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(2020)ThesisThere is limited biological and ecological data on hippos, most of which originates from riverine/lacustrine populations, with none on the Okavango Delta population in its unique wetland habitat. This thesis aimed to investigate the Delta’s hippo population (size/distribution) and examine small-scale seasonal variations in hippo pod dynamics, habitat selection, and behaviour. The research provides baseline ecological and behavioural data on hippos in wetland habitats and gives insight into their adaptability to changes in water availability. This is particularly important as the Delta’s waters are threatened by climate change and human pressure, which will reduce habitat for hippos. I utilised thirteen years of aerial survey data to examine temporal and spatial patterns of hippo populations in the Delta. Hippos preferentially occurred in large lagoons within seasonal swamps, avoiding the dense aquatic vegetation and deep water of the permanent swamp/main channels. Since the mid-1990s, Botswana’s hippo population has grown significantly, likely due to long-term increases in rainfall and inflow. The most recent survey (2018) emphasises Botswana as a stronghold for this species in Africa, however, the exceptionally small flood event of 2019 will likely have led to substantially reduced hippo numbers. This work demonstrates the value in long-term monitoring programs. I developed a method to monitor (count/age) hippos using a drone, achieving more accurate counts than ground and aerial surveys. Using this method, I examined seasonal changes in hippo pods (size/density/demographic composition/distribution) related to varying surface water availability. In the low flood season, hippos occurred in larger pods in higher densities, aggregating on the minimal water still available. All seasons were characterised by near-constant changes in pods, emphasising their dynamic nature and challenging the notion of stable hippo groupings. I conducted 24-hour activity budgets within the Delta and Chobe River to increase the currently limited knowledge of hippo behaviour and to investigate how behaviour changed temporally, spatially, and seasonally in variable landscapes. Large differences in behaviour between pods (even those within close proximity) indicate hippos are highly flexible, taking advantage of available resources, but also emphasising the effects of humans on hippo populations.
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Reassessing the role of competition in the evolution and expression of adaptive strategies in plants(2020)ThesisIn this thesis, I utilise the vast amount of competition literature that has accumulated to conduct four literature surveys testing the predictions of traditional strategy theory on the role of competition in the evolution of plant strategies and life histories. Traditional theory predicts that seedlings emerging from large seeds have the advantage over those emerging from small seeds in environments of dense vegetation. Through my synthesis I show that large seed size is associated with high competitive ability but only when plants are competing against other seedlings. My findings offer a new interpretation of seed size strategies suggesting that seedlings have little chance of establishing in dense communities but rather, mainly emerge in open spaces. Next I tested whether shade avoidance plasticity was an adaptive response under competition. Shade avoidance responses have often been thought of as a strategy plants use to outcompete their neighbours for light resources. I found that shade avoidance plasticity was not associated with an increase in competitive performance as has been predicted by theory but that instead the adaptive value of shade avoidance lies in gathering resources to allow earlier reproduction under competition. I tested if these findings extended to plasticity in general which theory predicts gives plants a competitive advantage by allowing them to adjust growth to acquire more of the available resources than their competitors. I found that plasticity was not associated with an increase in competitive ability in either short or long-lived species. Instead plasticity was correlated with increased reproductive efficiency in short-lived species whilst this did not occur in long-lived species. Finally, I tested whether functional traits specific leaf area (SLA) and maximum height were good predictors of competitive ability. I found that neither maximum height nor SLA were good predictors of competitive performance. My findings highlighted that the theoretical basis of our understanding of competition needs to be improved before we can effectively use functional traits to predict competitive outcomes. Overall, this thesis challenges some of the key foundational assumptions of strategy theory and illustrates the need for a change in the way we measure competitive ability.
