Forecasting intensifying disturbance effects on coral reefs

Neighbourhood benthic configuration reveals hidden co-occurrence social diversity

Ecological interactions among benthic communities are crucial for shaping marine ecosystems. Understanding these interactions is essential for predicting how ecosystems will respond to environmental changes, invasive species, and conservation management. However, determining the prevalence of species interactions at the community scale is challenging. To overcome this challenge, we employ tools from social network analysis, specifically exponential random graph modelling (ERGM). Our approach explores the relationships among animal and plant organisms within their neighbourhoods. Inspired by companion planting in agriculture, we use spatiotemporal co-occurrence as a measure of mixed species interaction. In other words, the variety of community interactions based on co-occurrence defines what we call 'co-occurrence social diversity'. Our objective is to use ERGM to quantify the proportion of interactions at both the simple paired level and the more complex triangle level, enabling us to measure and compare co-occurrence social diversity. Applying our approach to the Spanish coastal zone across eight sites, five depths, and sunlit/shaded aspects, we discover that 80% of sessile communities, consisting of over a hundred species, exhibit co-occurrence social diversity, with 5% of species consistently forming associations with other species. These organism-level interactions probably have a significant impact on the overall character of the site. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Exploring depth-related patterns of sponge diversity and abundance in marginal reefs

Marine sponges play a vital role in the reef's benthic community; however, understanding how their diversity and abundance vary with depth is a major challenge, especially on marginal reefs in areas deeper than 30 m. To help bridge this gap, we used underwater videos at 24 locations between 2- and 62-meter depths on a marginal reef system in the Southwestern Atlantic to investigate the effect of depth on the sponge metacommunity. Specifically, we quantified the abundance, density, and taxonomic composition of sponge communities, and decomposed their gamma (γ) diversity into alpha (α) and beta (β) components. We also assessed whether beta diversity was driven by species replacement (turnover) or by nesting of local communities (nestedness). We identified 2020 marine sponge individuals, which belong to 36 species and 24 genera. As expected, deep areas (i.e., those greater than 30 m) presented greater sponge abundance and more than eightfold the number of sponges per square meter compared to shallow areas. About 50% of the species that occurred in shallow areas (<30 m) also occurred in deep areas. Contrarily to expectations, alpha diversity of rare (0 D α), typical (1 D α), or dominant (2 D α) species did not vary with depth, but the shallow areas had greater beta diversity than the deep ones, especially for typical (1 D β) and dominant (2 D β) species. Between 92.7% and 95.7% of the beta diversity was given by species turnover both inside and between shallow and deep areas. Our results support previous studies that found greater sponge abundance and density in deep areas and reveal that species sorting is stronger at smaller depths, generating more beta diversity across local communities in shallow than deep areas. Because turnover is the major driver at any depth, the entire depth gradient should be considered in management and conservation strategies.

Disturbance theory for ecosystem ecologists: A primer

Understanding what regulates ecosystem functional responses to disturbance is essential in this era of global change. However, many pioneering and still influential disturbance-related theorie proposed by ecosystem ecologists were developed prior to rapid global change, and before tools and metrics were available to test them. In light of new knowledge and conceptual advances across biological disciplines, we present four disturbance ecology concepts that are particularly relevant to ecosystem ecologists new to the field: (a) the directionality of ecosystem functional response to disturbance; (b) functional thresholds; (c) disturbance-succession interactions; and (d) diversity-functional stability relationships. We discuss how knowledge, theory, and terminology developed by several biological disciplines, when integrated, can enhance how ecosystem ecologists analyze and interpret functional responses to disturbance. For example, when interpreting thresholds and disturbance-succession interactions, ecosystem ecologists should consider concurrent biotic regime change, non-linearity, and multiple response pathways, typically the theoretical and analytical domain of population and community ecologists. Similarly, the interpretation of ecosystem functional responses to disturbance requires analytical approaches that recognize disturbance can promote, inhibit, or fundamentally change ecosystem functions. We suggest that truly integrative approaches and knowledge are essential to advancing ecosystem functional responses to disturbance.

