School of BioSciences - Theses
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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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ItemUnderstanding and incorporating aphid parasitoids within IPM strategies in Australian grain crops( 2020)Aphids (Hemiptera: Aphididae) can be particularly devastating to grain crops, with their economic importance weighted on their ability to cause significant yield losses through a variety of methods. From feeding damage alone in 2012, cereal aphids caused an average annual loss of $14 million in Australian wheat crops. For over a century, growers have relied upon host plant resistance and chemical treatments to control invertebrate pests, however suppression of beneficial organisms and increased resistance within targeted species has created an ongoing battle with pest control. For example, the polyphagous green peach aphid (Myzus persicae (Sulzer)), often a pest of canola crops, has developed resistance to over 74 insecticides including carbamates, pyrethroids, and organophosphates around the world. Due to these issues, control of agricultural pests is now focussed on Integrated Pest Management (IPM) strategies, within which natural enemies can play a role as biological controls. Parasitoid wasps have had the most success as biological control organisms in the past, likely due to their host specificity. I spent three years collecting data on grain aphid pests and their associated natural enemies, paying particular attention to the hymenopteran parasitoids. I determined the distribution of grain aphids and their associated Aphidiinae within grain production landscapes around Australia, utilising historic data and citizen science. Additionally, I determined how aphid abundance and diversity, along with their associated parasitoids changed throughout the growing seasons. I created a key of aphid parasitoids (Hymenoptera: Aphidiinae) parasitizing aphids in Australian grain production landscapes. Finally, I determined the effects of seed treatments on specific natural enemies associated with M. persicae, identifying the difference between parasitoid and predator effects. My findings are informative for developing strategies to conserve those Aphidiinae species of particular importance in controlling aphid pests. Additionally, these results can assist with pest management decisions, enabling growers to implement IPM based on a greater breadth of knowledge.
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ItemPhylogenomics, molecular evolution and extinction in the adaptive radiation of murine rodents( 2020)Adaptive radiation plays a significant role in the generation of biological diversity, and the advent of modern sequencing approaches has unlocked a new genomic perspective on this process. Genomic-scale data from the across the diversity of adaptive radiations can provide unprecedented resolution of the phylogenetic, biogeographic and molecular context of diversification. Murine rodents (Murinae: Rodentia) are a recent and rapid adaptive radiation that make up > 10% of mammal species. Murines have repeatedly colonised new geographic areas and island systems in the Eastern Hemisphere, frequently as a result of overwater transitions. Recurring adaptive radiation, ecological character displacement, and convergent evolution across Murinae make them an ideal model for studying adaptive radiation, especially in the Indo-Australian region. Within broader Murinae, the Hydromyini are a speciose Australo-Papuan radiation that diversified following an overwater colonisation from Sunda to Sahul ca. 8 Ma. Previous multilocus studies did not provide sufficient phylogenetic resolution of the rapid diversification of Hydromyini, and did not adequately sample taxa to reconstruct their complex biogeographic history. In addition to unresolved biogeography, the endemic Australian clade within Hydromyini has suffered the highest rate of recent mammalian extinction in the world. The rapid decline of Australian rodents is thought to be primarily the result of predation by feral cats, combined with other factors such as anthropogenic land clearing. There is little information about the pace of decline in eight species that went extinct on the Australian mainland in the last 150 years, and it is unclear whether these species had suffered longer term declines that predate the arrival of Europeans into Australia in 1788. To resolve these outstanding issues, I develop a novel exon capture approach for murine rodents. Firstly, I investigate the degree of congruent and conflicting phylogenomic signal in a rapid radiation, using genus-level relationships in the Hydromyini as a model example. My results show that in a number of cases, strong conflict is not reflected in branch support metrics obtained using either maximum likelihood or summary coalescent approaches. This result is significant, as it suggests that approaches commonly used to estimate support in phylogenomic data can fail to detect uncertainty in the face of underlying genealogical heterogeneity. Further leveraging this novel exon capture design, I generate a robust phylogenomic tree based on > 350 samples across the Australo-Papuan continent, including extant and recently extinct species in Hydromyini. With these data, I reconstruct the species-level evolutionary and biogeographic history of the Hydromyini across Sahul, recovering numerous examples of overwater colonisation between regions. Consistent with the geomorphological hypothesis that the New Guinea lowlands emerged after the orogeny of the Central Cordillera, I find evidence for increasing ecological opportunity in the Hydromyini from approximately 5 Ma. This first species-level phylogenomic study spanning the entire Sahul region provides a baseline example for future comparative studies that seek to reconstruct the biogeographic drivers of diversification in Sahul at a continental scale. Using exon capture and whole-exome sequencing data from extinct and extant species, I place recently extinct Australian rodents in a phylogenomic context for the first time. I recover no marked evidence of genetic erosion in five extinct species at the time of specimen collection, in comparison to extant species with present-day low allelic diversity. This indicates that the decline of recently extinct Australian rodents occurred extremely rapidly, and its onset likely did not predate European settlement. Additionally, my results taxonomically resurrect a species from extinction, Gould’s mouse (Pseudomys gouldii), which survived as a single island population in Shark Bay, Western Australia (currently classified as P. fieldi). Finally, I generate whole exome data from 38 species in the global radiation of Murinae to examine patterns of positive selection and convergent evolution. I uncovered pervasive positive selection across genes associated with diet, digestion and taste across Murinae, and increased rates of adaptive evolution in carnivores compared to omnivores. Limited evidence for molecular convergence in worm-eating specialists Paucidentomys and Rhynchomys suggests a role for developmental phenotypic control in this striking example of ecological convergence. Broadly, my results indicate that the pronounced ecological and phenotypic shifts that are hallmarks of adaptive radiations may also drive corresponding shifts in the pace and pattern of molecular evolution across the genome. Together, the work in this thesis is fundamental to the understanding of diversification, adaptation and extinction in the Australo-Papuan region, and provides an extensive genomic resource for future studies.
