School of BioSciences - Theses
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ItemExpanding Our View of Algal-Bacterial Interactions Through Analysis of Molecular Data( 2023-04)Microalgae and bacteria have co-existed for millions of years and their interactions have significant bottom-up effects on ecosystem scale processes. Microalgae are highly diverse and innumerable, making it difficult to compile information on their interactions with equally ubiquitous and diverse bacteria. Furthermore, what we know so far about specific microalgal- bacterial interactions reflects only a small fraction of what potentially occurs in nature. In chapter 2, I performed a global screening for microalgae-bacteria associations using publicly available 16S rRNA metabarcoding data. The study aimed to discover previously unknown associations between microalgae and bacteria by using co-occurrence networks built from existing 16S rRNA gene-based metabarcoding datasets. This study identified a range of known and unknown associations between microalgae and bacteria, demonstrating the promise of 16S rRNA gene-based co-occurrence networks as a framework for hypothesis generation. In chapters 3 and 4, I studied the bacterial microbiome of Ostreobium, an alga living in coral skeleton. Ostreobium remains understudied despite extensive research on the coral holobiont. I hypothesized that the enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment. This would allow stronger associations between Ostreobium and the bacteria making it an ideal algal-bacterial system to investigate evolutionary concepts such as codivergence and phylosymbiosis.Phylosymbiosis captures the correlation between the host phylogeny and the relationships of microbial communities associated with those hosts. Phylosymbiosis may arise from stochastic processes as well as through long-term host-microbe associations such as codiversification or coevolution. Codiversification, which is usually an indicator of coevolution, occurs when the speciation of one organism leads to the speciation of the associated organisms. In chapter 3, I investigated the bacterial microbiome associated with several Ostreobium strains in cultures using 16S rRNA metabarcoding, characterizing the taxonomic composition, diversity, likely physical associations of the bacterial associates and phylosymbiotic signatures. The results of chapter 3 indicated that Ostreobium is associated with taxonomically diverse bacteria. However, Ostreobium consistently associated with only a few of these bacterial groups (34 bacterial taxa), revealing a core microbiome. The data showed that while some bacteria may be loosely attached, others are tightly attached or potentially intracellular. Together with the core microbiome these potentially tightly attached or intracellular bacteria were defined as the closely associated microbiome of Ostreobium. I discovered that the Ostreobium-bacterial associations prevalent in cultures are likely to appear in their natural environment by analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples. The results also indicated significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. In chapter 4, I used metagenome-assembled genomes (MAGs) to investigate the functional potential of the bacteria associated with Ostreobium and addressed the codiversification concept. Here, the genomes representing the closely associated bacterial taxa of Ostreobium were specifically studied. Their genomes harboured dissimilatory nitrate/nitrite reduction, urea hydrolysis and methylamine degrading genes showcasing the potential to provide Ostreobium with ammonia. In addition, the results indicated that bacterial genomes possess vitamin B12 synthesis potential. A significant number of MAGs contained genes to metabolize C1 compounds like methylamine, methanol, and methane suggesting C1 metabolism may be a common trait among bacteria. Additionally, the presence of eukaryotic-like proteins in these MAGs indicated that they have the genetic machinery to maintain putatively stable host associations. Finally, the cophylogenetic analyses to assess the phylogenetic congruence between Ostreobium hosts and the bacterial associates provided evidence for codiversification. Independent cophylogenetic assessment of microbial orders showed significant congruence between the Phycisphaerales and Ostreobium phylogenies and identified family SM1AO2 to be potentially co-diverging with Ostreobium. This PhD expands our knowledge of microalgal-bacterial interactions by revealing previously unknown associations and providing insights into their evolutionary and functional relationships.