Natural recovery of corals after severe disturbance

Ecosystem recovery from human-induced disturbances, whether through natural processes or restoration, is occurring worldwide. Yet, recovery dynamics, and their implications for broader ecosystem management, remain unclear. We explored recovery dynamics using coral reefs as a case study. We tracked the fate of 809 individual coral recruits that settled after a severe bleaching event at Lizard Island, Great Barrier Reef. Recruited Acropora corals, first detected in 2020, grew to coral cover levels that were equivalent to global average coral cover within just 2 years. Furthermore, we found that just 11.5 Acropora recruits per square meter were sufficient to reach this cover within 2 years. However, wave exposure, growth form and colony density had a marked effect on recovery rates. Our results underscore the importance of considering natural recovery in management and restoration and highlight how lessons learnt from reef recovery can inform our understanding of recovery dynamics in high-diversity climate-disturbed ecosystems.

Hot spots of bleaching in massive Porites coral colonies

Coral bleaching events have become more frequent and severe due to ocean warming. While the large-scale impacts of bleaching events are well-known, there is growing recognition of the importance of small-scale spatial variation in bleaching and survival probability of individual coral colonies. By quantifying bleaching in 108 massive Porites colonies spread across Lizard Island, Great Barrier Reef, during the 2016 bleaching event, we investigated how hydrodynamic exposure levels and colony size contribute to local variability in bleaching prevalence and extent. Our results revealed that exposed locations were the least impacted by bleaching, while lagoonal areas exhibited the highest prevalence of bleaching and colony-level bleaching extents. Such patterns of bleaching could be due to prolonged exposure to warm water in the lagoon. These findings highlight the importance of considering location-specific factors when assessing coral health and emphasize the vulnerability of corals in lagoonal habitats to rapid and/or prolonged elevated temperatures.

SMOTE-CD: SMOTE for compositional data

Compositional data are a special kind of data, represented as a proportion carrying relative information. Although this type of data is widely spread, no solution exists to deal with the cases where the classes are not well balanced. After describing compositional data imbalance, this paper proposes an adaptation of the original Synthetic Minority Oversampling TEchnique (SMOTE) to deal with compositional data imbalance. The new approach, called SMOTE for Compositional Data (SMOTE-CD), generates synthetic examples by computing a linear combination of selected existing data points, using compositional data operations. The performance of the SMOTE-CD is tested with three different regressors (Gradient Boosting tree, Neural Networks, Dirichlet regressor) applied to two real datasets and to synthetic generated data, and the performance is evaluated using accuracy, cross-entropy, F1-score, R2 score and RMSE. The results show improvements across all metrics, but the impact of oversampling on performance varies depending on the model and the data. In some cases, oversampling may lead to a decrease in performance for the majority class. However, for the real data, the best performance across all models is achieved when oversampling is used. Notably, the F1-score is consistently increased with oversampling. Unlike the original technique, the performance is not improved when combining oversampling of the minority classes and undersampling of the majority class. The Python package smote-cd implements the method and is available online.

Legacy effects of anthropogenic disturbances modulate dynamics in the world's coral reefs

Rapidly changing conditions alter disturbance patterns, highlighting the need to better understand how the transition from pulse disturbances to more persistent stress will impact ecosystem dynamics. We conducted a global analysis of the impacts of 11 types of disturbances on reef integrity using the rate of change of coral cover as a measure of damage. Then, we evaluated how the magnitude of the damage due to thermal stress, cyclones, and diseases varied among tropical Atlantic and Indo-Pacific reefs and whether the cumulative impact of thermal stress and cyclones was able to modulate the responses of reefs to future events. We found that reef damage largely depends on the condition of a reef before a disturbance, disturbance intensity, and biogeographic region, regardless of the type of disturbance. Changes in coral cover after thermal stress events were largely influenced by the cumulative stress of past disturbances and did not depend on disturbance intensity or initial coral cover, which suggests that an ecological memory is present within coral communities. In contrast, the effect of cyclones (and likely other physical impacts) was primarily modulated by the initial reef condition and did not appear to be influenced by previous impacts. Our findings also underscore that coral reefs can recover if stressful conditions decrease, yet the lack of action to reduce anthropogenic impacts and greenhouse gas emissions continues to trigger reef degradation. We uphold that evidence-based strategies can guide managers to make better decisions to prepare for future disturbances.

