Improved Coral Population Estimation Reveals Trends at Multiple Scales on Australia’s Great Barrier Reef

The global erosion of biodiversity presents unique challenges for identifying major changes in population dynamics, establishing their causes, and managing and conserving affected ecosystems at broad spatial scales. Adaptive learning approaches connecting different spatial scales through the transfer of hierarchical information are powerful tools to address such challenges. Here, we use a Semi-Parametric Bayesian Hierarchical (SPa-BaH) model to estimate coral cover trajectories using 16 years of a broad-scale survey on Australia’s Great Barrier Reef (GBR). The spatiotemporal variability of coral populations has been considered by separating three-tiered spatial scales and allowing for alternating phases of increasing and decreasing in the estimation of their trajectories. Model estimates revealed coral cover trajectories that were highly variable according to location but that fairly consistently declined at a regional spatial scale. Notwithstanding this general trend, individual reefs within subregions in the central part of the GBR often displayed different trajectory types between sites separated by only a few hundred meters. These coral dynamics were also associated with reduced recovery rates in the Cairns and Swain subregions. Our study highlights the importance of accounting for local variation in coral cover when estimating the spatiotemporal trends in coral cover trajectories, in this case, at the GBR scale. By retaining information at different hierarchical spatial scales, our SPa-BaH model supports better estimation of large-scale coral cover trajectories. The quantitative approaches developed here can also be applied to other species with complex dynamics thereby enhancing estimations of their trajectories at local- and larger-scales and options for their management.     

Modelling Coral Reef Futures to Inform Management: Can Reducing Local-Scale Stressors Conserve Reefs under Climate Change?

Climate change has emerged as a principal threat to coral reefs, and is expected to exacerbate coral reef degradation caused by more localised stressors. Management of local stressors is widely advocated to bolster coral reef resilience, but the extent to which management of local stressors might affect future trajectories of reef state remains unclear. This is in part because of limited understanding of the cumulative impact of multiple stressors. Models are ideal tools to aid understanding of future reef state under alternative management and climatic scenarios, but to date few have been sufficiently developed to be useful as decision support tools for local management of coral reefs subject to multiple stressors. We used a simulation model of coral reefs to investigate the extent to which the management of local stressors (namely poor water quality and fishing) might influence future reef state under varying climatic scenarios relating to coral bleaching. We parameterised the model for Bolinao, the Philippines, and explored how simulation modelling can be used to provide decision support for local management. We found that management of water quality, and to a lesser extent fishing, can have a significant impact on future reef state, including coral recovery following bleaching-induced mortality. The stressors we examined interacted antagonistically to affect reef state, highlighting the importance of considering the combined impact of multiple stressors rather than considering them individually. Further, by providing explicit guidance for management of Bolinao''s reef system, such as which course of management action will most likely to be effective over what time scales and at which sites, we demonstrated the utility of simulation models for supporting management. Aside from providing explicit guidance for management of Bolinao''s reef system, our study offers insights which could inform reef management more broadly, as well as general understanding of reef systems.     

Anticipative management for coral reef ecosystem services in the 21st century

Under projections of global climate change and other stressors, significant changes in the ecology, structure and function of coral reefs are predicted. Current management strategies tend to look to the past to set goals, focusing on halting declines and restoring baseline conditions. Here, we explore a complementary approach to decision making that is based on the anticipation of future changes in ecosystem state, function and services. Reviewing the existing literature and utilizing a scenario planning approach, we explore how the structure of coral reef communities might change in the future in response to global climate change and overfishing. We incorporate uncertainties in our predictions by considering heterogeneity in reef types in relation to structural complexity and primary productivity. We examine 14 ecosystem services provided by reefs, and rate their sensitivity to a range of future scenarios and management options. Our predictions suggest that the efficacy of management is highly dependent on biophysical characteristics and reef state. Reserves are currently widely used and are predicted to remain effective for reefs with high structural complexity. However, when complexity is lost, maximizing service provision requires a broader portfolio of management approaches, including the provision of artificial complexity, coral restoration, fish aggregation devices and herbivore management. Increased use of such management tools will require capacity building and technique refinement and we therefore conclude that diversification of our management toolbox should be considered urgently to prepare for the challenges of managing reefs into the 21st century.     

Supporting Fisheries Management by Means of Complex Models: Can We Point out Isles of Robustness in a Sea of Uncertainty?

