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Now showing 1 - 9 of 9
  • (2020) O'Reilly, Gabe
    Thesis
    Population genetics is a continuously advancing field of study. Population wide datasets, often with large numbers of genetic loci typed, are becoming increasingly more common due to advances in sequencing technologies making large scale data collection economically feasible. While large investment accelerates practical data collection, theoretical methods to make use of this growing pool of data should also be developed. The aim of this thesis is to develop several such methods, for use on population wide datasets, each to answer different questions a researcher might have about their study populations. Each chapter broadens the scope of analysis, with the second chapter investigating variation between the two genomes within each individual at one time in a single population, Chapter 3 will investigate variation of one population over generations, and Chapter 4 will look at variation between potentially subdivided populations over generations. In Chapter 2 I develop an analogue to traditional inbreeding measures, that works with data from multi-locus gene families typed by next generation sequencing. This type of data is currently not amenable to traditional inbreeding measurements. In Chapter 3, I developed predictive equations to Shannon’s Information (a measure of genetic diversity) to see if they could accurately predict how Shannon’s Information declines over time in a population, because a decline in genetic diversity is often linked with a decline in fitness of individuals in a population. In Chapter 4, I develop a method to detect whether a potential split event has actually led to genetic subdivision, preferably as early as possible, and possibly without genetic data from before the event. These processes analysed in these three chapters (inbreeding, genetic drift, and subdivision) are all often deleterious to populations by lowering the fitness of individuals in that population. The deleterious nature of these processes makes them of great interest for study, giving great utility to the methods proposed in this thesis.

  • (2023) Zillur Rahman, Kazi Mohammad
    Thesis
    Current healthcare infection surveillance rarely monitors the distribution of antimicrobial resistance (AMR) in bacteria beyond clinical settings in Australia and overseas. This results in a significant gap in our ability to fully understand and manage the spread of AMR in the general community. This thesis explores whether wastewater-based monitoring could reveal geospatial-temporal and demographic trends of antibiotic-resistant bacteria in the urban area of Greater Sydney, Australia. Untreated wastewater from 25 wastewater treatment plants sampled between 2017 and 2019 consistently contained extended-spectrum β-lactamases-producing Enterobacteriaceae (ESBL-E) isolates, suggesting its endemicity in the community. Carbapenem-resistant Enterobacteriaceae (CRE), vancomycin-resistant enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA) isolates were occasionally detected. Demographic and healthcare infection-related factors correlated with the ESBL-E load, and demographic variables influenced the VRE load. In contrast, the healthcare infection-related factor mainly drove the CRE load. These findings demonstrate the potential of wastewater-based surveillance to understand the factors driving AMR distribution in the community. The subsequent thesis work covers the genomic characterisation of selected ESBL-E and CRE wastewater isolates to reveal their nature, origin, and underlying resistance mechanisms. Phylogenetic analysis showed that Escherichia coli isolates were related to high-risk human-associated pandemic clones and non-human-associated clones. The Klebsiella pneumoniae and K. variicola isolates were related to globally disseminated and emerging human-associated clones, and some were detected for the first time in Australia. Genomic analysis also indicated novel resistance mechanisms against nitrofurantoin in E. coli, and against piperacillin/tazobactam and ticarcillin/clavulanic acid in Klebsiella isolates. The virulence gene content indicated that some E. coli and Klebsiella isolates were likely associated with infections, while the asymptomatic carriage was suggested for other isolates. These results demonstrate a clear potential for wastewater-based surveillance to monitor the emergence and dissemination of resistance in non-clinical isolates, and in particular, isolates from the community and non-human sources. The findings of this study can complement healthcare infection surveillance to inform management strategies to mitigate the emergence and dissemination of AMR and important human pathogens in the general community.