Being Bayesian in the 2020s: opportunities and challenges in the practice of modern applied Bayesian statistics

Building on a strong foundation of philosophy, theory, methods and computation over the past three decades, Bayesian approaches are now an integral part of the toolkit for most statisticians and data scientists. Whether they are dedicated Bayesians or opportunistic users, applied professionals can now reap many of the benefits afforded by the Bayesian paradigm. In this paper, we touch on six modern opportunities and challenges in applied Bayesian statistics: intelligent data collection, new data sources, federated analysis, inference for implicit models, model transfer and purposeful software products. This article is part of the theme issue 'Bayesian inference: challenges, perspectives, and prospects'.

Variation in the parasite communities of three co-occurring herbivorous coral reef fishes

Parasites are important, diverse, and abundant components of natural ecosystems and can influence the behaviour and health of their hosts, inter- and intraspecific interactions, and ultimately community structure. Coral reefs are one of the world's most biodiverse ecosystems, yet our understanding of the abundance, diversity, and composition of parasite communities of coral reef fishes is limited. Here, the authors aimed to compare the abundance, richness and composition of parasite communities among three co-occurring herbivorous coral reef fishes (the barred rabbitfish Siganus doliatus, Ward's damsel Pomacentrus wardi and the obscure damsel Pomacentrus adelus) from an inshore reef of the Great Barrier Reef (GBR). In total, 3978 parasites (3869 endoparasites and 109 ectoparasites) from 17 families were recovered from 30 individuals of each of the three fish species (mean = 44 ± 22 s.e. parasites per fish; range = 0-1947 parasites per fish). The parasite communities of P. wardi and P. adelus were characterised by pennellid copepods, derogenid and lecithasterid digeneans and were distinct from those of S. doliatus that were characterised by a higher abundance of atractotrematid and gyliauchenid digeneans. The abundance and family richness of all parasites were greatest in S. doliatus (abundance: 22.1 ± 5.0 parasites per fish; richness: 3.2 ± 0.3 families per fish), intermediate in P. wardi (abundance: 4.8 ± 1.1 parasites per fish; richness: 2.3 ± 0.3 families per fish) and lowest in P. adelus (abundance: 1.4 ± 0.4 parasites per fish; richness: 0.9 ± 0.2 families per fish). Similarly, the abundance of endoparasites was greatest in S. doliatus (19.7 ± 5.1 endoparasites per fish), intermediate in P. wardi (2.6 ± 0.7 endoparasites per fish) and lowest in P. adelus (1.2 ± 0.4 endoparasites per fish). Ectoparasite abundances were also lowest for P. adelus (0.2 ± 0.1 ectoparasites per fish), and S. doliatus and P. wardi had comparable abundances of ectoparasites (1.3 ± 0.3 and 2.1 ± 0.5 parasites per fish, respectively). Similarities between the parasite assemblages of the two pomacentrids may be related to their similar behaviours and/or diets vs. those of the larger-bodied and more mobile rabbitfish. Investigating the causes and consequences of variation in parasite communities across a broader range of fish species will be critical to understand the potential role of parasites in coral reef ecosystems.

Negative and positive interspecific interactions involving jellyfish polyps in marine sessile communities

Sessile marine invertebrates on hard substrates are one of the two canonical examples of communities structured by competition, but some aspects of their dynamics remain poorly understood. Jellyfish polyps are an important but under-studied component of these communities. We determined how jellyfish polyps interact with their potential competitors in sessile marine hard-substrate communities, using a combination of experiments and modelling. We carried out an experimental study of the interaction between polyps of the moon jellyfish Aurelia aurita and potential competitors on settlement panels, in which we determined the effects of reduction in relative abundance of either A. aurita or potential competitors at two depths. We predicted that removal of potential competitors would result in a relative increase in A. aurita that would not depend on depth, and that removal of A. aurita would result in a relative increase in potential competitors that would be stronger at shallower depths, where oxygen is less likely to be limiting. Removal of potential competitors resulted in a relative increase in A. aurita at both depths, as predicted. Unexpectedly, removal of A. aurita resulted in a relative decrease in potential competitors at both depths. We investigated a range of models of competition for space, of which the most successful involved enhanced overgrowth of A. aurita by potential competitors, but none of these models was completely able to reproduce the observed pattern. Our results suggest that interspecific interactions in this canonical example of a competitive system are more complex than is generally believed.

