Coral reefs support vast levels of biodiversity and provide valuable ecosystem services to millions of people but are increasingly threatened by global climate change and anthropogenic disturbances. Comprehensive and accurate biodiversity baselines are vital for effective ecosystem monitoring and molecular methods such as environmental DNA (eDNA) are promising new tools for this purpose.
This thesis aims to describe marine biodiversity in the remote Chagos Archipelago, over a broad temporal and spatial scale, and address methodological questions that will enhance our understanding of the ecology of eDNA and its applications in marine systems. Using eDNA collected every 6 hours at two coral reef sites, I aim to assess fine-scale changes in the eukaryotic communities detected. I show that sampling time has an effect on community richness and that the relative read frequency of eukaryotic taxa displays diurnal patterns in line with diurnal migrations. I present results from a mesocosm experiment testing the utility of marine sponges as natural samplers of eDNA and show the effect of DNA state on the capture and persistence of genetic material. Finally, I describe the diversity detected in the Chagos Archipelago using three eDNA metabarcoding assays. I record the distribution of several taxa of high conservation value, including endemic species and those facing anthropogenic pressures. I find that the beta diversity of microbial and eukaryotic communities varied over time, while fish communities were temporally stable but spatially distinct. Fish and microbial communities were also compositionally distinct around islands with invasive rats, highlighting
potential effects of seabird nutrients on community diversity.
This thesis adds to our knowledge of how eDNA persists and is captured in multiple sample types and utilises this method to provide molecular biodiversity baselines in a highly diverse but threatened coral
reef ecosystem.