School of BioSciences - Theses

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    Bioengineering coral-microalgae symbioses to improve the thermal bleaching resilience of adult corals
    Scharfenstein, Hugo ( 2023-12)
    Tropical coral reefs are hotspots of marine biodiversity valued for their ecological, socioeconomic and cultural significance. These ecosystems are supported by reef-forming corals (Scleractinia), which rely on photosymbionts (Symbiodiniaceae) for nutrition. Under stress, this intricate symbiosis can break down, resulting in coral starvation and possibly death. Vast swathes of coral reefs have been lost to anthropogenic activity. In the last decade, marine heatwaves – exacerbated by climate change – had the most widespread and devastating impact on coral cover. At current warming rates, coral reefs as we know them are projected to disappear before the turn of the century. To avert this decline, (human)-assisted evolution of coral thermal tolerance is actively researched as a strategy to mitigate worsening coral loss to marine heatwaves. Host-centric breeding and microbial manipulation methods are being explored to achieve this objective. This thesis focused on the enhancement of coral thermal tolerance through the manipulation of their algal symbiont communities. Algal symbiont manipulation is founded on the knowledge that coral thermal tolerance is largely underpinned by their Symbiodiniaceae community. Using experimental evolution, Symbiodiniaceae thermal tolerance can be enhanced in vitro. Preliminary studies demonstrated that introduction of heat-evolved photosymbionts into coral early life stages can boost host performance during thermal stress, with no apparent trade-off. However, key knowledge gaps need to be filled prior to the implementation of this strategy, some of which are addressed in this thesis. Chapter 1 provides an introduction to the coral-algal symbiosis, threats faced by corals, progress made in algal symbiont manipulation using experimentally evolved Symbiodiniaceae and the hurdles to implementation. In Chapters 2 and 3, novel strategies to increase the thermal tolerance of photosymbiont cultures are assessed. Mutagenesis prior to thermal selection yielded increased thermal tolerance, but it also led to trade-offs in growth and photochemical efficiency (Chapter 2). Selection under diurnal temperature fluctuations was identified as a promising strategy to experimentally evolve Symbiodiniaceae thermal tolerance (Chapter 3). In Chapter 4, I optimise a method (chemical bleaching) to remove the native photosymbionts from adult corals. I then demonstrate that a taxonomically diverse range of coral species can establish new symbioses with cultured Symbiodiniaceae, when these are heterologous to the host. In a team effort, novel pairings between adult corals and heat-evolved photosymbionts were generated and subjected to a simulated heatwave. In Chapter 5, I investigate the transcriptomic responses of these symbioses to heat. I identify a dampened response of heat-evolved photosymbionts to thermal stress, characterized by a reduced expression of oxidative stress and cellular damage response pathways. In Chapter 6, recommendations are provided to progress the experimental evolution of Symbiodiniaceae for coral reef restoration, and a preliminary assessment is made on the efficacy of heat-evolved photosymbiont lineages to improve adult coral thermal tolerance. Remaining challenges to the implementation of this strategy are also discussed. Overall, this thesis reduces the barriers to implementation of algal symbiont manipulation by delivering novel strategies for experimental evolution, and provides molecular evidence of reduced susceptibility of heat-evolved photosymbionts to thermal stress when in symbiosis.