Ecosystems are usually complex, nonlinear and strongly influenced by poorly known environmental variables. Among these systems, marine ecosystems have high uncertainties: marine populations in general are known to exhibit large levels of natural variability and the intensity of fishing efforts can change rapidly. These uncertainties are a source of risks that threaten the sustainability of both fish populations and fishing fleets targeting them. Appropriate management measures have to be found in order to reduce these risks and decrease sensitivity to uncertainties. Methods have been developed within decision theory that aim at allowing decision making under severe uncertainty. One of these methods is the information-gap decision theory. The info-gap method has started to permeate ecological modelling, with recent applications to conservation. However, these practical applications have so far been restricted to simple models with analytical solutions. Here we implement a deterministic approach based on decision theory in a complex model of the Eastern English Channel. Using the ISIS-Fish modelling platform, we model populations of sole and plaice in this area. We test a wide range of values for ecosystem, fleet and management parameters. From these simulations, we identify management rules controlling fish harvesting that allow reaching management goals recommended by ICES (International Council for the Exploration of the Sea) working groups while providing the highest robustness to uncertainties on ecosystem parameters.     

Assessing the Effectiveness of Local Management of Coral Reefs Using Expert Opinion and Spatial Bayesian Modeling

Multiple stressors are an increasing concern in the management and conservation of ecosystems, and have been identified as a key gap in research. Coral reefs are one example of an ecosystem where management of local stressors may be a way of mitigating or delaying the effects of climate change. Predicting how multiple stressors interact, particularly in a spatially explicit fashion, is a difficult challenge. Here we use a combination of an expert-elicited Bayesian network (BN) and spatial environmental data to examine how hypothetical scenarios of climate change and local management would result in different outcomes for coral reefs on the Great Barrier Reef (GBR), Australia. Parameterizing our BN using the mean responses from our experts resulted in predictions of limited efficacy of local management in combating the effects of climate change. However, there was considerable variability in expert responses and uncertainty was high. Many reefs within the central GBR appear to be at risk of further decline based on the pessimistic opinions of our expert pool. Further parameterization of the model as more data and knowledge become available could improve predictive power. Our approach serves as a starting point for subsequent work that can fine-tune parameters and explore uncertainties in predictions of responses to management.     

Population growth rates of reef sharks with and without fishing on the great barrier reef: robust estimation with multiple models

Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple assessment methods, to obtain robust estimates of population trends in species threatened by overfishing.     

Thermal stress induces persistently altered coral reef fish assemblages

Ecological communities are reorganizing in response to warming temperatures. For continuous ocean habitats this reorganization is characterized by large‐scale species redistribution, but for tropical discontinuous habitats such as coral reefs, spatial isolation coupled with strong habitat dependence of fish species imply that turnover and local extinctions are more significant mechanisms. In these systems, transient marine heatwaves are causing coral bleaching and profoundly altering habitat structure, yet despite severe bleaching events becoming more frequent and projections indicating annual severe bleaching by the 2050s at most reefs, long‐term effects on the diversity and structure of fish assemblages remain unclear. Using a 23‐year time series spanning a thermal stress event, we describe and model structural changes and recovery trajectories of fish communities after mass bleaching. Communities changed fundamentally, with the new emergent communities dominated by herbivores and persisting for >15 years, a period exceeding realized and projected intervals between thermal stress events on coral reefs. Reefs which shifted to macroalgal states had the lowest species richness and highest compositional dissimilarity, whereas reefs where live coral recovered exceeded prebleaching fish richness, but remained dissimilar to prebleaching compositions. Given realized and projected frequencies of bleaching events, our results show that fish communities historically associated with coral reefs will not re‐establish, requiring substantial adaptation by managers and resource users.     

Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories

Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters. Due to increasing frequencies of perturbations – anthropogenic and natural – many reefs are under threat. Such perturbations often have devastating effects on these unique ecosystems and especially if they occur simultaneously and amplify each other''s impact, they might trigger a phase shift and create irreversible conditions.We developed a generic, spatially explicit, individual-based model in which competition drives the dynamics of a virtual benthic reef community – comprised of scleractinian corals and algae – under different environmental settings. Higher system properties, like population dynamics or community composition arise through self-organization as emergent properties. The model was parameterized for a typical coral reef site at Zanzibar, Tanzania and features coral bleaching and physical disturbance regimes as major sources of perturbations. Our results show that various types and modes (intensities and frequencies) of perturbations create diverse outcomes and that the switch from high diversity to single species dominance can be evoked by small changes in a key parameter.Here we extend the understanding of coral reef resilience and the identification of key processes, drivers and respective thresholds, responsible for changes in local situations. One future goal is to provide a tool which may aid decision making processes in management of coral reefs.     