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(2020)ThesisYellowtail kingfish (Seriola lalandi, Valenciennes 1833; YTK) farming is considered the greatest opportunity for aquaculture expansion and diversification in Australia. Consequently, the demand for pelleted feed is expected to increase significantly for this species. Nutritional research on YTK has focused on macronutrient requirements and testing alternative protein and lipid sources to fishmeal and fish oil. However, there is a lack of information on micronutrient requirements and their effects on the growth and health of YTK. Therefore, it is important to acquire more knowledge on this topic to optimise the feed formulation for YTK. Choline is an essential nutrient typically supplemented in aquafeed and is abundant in raw materials such as fishmeal and soybean meal. Substituting raw materials for alternative food sources without knowing the choline requirement or its role in YTK performance might hinder YTK production. Accordingly, the main aim of this thesis was to improve our understanding of dietary choline on the growth performance and liver health of juvenile YTK at sub-optimal water temperatures. Liver was selected as a target organ because it is one of the major sites that facilitates various metabolic processes, including choline metabolism, and is susceptible to choline-deficiency induced liver disease. This thesis further explored the efficacy of using naturally-occurring stable isotopes to better understand the interactive effects of dietary choline and water temperature on nutrient assimilation of YTK. The aim was achieved and addressed by conducting two independent experiments with a series of interlinked studies. The research first determined the digestible choline requirement of YTK using a dose-response approach. The choline supplementation of a practical diet formulation at two temperatures (16 °Cand 24 °C) that bracket the culturing water temperatures commonly experienced by farmed YTK in Australia was also conducted. The digestible choline requirement of juvenile YTK was estimated to be 27.3 mg kgBW−1 d−1 or 1.94 g kg−1 diet (choline chloride supplementation: 0.0−10.0 g kg−1 diet), which is higher than for most finfish species. Choline and lipid apparent digestibility improved with increasing dietary choline. In contrast to many animal models, higher liver lipid deposition (in the form of free fatty acids and triacylglycerol) was associated with increasing dietary choline in YTK. However, this species did not exhibit signs of fatty liver disease related lesions which indicates that, if not beneficial, this amount of lipid is not detrimental to juvenile YTK. Upon further examination, dietary choline does not significantly alter the liver lipid composition but might protect liver health of YTK. This research confirmed that supplementing choline in fishmeal-based practical diets was necessary for juvenile YTK reared between 16 °C and 24 °C. Water temperature was largely responsible for the change in liver lipid composition and morphology; however, there was no indication of disease in fish fed practical diets. Importantly, this research demonstrated that the current industry practice of supplementing 3.0 g CC kg−1 diet to a fishmeal-based formula would ensure that the production performance and liver health of juvenile YTK are not compromised when cultured between 16 °C and 24 °C. Furthermore, using naturally-occurring stable isotopes, this research showed that fish had an affinity for assimilating certain raw materials such as sodium caseinate, poultry meal, meat meal, lupin, and wheat flour, irrespective of their inclusion levels. However, dietary choline content and water temperature did not significantly alter the assimilation of raw materials in the practical diet. The results indicate that higher inclusion of poultry meal, meat meal, lupin, and wheat flour in YTK feed is possible and might offer complementary information to digestibility studies. This thesis is the first to determine the choline requirement of YTK and established a scientific knowledge platform for further research on choline metabolism and its interaction with metabolically-linked nutrients. The research also provides scientifically-validated information that will help guide aquafeed formulation to reduce production costs and improve the growth performance and quality of YTK.
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(2021)ThesisThe Great Oxidation Event (GOE: c. 2.45-2.3 Ga) was accompanied by a series of global glaciations that placed significant environmental pressure on extant microbial life and, perhaps, led to the evolution of eukaryotes. However, the direct impact of the GOE on life remains unclear due to a lack of well-preserved, fossiliferous strata from this time. Here, a novel fossil form is described from the well-preserved shallow water part of a microbialite reef complex that lies between the 1st and 2nd of three global glaciations of the GOE, within the c. 2.4 Ga Turee Creek Group, Western Australia. Referred to as branching organic siliceous structures (BOSS), these novel fossils are organic-rich structures, up to 3 cm high, that are attached to the sides and tops of microbialites in up to 4 separate beds that have intercolumn sediment composed of phosphatic peloidal grainstone to pebble conglomerate. The unique occurrence of BOSS with phosphorite shows that they thrived in an oxygenated, nutrient-rich environment. BOSS display a range of morphology, from simple buds, through cylindrical or simple branching structures, to taller multi-level branching structures. The best-preserved BOSS are composed of kerogen-rich micrite with a faint texture of fine fibres that show a weakly radiating texture from the base to the outer, upper margins of BOSS. The interior parts of BOSS are commonly partially to wholly replaced by fine-grained silica (chalcedony to microquartz), which formed early in diagenesis, or possibly even during growth. Silica replacement of BOSS commenced as point-source growth of individual scattered spherulites and progressed to whole-scale replacement of the interior. BOSS interiors also contain two forms of pyrite: as necklaces of fine aggregates distributed in clusters; and as euhedral, sometimes zoned, grains in the exterior rinds of BOSS with silicified core zones. Sulfur isotopic data from the fine pyrite necklaces provides evidence of a sulfate reducing microbial community within BOSS. Petrographic analysis and morphological comparison show that BOSS are biological and dissimilar to any known type of abiological structure or microbialite. Rather, BOSS are most similar to eukaryotic algal-grade organisms based on their size, morphology and carbon isotope data. BOSS potentially illustrate that eukaryotes evolved up to 750 Ma earlier than previously recognised, coinciding with significant environmental change during the GOE.