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    Conservation of freshwater macroinvertebrates through molecular methods
    Tsyrlin, Edward ( 2023-09)
    Freshwater macroinvertebrates are a diverse group of aquatic animals that lack backbones, including insects, worms, crustaceans, and molluscs, with sizes larger than one-third of a millimetre. For over a century, this group has primarily served as an indicator of stream health, and for practical reasons, have been typically identified at the family level. While potentially suitable for generic ‘waterway health’ assessments, the recent evidence of the biodiversity loss within freshwater ecosystems globally, requires reliable methods that go beyond the family level to more accurately measure biodiversity, including species richness and composition within this group. To address this need, in Chapter 2, Marxan conservation planning software was used to analyse a dataset collected from 140 sites in Greater Melbourne, Australia, spanning from 1993 to 2009. Our analysis demonstrated the inadequacy of the family-level data analysis in assessing species-level diversity. Specifically, the minimum number of sites required to observe all families or all species in Greater Melbourne was compared to show that the use of family-level data leads to an insufficient sampling effort for the purpose of biodiversity assessments. Furthermore, the selection of 17% and 50% of optimal conservation sites using family-level data versus species-level data revealed that the use of family-level data would result in important omissions, jeopardizing the conservation of rare species in the Melbourne area. The adoption of DNA metabarcoding as a routine species identification method is advocated for biomonitoring, including biodiversity assessments. This approach offers greater insights into local and regional biodiversity values, facilitates the detection of subtle changes in site community composition, and reinvigorates the study of species-level taxonomy among freshwater macroinvertebrates. Subsequent studies in this thesis focus on employing molecular techniques to enhance our understanding of the biodiversity and taxonomy of critically endangered and poorly known freshwater macroinvertebrates. Chapter 3 aimed to improve our knowledge of the distribution of two endangered amphipod species, Austrogammarus australis and Austrogammarus haasei, also known as Dandenong and Sherbrooke amphipods, within the Dandenong Ranges, Victoria, Australia. While the previous delineation of A. haasei was well supported by the DNA analyses, A. australis was separated into six distinct genetic lineages. Three other genetically distinct groups were found outside of the Dandenong Ranges. Further research is required to taxonomically classify these lineages, potentially leading to changes in the conservation status and management priorities for these groups. This study highlights the value of DNA barcoding techniques for detecting cryptic species, particularly when these species already hold conservation significance. In Chapter 4, DNA barcoding was also employed to detect environmental DNA (eDNA) of another critically endangered freshwater invertebrate, the Mount Donna Buang wingless stonefly (Riekoperla darlingtoni), to potentially identify new populations outside its known range. The survey revealed two new localities located 2.5 km west of previously known populations, expanding the extent of occurrence to 0.37 square km, across a total of five localities. A significant decline in the abundance of the main population correlated with climate warming. This study demonstrated that eDNA survey methods are sensitive and reliable for detecting freshwater invertebrate species occurring at low densities and difficult to sample habitats, compared to conventional methods. These results provided the necessary data for a submission to list the species under the Australian federal Environment Protection and Biodiversity Conservation Act (EPBC) 1999. The study also contributed to a case to protect the species from a proposed development within its range and attracted international recognition to this unique and vulnerable species through the IUCN. Chapter 5 addresses the common challenge of associating aquatic juvenile and terrestrial adult life stages. DNA barcoding has the advantage of reducing the need for rearing juvenile stages by associating both stages through their DNA. Additionally, DNA data facilitated the examination of relationship among the species in this study. This approach was applied to associate larval stages with previously described adults and to redescribe the larval stage of the diving beetle Chostonectes nebulosus. An identification key to all known Chostonectes was constructed using morphological characters. The increasingly pivotal role of DNA methods in detecting and discovering freshwater macroinvertebrate species is highlighted throughout the manuscript. These methods are expected to greatly improve the assessment and management of invertebrate diversity, laying a solid foundation for making well-informed decisions in conservation management and shaping evidence-based environmental policies.