Minor Genetic Consequences of a Major Mass Mortality: Short-Term Effects in Pisaster ochraceus

AbstractMass mortality events are increasing globally in frequency and magnitude, largely as a result of human-induced change. The effects of these mass mortality events, in both the long and short term, are of imminent concern because of their ecosystem impacts. Genomic data can be used to reveal some of the population-level changes associated with mass mortality events. Here, we use reduced-representation sequencing to identify potential short-term genetic impacts of a mass mortality event associated with a sea star wasting outbreak. We tested for changes in the population for genetic differentiation, diversity, and effective population size between pre-sea star wasting and post-sea star wasting populations of Pisaster ochraceus-a species that suffered high sea star wasting-associated mortality (75%-100% at 80% of sites). We detected no significant population-based genetic differentiation over the spatial scale sampled; however, the post-sea star wasting population tended toward more differentiation across sites than the pre-sea star wasting population. Genetic estimates of effective population size did not detectably change, consistent with theoretical expectations; however, rare alleles were lost. While we were unable to detect significant population-based genetic differentiation or changes in effective population size over this short time period, the genetic burden of this mass mortality event may be borne by future generations, unless widespread recruitment mitigates the population decline. Prior results from P. ochraceus indicated that natural selection played a role in altering allele frequencies following this mass mortality event. In addition to the role of selection found in a previous study on the genomic impacts of sea star wasting on P. ochraceus, our current study highlights the potential role the stochastic loss of many individuals plays in altering how genetic variation is structured across the landscape. Future genetic monitoring is needed to determine long-term genetic impacts in this long-lived species. Given the increased frequency of mass mortality events, it is important to implement demographic and genetic monitoring strategies that capture baselines and background dynamics to better contextualize species' responses to large perturbations.

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.

Algal turf structure and composition vary with particulate loads on coral reefs

Algal turfs trap and retain particulates, however, little is known about the relationship between particulate accumulation and taxonomic composition of algal turfs. We investigated how particulate mass related to algal turf structure (length and density) and community composition (taxonomic and functional) on two disparate reefs. Particulate mass was positively related to algal turf length. By contrast, the relationship between particulate mass and turf density was more complex and followed a negative parabolic shape; density increased with particulate mass before stabilising and then declining. Community analyses showed taxonomic, but not functional group compositions differed significantly between reefs and with increasing particulate mass. Our results suggest high loads of particulates accumulated in algal turfs are related to a longer, lower density turf structure, typified by filamentous forms such as Cladophora. Changes in algal turf structure and composition could have a variety of bottom-up influences on coral reef ecosystems.

Coral Reef Bleaching under Climate Change: Prediction Modeling and Machine Learning

The coral reefs are important ecosystems to protect underwater life and coastal areas. It is also a natural attraction that attracts many tourists to eco-tourism under the sea. However, the impact of climate change has led to coral reef bleaching and elevated mortality rates. Thus, this paper modeled and predicted coral reef bleaching under climate change by using machine learning techniques to provide the data to support coral reefs protection. Supervised machine learning was used to predict the level of coral damage based on previous information, while unsupervised machine learning was applied to model the coral reef bleaching area and discovery knowledge of the relationship among bleaching factors. In supervised machine learning, three widely used algorithms were included: Naïve Bayes, support vector machine (SVM), and decision tree. The accuracy of classifying coral reef bleaching under climate change was compared between these three models. Unsupervised machine learning based on a clustering technique was used to group similar characteristics of coral reef bleaching. Then, the correlation between bleaching conditions and characteristics was examined. We used a 5-year dataset obtained from the Department of Marine and Coastal Resources, Thailand, during 2013–2018. The results showed that SVM was the most effective classification model with 88.85% accuracy, followed by decision tree and Naïve Bayes that achieved 80.25% and 71.34% accuracy, respectively. In unsupervised machine learning, coral reef characteristics were clustered into six groups, and we found that seawater pH and sea surface temperature correlated with coral reef bleaching.

