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Includes bibliographical references. ; Life-history studies have informed all areas of aquatic ecological research, whilst also providing information relevant for conservation and management of aquatic systems. Given the large research gap that has existed in this regard for Southern Hemisphere lotic systems, there has been an urgent need to gather such data if effective management policies are to be implemented regionally, especially in the face of ongoing development, anthropogenic impacts, and global climate change. Furthermore, there has been a growing awareness of the need to incorporate thermal guidelines into legislation regarding environmental flows and associated water management plans. In South Africa radical new legislation introduced in 1996 resulted in rivers and aquatic ecosystems being given a right to water of their own- essentially environmental flows, required to protect the aquatic ecosystems associated with the water resource, that are determined separately for all or part of any significant water resource. This water, including both the quantity and quality, is referred to as the "Ecological Reserve." Baseline information on the relationship between temperature and life-history patterns of aquatic insects is required to inform the incorporation of thermal guidelines in the Ecological Reserve determination process. Assuming such information can be gathered, a problem arises as to how the data can be interpreted and incorporated into management guidelines. For instance if representatives of widespread species occurring throughout a country are collected from a single location (say perhaps a single province in South Africa) and then analysed in terms of their thermal limits for growth – would these limits hold true for that same species where it occurs elsewhere? Intra-specific variability, cryptic species and broader phylogenetic constraints all influence the thermal limits of species and need to be considered when examining thermal influences on life-history patterns. This thesis aimed to test the overarching hypothesis that while the life-history traits of aquatic insects could be constrained to some degree by their evolutionary history, they would also be impacted by thermal and hydrological regimes, inducing a degree of plasticity in their life cycles. This hypothesis was tested by examining the key life-history traits of three representative taxa of aquatic insect, namely Lestagella penicillata (Ephemeroptera), Aphanicercella spp. (Plecoptera) and Chimarra ambulans (Trichoptera), and how they are driven by environmental and genetic factors in six rivers situated in the south-western Cape Province of South Africa.

Environmental DNA, or eDNA, methodologies can enable the rapid detection of a target species without either visual or physical confirmation of the species presence. Over the last decade, targeted quantitative PCR (qPCR) assays have become an increasingly useful method employed by government and non-government agencies alike for purposes such as protecting and preserving ecosystems from invasive species, or for the conservation of endangered species. As the application of eDNA to answer ecological questions pushes the limits of qPCR-based detection, there is a pressing need to standardise the way qPCR results are reported and interpreted, as well as the way qPCR assays are evaluated for use outside of the remit of the original study.Natural England is one such government agency who have begun to use eDNA methodologies more widely to answer ecological questions. However, while some qPCR assays available for detecting the presence or absence of species such as the great crested newt (Triturus cristatus) have been specified, validated and quality assured to a high degree (Biggs et al. 2014), existing qPCR assays for other species are generally less well developed and validated. Additionally, for some species there are multiple qPCR assays available, with each being developed and validated to different stages. As such, Natural England identified a need to understand how the data derived from eDNA should be interpreted dependent on the level of qPCR assay development, and ultimately the confidence they can have in the accuracy of resulting data, including the associated risk of false positives or false negatives.NatureMetrics has developed a prototype web-based tool and protocol (European Technical Readiness Level 5) which would enable end users such as Natural England to inform their interpretation of qPCR results. The prototype is currently in the beta testing stage and is expected to be available in the coming months. The web-based tool will simplify qPCR assay evaluation, enabling end users to select the most appropriate qPCR assay for their needs, as well as standardise the reporting and interpretation of their qPCR results by generating a report at both the sample and site level from the inputted qPCR data.

Environmental DNA, or eDNA, methodologies can enable the rapid detection of a target species without either visual or physical confirmation of the species presence. Over the last decade, targeted quantitative PCR (qPCR) assays have become an increasingly useful method employed by government and non-government agencies alike for purposes such as protecting and preserving ecosystems from invasive species, or for the conservation of endangered species. As the application of eDNA to answer ecological questions pushes the limits of qPCR-based detection, there is a pressing need to standardise the way qPCR results are reported and interpreted, as well as the way qPCR assays are evaluated for use outside of the remit of the original study.Natural England is one such government agency who have begun to use eDNA methodologies more widely to answer ecological questions. However, while some qPCR assays available for detecting the presence or absence of species such as the great crested newt (Triturus cristatus) have been specified, validated and quality assured to a high degree (Biggs et al. 2014), existing qPCR assays for other species are generally less well developed and validated. Additionally, for some species there are multiple qPCR assays available, with each being developed and validated to different stages. As such, Natural England identified a need to understand how the data derived from eDNA should be interpreted dependent on the level of qPCR assay development, and ultimately the confidence they can have in the accuracy of resulting data, including the associated risk of false positives or false negatives.NatureMetrics has developed a prototype web-based tool and protocol (European Technical Readiness Level 5) which would enable end users such as Natural England to inform their interpretation of qPCR results. The prototype is currently in the beta testing stage and is expected to be available in the coming months. The web-based tool will simplify qPCR assay evaluation, enabling end users to select the most ...