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    The influence of circadian clock variation on local adaptation in Arabidopsis and agronomic traits in wheat
    Buckley, Christopher Robert ( 2023-11)
    Plants have evolved diverse mechanisms to cope with changes in their environment. Among the most important of these, the plant circadian clock adjusts physiology and development in response to daily and seasonal environmental rhythms. The cues perceived by plant circadian clocks are non-uniform across the biogeographical environment, and variation of circadian function is required between and within species. The overarching aim of this thesis was to identify how this functional clock variation arises in plants. Extant phenotypic variation in circadian rhythms across a naturally occurring species, Arabidopsis thaliana, and a cultivated species, bread wheat (Triticum aestivum), was quantified and compared. The respective contributions of this variation to local adaptation in Arabidopsis and agronomic traits in wheat were rigorously assessed. In Chapter 2, a transient luciferase imaging assay was used to measure circadian rhythms of 287 natural Arabidopsis accessions. Through genome-wide association mapping, three SNPs were identified in the evening-expressed clock gene EARLY FLOWERING 3 (ELF3) that were highly associated with variation in circadian period. Accessions harbouring these SNPs primarily occupy continental climates of Eastern Europe and Central Asia, and through physiological and population genetic analyses, evidence is provided that ELF3 has aided local adaptation to highly seasonal climates. The circadian rhythms of elite Australian wheat cultivars were measured using delayed leaf fluorescence in Chapter 3, and a large range in circadian period was detected. By leveraging existing and novel clock gene markers, specific combinations of clock gene alleles (chronotypes) were defined that are associated with circadian period. To test the importance of circadian rhythm variation to agricultural traits, the timing of leaf senescence and grain nutrition traits were measured across the same cultivars, and strong associations with circadian period were observed. A specific effect on timing of senescence and grain protein content was found for a widespread deletion in TaELF3-D1 using pairs of near-isogenic lines (NILs). To define the global transcriptional response of circadian rhythms to senescence, in Chapter 4 48-hour ‘circadian transcriptomes’ were generated in both mature and senescent flag leaves. This analysis revealed that the output of the clock expands and diversifies at senescence, and this response is associated with increasing rhythmicity of WRKY transcription factor expression. The average circadian period of transcripts shortens by 0.5 h in senescent tissue, akin to previous studies of circadian rhythms during ageing. Interestingly, the pace of circadian oscillator genes is largely unchanged. Instead, clock genes are enriched amongst transcripts that exhibit significant advancement of phase, which is perhaps a driver of the changing period of global gene expression. These findings demonstrate abundant phenotypic variation in the circadian clocks of naturally occurring and domesticated plant species. This variation is not only consequential for traits related to seasonal development (e.g. flowering or senescence); it can also have pleiotropic effects on traits like response to high temperature and nutrient use efficiency. Clock gene variation has been co-opted by the forces of natural and artificial selection and thus holds promise for the finetuning of agricultural traits in future changing environmental conditions.
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    Development of bacterial probiotics to increase thermal bleaching tolerance of corals
    Doering, Talisa ( 2023-12)
    Coral reefs host >30% of all marine eukaryotic species and hold significant ecological, economic, cultural and spiritual value. However, coral reefs are vanishing due to climate change-induced coral bleaching (i.e. the loss of photosymbiotic algae from the coral tissues) and mortality. Current models predict that coral reefs will be lost within this century if no action is taken. Besides reducing greenhouse gas emissions, the development of strategies that improve coral thermal tolerance is imperative as long-lived corals are not likely to naturally adapt in time to current rates of ocean warming. The health and survival of reef building corals depend on the symbioses with a diversity of microorganisms, such as photosynthetic algae and bacteria. Within the scope of assisted evolution approaches for corals, the manipulation of the coral bacterial microbiome via the use of probiotics, i.e. the addition of beneficial living microorganisms to improve host fitness, is still at the beginning. With the overall objective of developing bacterial probiotics to mitigate bleaching, this thesis (1) examined the cellular mechanisms of coral bleaching in two cnidarian models, the sea anemone Exaiptasia diaphana and the scleractinian coral Galaxea fascicularis, (2) identified G. fascicularis as a new coral model for developing bacterial probiotics, (3) cultured and genomically identified G. fascicularis-associated bacterial probiotic candidates and their traits, and (4) examined uptake and temporal association of four probiotic candidates with the coral host over 5.8 months. The findings of this thesis verified a key role of reactive oxygen species (ROS) in thermal bleaching of G. fascicularis and demonstrated a diverse potential of associated bacteria to mitigate bleaching, for instance through ROS-scavenging. Further, my findings demonstrated a potential of the probiotic strains Endozoicomonas sp., Ruegeria sp. and Roseibium sp. to remain associated with the coral for one to at least six months post-inoculation under ambient conditions. Further study is required to test whether these can confer thermal bleaching tolerance to the coral host. This thesis has provided important new knowledge that will help assess whether bacterial probiotics is a viable intervention for coral reefs.