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ItemNo Preview AvailableIntrinsic and extrinsic modulators of Müller glia behaviour during retinal regeneration( 2022-12)Loss or dysfunction of the neurons in the retina leads to significant and irreversible vision impairment. Due to the variety of causes of this vision loss, ranging from genetic disease, environmental perturbations as well as ageing, a one-size-fits-all therapeutic approach does not currently exist. However, an exciting potential treatment involves activation of resident stem cells that already exist in the retina to replace these lost neurons. Muller glia are an abundant cell type in the retina of all vertebrate species, and in the established model system zebrafish (Danio rerio), Muller glia can successfully contribute to retinal regeneration and thus restoration of visual function. This is achieved through cellular reprogramming, whereby zebrafish Muller glia adopt a stem cell-like state and give rise to daughter progenitors through cell division, which can differentiate into mature retinal neurons. Despite an inability for human Muller glia to intrinsically regenerate the retina, factors crucial for driving this zebrafish Muller glia activation have been able to improve the neurogenic ability of mammalian Muller glia as seen in rodent systems. Therefore, enhancing our understanding of factors that influence Muller glia-driven regeneration in the zebrafish is crucial to designing future therapeutic strategies to treat neuron loss in the human retina. This thesis examines the current efforts determining factors that influence Muller glia-driven regeneration in the vertebrate retina, summarises research investigating key aspects of Muller glia behaviour in zebrafish retina regeneration, and discusses future directions for this research field to consider. Chapter 1 introduces the retina with an emphasis on the photoreceptor cells, the zebrafish model system, and the current understanding of Muller glia-driven regeneration in zebrafish, chick, and rodent systems. Chapter 2 provides evidence into the heterogeneity that exists among Muller glia in the zebrafish retina, how this heterogeneity can influence Muller glia activation, and the gene expression changes that drive this activation. Chapter 3 investigates external factors that can influence the behaviour of Muller glia following neuronal injury, with a focus on immune cells and debris clearance. Chapter 4 focuses on the fate of daughter progenitor cells derived from Muller glia in the regenerating zebrafish retina and how this progenitor fate can be influenced by the injury environment. Chapter 5 discusses future avenues to pursue from this research, as well as relevance in designing future therapeutic strategies to stimulate effective Muller glia-driven regeneration.
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ItemConflict and concordance in the evolutionary process: exploring the effects of separate sexes in Drosophila melanogaster( 2023-03)Differences in how selection acts on males and females are crucially important to many questions in evolutionary biology, including the evolutionary origins of sexual reproduction, and the maintenance of genetic variance in the face of selection. Theory predicts stronger total selection (i.e. natural and sexual) on the phenotypic effects of alleles when they are expressed in males, because males are typically subject to more intense sexual selection than females. However, selection among males does not always increase the fitness of their daughters, because alleles can differentially affect the sexes. Because selection acts on phenotypes produced by many alleles, this can result in mutually non-exclusive, conflicting fitness outcomes for females. For example, selection among males may favour alleles that increase male reproductive success and female fitness, such that natural and sexual selection align (‘good genes’ effects). In this case, selection among males reduces genetic load and increases population viability. Simultaneously, selection can also favour alleles that increase male reproductive success but reduce female fitness (intralocus sexual conflict). This latter scenario increases genetic load in females and may increase the risk of population extinction. Teasing apart the joint action of sexually concordant and antagonistic selection is a considerable challenge. However, new community resources, genetic tools and quantitative genetic methods provide the opportunity to resolve this confound. In this dissertation, I investigated the evolutionary ramifications of males, and the sexes sharing a genome, using multiple approaches. In Chapter 1, I summarise my main findings, provide a short primer on the evolutionary process and detail how this is affected by selection acting on separate sexes. I particularly focus on how differences between the sexes produce intralocus sexual conflict and the purging of mutation load through sexual selection. In my first data chapter (Chapter 2), I collated sex-specific breeding values for hundreds of traits in the Drosophila Genetic Reference Panel and used the Secondary Theorem of Natural Selection to estimate how these traits would respond to selection in a laboratory environment. I found that the expected response to selection is stronger in males than it is in females, and that very few traits are expected to respond to selection in opposite directions in males and females. I then explored the fitness consequences of intralocus sexual conflict in greater detail (Chapter 3), using an experimental evolution approach in Drosophila melanogaster that enforced female-limited, male-limited and unconstrained inheritance of the major autosomes, using an innovative breeding design. Contrary to earlier research, limiting the selective response to males did not increase male fitness. Moreover, a female-limited selection response also resulted in no increase to female fitness. I then capitalised on these ‘sex-limited evolution’ populations in Chapter 4, where I explored whether passing the autosomal genome through males reduced the load of deleterious mutations in the population. I found that a male-limited selection response history reduced mutation load relative to control and potentially also female-limited selection histories. In a final experiment, I investigated whether sexual selection enhances purging of a particularly deleterious gene complex that is associated with a sperm-killing selfish allele. Through manipulative experiments and a population genetic model, I tested the prediction that sperm competition and cryptic female choice could curtail the spread of the selfish allele complex. I showed that sexual selection acting among males can reduce the frequency of the selfish allele, which likely has a positive effect on population viability (Chapter 5). My findings suggest that the selective response is greater in males than it is in females, and that this extends beyond traits with direct links to male reproductive success. Furthermore, this stronger selection among males appears to purge deleterious mutations from the gene pool, to a greater extent than occurs in response to selection among females. Finally, the benefits of an evolutionary response in males extend to females, and these benefits appear to outweigh the relatively benign fitness consequences of segregating sexually antagonistic alleles (or lack thereof) in my experimental Drosophila populations.
