Advancing methods in marine conservation planning with ecological connectivity and environmental DNA

Conservation planning identifies important areas for protection to stem the global loss of marine biodiversity. How protected areas are designed changes as new technologies improve our understanding of population dynamics and ecological processes. The interconnectedness of fragmented marine habitats is now widely documented, with the implication that dispersing species can benefit from networks of well-connected protected areas. At the same time, the ability to detect species occurrence and the taxonomic scope of biodiversity assessment has been revolutionised by environmental DNA. Here, I investigate how current practices in designing marine protected areas can be improved based on these novel understandings. In the first three chapters, I illustrate how larval dispersal can inform the management of coral reefs and reef-associated species. First, I show how dispersal connectivity can be used at multiple spatial scales of spatial planning, with a case study of marine reserve establishment in Southeast Sulawesi, Indonesia. I describe how to combine regional identification of protected area networks with local delineation of marine reserves using detailed habitat data. Second, I compare the performance of two conceptually different approaches to integrating connectivity in spatial prioritisation tools, using Marxan. Conservation priorities can either be identified based on site-specific features of connectivity, or through a spatial dependency-based approach of selecting clusters of strongly connected habitat patches. I demonstrate that features and spatial dependency can all perform best in different contexts, depending on the conservation objectives, habitat degradation, and species dispersal capabilities. Third, I explore how temporal variability of larval dispersal impacts expected reserve benefits. I show how in certain cases, using a mean of dispersal connectivity is suboptimal before suggesting how more temporally stable reserve networks can be designed. In the final chapter, I evaluate how biodiversity assessments with environmental DNA analyses can inform spatial planning and how the resulting conservation priorities compare to those based on traditional visual census surveys. I show that both survey techniques identify unique taxonomic groups and have relatively low co-detection of shared groups, suggesting that these techniques should be used in combination to set conservation priorities. Overall, this research aims to promote the wider uptake of larval dispersal and environmental DNA in conservation planning for marine ecosystems.