Prospects for integrating environmental DNA metabarcoding into the conservation of marine megafauna

Marine megafauna include some of the most threatened taxa globally, risking the loss of key ecosystem functions and services that they provide unless conservation action can reverse their declining population statuses. Marine protected areas (MPAs) are the most popular tool implemented to conserve marine megafauna, but it remains unclear how effectively current MPA systems are capturing the requirements of marine megafauna due to incomplete knowledge of their distributions and limited long-term monitoring post-introduction of conservation measures. Environmental DNA (eDNA) offers a novel way to survey the marine environment, improving the detectability of rare species and observing changes across whole ecosystems simultaneously. The aim of my thesis was to explore how eDNA metabarcoding could improve the conservation of marine megafauna. I addressed this aim across four main research questions: 1) Can simultaneous monitoring of marine megafauna and their prey with eDNA metabarcoding improve understanding of their fine-scale habitat use? 2) Does the structure and complexity of cetaceans’ ecosystems change spatially and temporally, and how does this effect vulnerability to climate change? 3) Can we retrieve high quality species distributions from commercial vessel surveys, permitting eDNA surveys to be upscaled across greater spatiotemporal resolutions? 4) How does improved spatiotemporal and taxonomic coverage offered by eDNA impact spatial priority area designations within a marine spatial planning framework? eDNA revealed previously unknown patterns in the spatiotemporal availability of key prey species for cetaceans that improved understanding of their habitat use within a newly designated marine protected area. These prey species are highly connected and important ecosystem components but are particularly vulnerable to climate change so future changes to the ecosystem structure can be expected. Accessing spatiotemporal scales relevant to marine megafauna distributions often relies on expensive dedicated research vessels, but, using a simulation approach, I demonstrate that commercial vessels offer viable alternative survey platforms. Sampling along commercial routes that cover environmental variability and community composition adequately can predict species distributions as accurately as comparative non-spatially biased samples. Commercial vessels coupled with advances in automating eDNA sample processing offers a promising avenue to increase regular monitoring of the marine environment, especially in areas that are often under sampled and otherwise inaccessible. Marine spatial planning often implements coarse ecological data, such as habitat types or bioregions, to identify priority areas for conservation management. eDNA surveys can improve taxonomic coverage and understanding of species distributions. I showed that considering taxonomic groups (marine mammals, elasmobranchs, teleost fishes) separately more effectively identified spatial priority areas for the different groups which were missed in spatial priority areas designed for all taxa simultaneously. Including conservation objectives specific to different marine megafauna taxa will achieve more effective conservation that incorporates their contrasting and specialised life histories and habitat requirements.