Given the recent trend towards establishing very large marine protected areas (MPAs) and the high potential of these to contribute to global conservation targets, we review outcomes of the last decade of marine conservation research in the British Indian Ocean Territory (BIOT), one of the largest MPAs in the world. The BIOT MPA consists of the atolls of the Chagos Archipelago, interspersed with, and surrounded by, deep oceanic waters. Islands around the atoll rims serve as nesting grounds for sea birds. Extensive and diverse shallow and mesophotic reef habitats provide essential habitat and feeding grounds for all marine life, and the absence of local human impacts may improve recovery after coral bleaching events. Census data have shown recent increases in the abundance of sea turtles, high numbers of nesting seabirds and high fish abundance, at least some of which is linked to the lack of recent harvesting. For example, across the archipelago the annual number of green turtle nests (Chelonia mydas) is ~20,500 and increasing and the number of seabirds is ~1 million. Animal tracking studies have shown that some taxa breed and/or forage consistently within the MPA (e.g. some reef fishes, elasmobranchs and seabirds), suggesting the MPA has the potential to provide long-term protection. In contrast, post-nesting green turtles travel up to 4000 km to distant foraging sites, so the protected beaches in the Chagos Archipelago provide a nesting sanctuary for individuals that forage across an ocean basin and several geopolitical borders. Surveys using divers and underwater video systems show high habitat diversity and abundant marine life on all trophic levels. For example, coral cover can be as high as 40-50%. Ecological studies are shedding light on how remote ecosystems function, connect to each other and respond to climate-driven stressors compared to other locations that are more locally impacted. However, important threats to this MPA have been identified, particularly global heating events, and Illegal, Unreported and Unregulated (IUU) fishing activity, which considerably impact both reef and pelagic fishes.

1. Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology-based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology-based protocols currently used by ecological surveyors is essential to determine whether this DNA-based approach is suitable for long-term monitoring of the marine ecosystems. 2. We compared metabarcoding and morphology-based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un-sieved samples in our metabarcoding analysis. We found that while metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples. 4. Synthesis and applications. We show that metabarcoding using the cytochrome c oxidase I (COI) marker provides a more holistic, community-based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates that need to be addressed before metabarcoding can replace traditional methods. Ultimately, with these limitations taken into consideration, resolving community-wide diversity patterns with metabarcoding could improve the management of non-protected marine habitats in the United Kingdom.

In a time of unprecedented ecological change, understanding natural biophysical relationships between reef resilience and physical drivers is of increasing importance. This study evaluates how wave forcing structures coral reef benthic community composition and recovery trajectories after the major 2015/2016 bleaching event in the remote Chagos Archipelago, Indian Ocean. Benthic cover and substrate rugosity were quantified from digital imagery at 23 fore reef sites around a small coral atoll (Salomon) in 2020 and compared to data from a similar survey in 2006 and opportunistic surveys in intermediate years. Cluster analysis and principal component analysis show strong separation of community composition between exposed (modelled wave exposure > 1000 J m−3) and sheltered sites (< 1000 J m−3) in 2020. This difference is driven by relatively high cover of Porites sp., other massive corals, encrusting corals, soft corals, rubble and dead table corals at sheltered sites versus high cover of pavement and sponges at exposed sites. Total coral cover and rugosity were also higher at sheltered sites. Adding data from previous years shows benthic community shifts from distinct exposure-driven assemblages and high live coral cover in 2006 towards bare pavement, dead Acropora tables and rubble after the 2015/2016 bleaching event. The subsequent recovery trajectories at sheltered and exposed sites are surprisingly parallel and lead communities towards their respective pre-bleaching communities. These results demonstrate that in the absence of human stressors, community patterns on fore reefs are strongly controlled by wave exposure, even during and after widespread coral loss from bleaching events.