School of BioSciences - Theses

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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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    Birds in the sky, fish in the sea, money in the bank: quantitative methods for more effective conservation
    Ryan, Gerard Edward ( 2021)
    My approach in this thesis was to explore how to wring more information out of existing data to reduce uncertainty, improve decision-making and hope to generate better conservation outcomes. I explore and develop a range of quantitative tools to this end. I look at three key areas: dealing with uncertainty, structuring decision making, and improving the use of existing information. I consider these concepts over three thematic case studies: monitoring the abundance of three vulture species in Cambodia, trading-off the costs and benefits of releasing information publicly when a new species or population is discovered, and comparing use of optimisation and project prioritisation protocols to allocate funding to species conservation efforts. In the first case-study, I develop new Bayesian hierarchical model to estimate vulture abundance, and compare the inferences available from this approach with less specialised approaches previously used. In the second case-study I develop a decision-making framework to allow decision-makers to explicitly trade-off costs and benefits, and apply the method to data collected from informants who have made these types of decisions themselves. In the final section, I explore whether additional information can improve optimisation to allocate funding, and compare performance in terms of expected avoided extinctions of the optimisation approach with a project prioritisation protocol. I find that there is indeed much more we can learn from the information we have. But this is not a free lunch – work needs to be done to uncover opportunities, and technical skills are often needed to make best use of them, and assumptions must often be made to draw conclusions.