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ItemMove it or lose it: how and when to use targeted gene flow( 2023-04)A myriad of threats are currently assailing threatened and soon to be threatened populations. Habitat removal, climate change, wildlife disease and the invasion of non-native species are all placing increased pressure on the systems we undervalue for their role in providing clean air, water, carbon sequestration and natural beauty. Many populations, however, contain individuals expressing traits that enable them to survive and reproduce even in the presence of these existential threats. Unfortunately, many of these adaptive traits are rare in endangered populations. But useful variation in traits doesn't only occur within populations: geographic trait variation is ubiquitous and can arise from a number of different processes, including natural selection, spatial sorting, and drift. Natural selection allows populations to adapt to local environmental conditions and can lead to locally adapted variants. Spatial sorting, the spatial analogue to natural selection, can also lead to predictable geographic variation in traits across space, as invasion and recolonisation select for increased dispersal. Both of these forms of selection result in predictable trait variation that conservation biologists can harness to promote conservation benefits. Geographic variation might also arise through drift, but such variation is much less predictable. Once geographic variation exists, it is possible to harness such variation to affect conservation goals. This idea -- targeted gene flow -- has the objective of identifying and harnessing geographic trait variation to promote conservation benefit. Current work on targeted gene flow has focused on understanding how species respond to certain threats and on exploring the use of targeted gene flow to boost adaptive potential in threatened populations. In this thesis, I explore the utility of applying targeted gene flow to two different conservation problems: i) can targeted gene flow be deployed to facilitate evolutionary rescue in response to rapid (and flexible) environmental change? and ii) can targeted gene flow be deployed to directly mitigate a threatening process? To answer these questions, I use a blend of field studies and simulation models focused on the introduced pest, the Cane Toad (Rhinella marina). This thesis starts by providing the reader with background information and current applications of targeted gene flow, as well as identifying and framing the need for novel measures to reduce the impacts of cane toads in Australia. To explore this use case, we first need to understand how to apply targeted gene flow in an optimal fashion, as well as how to measure any benefits. In the opening data chapter of my thesis, I set out to understand how to optimally deploy targeted gene flow and build upon initial work in this area to examine how targeted gene flow should be deployed against differing threat profiles. I find that the optimal timing and size of a targeted gene flow action is highly sensitive to the maximum rate of change of the threat across time, and that if conducted correctly, targeted gene flow can provide enough adaptive potential to stave off extinction whilst retaining almost all of the genetic diversity of the population under threat. This measure, the expected benefit, is a novel metric to benchmark the effectiveness of targeted gene flow applications. In the subsequent chapters of this thesis, I extend the notion of targeted gene flow to a different context: reducing the dispersal ability of invasive species. Cane toads are one of the most harmful introduced species in Australia. Decades of sustained investment in cane toad control, research and management has unearthed a number of effective strategies for the local control of cane toad populations, but no landscape level solution currently exists. In chapter three, I quantify the financial benefit of keeping areas toad-free. I conduct field studies to generate estimates of toad density and detectability, before combining these with removal and cost models to provide an estimate of the value of cane toad quarantine across offshore islands as well as a potential toad-free haven on the mainland: the Pilbara region of Western Australia. My final chapter explores how targeted gene flow can be deployed to increase the effectiveness of a landscape barrier designed to contain the toad invasion and so create a toad-free haven over 265,000 km2 of the Australian mainland. This chapter provides the first case study of how targeted gene flow can be deployed to directly mitigate a threatening process. In doing so, I provide the first evidence that targeted gene flow can be used to directly reduce the negative impacts of an invasive species, through driving down their dispersal ability, and in doing so render landscape barriers substantially more effective. This thesis shares the process of exploring a new application of targeted gene flow, from theoretical conception to an applied trial. I provide the first evidence that targeted gene flow can be used to reduce the ability of an invasive species to move across the landscape, alongside extensions to the current framework surrounding how to optimally implement targeted gene flow to aid threatened populations. The resulting strategies are not limited to the impacts of cane toads but instead have application to a wide range of conservation scenarios. Generally, my thesis develops the under-appreciated idea that, by being creative with geographic trait variation, we have a powerful and cost-effective tool for conserving biodiversity.
