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Coral reefs are among the most biodiverse ecosystems on the planet. Almost a third of tropical reefs lie in the Coral Triangle (CT), the epicenter of marine biodiversity, and are substantially threatened by human activity. Timor-Leste became independent in 2002 and is the newest of six nations in the CT, which include Indonesia, Malaysia, the Philippines, Papua New Guinea, and the Solomon Islands. It is important to establish a baseline for the current composition and state of coral reefs. For this thesis, the following specific objectives related to the coral reefs along the north coast of Timor-Leste were addressed: (1) assess coral reef variability based on kilometer-scale phototransects and explore environmental drivers of differences; (2) explore how the variation in the diversity of marine cryptic invertebrates varies at local scales over the same regions; and (3) quantify the condition of corals (coral health) using coral disease surveys alongside and measurements of water quality and temperature in the capital area of Dili, taken before and after the global bleaching event in 2016. The benthic structure of outer reef slope communities along the north coast was analyzed using kilometer-scale phototransects (each 1.5-2 km) collected from the 2014 XL Catlin Seaview Survey. Chapter 2 analyzed over 20,000 benthic photos using machine learning techniques, which revealed significant coral cover in Timor-Leste ranging from 5.4 to 33.0%, comparable to coral cover in other regions of the Indo-Pacific and CT. Wave exposure, distance to nearest river, and human population density were explored as potential drivers of benthic composition. A linear mixed-effects model tested the same covariates plus the ratio of branching to massive corals (i.e., structural complexity) on total coral cover. All parameters significantly explained benthic composition while there was a significant positive effect from wave exposure on coral cover that interacted with structural complexity where the effect was greatest on more complex reefs. This was due to the low incidence of storms and the comparatively protected north coast.Marine cryptic invertebrate biodiversity was explored in Chapter 3 using Autonomous Reef Monitoring Structures (ARMS) and genetic DNA barcoding of brachyuran crabs for outer reef slope sites in Timor-Leste. This was accomplished in collaboration with the US National Oceanic and Atmospheric Administration and the Smithsonian Institution National Museum of Natural History. Three size fractions (i.e., two meiofaunal and one sessile) from the ARMS were DNA metabarcoded. The results indicated several interesting trends that corroborate the biogeographic pattern of maximal diversity in the CT. For example, rarefaction curves of crabs and metabarcodes did not reach asymptotes meaning greater sampling would likely uncover more species. There was a high degree of unique operational taxonomic units (37% for brachyuran crabs) and diversity was greater than other Indo-Pacific sites as expected. The metabarcoding resulted in 19% unclassified operational taxonomic units, indicating the cryptic biodiversity of reefs is under-sampled with biodiversity being much more than previously quantified. The relationship between cryptofaunal diversity and coral cover was inconclusive. However, there was further evidence that rubble habitats promote the greatest diversity of coral reef cryptofauna.Reef condition in Timor-Leste was the focus of Chapter 4. The condition of four reefs was surveyed in November 2015 and July 2017. Temperature and nutrient data were also collected in 2015. Both surveys revealed disease prevalence was low, but had higher levels of compromised health (e.g., algal overgrowth). Interestingly, the isotope signature of nitrogen along the north coast did not match that expected for coastal pollution (8-30‰) but did match that expected from oceanic sources (2-6‰). Heat stress during the 2016-2017 global bleaching event was also quantified in Timor-Leste. Surveys before and after the event did not indicate high bleaching mortality as predicted by the Coral Reef Watch Timor-Leste (CRWTL) satellite sea surface temperature. CRWTL was significantly higher (> 1˚C) than in situ temperature during the austral summer. Both the temperature and nutrient data indicate seasonal oceanographic processes such as upwelling influence shallow reefs along the north coast.As local and global conditions change along the coastline of developing nations such as Timor-Leste, understanding the condition of reefs becomes critical. This thesis undertook the largest survey of coral reefs in the history of Timor-Leste. This study revealed rich coral reefs relatively high in biodiversity that are comparatively protected from climate change-induced ocean warming. The findings emphasize Timor-Leste’s significance as one of 50 coral reef world regions that are relatively less vulnerable to recent climate change impacts from a systematic global analysis. As such, immediate conservation priorities for Timor-Leste should focus on addressing localized anthropogenic pressures including sedimentation and overfishing. The balance between communities, ecosystems, and sustainable economies, must be further investigated using the wealth of Traditional Knowledge such as tara bandu customary law to build strong and resilient socio-ecological systems. All of this must be seen in the context of strong, intergovernmental action that is needed to address global climate change.