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    Modelling gene-environment interactions for myopia development in zebrafish
    Xie, Jiaheng ( 2023-10)
    Myopia prevalence is increasing dramatically and is expected to affect up to 5 billion people by 2050. Myopia occurs when excessive eye growth leads to the light sensing retinal photoreceptors being located behind the visual input focal plane, resulting in blurred distance vision. It is thought that prolonged exposure to aberrant visual environments impairs emmetropisation processes leading to a mismatch between eye size to its optical power. Therefore, myopia can be induced environmentally in animal models by manipulating visual cues. There is ample evidence that emmetropisation relies on gene-environment interactions, but the underlying mechanisms remain largely unknown. Recent human genome-wide association studies (GWAS) have identified a large number of novel genetic variants associated with myopia. To understand the role of these genes in myopia development, high-throughput vertebrate models are needed for large-scale in vivo investigation of genes-environment interactions. In this project, a high-throughput gene manipulation and multi-level analysis platform was developed to show that modifying a GWAS-associated gene pdzk1, which has been linked to visual endophenotypes (e.g., contrast sensitivity) of neurodevelopmental disorders (e.g., schizophrenia and autism), resulted in zebrafish visual dysfunction (optomotor response and electroretinography; Chapter 2). Using a novel dark-rearing paradigm, robust myopia phenotypes were generated, with clear refractive anomalies as well as functional and anatomical sequalae (Chapter 3). Next, a CRISPR approach was employed to modify a GWAS-identified myopia-risk gene, EGF containing fibulin extracellular matrix protein 1 (efemp1) only in the retina. Retina-specific efemp1 mutant showed impaired eye growth regulation that was dependent on visual input (Chapter 4). Finally, using restricted-wavelength rearing along with disruption of retinal short-wavelength cone photoreceptors (S-cones), it was possible to show that S-cones play a crucial role in visually driven ocular development in zebrafish (Chapter 5). The availability of gene editing tools in zebrafish coupled with multi-level phenotypic assessment tools, and robust environmental myopia models provide an excellent platform for large-scale in vivo investigation of gene-environment interactions in myopia development. This platform has been used here to highlight the importance of the efemp1 gene and S-cones to myopia development and also provided insights as to the molecular mechanisms and the anatomical substrates through which they might modify eye growth in myopia.
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    The role of lipids in the formation of beneficial interactions between plant roots and soil microbiota under heat stress
    Macabuhay, Allene Andaya ( 2022-11)
    Climate change, which is characterized by the rise of global atmospheric temperatures known as global warming, has serious detrimental effects on crop production because of the direct influence of elevated temperature on plant development. One novel strategy to increase crop productivity while mitigating heat stress is the use of soil microbes, which is slowly gaining popularity because of its low-cost approach, availability, sustainability, and quick turnover. Specific soil microbes can form symbiotic relationships with the roots, whose beneficial effects on plant growth and development, as well as on plant responses to biotic and abiotic stresses, lead to improved plant performance. The plant-microbe interaction is complex and involves below-ground communication, followed by modifications of molecular, biochemical, and morphological processes in the plant. Plant roots display extreme plasticity in adapting to a range of environmental stimuli and are therefore important indicators of plant-level responses to microbial colonization, via changes in architecture and metabolic processes. Lipids, which are essential constituents of the plasma membrane with diverse functions in cellular processes and homeostasis, have been proposed to play significant roles in the rhizosphere. Because heat stresses have a profound effect on membrane stability and lipid composition, rising global temperatures are likely to impact the formation of plant-microbe symbiosis. This study aimed to characterize and quantify the bacteria-induced growth promotion and heat tolerance in plants, and to investigate how plant root lipid profiles are altered under both bacteria and high-temperature conditions. For that, advanced phenotyping and lipidomics technology were employed to monitor plant responses to developmental and environmental changes. By using the high-resolution, high-throughput phenotyping platform GrowScreen-Agar II, an open-top plant-bacteria co-cultivation system was optimized utilizing the model plant Arabidopsis thaliana and the plant-growth-promoting rhizobacteria (PGPR) Paraburkholderia phytofirmans PsJN. This allowed for in-depth, tissue- and time-specific root-and-shoot morphological trait characterization, which elucidated the dynamics of bacterial promotion on plant growth. We have quantified the magnitude of bacterial-induced plant stimulation between ambient and elevated temperatures, confirming the excellent benefit of the PGPR in ameliorating the adverse effects of heat stress. These morphological traits were also associated with the root lipid profile using state-of-the-art lipidomics technology, which revealed specific lipid species and their functions in this tripartite interaction. Knowledge gained from this study, besides being fundamental in the understanding of plant-microbe interactions, can also inform research agenda of future directions for microbial studies as potential agricultural and biotechnological solutions in the endeavor to address global food security under climate change.
