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

Combining environmental DNA and visual surveys can inform conservation planning for coral reefs

Environmental DNA (eDNA) metabarcoding has the potential to revolutionize conservation planning by providing spatially and taxonomically comprehensive data on biodiversity and ecosystem conditions, but its utility to inform the design of protected areas remains untested. Here, we quantify whether and how identifying conservation priority areas within coral reef ecosystems differs when biodiversity information is collected via eDNA analyses or traditional visual census records. We focus on 147 coral reefs in Indonesia’s hyper-diverse Wallacea region and show large discrepancies in the allocation and spatial design of conservation priority areas when coral reef species were surveyed with underwater visual techniques (fishes, corals, and algae) or eDNA metabarcoding (eukaryotes and metazoans). Specifically, incidental protection occurred for 55% of eDNA species when targets were set for species detected by visual surveys and 71% vice versa. This finding is supported by generally low overlap in detection between visual census and eDNA methods at species level, with more overlap at higher taxonomic ranks. Incomplete taxonomic reference databases for the highly diverse Wallacea reefs, and the complementary detection of species by the two methods, underscore the current need to combine different biodiversity data sources to maximize species representation in conservation planning

The inclusion of fisheries and tourism in marine protected areas to support conservation in Indonesia

With the rapid growth of Indonesia’s marine protected area (MPAs) estate in Indonesia, reaching 23.9 million hectares by January 2020, attention needs to be focused on strengthening the effectiveness of MPA management. Consolidating and expanding protection of Indonesia’s marine resources is critical with increasing pressure from a fast-expanding population, illegal, unreported, and unregulated fishing, pollution, coastal development, unsustainable tourism and climate change. Biodiversity conservation must therefore concurrently consider multiple economic sectors such as fisheries and tourism, and their synergies with MPA management. This paper aims to outline the current landscape of fisheries and marine tourism pertaining to area-based conservation in Indonesia, to inform and support improved integration into effective MPA management. Four areas to focus efforts were identified: diversification of governance types of community-based management, improved coordination between fisheries and MPAs during planning and management implementation, the development and support of pathways for sustainable tourism, and planning for future conditions. Sustainable development for fisheries and tourism must be incorporated into all aspects of MPA management, whilst recognising that current management systems are insufficient to ensure long-term sustainability for natural resources and local communities, and strategies need to increase resilience of social-ecological systems in anticipation of future conditions

Macroalgae exhibit diverse responses to human disturbances on coral reefs

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships betweenspecific macroalgae taxa and local human-driven disturbance. Using genus-level monitoring data from 1,205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationshipsbetween the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responsesto human disturbances impedes the ability to diagnose and respond appropriately to these threats

Macroalgae exhibit diverse responses to human disturbances on coral reefs

Scientists and managers rely on indicator taxa such as coral and macroalgal cover to evaluate the effects of human disturbance on coral reefs, often assuming a universally positive relationship between local human disturbance and macroalgae. Despite evidence that macroalgae respond to local stressors in diverse ways, there have been few efforts to evaluate relationships between specific macroalgae taxa and local human‐driven disturbance. Using genus‐level monitoring data from 1205 sites in the Indian and Pacific Oceans, we assess whether macroalgae percent cover correlates with local human disturbance while accounting for factors that could obscure or confound relationships. Assessing macroalgae at genus level revealed that no genera were positively correlated with all human disturbance metrics. Instead, we found relationships between the division or genera of algae and specific human disturbances that were not detectable when pooling taxa into a single functional category, which is common to many analyses. The convention to use percent cover of macroalgae as an indication of local human disturbance therefore likely obscures signatures of local anthropogenic threats to reefs. Our limited understanding of relationships between human disturbance, macroalgae taxa, and their responses to human disturbances impedes the ability to diagnose and respond appropriately to these threats