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ItemGenomically informed gene drive modelling( 2022)CRISPR/Cas gene drives are a focus of genetic biocontrol for pest species. They have the potential to radically affect pest species, by making them more manageable or by eradicating them. However, it is not yet fully understood how the elements of a gene drive interact to guide the progression of a gene drive. We explored how we can design gene drives that are safer, either by being temporally limiting or spatially limiting, through a modelling framework. Our modelling included a range of variables, with the addition of genomic information to infer the homing efficiency of the gene drive. We showed that there was no single variable that differentiated between the outcomes of a gene drive. Granted some variables were more influential in determining the outcome than others. The degree of dominance of the selection coefficient was shown to be strongly influential on the equilibrium outcome. While the interaction between conversion efficiency and resistance was shown to strongly influence the Temporary outcome. Furthermore, we showed that internal dynamics of a gene drive can be regulated by the variables of the gene drive. This provided insight into where effort should be directed in gene drive design to achieve the intended outcome of a gene drive, as well as controlling the progression to that outcome. The inclusion of genomic data in CRISPR gene drive modelling allowed for localisation of the gene drive due to genetic variation alone. Finding loci in the genome where there were allele frequencies differences allowed us to model gene drives that were highly efficient in the target population and poorly efficient in off-target populations. This conversion efficiency differential allowed for sustained gene drive localisation in spite of migration and selection. Population suppression was explored in our modelling to better understand how we could create sustained localised suppression. We showed sustained population suppression was possible through incomplete distortion of the sex ratio of the progeny. A deterministic gene drive model was developed to solve for equilibrium points for a range of migration rates and selection coefficients. These equilibria can be used as thresholds for gene drive design and monitoring. This work aims to further develop our understanding of how gene drives are likely to progress when released. We focussed on characterising which aspects of a gene drive were most important in determining both their progression and outcome. The inclusion of genetic information in our modelling revealed a new avenue that can be exploited to achieve gene drive localisation. This modelling work will aid in the design process of gene drives to increase our confidence that gene drives will work as intended.
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ItemExploring the cancer transcriptome with novel bioinformatics approaches( 2022)Currently three out of every 10 deaths within Australia will be a direct consequence of cancer. Cancer is a complex and genetically heterogeneous disease that is, as a consequence, effectively unique to each individual. However, there are common driving events, phenotypes, and risks that can segregate cancer within tumour types and subtypes. These groupings are beneficial as they can both inform treatment regimes and yield new targets for pharmaceutical development. Next Generation Sequencing (NGS) of RNA has enabled measurement of the abundance and makeup of a sample’s transcriptome, which through bioinformatics analysis, can reveal the rich interplay between genetic mutations and their functional and phenotypic consequences. This thesis focuses on three key transcriptome projects. The first project developed the ALLSorts software which is the first publicly available and open-source classifier for determining subtypes of B-Cell Acute Lymphoblastic Leukemia (B-ALL). The purpose of this tool is to provide researchers with an accurate method for using transcriptome data to quickly label B-ALL samples according to 18 subtypes. Subtyping is becoming part of clinical standard-of-care, informing targeted pharmaceutical treatment and/or treatment intensity. The second project, Slinker, is a publicly available and open source visualisation tool that can be applied to any gene that highlights splicing variation between a case and controls. Novel splicing is regularly observed across a variety of diseases, including cancer, and can lead to a significant alteration of the final transcript, possibly transforming it into a pathogenic driver. Slinker is novel in that it utilises the superTranscritome method to create succinct visualisations by removing redundant features. The final project in this thesis is an analysis of the utility of long read transcripts as a transcriptomic reference, specifically within a spatial context. Three references were compared: the hg38 reference transcriptome, the long reads themselves as a reference, and both combined. Each had gene expression quantified through highly accurate, short read technology. The combined reference resulted in both a higher mapping rate and novel expressed sequences, of which one belongs to a gene that is a known prognostic marker for the oropharyngeal head and neck cancers that this method was applied to.