  • (2022) Stuart, Katarina
    Thesis
    Few invasive birds are as globally successful or as well-studied as the European (or common) starling (Sturnus vulgaris). Native to the Palaearctic, the starling has been a prolific invader in North and South America, southern Africa, Australia, and the Pacific Islands, while facing population declines of >50% in some native regions. Starlings present an invaluable opportunity to examine questions regarding rapid adaptation and evolution within invasive populations, and to gain insight into genetic responses to novel selective regimes. My research focuses primarily on the invasive starling population in Australia and aims to investigate the genetics underlying their evolution, using a range of genomic approaches. First, I generated high-quality genomic resources (transcriptome and genome) to facilitate evolutionary studies on this species. I then used reduced representation sequencing to assess population structure and patterns of putative selection in Australia. I found that introduction history can confound the identification of signals of selection. By comparing single nucleotide polymorphism (SNP) variation in native range historical samples and contemporary samples from the native and introduced Australian ranges, I identified instances of divergent and parallel evolution across both contemporary populations. I used whole genome resequencing to contrast patterns of SNPs and structural variants in native and in invasive populations in North America and Australia. I identified putatively adaptive structural variants and assessed the roll of balancing selection, which may facilitate rapid adaptation in the Australian range. Finally, I examined matched genetic, morphological, and environmental data to reveal that vegetation and rainfall variability appear to be important in shaping starling morphology and genetic variability. I identified patterns of biologically important phenotypic traits in the Australian invasive range that varied with underlying genetic patterns (implying heritability) or only with environmental gradients (implying plasticity). Overall, my research illuminates mechanisms and patterns of genetic change in native and invasive starling populations and may inform management of this species. More broadly, this research provides an important perspective on the role of rapid evolution in the persistence of introduced species, and the environmental factors that may shape range shifts and evolution across taxa.

  • (2022) Zhang, Shan
    Thesis
    Marine sponges (phylum Porifera) often form stable symbioses with unique and complex microbial communities. Sponges have also been increasingly recognized as important model organisms for understanding symbiosis processes. To improve our understanding of the adaptation of sponge-associated symbionts to a symbiotic lifestyle and the associated metabolic interactions, I have applied comparative genomics and metabolomics as well as genome-scaled metabolic network modelling to the spongeassociated microbial symbionts. Firstly, to better understand how sponge-associated microorganisms adapt to a symbiotic lifestyle, in Chapter 2 I performed comparative analyses of metagenomeassembled genomes (MAGs) from three different sponge-associated Nitrososphaeria (formerly Thaumarchaeota) and their free-living counterparts. The results revealed several functional features related to a sponge-associated lifestyle, including nutrients transport, restriction-modification, defense mechanisms, and protein-protein interactions. Distinct characteristics were found among the three species, indicating that they have reached different stages of adaptation and/or occupied different ecological niches in their hosts. In addition, in Chapter 3, I performed comparative metabolomic analyses of whole sponge tissues and fractionated microbial cells from six co-occurring sponge species to determine the biological and ecological roles, as well as the true producers of spongederived metabolites. The results showed that all investigated sponge species appear to have metabolic interactions with their symbionts by providing nutrients (e.g., carbohydrates). Antagonistic activities were detected in both sponge hosts and microbial symbionts, suggesting that sponge holobionts can protect themselves against invasive species. Sponge hosts were also predicted to recognize self from non-self by producing mannose, a molecule that mediates cell-cell recognition and adhesion. Additionally, several antioxidants appeared to be produced by microbial symbionts, suggesting that symbionts may have a defensive response to oxidative stress. Lastly, to investigate metabolic interactions within the sponge holobionts, in Chapter 4 I developed a genome-scale metabolic network model for an eight-species microbiome associated with the sponge Stylissa flabelliformis. This microbiome was composed of an ammonia-oxidizing archaea (AOA) and seven bacteria species, including a nitrite-oxidizing bacteria (NOB), a photosymbiont, a denitrifying species and four sulfur-oxidizing bacteria (SOB). The results predicted that certain amounts of spongederived ammonium and hypotaurine are necessary to maintain a stable community structure. The AOA, NOB, SOB and the photosymbiont were predicted to live mixotrophically via cross-feeding interactions. Assuming that the sponge host could consume symbionts as particulate organic matters, it was predicted that under steady-state conditions, the sponge holobiont would still lose a considerable amount of carbon due to symbiont respiration, nitrite and nitric oxide due to denitrification, as well as sulfite and sulfate due to sulfite oxidation, implying that the sponge host would have to obtain extra carbon source, or provide sulfur- and nitrogen-free/poor metabolites to the microbiome. Overall, this work has provided novel evolutionary and ecological insights into the relationship between sponges and their symbionts, the putative biological activities and sources of sponge-derived metabolites, as well as the metabolic interactions that may occur within the sponge holobiont.