Coral reefs promote the evolution of morphological diversity and ecological novelty in labrid fishes

Although coral reefs are renowned biodiversity hotspots it is not known whether they also promote the evolution of exceptional ecomorphological diversity. We investigated this question by analysing a large functional morphological dataset of trophic characters within Labridae, a highly diverse group of fishes. Using an analysis that accounts for species relationships, the time available for diversification and model uncertainty we show that coral reef species have evolved functional morphological diversity twice as fast as non-reef species. In addition, coral reef species occupy 68.6% more trophic morphospace than non-reef species. Our results suggest that coral reef habitats promote the evolution of both trophic novelty and morphological diversity within fishes. Thus, the preservation of coral reefs is necessary, not only to safeguard current biological diversity but also to conserve the underlying mechanisms that can produce functional diversity in future.     

Population control based on abundance estimates: Frequency does not compensate for uncertainty

For decision making processes related to a sustainable harvest, two aspects are of fundamental importance: first, the insufficient accuracy of abundance estimates and second, the fact that an increased mortality will not necessarily decrease the population size. To optimise decision making, we investigated how uncertainty, namely incomplete information and inadequate understanding about the conditions and the relationships between system components, affect the feasibility of population control. To this end, we developed an age-structured population model for roe deer, one of the most common ungulates in Europe. The model simulates hunting processes that are affected by uncertainties related to abundance estimates and species demography. The results indicated that uncertainty related to abundance estimates largely reduced the ability to achieve target population densities. Surprisingly, this effect was not weakened by more frequent estimations. We conclude that decreasing the interval of abundance estimates counterintuitively cannot compensate for lacking accuracy. This novel aspect should therefore be considered in the management of dynamic ecological systems.     

Temporal patterns in coral reef, seagrass and mangrove communities from Chengue bay CARICOMP site (Colombia): 1993-2008

Few monitoring programs have simultaneously assessed the dynamics of linked marine ecosystems (coral reefs, seagrass beds and mangroves) to document their temporal and spatial variability. Based on CARICOMP protocol we evaluated permanent stations in coral reefs, seagrass beds and mangroves from 1993 to 2008 in Chengue Bay at the Tayrona Natural Park, Colombian Caribbean. Overall, the studied ecosystems showed a remarkable stability pattern over the monitoring period. While there were annual variations in coral reefs (coral cover) and mangroves (litterfall) caused by hurricane Lenny in 1999, particular trends in seagrass (leaf area index and leaf productivity) appear to reflect the natural variability in this ecosystem. We suggest that monitoring sites at the three marine ecosystems had in general a healthy development in the last 16 years. Our results are critical to locally improve the management strategies (Tayrona Natural Park) and to understand the long-term dynamics of closely associated marine ecosystems in the Caribbean.     

Caribbean reefs of the Anthropocene: Variance in ecosystem metrics indicates bright spots on coral depauperate reefs

Dramatic coral loss has significantly altered many Caribbean reefs, with potentially important consequences for the ecological functions and ecosystem services provided by reef systems. Many studies examine coral loss and its causes—and often presume a universal decline of ecosystem services with coral loss—rather than evaluating the range of possible outcomes for a diversity of ecosystem functions and services at reefs varying in coral cover. We evaluate 10 key ecosystem metrics, relating to a variety of different reef ecosystem functions and services, on 328 Caribbean reefs varying in coral cover. We focus on the range and variability of these metrics rather than on mean responses. In contrast to a prevailing paradigm, we document high variability for a variety of metrics, and for many the range of outcomes is not related to coral cover. We find numerous “bright spots,” where herbivorous fish biomass, density of large fishes, fishery value, and/or fish species richness are high, despite low coral cover. Although it remains critical to protect and restore corals, understanding variability in ecosystem metrics among low‐coral reefs can facilitate the maintenance of reefs with sustained functions and services as we work to restore degraded systems. This framework can be applied to other ecosystems in the Anthropocene to better understand variance in ecosystem service outcomes and identify where and why bright spots exist.     