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(2021)ThesisMistletoes exert a pervasive influence over many aspects of an ecosystem but the positive effects of mistletoe have historically been underappreciated. This is because of the nature of mistletoes as hemiparasites, and how an overabundance of mistletoe can debilitate the functioning of its host. However, different host species respond to different mistletoe infections in different ways. In this thesis, I sought to understand more about the functional role of the pale-leaf mistletoe (Amyema maidenii) that parasitises mulga trees (Acacia aneura) in arid zone Australia. Firstly, I used the host quality hypothesis as a framework to evaluate the relative abundance of the pale-leaf mistletoe in mulga trees. Secondly, I conducted an experimental mistletoe removal study to test the theory that mistletoes can influence the microclimate of its host, thereby facilitating habitat use of a free ranging animal. The first study revealed that mistletoes aggregate on taller mulga trees, where the negative effects of mistletoe infection are more likely to occur. In the experimental removal study, my results evidence a novel pathway for how mistletoes can modulate the microclimate beyond its own physical structure, creating a distinctly cooler understorey microclimate at the host-scale. In trees where mistletoe was present, kangaroos (red kangaroo – Osphranter rufus) also preferentially rested beneath these trees when compared to trees where mistletoe was removed. I conclude that the pale-leaf mistletoe is an important constituent within arid zone Australia but this is likely mediated by different mechanisms. Results from my first study suggest that the pale-leaf mistletoe may have an important negative role as they aggregate on taller trees, thereby increasing the likelihood that they may debilitate the functioning of taller host trees. On the other hand, results from the second study provides further support for the theory that mistletoes function as a keystone resource, structuring species interactions and positively influencing ecosystem functioning. More broadly, results from the second study emphasise the prevalence of positive interactions within ecological communities and how they can occur in unexpected ways and between organisms that never come into direct contact.
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(2021)ThesisThis thesis examines the potentially achievable prediction skill of temperature and precipitation on interannual to decadal time scales by analyzing predictability in perfect-model experiments using coupled climate models. I develop a framework which (1) compares perfect‐model prediction experiments with predictions of the real world, and (2) assesses the added value from capturing the initial state in the climate system in decadal predictions. I find that for the annual average near‐surface air temperature, ideal initialization may substantially improve the predictions during the first two forecast years particularly in parts of the Southern Ocean, the Indian Ocean, the tropical Pacific and North Atlantic, and some surrounding land areas. On longer time scales, the predictions rely more on model performance in simulating low‐frequency variability and long‐term changes due to external forcing. This thesis also investigates conditional predictability dependent on initial states, in particular multi-year predictability conditional on the state of the El Niño–Southern Oscillation (ENSO) at the time of prediction initialization. I find that predictions starting with El Niño or La Niña conditions exhibit higher skill in predicting near-surface air temperature and precipitation multiple years ahead, compared to predictions initialized with neutral ENSO conditions. This thesis also compares the predictability for mean and extreme temperature and precipitation on interannual to decadal time scales. The results show that both the mean and likelihood of near-surface air temperature extremes are predictable in many regions in the first lead year, while the areas exhibiting precipitation predictability tend to be mostly located in low-latitude regions. On decadal time scales, significant potential prediction skill for mean and extreme temperatures is found over the North Atlantic and the Southern Ocean and also over some land areas. Indices of moderate temperature extremes tend to show a higher predictability than the mean. This work suggests potentially improvable skill of current decadal prediction systems under the assumption of idealized initialization and identifies climate states that enable more skillful predictions relative to other climate states. This will ultimately lead to improved decadal forecasts, something that is critical for decision-makers requiring information on climate parameters for future planning across a range of sectors, such as water and bushfire management and agriculture.