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ItemHeterozostera resilience( 2019)Seagrass perform critical provisioning, regulating, cultural and supporting ecological functions and services humans rely on worldwide. Unfortunately, many seagrass ecosystems are vulnerable to disturbance and are being lost at alarming rates. Some seagrass species have been listed by the International Union for the Conservation of Nature as threatened and endangered where population sizes are small or are highly restricted in geographic distribution. For several other species, there is not enough data to determine whether a species is at risk or not. When ecological resilience thresholds for species survival and reproduction are exceeded, declines in seagrass may occur. Declines over time and space may be episodic or ongoing and occur as a result of impacts from both natural and anthropogenic stressors, such as turbidity, eutrophication, hypersalinity and urbanization. Increasing global change phenomena are expected to exacerbate declines of seagrass in many parts of the world, and vast losses of seagrass have functional implications for other ecosystems and organisms. Heterozostera are unique seagrass broadly distributed throughout coastal southern latitudes especially in Australia. Only three populations of Heterozostera are found outside of Australia, in a small region of the eastern Pacific in Chile. The populations are made up of 2 nonflowering clones. Therefore, Heterozostera of Australia may be functionally endemic to southern Australia, including Tasmania. Substantial loss of Heterozostera has been reported from the middle of Heterozostera's range in several locations of Victoria, Australia. Subsequent recovery of diminished populations has been slow in some sites, especially in Western Port, Victoria. Few published accounts related to resilience, including seagrass population monitoring for conservation and restoration of Heterozostera in the southern hemisphere have been completed. The aim of this thesis is to advance basic botanical research on Heterozostera in support of taxonomic resolution and the development of conservation strategies, especially those focused on modeling and applied seagrass resilience and restoration in Australia. More studies are needed to contribute to the development of restoration and resilience management strategies for lesser studied southern hemisphere seagrass ecosystems, and this work supports the generation of additional discoveries. Specifically, the objective of this dissertation is to identify and examine the autoecology and resilience Heterozostera, including sexual and clonal reproductive success under variable environmental cues. In all, five comprehensive studies of Heterozostera biogeography and biology are included in this dissertation, along with a theoretical framework and summary exploring the roles of environmental parameters in the autoecology of resilience for temperate Australian Heterozostera. Chapter 1 presents a review of research in support of Australian Zosteraceae, including trends and gaps in our understanding of seagrass resilience mechanisms, including both resistance and recovery pathways in Heterozostera. Chapter 2 details the results of an extensive survey of existing sediment and nutrient conditions for Heterozostera populations across 15 seagrass meadows located in southeastern Australia's Port Phillip Bay. Chapter 3 summarizes a series of experiments aimed at discovering effective Heterozostera seed storage and collection protocols for use in land based aquaculture, and specifically examining the potential roles of seed colour, sterilisation and refrigeration with the goal of improving long term seed viability. Chapter 4 contains a fully factorial germination assay undertaken to identify potential cues to Heterozostera germination, including sediment type and sterilization, nutrient loads, and refrigeration. Chapter 5 details a germination experiment using a 2 ppm copper sulphate (CuSO4) solution to cue germination of Heterozostera seed. Lastly, Chapter 6 explores the rates of asexual growth and survival of three types of clonal reproductive Heterozostera propagules (rhizome, plantlet and shoot). This work provides novel information about several topics of research with regard to the autoecology of Heterozostera including: (1) species identification, (2) species ecology and biogeography, (3) reproductive material collection and storage, (4) seed germination, and (5) clonal transplanting. This research demonstrates Heterozostera is capable of widespread recovery across a range of sediment and nutrient conditions. Continued work on lesser known Heterozostera species (H. tasmanica and H. polychlamys), and other rarer seagrasses world-wide are critical for understanding the potential loss of resilience and increased vulnerability (or conversely, the potential for recovery, adaptation and survival) of threatened and endangered seagrass populations with limited global dispersal. Collectively these studies details methods to support future Heterozostera research in both laboratory and field settings where culture of reproductive materials are required. In addition, the outcomes from this research provides novel information in support of progressing insitu seeding and transplanting efforts aimed to improve operation of land based seagrass nurseries and research studies. Novel evidence builds support that Heterozostera nigricaulis as a functionally resilient species of seagrass, largely due to its ability to inhabit variable ecological conditions and to utilize multiple sexual and asexual reproductive strategies to recover populations following disturbances.