applied in the South Pacific (Chapter 2); however, overcoming the challenges posed by very short and non-continuous records required adaptations to existing methods (Chapter 3) and the development of new methods (Chapter 5). In the final two chapters, the thesis focuses on how catchment-scale tree-ring reconstructions can be most useful to water managers. In these chapters, methods of identifying, explaining, and representing extreme event frequency, return periods, and trends are explored, as are methods for using paleoclimate data along with climate model projections to help contextualise future risks of climate change. Overall, this thesis highlights the enormous potential of remote tree-rings for improving our understanding of past climate in the South Pacific. The reconstructions consistently demonstrate that the instrumental period underestimates the full range of natural climate variability and shows how century-long records provided by tree rings can help us better understand past climate drivers, contextualise the instrumental period, and refine estimates of future climate risks. This thesis builds upon a growing body of work that demonstrates the considerable value of tree-ring based reconstructions for current and future water resource decision making, most notably in remote regions that are highly vulnerable to climate change but where there are limited instrumental records. Maximising the potential of tree-ring data for water management will require ongoing collaboration between dendrochronologists and water managers.

  • (2022) Oudone, Phetdala
    Thesis
    Dissolved 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.

  • (2022) Teece, Bonnie
    Thesis
    This thesis investigates the reliability of organic biosignatures in geological materials that span most of Earth’s geological record. The aim is to determine the syngeneity and reliability of organic matter (OM) and the best techniques to use on geological materials with different compositions and thermal histories. Active to recently fossilised (<14 ka) hot spring sinter samples from El Tatio, Chile, Taupo Volcanic Zone (TVZ), New Zealand, and Yellowstone National Park (YNP) were examined as these are key astrobiological targets due to their excellent preservation potential. El Tatio and TVZ samples were analysed using gas chromatography-mass spectrometry (GC-MS). TVZ samples returned aromatic hydrocarbon ratios, low isoprenoid/n­-alkane ratios, and smooth n-alkane distributions, that indicate OM had reached the oil window despite lack of burial. Surface samples from three localities in YNP record a similar complex history. Raman spectrometry and GC-MS results (hopane ratios and low isoprenoid/n-alkane ratios) are again indicative of the oil window. Thus, some of the preserved OM in hot springs was transported into the samples from hot subsurface reservoirs. GC-MS analyses of Jurassic (~178 – 151 Ma) sinter from Argentina show that the proximal sinter apron contains a low abundance of compounds with mixed thermal maturities, whereas the cooler distal apron contains thermally immature OM and a wide variety of hydrocarbons. These results indicate that the distal apron of fossil sinters is an attractive target for organic biosignature research. The reliability of OM in ancient rocks was tested on samples of three distinct fossil types from an overmature c. 2.4 Ga microbialite reef in the Turee Creek Group, Western Australia using in situ micro-Fourier transform infrared spectrometry (micro-FTIR) and flash pyrolysis GC-MS. Micro-FTIR revealed differences in branching and chain length of the hydrocarbon moiety, but anthropogenic contaminants were also detected. This thesis highlights the need for a whole system approach when considering the origin of OM in geological materials. The veracity of results depends on a thorough understanding of both the environmental context and geological history, and on bespoke analytical approaches to increase confidence in biosignature detection.

  • (2023) Pollo, Pietro
    Thesis
    Evolutionary 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.

  • (2023) Lu, Xinyi
    Thesis
    Methane (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.

  • (2023) Chen, Stephanie
    Thesis
    There 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.