  • (2023) Hudson, Jennifer
    Thesis
    Disease outbreaks affecting marine organisms represent a serious concern for the ecological functioning and economic value of coastal ecosystems. In particular, diseases affecting foundational species such as macroalgae, can threaten the health and productivity of temperate marine ecosystems and have far reaching consequences for ocean life. Therefore, the aim of this thesis was to investigate the molecular mechanisms determining host-pathogen interactions between the model red macroalga, Delisea pulchra and Aquimarina sp. AD1 (Bacteroidota), an etiological agent of bleaching disease. Members of phylum Bacteroidota are an abundant and diverse group of marine bacteria, yet little is known about their virulence strategies. A systematic review of the literature revealed that members of this phylum are inherent opportunists, with disease being an outcome of complex host-pathogen-environment interactions. Moreover, virulence is motivated by the nutritional acquisition of host polymers, with pathogenic Bacteroidota employing a suite of specialised polymer degrading functions to elicit host damage. Using this framework, a comparative genome analysis approach between Aquimarina sp. AD1, a closely related pathogen Aquimarina sp. BL5 and a non-pathogen, Aquimarina sp. AD10, identified an array of traits that may contribute to the virulence of Aquimarina sp. AD1 and BL5, including the capacity to degrade host polysaccharides. Further phenotypic investigation of the agarolytic profile revealed that Aquimarina sp. AD1 is highly adapted to growth on agar substrates, encoding several specialised agarolytic functions that were absent in the related non-pathogen, which are hypothesised to contribute to the virulence of this algal pathogen. Lastly, the transcriptional response of D. pulchra following exposure to Aquimarina sp. AD1, compared to Aquimarina sp. AD10, was investigated under the conditions of thermal stress that is associated with the onset disease. A downregulation of genes encoding for protein metabolism, cellular stress response, energy generation and photosynthesis was observed in the alga. This response was predicted to interfere with the algal pathogen-defences which may ultimately lead to tissue damage and bleaching symptoms. By investigating both the host and pathogen factors determining disease outcomes, this thesis advances our understanding of disease in this model host-pathogen system, and further expands our understanding of virulence in this group of marine pathogens.

  • (2023) Li-Williams, Scarlett
    Thesis
    Rusa deer (Cervus timorensis) were introduced to Australia in the late 1800s to early 1900s for game hunting, aesthetic purposes, and farming. Since their introduction, their distribution has increased, especially in peri-urban landscapes across the state of New South Wales (NSW), eastern Australia, causing negative environmental and socio-economic impacts. Effective management of deer in peri-urban landscapes requires strong knowledge on the spatial ecology of the target species, which can be challenging. Characterising the genetic structure and patterns of gene flow in a population can help to identify landscape features affecting movement, and this information can be useful for devising effective management strategies for invasive populations. In this thesis, I used reduced representation sequencing data (DArT-seq) to investigate population structure, characterise dispersal, and investigate if natural and artificial landscape features affected gene flow in peri-urban rusa deer invading the Illawarra region of NSW. I then used landscape resistance models to determine how specific landscape features affect connectivity in this species. In addition, I explored the potential impact of model selection criteria for landscape genetic analyses. Genetic diversity was highest in the north of the Illawarra region, near an original introduction site. When investigating genetic structure (without landscape data), a railway line demarcated restricted gene flow whilst natural features did not appear to restrict gene flow. Using landscape genetics, both natural and artificial features appeared to impact connectivity. The artificial structures present in Illawarra and topographic ruggedness have a potential barrier effect to gene flow, and tree cover may be facilitating gene flow. Model selection based on information criterion were robust, however multicollinearity in landscape variables influenced model choice selection. In conclusion, the genetic structure of the Illawarra rusa deer population was consistent with individuals spreading south from their introduction site in Royal National Park. The population was not panmictic, and both artificial and natural landscape features (associated with urbanisation and terrain ruggedness) were associated with increased spatial genetic structure.I identified three potential management units on which to prioritise management efforts to reduce further environmental and socio-economic impact of invasive rusa deer.