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ItemDeciphering the molecular mechanisms underpinning oil biosynthesis in Salvia hispanica L. (Chia)( 2022)Salvia hispanica L. (chia) is an oil seed plant rich in omega-3 polyunsaturated fatty acids, proteins, and antioxidants. Daily consumption of chia seeds has been associated with health benefits related to cardiovascular system and cognitive function. The link observed between the nutraceutical composition of chia seeds and the health benefits associated with it prompted extensive research into the contents of chia seeds. The study of oil biosynthesis pathways in the model organism Arabidopsis thaliana as well as other oil seed plants has been an active research area aiming to unravel the mechanisms of oil production. However, the underlying genetic mechanisms that regulate oil biosynthesis, particularly in non-model organisms such as S. hispanica, are little understood. One of the several biological roles assigned to plant lipids is their involvement in abiotic stress responses. The cause-effect relationship of oil biosynthesis and stress response in plants becomes particularly important under extreme environmental conditions. The rise in global temperature is thus threatening the yield and quality of S. hispanica’s seed oil quality. The genetic make-up of S. hispanica was unstudied prior to this PhD study, thereby hindering the discovery of genes and regulatory elements that determine its unique traits. Advances in high-throughput genomic technologies including Illumina short-read sequencing, Oxford Nanopore Technology long-read sequencing, and Hi-C chromosome conformation capture technique enabled the creation of a high-quality near-complete chromosome-level reference genome for S. hispanica. The evolutionary study of the S. hispanica genome through comparative genomics revealed novel aspects related to the omega-3 fatty acid accumulation in chia seeds. The hypothesis that due to a recent whole genome duplication highly expressed genes regulate oil biosynthesis was rejected. Instead, the evolutionary expansion of the stearoyl-ACP desaturase (SAD) gene family due to tandem duplications was identified as the key factor of efficient oil biosynthesis in S. hispanica. Along with global warming, heat waves in the Kimberly region of Australia are anticipated, their effect is a major concern for chia growers. In this thesis, an integrated transcriptomic (RNAseq) and lipidomic (LC-MS) approach was used to demonstrate an effective basal thermotolerance in S. hispanica in response to heat shock and prolonged heat stress. The successful recovery of lipids and transcripts in S. hispanica leaves that undergone heat stress is proposed to be associated with Ca2+ signalling and cytosolic transport pathways as well as two distinct membrane lipid-remodelling mechanisms. An increase in the abundance of unsaturated lipids, dominated by the triacylglycerol (TG) family, is proposed to cause stabilisation of membrane fluidity. In parallel, an analysis of differentially expressed genes indicated that the phospholipid diacylglycerol acyltransferase (PDAT) and the diacylglycerol O-acyltransferase (DGAT) genes play a pivotal role in heat induced biosynthesis of TGs in the endoplasmic reticulum and detoxifying the chloroplast from free fatty acids. The reference genome of S. hispanica generated as part of this PhD study will greatly assist the plant science and plant breeding communities to study the molecular mechanisms of S. hispanica in the future. Features of the generated high quality Hi-C contact map such as chromosomal territories and regulatory interaction of enhancers and promoters will provide new insight into the molecular genetics underlying the unique traits of S. hispanica. This dissertation further contributes to a better understanding of fatty acid biosynthesis in S. hispanica and the role of lipids in response to heat stress in general. Together the results of this PhD will aid the development of novel agronomical crops with improved seed oil content or enhanced resistance to abiotic stresses while mitigating the detrimental impacts of climate change.