A tale of two reef systems: Local conditions, disturbances, coral life histories, and the climate catastrophe

Coral reefs have evolved over millennia to survive disturbances. Yet, in just a few decades chronic local pressures and the climate catastrophe have accelerated so quickly that most coral reefs are now threatened. Rising ocean temperatures and recurrent bleaching pose the biggest threat, affecting even remote and well-managed reefs on global scales. We illustrate how coral bleaching is altering reefs by contrasting the dynamics of adjacent reef systems over more than two decades. Both reef systems sit near the edge of northwest Australia's continental shelf, have escaped chronic local pressures and are regularly affected by tropical storms and cyclones. The Scott reef system has experienced multiple bleaching events, including mass bleaching in 1998 and 2016, from which it is unlikely to fully recover. The Rowley Shoals has maintained a high cover and diversity of corals and has not yet been impacted by mass bleaching. We show how the dynamics of both reef systems were driven by a combination of local environment, exposure to disturbances and coral life history traits, and consider future shifts in community structure with ongoing climate change. We then demonstrate how applying knowledge of community dynamics at local scales can aid management strategies to slow the degradation of coral reefs until carbon emissions and other human impacts are properly managed.

Coral micro- and macro-morphological skeletal properties in response to life-long acclimatization at CO2 vents in Papua New Guinea

This study investigates the effects of long-term exposure to OA on skeletal parameters of four tropical zooxanthellate corals naturally living at CO₂ seeps and adjacent control sites from two locations (Dobu and Upa Upasina) in the Papua New Guinea underwater volcanic vent system. The seeps are characterized by seawater pH values ranging from 8.0 to about 7.7. The skeletal porosity of Galaxea fascicularis, Acropora millepora, massive Porites, and Pocillopora damicornis was higher (up to ~ 40%, depending on the species) at the seep sites compared to the control sites. Pocillopora damicornis also showed a decrease of micro-density (up to ~ 7%). Thus, further investigations conducted on this species showed an increase of the volume fraction of the larger pores (up to ~ 7%), a decrease of the intraskeletal organic matrix content (up to ~ 15%), and an increase of the intraskeletal water content (up to ~ 59%) at the seep sites. The organic matrix related strain and crystallite size did not vary between seep and control sites. This multi-species study showed a common phenotypic response among different zooxanthellate corals subjected to the same environmental pressures, leading to the development of a more porous skeletal phenotype under OA.

Dangerous demographics in post-bleach corals reveal boom-bust versus protracted declines

Thermal-stress events have changed the structure, biodiversity, and functioning of coral reefs. But how these disturbances affect the dynamics of individual coral colonies remains unclear. By tracking the fate of 1069 individual Acropora and massive Porites coral colonies for up to 5 years, spanning three bleaching events, we reveal striking genus-level differences in their demographic response to bleaching (mortality, growth, and recruitment). Although Acropora colonies were locally extirpated, substantial local recruitment and fast growth revealed a marked capacity for apparent recovery. By contrast, almost all massive Porites colonies survived and the majority grew in area; yet no new colonies were detected over the 5 years. Our results highlight contrasting dynamics of boom-and-bust vs. protracted declines in two major coral groups. These dangerous demographics emphasise the need for caution when documenting the susceptibility and perceived resistance or recovery of corals to disturbances.

Collapsing ecosystem functions on an inshore coral reef

Ecosystem functions underpin productivity and key services to humans, such as food provision. However, as the severity of environmental stressors intensifies, it is becoming increasingly unclear if, and to what extent, critical functions and services can be sustained. This issue is epitomised on coral reefs, an ecosystem at the forefront of environmental transitions. We provide a functional profile of a coral reef ecosystem, linking time-series data to quantified processes. The data reveal a prolonged collapse of ecosystem functions in this previously resilient system. The results suggest that sediment accumulation in algal turfs has led to a decline in resource yields to herbivorous fishes and a decrease in fish-based ecosystem functions, including a collapse of both fish biomass and productivity. Unfortunately, at present, algal turf sediment accumulation is rarely monitored nor managed in coral reef systems. Our examination of functions through time highlights the value of directly assessing functions, their potential vulnerability, and the capacity of algal turf sediments to overwhelm productive high-diversity coral reef ecosystems.