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    Deciphering how CELLULOSE MICROTUBULE UNCOUPLING 1 (CMU1) controls pavement cell shape and root skewing via microtubule (MT) stability
    Chen, Hsiang-Wen ( 2023-07)
    The cell wall is a specialised structure that contributes not only to plant life but also to practical uses for our society. One of the most vital components in the cell wall is cellulose, synthesised by Cellulose Synthase (CESA) proteins that form large complexes that move along cortical microtubules (MTs) at the plasma membrane. The MT-steered trajectories of the CESAs are assisted by several MT-binding proteins, including Cellulose-Microtubule Uncoupling (CMU) 1 & 2, Companions of Cellulose synthase (CC) and Cellulose Synthase Interactive (CSI) proteins. Our lab has previously published studies on the in vivo interaction between CMU1 and MTs (Liu et al., 2016). However, many questions remained about the mechanism of interaction between CMU1 and MTs, and how these interactions contribute to plant growth and development. Chapter 1 offers a concise introduction to plant cell wall cellulose and the cytoskeleton, focusing specifically on the connection between the cellulose synthase complex and microtubules. There are four basic features that are presented, including a quick overview of the primary and secondary cell walls, the cytoskeleton in planta, the relationship between microtubule-associated proteins (MAPs) and cellulose, common phenotypes caused by microtubule disruption, and the goals of this research project are all topics that are covered in this thesis. In Chapter 2, the phenotypes of cmu mutants were investigated in vivo using a variety of techniques, including a root skewing assay, a root penetration experiment, root length and angle measurements, and cotyledon pavement cell analysis. Circularity and relative completeness of the pavement cells were significantly different between Col-0 and cmu mutants. In addition, the rate of microtubule polymerization was three times faster in the cmu1cmu2 mutants than in wild type. These findings imply that alterations in microtubules may cause pavement cells to become more round. In Chapter 3, two proteins, His-tag CMU1 full length (FL) and His-tag CMU1-FL-GFP, were expressed and purified. The His-CMU1-FL-GFP protein was discovered to attach to microtubules (MTs) in vitro. Using SDS-page and microscopy, I documented that the His-CMU1-FL protein caused MTs to bundle together. GFP served as a visual indicator to validate the binding and bundling of CMU1 to the MTs and a photobleaching experiment indicated that CMU1 proteins were capable of binding and bundling MTs. These results suggest that, when interacting with microtubules, CMU1 proteins are capable of both binding and bundling. In Chapter 4, to discover whether part of the CMU1 FL protein was capable of binding and bundling MTs, the variants of CMU1 FL, including the N terminus, Tetratricopeptide repeat (TPR) domain, and C terminus, with or without GFP and a His-tag were purified. The findings of the MT binding experiment indicated that the CMU1 TPR domain had the greatest binding capacity. The MT bundling test further showed that the TPR domain of CMU1 has greater bundling capacity than the N or C termini. In addition, the GFP version demonstrated that the TPR domain of CMU1 decorated MTs. This suggests that the TPR domain of CMU1 is primarily responsible for CMU1 MT binding and bundling in vitro. In Chapter 5, studies conducted in vitro and in vivo indicate that the MAP IQ-domain 2 (IQD2) protein interacts with CMU1. The phenotypes of the cmu1 and iqd2 mutants were examined in vivo using similar techniques as Chapter 2. Col-0 wild type, cmu mutants, and iqd2 mutants vary significantly in terms of the circularity and relative completeness of the pavement cells. Experiments conducted in vitro further showed that the presence of IQD2 promotes the binding and bundling of CMU1 to microtubules. In Chapter 6, the results of this study are summarized into a model of CMU1 and IQD2 function in microtubule regulation, cell wall synthesis, and plant growth and development. Some suggestions for future research possibilities are also proposed to test this model.
