A protocol for the large‐scale analysis of reefs using Structure from Motion photogrammetry

1. Substrate complexity is an essential metric of reef health and a strong predictor of several ecological processes connected to the reef, including disturbance, resilience, and associated community abundance and diversity. / 2. Underwater Structure from Motion (SfM) photogrammetry has been growing rapidly in use over the last 5 years due to advances in computing power, reduced costs of underwater digital cameras and a push for reproducible data. This has led to the adaptation of an originally terrestrial survey technique into the marine realm, which can now be applied at the habitat scale. / 3. This technique allows researchers to make detailed 3D reconstructions of reef surfaces for morphometric analysis of reef physical structure and perform large‐scale image‐mosaic mapping. SfM is useful for both reef‐scale and colony‐scale assessments, where visual or acoustic methods are impractical or not sufficiently detailed. / 4. Here we provide a protocol for the collection, analysis and display of 3D reef data, focussing on large‐scale habitat assessments of coral reefs using primarily open‐source software. We further suggest applications for other underwater environments and scales of assessment, and hope this standardized protocol will help researchers apply this technology and inspire new avenues of ecological research

Mushroom to manoeuvre? Using photogrammetry to track the movement and survival of free-living corals

Mushroom corals can play an important role in tropical reef ecosystems by providing habitat and performing important ecological functions. Unlike most stony corals, free-living mushroom corals can move, both passively and actively, and can use this ability to escape competition or harmful environments. However, as their movement is typically slow, occurs over relatively small scales, and is traditionally hard to measure, their movement ecology is little researched. Nevertheless, quantitative geospatial data on species’ movement, distribution, survival, and interaction can improve mechanistic modelling of community dynamics in various environments. We use ‘structure from motion’ photogrammetry to track 51 individual corals’ 3D movement and survival over one year within an isolated and enclosed lagoon. This technique essentially provides a large-scale quantitative community time-lapse and allows detailed individual level life-history data to be collected over spatial and temporal scales that were previously impractical

Evaluating the efficacy of small-scale marine protected areas for preserving reef health: A case study applying emerging monitoring technology

Marine protected areas (MPAs) are widely used as management tools to conserve species and ecosystems at risk from human impact. Coastal managers often focus MPA designation on biogenic reef environments due to their value and sensitivity to damage. However, difficulties in enforcement and a lack of capacity to adequately monitor MPAs often make it hard for managers to assess the effectiveness of MPAs, particularly in under‐resourced, low‐income coastal countries. Reef community data were collected at three long‐term managed reserves within the Western Visayas region of the central Philippines in order to assess the state of reef community structure inside and outside of these small‐scale locally managed MPAs. In addition, 3D structural data were captured using recently developed 'Structure from Motion' photogrammetry techniques, demonstrating how multiple quantitative metrics of physical structural complexity and health can be recorded in such analyses. These community‐run MPAs were shown to be effective even when small (10–20 ha). Mean fish biomass density was five times greater within present‐day protected sites, alongside significantly increased levels of fish diversity, richness, and size. No significant structural differences were observed inside and outside of MPAs; however, average reef rugosity, height, and roughness were significantly higher in unfished reefs compared to blast‐fished reefs. Reef substrate complexity, coral composition, and level of management, were also shown to structure fish community assemblages, with the link between reef structure and fish richness/abundance disrupted outside of MPAs. The Structure from Motion technique allows a greater range of quantitative morphometrics to be assessed than traditional methods and at relatively low cost. The technique is rapid, non‐destructive and can be archived, increasing the value of data for managers wishing to quantify reef health and efficiently monitor benthic changes through time. We discuss both the limitations and benefits of this technology's future use

A review of a decade of lessons from one of the world’s largest MPAs: conservation gains and key challenges

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordtribute 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 fsh 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 clutches (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 fshes, 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 identifed, particularly global heating events, and Illegal, Unreported and Unregulated (IUU) fshing activity, which considerably impact both reef and pelagic fshes.Bertarelli Foundatio

A review of a decade of lessons from one of the world's largest MPAs: conservation gains and key challenges

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 clutches (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