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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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(2022)ThesisAs a dominant terrestrial ecosystem of the Earth, forest environments play profound roles in ecology, biodiversity, resource utilization, and management, which highlights the significance of forest characterization and monitoring. Some forest parameters can help track climate change and quantify the global carbon cycle and therefore attract growing attention from various research communities. Compared with traditional in-situ methods with expensive and time-consuming field works involved, airborne and spaceborne remote sensors collect cost-efficient and consistent observations at global or regional scales and have been proven to be an effective way for forest monitoring. With the looming paradigm shift toward data-intensive science and the development of remote sensors, remote sensing data with higher resolution and diversity have been the mainstream in data analysis and processing. However, significant heterogeneities in the multi-source remote sensing data largely restrain its forest applications urging the research community to come up with effective synergistic strategies. The work presented in this thesis contributes to the field by exploring the potential of the Synthetic Aperture Radar (SAR), SAR Polarimetry (PolSAR), SAR Interferometry (InSAR), Polarimetric SAR Interferometry (PolInSAR), Light Detection and Ranging (LiDAR), and multispectral remote sensing in forest characterization and monitoring from three main aspects including forest height estimation, active fire detection, and burned area mapping. First, the forest height inversion is demonstrated using airborne L-band dual-baseline repeat-pass PolInSAR data based on modified versions of the Random Motion over Ground (RMoG) model, where the scattering attenuation and wind-derived random motion are described in conditions of homogeneous and heterogeneous volume layer, respectively. A boreal and a tropical forest test site are involved in the experiment to explore the flexibility of different models over different forest types and based on that, a leveraging strategy is proposed to boost the accuracy of forest height estimation. The accuracy of the model-based forest height inversion is limited by the discrepancy between the theoretical models and actual scenarios and exhibits a strong dependency on the system and scenario parameters. Hence, high vertical accuracy LiDAR samples are employed to assist the PolInSAR-based forest height estimation. This multi-source forest height estimation is reformulated as a pan-sharpening task aiming to generate forest heights with high spatial resolution and vertical accuracy based on the synergy of the sparse LiDAR-derived heights and the information embedded in the PolInSAR data. This process is realized by a specifically designed generative adversarial network (GAN) allowing high accuracy forest height estimation less limited by theoretical models and system parameters. Related experiments are carried out over a boreal and a tropical forest to validate the flexibility of the method. An automated active fire detection framework is proposed for the medium resolution multispectral remote sensing data. The basic part of this framework is a deep-learning-based semantic segmentation model specifically designed for active fire detection. A dataset is constructed with open-access Sentinel-2 imagery for the training and testing of the deep-learning model. The developed framework allows an automated Sentinel-2 data download, processing, and generation of the active fire detection results through time and location information provided by the user. Related performance is evaluated in terms of detection accuracy and processing efficiency. The last part of this thesis explored whether the coarse burned area products can be further improved through the synergy of multispectral, SAR, and InSAR features with higher spatial resolutions. A Siamese Self-Attention (SSA) classification is proposed for the multi-sensor burned area mapping and a multi-source dataset is constructed at the object level for the training and testing. Results are analyzed by different test sites, feature sources, and classification methods to assess the improvements achieved by the proposed method. All developed methods are validated with extensive processing of multi-source data acquired by Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR), Land, Vegetation, and Ice Sensor (LVIS), PolSARproSim+, Sentinel-1, and Sentinel-2. I hope these studies constitute a substantial contribution to the forest applications of multi-source remote sensing.
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(2021)ThesisSince Johan Hjort first proposed his ‘critical period’ hypothesis in the early 1900’s, fisheries scientists have recognised the importance of the early-life stages of fish in determining year-to-year variation in recruitment. Despite this, our ability to forecast larval success remains limited. This is particularly true in the Australian context, where larval fish monitoring programs have only recently been established. This thesis aims to contribute knowledge regarding the population dynamics of larval fishes off eastern Australia. To achieve this, I utilise a new larval fish assemblage database, develop new modelling techniques, and conduct three sampling voyages to test my models on original data. The work is presented across 4 independent research chapters. In Chapter 2, I characterise patterns in the distribution of larval fish over 15° of latitude with highly variable conditions driven by the East Australian Current, using a newly available larval fish database supplemented with recently collected samples. Along eastern Australia, generalized additive models reveal that larval abundance and diversity is higher in the north and decreases poleward for most of the year, establishing a baseline trend for the region. This pattern reverses in summer, when spawning events occur around Tasmania, which could change as the East