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    Analysis on the role of Enteroblasts in epithelial homeostasis in the adult Drosophila midgut
    Zhu, Qiuyun ( 2023-06)
    Epithelial tissue functions as a protective barrier to the outside world, thus proper maintenance of epithelial homeostasis is essential for animal health and wellbeing. In response to damage or programmed cell death, the functional and structural integrity of an epithelium is maintained through cell turnover. In this project, we utilised the adult Drosophila midgut as a model to study homeostatic maintenance in an adult tissue, with particular focus on the role of the Enteroblast (EB), as it was reported to function as a reservoir for damage-induced tissue repair (Antonello et al., 2015). The process whereby EBs differentiate and give rise to new Enterocytes (ECs) is known as a Mesenchymal-Epithelial Transition (MET), and is an essential component for their proper incorporation into the existing epithelium. In this project, we built upon the current knowledge of the transcription factors and signalling pathways that drive EB MET and focused our investigations on the complex morphogenetic behaviour of EB cells. To this end, we have established an analysis pipeline that combines machine learning segmentation with cellular morphometric and spatial distributions analysis. Using this pipeline, we first uncovered a previously unreported bimodal distribution pattern for wildtype EBs which is associated with midgut regeneration status. In “quiescent” midguts, EBs were evenly spread out and new ECs were rare. In “regenerative” midguts, EBs were often found in groups, made up of EBs in various stages of their MET as well as new ECs, which we termed “MET regenerative clusters”. Next, using time-lapse imaging, we have established that EBs are motile in nature, and exhibit increased cytoplasmic movements when subjected to artificial tissue damage. With these findings, we proposed a working model linking midgut damage (i.e. EC loss) to regenerative cluster formation through the directional migration of nearby EBs. Furthermore, by applying the pipeline to EBs with target gene RNAi knockdowns, we identified Septate Junction (SJ) component Discs Large (dlg) to be a novel EB MET regulator. The presence of dlg-deficient cells disrupts normal midgut epithelial structure (i.e. a multilayered epithelium was observed), and such cells often exhibit polarity and junctional defects. Loss of dlg is also linked to apical membrane thinning and subsequent luminal extrusions. Signalling pathways linked to midgut stress responses were examined and we found the dlg-/- phenotype to be associated with JAK/STAT and JNK activation. Finally, to make further progress on our working model, we present the design of the TALGAR system (Targeted Apoptosis using LexA with GAL4 Analysis of Response) which allows for the induction of reproducible and temporally-regulated site-specific damage, as well as the ability to examine live EB cell dynamics and perform target gene manipulations. The TALGAR system was not completed due to time constraints but progress towards the goal was made and is described. Our work highlights the utility of the Drosophila model to further our understanding of epithelial homeostasis, and the importance of quiescent basal progenitors such as EBs in response to damage. The discovery of regenerative clusters opens up a new avenue for studying the triggers of regeneration, an area that has previously been difficult to address. As mechanisms of regeneration are conserved across evolution, this can pave the way for further research, and highlights the importance of MET in wounding and repair. It is also intriguing that the function of a junctional protein includes a role in the regulation of cell MET status. One of the many interesting questions left to be explored is whether other junctional proteins also regulate MET.