Kenyan coral reef lagoon fish: effects of fishing,substrate complexity,and sea urchins

Population density, number of species, diversity, and species-area relationships of fish species in eight common coral reef-associated families were studied in three marine parks receiving total protection from fishing, four sites with unregulated fishing, and one reef which recently received protection from fishing (referred to as a transition reef). Data on coral cover, reef topographic complexity, and sea urchin abundance were collected and correlated with fish abundance and species richness. The most striking result of this survey is a consistent and large reduction in the population density and species richness of 5 families (surgeonfish, triggerfish, butterflyfish, angelfish, and parrotfish). Poor recovery of parrotfish in the transition reef, relative to other fish families, is interpreted as evidence for competitive exclusion of parrotfish by sea urchins. Reef substrate complexity is significantly associated with fish abundance and diversity, but data suggest different responses for protected versus fished reefs, protected reefs having higher species richness and numbers of individuals than unprotected reefs for the same reef complexity. Sea urchin abundance is negatively associated with numbers of fish and fish species but the interrelationship between sea urchins, substrate complexity, coral cover, and management make it difficult to attribute a set percent of variance to each factor-although fishing versus no fishing appears to be the strongest variable in predicting numbers of individuals and species of fish, and their community similarity. Localized species extirpation is evident for many species on fished reefs (for the sampled area of 1.0 ha). Fifty-two of 110 species found on protected reefs were not found on unprotected reefs.     

Multiple feedbacks and the prevalence of alternate stable states on coral reefs

The prevalence of alternate stable states on coral reefs has been disputed, although there is universal agreement that many reefs have experienced substantial losses of coral cover. Alternate stable states require a strong positive feedback that causes self-reinforcing runaway change when a threshold is passed. Here we use a simple model of the dynamics of corals, macroalgae and herbivores to illustrate that even weak positive feedbacks that individually cannot lead to alternate stable states can nonetheless do so if they act in concert and reinforce each other. Since the strength of feedbacks varies over time and space, our results imply that we should not reject or accept the general hypothesis that alternate stable states occur in coral reefs. Instead, it is plausible that shifts between alternate stable states can occur sporadically, or on some reefs but not others depending on local conditions. Therefore, we should aim at a better mechanistic understanding of when and why alternate stable states may occur. Our modelling results point to an urgent need to recognize, quantify, and understand feedbacks, and to reorient management interventions to focus more on the mechanisms that cause abrupt transitions between alternate states.     

Assessing uncertainties in land cover projections

Understanding uncertainties in land cover projections is critical to investigating land‐based climate mitigation policies, assessing the potential of climate adaptation strategies and quantifying the impacts of land cover change on the climate system. Here, we identify and quantify uncertainties in global and European land cover projections over a diverse range of model types and scenarios, extending the analysis beyond the agro‐economic models included in previous comparisons. The results from 75 simulations over 18 models are analysed and show a large range in land cover area projections, with the highest variability occurring in future cropland areas. We demonstrate systematic differences in land cover areas associated with the characteristics of the modelling approach, which is at least as great as the differences attributed to the scenario variations. The results lead us to conclude that a higher degree of uncertainty exists in land use projections than currently included in climate or earth system projections. To account for land use uncertainty, it is recommended to use a diverse set of models and approaches when assessing the potential impacts of land cover change on future climate. Additionally, further work is needed to better understand the assumptions driving land use model results and reveal the causes of uncertainty in more depth, to help reduce model uncertainty and improve the projections of land cover.     

Prioritizing key resilience indicators to support coral reef management in a changing climate

Managing coral reefs for resilience to climate change is a popular concept but has been difficult to implement because the empirical scientific evidence has either not been evaluated or is sometimes unsupportive of theory, which leads to uncertainty when considering methods and identifying priority reefs. We asked experts and reviewed the scientific literature for guidance on the multiple physical and biological factors that affect the ability of coral reefs to resist and recover from climate disturbance. Eleven key factors to inform decisions based on scaling scientific evidence and the achievability of quantifying the factors were identified. Factors important to resistance and recovery, which are important components of resilience, were not strongly related, and should be assessed independently. The abundance of resistant (heat-tolerant) coral species and past temperature variability were perceived to provide the greatest resistance to climate change, while coral recruitment rates, and macroalgae abundance were most influential in the recovery process. Based on the 11 key factors, we tested an evidence-based framework for climate change resilience in an Indonesian marine protected area. The results suggest our evidence-weighted framework improved upon existing un-weighted methods in terms of characterizing resilience and distinguishing priority sites. The evaluation supports the concept that, despite high ecological complexity, relatively few strong variables can be important in influencing ecosystem dynamics. This is the first rigorous assessment of factors promoting coral reef resilience based on their perceived importance, empirical evidence, and feasibility of measurement. There were few differences between scientists' perceptions of factor importance and the scientific evidence found in journal publications but more before and after impact studies will be required to fully test the validity of all the factors. The methods here will increase the feasibility and defensibility of including key resilience metrics in evaluations of coral reefs, as well as reduce costs. Adaptation, marine protected areas, priority setting, resistance, recovery.     