Australian Current strengthens with climate change. Existing methods for estimating mortality rates, such as catch-curves, require large sample sizes, as they work by grouping individuals into age bins to determine a frequency distribution. Yet, sampling enough larvae is often not possible at fine scales within the constraints of research projects. Drawing on size distribution theory, and improved computational techniques, in Chapter 3 I develop a novel method to simultaneously estimate growth and mortality of fish larvae which improves certainty in estimates with fewer fish available. Using Bayesian inference methods, I show how growth and mortality can be estimated from a continuous distribution of sizes removing the need to bin data. Furthermore, these new models are flexible and can estimate non-linear growth and mortality functions. The ratio of larval growth to mortality, or its inverse, is used to indicate changes in cohort biomass and is referred to as a cohort’s “recruitment potential”. Most studies observing this metric have focused on variation at survey-level or annual scales, which may ignore crucial variability in cohort success at finer spatiotemporal scales relevant to individual larvae. By sampling larval Pacific sardine (Sardinops sagax) off southeast Queensland, in Chapter 4 I demonstrate that vital rates of cohort success vary at scales smaller than features that are generally considered to be oceanographic habitats (i.e., eddies and shelf waters). While growth rates are more consistent among features, rates of mortality are highly variable, highlighting the importance of incorporating mortality estimates in attempts to understand cohort success in field studies. Building on the understanding that size-spectra are remarkably consistent in marine ecosystems, in Chapter 5 I test the hypothesis that the slope of the plankton spectra provides a valuable diagnostic tool for rapidly assessing growth and mortality of larval fishes in situ. To test this, I sampled larval Pacific sardine and plankton simultaneously on three voyages along eastern Australia, using a bongo net with an interior finer-mesh net. Contrary to expectations, results from this study demonstrate a negative relationship between the slope of plankton size spectra and recruitment potential of larval Pacific sardine of equivalent size. This may result from high susceptibility of larval Pacific sardine to predation, owing to the thin body shape and poor swimming ability characteristic of clupeid larvae. Several stronger relationships between larval growth and mortality, and physical oceanographic parameters were evident. Together, these results indicate that years where spawning occurs predominantly in shelf areas with a lower concentration of large predatory zooplankton, and, the East Australian Current is meandering further from the shelf break than normal, could provide the necessary conditions allowing for exceptional levels of Pacific sardine recruitment off eastern Australia. My thesis suggests plankton size spectra are unlikely to reflect recruitment potential directly, at least for Pacific sardine. However, incorporating some size-based aspects of the plankton community into a broader modelling framework could further our ability to determine how larval success varies across a seascape. Improvements in the resolution of vital rate estimates, and of spatially explicit modelling procedures, might accurately predict larval success although data is currently unavailable. Therefore, continued sampling larval fishes and estimation of vital rates is required. While data from international programs such as CalCOFI provide a strong starting point, continuation of larval fish monitoring programs in Australia will provide an avenue to further explore forecasting of larval success
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(2022)ThesisThe Southern Hemisphere extratropical westerly winds are the strongest time-averaged surface winds on Earth, having a profound impact on weather systems, ocean circulation, Antarctic sea-ice as well as oceanic uptake of heat and carbon. The westerly winds have shown poleward intensification in the last few decades driven primarily by stratospheric ozone depletion with a secondary role played by increasing greenhouse gases. In recent years we have seen early signs of ozone recovery as a result of the Montreal Protocol. Part 1 of this thesis demonstrates that by curbing CFC emissions, the Montreal Protocol also played a critical role in mitigating future surface climate change, equivalent to approximately 25% reduction in global surface warming by 2050. A major feature of the Southern Hemisphere extratropical atmospheric circulation is its strong zonal coherence. However, there are notable zonal asymmetries embedded in the flow, with two important examples being the zonal wave 3 (ZW3) and Amundsen Sea Low (ASL). Although these features have received significant attention from the scientific community, the mechanisms responsible for their presence are still not clear. In Part 2, model experiments suggest that the ZW3 pattern is generated remotely by tropical deep convection and not by the presence of three extratropical landmasses as had previously been assumed. Quantification of ZW3 impacts requires a way to consistently characterize this variability. In Part 3, I formulate a new index for ZW3 which accounts for variability in the structure, phase and amplitude of ZW3. In Part 4, I provide evidence that in contrast to ZW3, the ASL is generated primarily by the interaction between westerly winds and Antarctic orography. Zonally asymmetric features are not only present in the mean circulation but also in the past and projected westerly wind changes in the Southern Hemisphere. These are characterized in Part 5 in reanalysis and models. Following on from this, I demonstrate in ocean model simulations that future projected zonally asymmetric atmospheric changes can drive substantial changes in the ocean circulation in the Pacific and Indian Oceans, accounting for more than 30% of the projected surface ocean warming around parts of Australia (Part 6).