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    Ecological genomics, behaviour and control of Aedes notoscriptus, a neglected disease transmitting mosquito from Australia
    Paris, Véronique ( 2023-07)
    Mosquitoes are significant disease vectors, spreading pathogens that cause diseases like malaria, dengue, and Zika worldwide. In Australia, local mosquito species play a crucial role in disease transmission. Effective control strategies must consider the ecological characteristics of the target species and the surrounding environment. The first part of this thesis focused on studying the population structure and dispersal patterns of the Australian Backyard mosquito (Aedes notoscriptus) at fine and global scales. Notably, this species displays higher dispersal capabilities compared to the primary dengue-transmitting mosquito, Ae. aegypti. By combining mitochondrial DNA (mtDNA) and genome-wide single nucleotide polymorphisms (SNPs), I found evidence for cryptic mtDNA lineages of Ae. notoscriptus with varying geographical distributions. Additionally, SNP analysis identifies six distinct genomic groups that do not consistently align with the mtDNA lineages. The discordance between mtDNA and nuclear DNA is not attributed to Wolbachia infections but may be influenced by factors such as sex-specific asymmetries and human-assisted displacement. Furthermore, insights into invasive Ae. notoscriptus populations in New Zealand and the USA suggest their likely origin in Victoria, Australia. Additionally, I tested a novel mosquito trap design by evaluating its effectiveness through field and laboratory studies. The findings indicate that this system effectively reduces the number of Ae. notoscriptus eggs in the field. Furthermore, by reviewing existing literature, conducting human-baited field trials, and performing laboratory experiments, I found that the levels of male mosquito attraction to humans seems to be highly species specific, which is important for the effective and sustainable management of male mosquito releases to control population sizes and disease transmission.
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    Restoration of kelp beds on degraded temperate rocky reefs
    Graham, Tristan David John ( 2023-04)
    The loss of kelp beds has been observed across the globe, often as a result of overgrazing by urchins, but also facilitated by other factors that reduce kelp bed resilience. While kelps are restricted to temperate waters, their local distribution and abundance are limited by the availability of suitable substrate, light conditions, and wave climate. Natural recovery of kelp beds can be limited by short dispersal distances for spores, and the stabilizing feedbacks of alternate reef states. The loss of ecosystem services provided by kelp beds and the lack of natural recovery is driving interest in restoration among land managers and researchers. Restoration attempts for these temperate rocky reef ecosystems to date have had mixed success, and lessons learned may be location specific, requiring further work to inform restoration efforts in different systems. The study area for this thesis is Port Phillip Bay, part of the Great Southern Reef (GSR) which stretches across southern Australia. Ecklonia radiata is the dominant kelp across the GSR, and Heliocidaris erythrogramma is the urchin of concern in Port Phillip Bay. Ecklonia radiata is a relatively small kelp with large morphological diversity across environmental gradients. Port Phillip Bay has a history of anthropogenic environmental disturbances including catchment-based pollution, introduction of invasive species, and removal of several large fishes through overfishing. In recent years, overgrazing by H. erythrogramma has been blamed for vast losses of E. radiata cover in the Bay. I begin this thesis by conducting a baseline survey of reef condition, urchin density, and urchin roe marketability across Port Phillip Bay. This allowed identification of specific management actions at a small (1 ha) spatial scale. I then explore three specific components of kelp restoration: 1) the use of kelp mimics to reduce sediment accumulation in the absence of an adult kelp bed; 2) the spatial scales over which natural recruitment can occur, and preferences for different substrate orientations and levels of shading; and 3) factors affecting success of transplanting juvenile kelp for restoration. The final chapter draws together the lessons from these four chapters in a management plan for kelp forests and urchins. Specific management actions were categorized at a 1 ha scale, allowing areas at highest risk to be identified, and actions to be prioritized based on management priorities and available resources. I observed divergent effects on sediment accumulation across sites, suggesting the artificial kelp behaves differently in slightly different environmental conditions. I observed most new kelp recruited within tens of meters from the nearest kelp bed, but densities and distances could not be explained by modelled local currents. I confirm the reduced sediment accumulation and low light conditions under a kelp canopy are associated with higher recruitment, and found vertical surfaces saw a tenfold increase in recruit density. However, I did not separate the effects, so the higher recruitment may have been due to one factor and in spite of the other. My transplant study demonstrated a potentially scalable restoration technique and highlighted the sensitivity of restoration spatial and temporal context. I also identified shallow exposed bommies as a potential source of juvenile sporophytes where high recruitment is coupled with very low likelihood of survival to maturity. Insights from this thesis can inform small scale interventions within the broader context of the Bay. My thesis identifies specific small scale kelp management actions appropriate within the broader context of Port Phillip Bay, but the lessons can be translated for application more broadly. My findings, some of which contrasts with previous studies, highlight the nuances in management of complex temperate reef ecosystems.