El Niño Southern Oscillation global coral bleaching events are increasing in frequency; however, the severity of bleaching is not geographically uniform. There were two major objectives of the present project: 1) assess the state of reefs and coral health at several sites and 2) explore water quality and climate change impacts on Timorese reefs. The impacts of climate change (principally by following coral mortality) were surveyed on coral reefs before and after the 2016–2017 underwater heatwave, using temperature loggers deployed between surveys which were compared to Coral Reef Watch (CRW) experimental virtual station sea surface temperature (SST). CRW is an important and widely used tool; however, we found the SST was significantly warmer (> 1°C) than in situ temperature during the austral summer accruing 5.79 degree heating weeks. In situ temperature showed no accumulation. Change in coral cover between surveys was attributed to reef heterogeneity. There were significant differences in coral cover, coral diversity, and nutrient concentrations between site and depth and a low prevalence of disease recorded in both years. The comparison of temperature and SST indicate that bleaching stress in Timor-Leste is potentially mitigated by seasonal and oceanographic dynamics. This is corroborated by Timor-Leste’s location within the Indonesian ThroughFlow. Timor-Leste is a climate refugium and the immediate conservation work lies in the management of localized anthropogenic impacts on coral reefs such as sedimentation and fishing.

Addressing the global decline of coral reefs requires effective actions from managers, policymakers and society as a whole. Coral reef scientists are therefore challenged with the task of providing prompt and relevant inputs for science-based decision-making. Here, we provide a baseline dataset, covering 1300 km of tropical coral reef habitats globally, and comprised of over one million geo-referenced, high-resolution photo-quadrats analysed using artificial intelligence to automatically estimate the proportional cover of benthic components. The dataset contains information on five major reef regions, and spans 2012–2018, including surveys before and after the 2016 global bleaching event. The taxonomic resolution attained by image analysis, as well as the spatially explicit nature of the images, allow for multi-scale spatial analyses, temporal assessments (decline and recovery), and serve for supporting image recognition developments. This standardised dataset across broad geographies offers a significant contribution towards a sound baseline for advancing our understanding of coral reef ecology and thereby taking collective and informed actions to mitigate catastrophic losses in coral reefs worldwide., Measurement(s) ecosystem • coral reef • composition Technology Type(s) automated image annotation • machine learning Factor Type(s) year of data collection • geographic location Sample Characteristic - Organism Anthozoa • Algae • Porifera Sample Characteristic - Environment marine coral reef biome • marine coral reef fore reef Sample Characteristic - Location Atlantic Ocean • Eastern Australia • Indian Ocean • Southeast Asia • Pacific Ocean • Great Barrier Reef Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13007516

