Optimizing eDNA methods to assess marine ecosystem health
Date
2025
Authors
Acharya-Patel, Neha
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Abstract
The world is losing biodiversity at an unprecedented rate due to climate change and anthropogenic development. The global implications of these losses are catastrophic, and drastic improvements are needed in conservation and biomonitoring methods to track these changes. My PhD research focuses on optimizing environmental DNA (eDNA) methods as a scalable biomonitoring method. eDNA, which refers to genetic material that can be extracted from environmental samples, can provide insight into species occupancy, composition, and abundance. To perform this research, we developed many sensitive and robust qPCR assays using a whole mitogenome approach and a rigorous validation pipeline. The thesis explores the application of eDNA methods to address different conservation challenges in four marine ecosystems. First, we examined the distribution of the Olympia oyster (Ostrea lurida) in Barkley Sound, BC, employing a targeted eDNA assay and exploring how tidal and freshwater dynamics affect DNA signal strength. Second, we evaluated DNA extraction methods for detecting sea otter (Enhydra lutris) DNA in sediments, contributing to the understanding of species distribution and improving protocols for degraded marine mammal DNA detection. Third, we investigated the impacts of marine pollution in the Pacific Northwest by developing sensitive eDNA assays for indicator species, correlating their abundance with ecological responses to organic enrichment. Finally, we compared eDNA surveys to SCUBA diving for surveying rockfish species, demonstrating that eDNA can capture greater species richness while addressing challenges in species identification amongst a large closely related genus.
Overall, this research illustrates the potential of eDNA as an efficient tool for marine conservation, highlighting its application across different environments and conservation contexts. The findings provide critical insights for monitoring marine biodiversity and inform management strategies to protect vulnerable species and ecosystems.
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Keywords
Environmental DNA, Biodiversity, Conservation, Biology, Marine research, Molecular ecology, Ocean