Algal turf productivity on coral reefs: A meta-analysis

Algal turfs are an abundant and highly productive component of coral reef ecosystems. However, our understanding of the drivers that shape algal turf productivity across studies and among reefs is limited. Based on published studies we considered how different factors may shape turf productivity and turnover rates. Of the factors considered, depth was the primary driver of turf productivity rates, while turnover was predominantly related to turf biomass. We also highlight shortcomings in the available data collected on turf productivity to-date; most data were collected prior to global coral bleaching events, within a limited geographic range, and were largely from experimental substrata. Despite the fact turfs are a widespread benthic covering on most coral reefs, and one of the major sources of benthic productivity, our understanding of their productivity is constrained by both a paucity of data and methodological limitations. We offer a potential way forward to address these challenges.

Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium

Background

Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features.

Results

Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species.

Conclusions

Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-00994-6.

Biophysical and anthropogenic influences on the status of Tonga's coral reefs and reef fish fishery

Despite increasing threats to Tonga's coral reefs from stressors that are both local (e.g. overfishing and pollution) and global (e.g. climate change), there is yet to be a systematic assessment of the status of the country's coral reef ecosystem and reef fish fishery stocks. Here, we provide a national ecological assessment of Tonga's coral reefs and reef fish fishery using ecological survey data from 375 sites throughout Tonga's three main island groups (Ha'apai, Tongatapu and Vava'u), represented by seven key metrics of reef health and fish resource status. Boosted regression tree analysis was used to assess and describe the relative importance of 11 socio-environmental variables associated with these key metrics of reef condition. Mean live coral cover across Tonga was 18%, and showed a strong increase from north to south correlated with declining sea surface temperature, as well as with increasing distance from each provincial capital. Tongatapu, the southernmost island group, had 2.5 times greater coral cover than the northernmost group, Vava'u (24.9% and 10.4% respectively). Reef fish species richness and density were comparable throughout Tongatapu and the middle island group, Ha'apai (~35 species/transect and ~2500 fish/km2), but were significantly lower in Vava'u (~24 species/transect and ~1700 fish/km2). Spatial patterns in the reef fish assemblage were primarily influenced by habitat-associated variables (slope, structural complexity, and hard coral cover). The biomass of target reef fish was greatest in Ha'apai (~820 kg/ha) and lowest in Vava'u (~340 kg/ha), and was negatively associated with higher human influence and fishing activity. Overall mean reef fish biomass values suggest that Tonga's reef fish fishery can be classified as moderately to heavily exploited, with 64% of sites having less than 500 kg/ha. This study provides critical baseline ecological information for Tonga's coral reefs that will: (1) facilitate ongoing management and research; and (2) enable accurate reporting on conservation targets locally and internationally.

A contemporary baseline record of the world's coral reefs

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

Coral Reef Community Changes in Karimunjawa National Park, Indonesia: Assessing the Efficacy of Management in the Face of Local and Global Stressors

Karimunjawa National Park is one of Indonesia’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’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 ± 0.12% (Standard Deviation, SD) to 26.3 ± 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.

Towards modelling the future risk of cyclone wave damage to the world's coral reefs

Tropical cyclones generate extreme waves that can damage coral reef communities. Recovery typically requires up to a decade, driving the trajectory of coral community structure. Coral reefs have evolved over millennia with cyclones. Increasingly, however, processes of recovery are interrupted and compromised by additional pressures (thermal stress, pollution, diseases, predators). Understanding how cyclones interact with other pressures to threaten coral reefs underpins spatial prioritization of conservation and management interventions. Models that simulate coral responses to cumulative pressures often assume that the worst cyclone wave damage occurs within ~100 km of the track. However, we show major coral loss at exposed sites up to 800 km from a cyclone that was both strong (high sustained wind speeds >=33 m/s) and big (widespread circulation >~300 km), using numerical wave models and field data from northwest Australia. We then calculate the return time of big and strong cyclones, big cyclones of any strength and strong cyclones of any size, for each of 150 coral reef ecoregions using a global data set of past cyclones from 1985 to 2015. For the coral ecoregions that regularly were exposed to cyclones during that time, we find that 75% of them were exposed to at least one cyclone that was both big and strong. Return intervals of big and strong cyclones are already less than 5 years for 13 ecoregions, primarily in the cyclone-prone NW Pacific, and less than 10 years for an additional 14 ecoregions. We identify ecoregions likely at higher risk in future given projected changes in cyclone activity. Robust quantification of the spatial distribution of likely cyclone wave damage is vital not only for understanding past coral response to pressures, but also for predicting how this may change as the climate continues to warm and the relative frequency of the strongest cyclones rises.