Ecosystem monitoring is central to effective management, where rapid reporting is essential to provide timely advice. While digital imagery has greatly improved the speed of underwater data collection for monitoring benthic communities, image analysis remains a bottleneck in reporting observations. In recent years, a rapid evolution of artificial intelligence in image recognition has been evident in its broad applications in modern society, offering new opportunities for increasing the capabilities of coral reef monitoring. Here, we evaluated the performance of Deep Learning Convolutional Neural Networks for automated image analysis, using a global coral reef monitoring dataset. The study demonstrates the advantages of automated image analysis for coral reef monitoring in terms of error and repeatability of benthic abundance estimations, as well as cost and benefit. We found unbiased and high agreement between expert and automated observations (97%). Repeated surveys and comparisons against existing monitoring programs also show that automated estimation of benthic composition is equally robust in detecting change and ensuring the continuity of existing monitoring data. Using this automated approach, data analysis and reporting can be accelerated by at least 200x and at a fraction of the cost (1%). Combining commonly used underwater imagery in monitoring with automated image annotation can dramatically improve how we measure and monitor coral reefs worldwide, particularly in terms of allocating limited resources, rapid reporting and data integration within and across management areas.

Coral reefs are highly vulnerable habitats, threatened by climate change and local anthropogenic impacts. Management is imperative, and spatial prioritisation apportions the area of interest to inform investments of scarce conservation resources. Spatially delineated planning units used to make management decisions are typically large enough to contain significant natural variabilities, but the ecological significance of such variance is seldom considered in planning decisions. On coral reefs, the patchiness of habitat quality within planning units matters both ecologically and functionally. Here, we show that considering within-planning unit variance in spatial prioritisation influences the location and design of reserve networks. Studying Timor-Leste, we statistically model the average and variance in coral cover. We compare conservation priority areas for scenarios informed by coral cover and variance to a baseline scenario with the spatial prioritisation software Marxan. To further explain these differences, and to show the value of including coral variance as a metric in spatial prioritisation, we created a reserve quality score. We show that the similarity between reserve networks was only 57% for protection, and 44% for restoration objectives. For both objectives, the inclusion of cover variance improves the conservation benefit of management. This project has shown a novel way to target areas for restoration. These results demonstrate that not only is mean coral cover (and, by extension, reef condition) a key criterion in selecting marine conservation actions, but its variance must be considered in spatial conservation prioritisation to improve both the efficiency and benefit of management actions within marine reserve networks.

Karimunjawa National Park is one of Indonesia&rsquo, s oldest established marine parks. Coral reefs across the park are being impacted by fishing, tourism and declining water quality (local stressors), as well as climate change (global pressures). In this study, we apply a multivariate statistical model to detailed benthic ecological datasets collected across Karimunjawa&rsquo, s coral reefs, to explore drivers of community change at the park level. Eighteen sites were surveyed in 2014 and 2018, before and after the 2016 global mass coral bleaching event. Analyses revealed that average coral cover declined slightly from 29.2 &plusmn, 0.12% (Standard Deviation, SD) to 26.3 &plusmn, 0.10% SD, with bleaching driving declines in most corals. Management zone was unrelated to coral decline, but shifts from massive morphologies toward more complex foliose and branching corals were apparent across all zones, reflecting a park-wide reduction in damaging fishing practises. A doubling of sponges and associated declines in massive corals could not be related to bleaching, suggesting another driver, likely declining water quality associated with tourism and mariculture. Further investigation of this potentially emerging threat is needed. Monitoring and management of water quality across Karimunjawa may be critical to improving resilience of reef communities to future coral bleaching.

Sewage pollution threatens the health of coastal populations and ecosystems, including coral reefs. We investigated spatial patterns of sewage pollution in Puako, Hawaii using enterococci concentrations and δ(15)N Ulva fasciata macroalgal bioassays to assess relationships with the coral disease Porites lobata growth anomalies (PGAs). PGA severity and enterococci concentrations were high, spatially variable, and positively related. Bioassay algal δ(15)N showed low sewage pollution at the reef edge while high values of resident algae indicated sewage pollution nearshore. Neither δ(15)N metric predicted PGA measures, though bioassay δ(15)N was negatively related to coral cover. Furthermore, PGA prevalence was much higher than previously recorded in Hawaii and the greater Indo-Pacific, highlighting Puako as an area of concern. Although further work is needed to resolve the relationship between sewage pollution and coral cover and disease, these results implicate sewage pollution as a contributor to diminished reef health.