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ItemDissecting the contribution of structural gene and regulatory variation in metabolic resistance to insecticides in Drosophila melanogaster( 2022)Strong selection pressure imposed by insecticide usage has allowed resistance to evolve and spread in insect populations. One mechanism underlying resistance, increased insecticide metabolism, is often linked to increased expression or activity of enzymes belonging to four major families: cytochrome P450s, esterases, glutathione S-transferases and uridine diphosphate-glycosyltransferases. There is a growing body of evidence that the capacity for metabolic enzymes to confer insecticide resistance is a by-product of their evolved capacity to metabolise xenobiotics present in the natural environment. This has led to the hypothesis that insect populations may contain an array of metabolic enzymes that can potentially provide resistance to insecticides, despite not being optimised for insecticide metabolism in terms of their expression or structure. This raises questions about the genetic changes required for metabolic resistance to evolve and the number of enzymes in a given species that have the potential to confer resistance. This study addresses these questions by exploiting two well-defined model systems – the resistance genes Cyp6g1 in Drosophila melanogaster and LcaE7 in Lucilia cuprina. A multi-faceted approach using in vivo, in vitro, and in silico techniques has been deployed to explore these questions. The first aim of this study was to evaluate the resistance potential of five D. melanogaster P450 genes closely related to Cyp6g1. This was achieved through transgenic overexpression regulated by the Accord promoter responsible for elevated levels of Cyp6g1 expression in natural populations of D. melanogaster. Homology models were also created for all six of these P450s. Of these genes, only Cyp6g1 and Cyp6g2 were able to confer resistance towards the insecticides tested - nicotine and the neonicotinoids, imidacloprid and nitenpyram. The second aim investigates the structure-function relationship of CYP6G1. Molecular docking alongside site-directed mutagenesis experiments were able to demonstrate that Phe123, Phe124, Thr219, and Val377 are involved in the metabolism of imidacloprid. Moreover, CYP6G1 variants with an increased capacity for imidacloprid metabolism were generated via Phe220Pro or Val308Ser replacements. However, only one of these mutations, Phe220Pro, confers increased levels of imidacloprid resistance. The third aim explores whether a highly efficient organophosphate hydrolase LcaE7 variant (R9) produced through laboratory-directed evolution could confer resistance when placed in an in vivo D. melanogaster system. Despite having very high levels of activity, this LcaE7 variant conferred lower than expected levels of organophosphate resistance. Activity-stability trade-offs in this evolved variant has reduced its capacity for organophosphate resistance, hence it is unlikely to arise and spread in natural populations of L. cuprina. The findings from this study further our understanding of the evolutionary options available for metabolic resistance and contribute to the capacity to predict the nature of resistance that may evolve, leading to better resistance management strategies.
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ItemQuaternary diversity dynamics of Australian reptiles( 2022)Predicting the outcomes of anthropogenic impacts on ecosystems is an essential step to counteract the recent biodiversity crisis. The Quaternary fossil record offers a unique opportunity to formulate such predictions by testing how ecological communities and / or species distributions change through time, e.g., in response to the repeated and intensifying shifts in global climate during the glacial-interglacial cycles. Such paleoecological information is particularly critical for ectothermic vertebrates, such as reptiles and amphibians collectively known as herpetofauna, as these groups comprise a high number of threatened species and are particularly sensitive to changing climates. Yet, in most cases, the investigation of long-term faunal dynamics requires a morphology-based taxonomic or ecological identification of fossilized elements. For herpetofauna this has been notoriously difficult, due to a lack of comparative knowledge about the osteological variation in modern taxa, underdeveloped osteological museum collections, and the prevalence of cryptic diversity. These difficulties pose a major challenge when paleontological data are intended to inform conservation, because applied conservation measures fundamentally rely on (species-level) taxonomy (e.g., the IUCN Red List). In this thesis, I test the recognizability of herpetofaunal species in the Quaternary Australian fossil record and apply alternative methods for inferring climate-related faunal dynamics, through a combination of quantitative paleontological and neontological methods. Australia is ideal for such an analysis as the continent comprises an exceptionally high herpetofaunal diversity as well as numerous Quaternary fossil sites, preserving a relatively continuous temporal sequence of reptile and amphibian fossils. I show in Chapter 1 that faunal change can be detected at higher taxonomic levels (above the species-level) and that changes in relative abundance of different reptile subfamilies over time correspond to changing aridity throughout a fossil deposit in western Victoria. This suggests that historical baselines for evaluating the stability of modern ecosystems may be established even in the absence of species-level taxonomic resolutions. The central aspect of this