  • (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.

  • (2022) Leong, Rick
    Thesis
    Foundation species such as trees, corals, kelp and seagrasses are found across multiple spatial scales (i.e., local to biogeographic scales) and provide many ecosystem services. Understanding species distributions across multiple spatial scales can inform species resilience and important spatial scales for restoration and management of threatened foundation species. However, only few studies have investigated their distribution patterns across all spatial scales they exist in. The Sydney Rock Oyster, Saccostrea glomerata, is a threatened, reef-building, intertidal foundation species that is found on the Australian south-eastern coast. Remnant reefs in different estuaries consist of patches of different shapes, size and distances (i.e., connectivity) from one another. In this thesis, I utilised this spatial variation to investigate how oyster population characteristics (e.g., body size and density), population processes (e.g., recruitment) and biodiversity provision by remnant S. glomerata reefs vary within patches (e.g., surface elevation), with patch-scale attributes (e.g., patch-area), among patches (e.g., distance between patches) and on a regional scale (i.e., among estuaries). My major finding was that variation at the largest scale (among estuaries) was the best predictor of body size and density of oysters, faunal communities and oyster recruitment. Although smaller scales (i.e., scales within estuary) relationships also occurred for all metrics, these were often in different directions (positive, negative or neutral) across estuaries. This suggests that larger scale processes are setting the context to smaller scale effects on metrics recorded. To investigate the effect of larger scale processes on oyster recruitment, I conducted a field experiment across six estuaries. The major finding was that oyster recruitment across these estuaries was negatively correlated to sedimentation loads in each estuary. In summary, my thesis highlights the need to understand ecological patterns of foundation species across multiple spatial scales and the influence of large-scale processes that may drive ecological patterns at smaller scales. From a restoration perspective, prioritising important spatial scales that maximise population characteristics and ecosystem functions, especially the recruitment of the target species can aid in efforts to promote long-term oyster reef sustainability, enhance restoration success and the services they provide.

  • (2023) Eyck, Harrison
    Thesis
    The cane toad (Rhinella marina) is a major driver of species’ declines and adaptation in its invasive range in Australia. However, much of this research is focused on vertebrates, and we know relatively little about how it has impacted micro-organisms, such as nematodes. My thesis focuses on the relationship between cane toads and two nematode species. The first is the parasitic lungworm Rhabdias pseudosphaerocephala, which cane toads brought with them from South America. The second is a previously undescribed free-living nematode designated Au20MP, which I found living in cane toad faeces in the Northern Territory, Australia. Using infection experiments, I sought to determine what traits in the host-parasite relationship between toads and lungworms have led to the emergence of a co-evolutionary arms race at their range-edge in Australia. I found that this arms race is primarily driven by differences in toad immune function between range-edge and range-core populations. Second, I assembled the R. pseudosphaerocephala genome, and used this to characterise genetic differences between range-core and range-edge populations, which also differ extensively in phenotype and infectivity. I also investigated the diversity within Australia of the cryptic, co-introduced South American native R. pseudosphaerocephala. Within Australia, I found evidence of a single taxonomic group, and my analyses suggest a genetic bottleneck has occurred on the range-edge. I phylogenomically placed the Rhabdiasidae within the suborder Rhabditina. I then generated a draft genome assembly of Au20MP, and phylogenomically identified this previously undescribed species as a member of the globally widespread Panagrolaimidae, known for their extreme environmental tolerance and reproductive diversity. Finally, I used behavioural trials to demonstrate that Au20MP actively seeks out toad faeces, and develops preferences for toads from populations that it has previously encountered, indicating that this species may exploit toads as a source of food in the wild. My thesis advances the understanding of the evolution of host-parasite interactions, nematode genomics, systematics, and behaviour. These findings highlight the behavioural and genomic adaptability of nematodes, and suggest that interactions between invaders and nematodes are commonplace, and could have wide-ranging consequences due to the abundance of nematodes in almost every habitat on Earth.