Evaluation of habitat suitability index models by global sensitivity and uncertainty analyses: a case study for submerged aquatic vegetation

Habitat suitability index (HSI) models are commonly used to predict habitat quality and species distributions and are used to develop biological surveys, assess reserve and management priorities, and anticipate possible change under different management or climate change scenarios. Important management decisions may be based on model results, often without a clear understanding of the level of uncertainty associated with model outputs. We present an integrated methodology to assess the propagation of uncertainty from both inputs and structure of the HSI models on model outputs (uncertainty analysis: UA) and relative importance of uncertain model inputs and their interactions on the model output uncertainty (global sensitivity analysis: GSA). We illustrate the GSA/UA framework using simulated hydrology input data from a hydrodynamic model representing sea level changes and HSI models for two species of submerged aquatic vegetation (SAV) in southwest Everglades National Park: Vallisneria americana (tape grass) and Halodule wrightii (shoal grass). We found considerable spatial variation in uncertainty for both species, but distributions of HSI scores still allowed discrimination of sites with good versus poor conditions. Ranking of input parameter sensitivities also varied spatially for both species, with high habitat quality sites showing higher sensitivity to different parameters than low‐quality sites. HSI models may be especially useful when species distribution data are unavailable, providing means of exploiting widely available environmental datasets to model past, current, and future habitat conditions. The GSA/UA approach provides a general method for better understanding HSI model dynamics, the spatial and temporal variation in uncertainties, and the parameters that contribute most to model uncertainty. Including an uncertainty and sensitivity analysis in modeling efforts as part of the decision‐making framework will result in better‐informed, more robust decisions.     

High resilience masks underlying sensitivity to algal phase shifts of Pacific coral reefs

A single ecosystem can exhibit great biogeographic and environmental variability. While a given ecological driver might have a strong impact in one region, it does not necessarily hold that its importance will extend elsewhere. Coral reefs provide a striking example in that coral communities have low resilience in the Atlantic and remarkable resilience in parts of the species‐rich Pacific. Recent experimental evidence from the Atlantic finds that fishing of large herbivorous fish can be a strong driver of coral resilience. Here, we repeat the Atlantic experiment in the highly resilient forereef of Moorea (French Polynesia), which has repeatedly recovered from disturbances. A combination of cages, fish deterrents (FDs), and controls allowed us to simulate the consequences of fishing large herbivores on algal assemblages, coral recruitment, and the demographic rates of coral juveniles. We find that the impacts of removing large herbivorous reef fish vary with early coral ontogeny. Reduced herbivore access led to a modest macroalgal bloom and reduction in coral recruitment. However, larger juvenile corals (> 1 cm diameter) survived better and grew faster under these conditions because of a reduction in corallivory. To determine the net impact of losing larger herbivorous fish, we combined experimental results with estimated demographic parameters in an individual‐based model. Simulating coral recovery trajectories for five years, we find that protecting larger reef fish led to better recovery in 66–99% of simulations, depending on underlying assumptions (with the more credible assumptions being associated with greater likelihood of net positive impacts). While we find that fishing effects are detrimental to corals in both the Atlantic and Pacific systems studied, the nature of the interactions varied markedly. In the identical previously‐published study in the Atlantic, macroalgae exhibited a rapid bloom and caused a sufficiently large reduction in coral recruitment to force a predicted ecosystem shift to an alternative attractor. The commensurate macroalgal bloom in Moorea was weak yet the corals were two orders of magnitude more sensitive to its presence. We do not suggest that a reduction in recruitment in Moorea will lead to alternative attractors but the long‐term risks of a reduction in recovery rate are cause for concern as rates of coral mortality are projected to increase. The emerging picture is that Pacific reefs are less likely to experience macroalgal blooms but are surprisingly sensitive to such blooms if they occur.     

Shifting paradigms in restoration of the world's coral reefs

Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine‐protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014–2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.     

On the evolution of fish–coral interactions

The biodiversity of tropical reefs is typified by the interaction between fishes and corals. Despite the importance of this ecological association, coevolutionary patterns between these two animal groups have yet to be critically evaluated. After compiling a large dataset on the prevalence of fish–coral interactions, we found that only a minority of fish species associate strongly with live corals (~5%). Furthermore, we reveal an evolutionary decoupling between fish and coral lineage trajectories. While fish lineages expanded in the Miocene, the bulk of coral diversification occurred in the Pliocene/Pleistocene. Most importantly, we found that coral association did not drive major differences in fish diversification. These results suggest that the Miocene fish diversification is more likely related to the development of novel, wave-resistant reef structures and their associated ecological opportunities. Macroevolutionary patterns in reef fishes are thus more strongly correlated with the expansion of reefs than with the corals themselves.