thesis is addressed in Chapters 2 and 3. Using a quantitative approach based on 3D geometric morphometrics, I leverage digital morphological data (CT scans) to test how reliable individual bones of agamids (Chapter 2) and varanids (Chapter 3) can be assigned to (modern) lower-level taxonomic or ecological categories. My results show that genus- or subgenus-level as well as ecological identifications can be confidently achieved in most cases (> 90%). Thus, these categories constitute appropriate groupings for the investigation of temporal diversity dynamics. In contrast, species-level identifications were generally less reliable and sensitive to incompleteness of the bones or sample size. These results add to the long-standing question of transferability of modern species boundaries to the fossil record and imply that a comparison of modern and past (species-level) biodiversity may be prone to identification errors, at least within these groups. Finally, in Chapter 4, I integrated fossil occurrences, generated through the quantitative identification framework developed in the previous chapters, with (paleo-)species-distribution modelling, population genomics and osteological data of modern specimens to examine the decline of the threatened Mountain Dragon (Rankinia diemensis). This integrative approach revealed a strong link between Quaternary climate change and ongoing habitat loss and fragmentation in this temperate-adapted agamid lizard. My results suggest that increasing temperatures will likely force R. diemensis to further shift its distribution to higher altitudes, leading to a reduction of suitable habitat and increasing fragmentation of populations as global warming proceeds. Overall, my thesis provides new insights into the possibilities and limitations of the Quaternary Australian herpetofaunal fossil record in a conservation-paleobiological context, as well as an extensive resource of virtual morphological data and a quantitative methodological framework for future research.
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ItemLight manipulation by Christmas beetles: quantification, mechanisms and ecological relevance( 2022)The brilliant and colourful appearances of Christmas beetles (Scarabeidae - Rutelinae) are famous for decorating eucalyptus trees during the Australian summer. Millions of years of evolution perfected the design of their hardened fore wings (elytra) to manipulate light and create striking optical effects. However, little is known about the exact underlying nanostructures or the ecological variables driving their evolution. Despite the recent increase in biophotonics studies, this remains the case for many organisms with striking colourful appearances. By studying light manipulation in Christmas beetles, I aim to develop methods and concepts generalisable to other organisms. Christmas beetles produce a wide variety of optical effects including saturated colours, black, and pearlescent white. Some species look mirror-like and metallic gold or brass. Moreover, these colours change with the viewing or illumination angle. Christmas beetles can also interact with long wavelengths outside of the human-visible spectrum, in the near-infrared (NIR), and reflect circularly polarised light, which makes them appear as different colours through the right and left lenses of 3D cinema glasses. To better understand this diversity, I proposed a method for its quantification, studied some of its underlying mechanisms and tested if it can be explained by ecological differences. To characterise the beetles’ optical effects, I proposed a generalization of existing spectroscopy methods and parameters to describe reflection profiles across the visible and NIR spectrum, regardless of their underlying mechanism. Ultimately these methods break down complex optical effects into simpler traits and can facilitate comparison between studies. The proposed terminology attempts to conceptually unify disparate fields (biology and optics) and allows a clear distinction with terms used to describe colour perception. To study the optical mechanisms in Christmas beetles, I analysed the architecture of their elytra. I discovered that unlike scarab beetles studied to date, three different Christmas beetle species use multicomponent photonic systems, with an upper layer acting as a green pigment-based filter and an underlaying broadband reflector, that particularly enhances NIR reflectance. For beetles with spiral nanostructures, I found a trade-off between polarisation and NIR reflectance. This diversity of photonic structures shows that beetles are a promising model for understanding complex optical properties of natural materials. To investigate ecological correlates of the optical effects in Christmas beetles, I used a biophysical essay and a phylogenetic comparative analysis. High reflectance reduced heating of the beetle elytra under controlled conditions, but I did not find any evidence that highly reflective species occur in hotter environments. Christmas beetles do not follow a simple eco-geographical pattern, possibly because their optical effects respond to species-specific combinations of environmental challenges. I demonstrated that diversity in optical effects and photonic mechanisms is more than meets the eye, even for a small group such as Christmas beetles. My thesis highlights the value of a cross-disciplinary approach where optical methods can spark stimulating biological questions and the comparative study of phylogenetically related species can inform species selection for photonics studies. The resulting conversation between the two disciplines accelerates progress in the search for the biological function of striking optical effects.