Cross-scale Habitat Structure Drives Fish Body Size Distributions on Coral Reefs

Divergent responses of pelagic and benthic fish body-size structure to remoteness and protection from humans

Animal body-size variation influences multiple processes in marine ecosystems, but habitat heterogeneity has prevented a comprehensive assessment of size across pelagic (midwater) and benthic (seabed) systems along anthropic gradients. In this work, we derive fish size indicators from 17,411 stereo baited-video deployments to test for differences between pelagic and benthic responses to remoteness from human pressures and effectiveness of marine protected areas (MPAs). From records of 823,849 individual fish, we report divergent responses between systems, with pelagic size structure more profoundly eroded near human markets than benthic size structure, signifying greater vulnerability of pelagic systems to human pressure. Effective protection of benthic size structure can be achieved through MPAs placed near markets, thereby contributing to benthic habitat restoration and the recovery of associated fishes. By contrast, recovery of the world's largest and most endangered fishes in pelagic systems requires the creation of highly protected areas in remote locations, including on the High Seas, where protection efforts lag.

Habitat structure shapes temperate reef assemblages across regional environmental gradients

Intertidal artificial habitats are proliferating, but are generally simpler in structure and host lower biodiversity than natural rocky reefs. Eco-engineering aims to enhance the biodiversity of coastal infrastructure, often through physical structural modifications that mimic topographic properties of natural shores. Relationships between biotic assemblages and structural properties of natural and artificial reefs have been extensively studied at sampling scales of up to 1 m2. But evidence that quantified local structural variation has an appreciable influence on biotic assemblages, at a shore-wide scale across regional environmental gradients, is lacking. Here we addressed this knowledge gap with an observational study at 32 natural and artificial intertidal reef sites in Wales, UK. We used multivariate community analysis and permutation tests to examine associations between local physical structure, regional environmental variables and sessile biotic assemblages. A potential influence of local habitat structure on assemblage composition was evident across regional-scale environmental gradients. Compared to natural sites, artificial reefs had lower taxonomic richness, distinct and more variable assemblage composition, and different physical structure. After removing the effect of habitat (natural or artificial), canonical correspondence analysis showed that environmental variables (wave exposure, sea surface temperature and salinity variation), along with two metrics of physical structure (standard deviation in log-transformed detrended roughness and skewness of surface verticality, both at 0.5 m scale), explained 40 % of the variation in assemblage composition among sites. The two structural metrics independently explained 14.5 % of the variation. Associations identified between individual taxa and environmental variables indicated that sites with a higher proportion of horizontal surfaces hosted more canopy macroalgae, which in turn support other algae and invertebrates. Our findings provide evidence to inform scaling-up of structural eco-engineering interventions from experimental contexts to enhance the biodiversity of coastal infrastructure across regional extents.

Habitat traits and predation interact to drive abundance and body size patterns in associated fauna

Habitat-forming organisms provide three-dimensional structure that supports abundant and diverse communities. Variation in the morphological traits of habitat formers will therefore likely influence how they facilitate associated communities, either via food and habitat provisioning, or by altering predator-prey interactions. These mechanisms, however, are typically studied in isolation, and thus, we know little of how they interact to affect associated communities. In response to this, we used naturally occurring morphological variability in the alga Sargassum vestitum to create habitat units of distinct morphotypes to test whether variation in the morphological traits (frond size and thallus size) of S. vestitum or the interaction between these traits affects their value as habitat for associated communities in the presence and absence of predation. We found morphological traits did not interact, instead having independent effects on epifauna that were negligible in the absence of predation. However, when predators were present, habitat units with large fronds were found to host significantly lower epifaunal abundances than other morphotypes, suggesting that large frond alga provided low-value refuge from predators. The presence of predators also influenced the size structure of epifaunal communities from habitat units of differing frond size, suggesting that the refuge value of S. vestitum was also related to epifauna body size. This suggests that habitat formers may chiefly structure associated communities by mediating size-selective predation, and not through habitat provisioning. Furthermore, these results also highlight that habitat traits cannot be considered in isolation, for their interaction with biotic processes can have significant implications for associated communities.

Safeguarding nutrients from coral reefs under climate change

The sustainability of coral reef fisheries is jeopardized by complex and interacting socio-ecological stressors that undermine their contribution to food and nutrition security. Climate change has emerged as one of the key stressors threatening coral reefs and their fish-associated services. How fish nutrient concentrations respond to warming oceans remains unclear but these responses are probably affected by both direct (metabolism and trophodynamics) and indirect (habitat and species range shifts) effects. Climate-driven coral habitat loss can cause changes in fish abundance and biomass, revealing potential winners and losers among major fisheries targets that can be predicted using ecological indicators and biological traits. A critical next step is to extend research focused on the quantity of available food (fish biomass) to also consider its nutritional quality, which is relevant to progress in the fields of food security and malnutrition. Biological traits are robust predictors of fish nutrient content and thus potentially indicate how climate-driven changes are expected to impact nutrient availability within future food webs on coral reefs. Here, we outline future research priorities and an anticipatory framework towards sustainable reef fisheries contributing to nutrition-sensitive food systems in a warming ocean.

Small predators dominate fish predation in coral reef communities

Ecosystem processes are challenging to quantify at a community level, particularly within complex ecosystems (e.g., rainforests, coral reefs). Predation is one of the most important types of species interactions, determining several ecosystem processes. However, while it is widely recognised, it is rarely quantified, especially in aquatic systems. To address these issues, we model predation on fish by fish, in a hyperdiverse coral reef community. We show that body sizes previously examined in fish-fish predation studies (based on a metanalysis), only represent about 5% of likely predation events. The average fish predator on coral reefs is just 3.65 cm; the average fish prey just 1.5 cm. These results call for a shift in the way we view fish predation and its ability to shape the species or functional composition of coral reef fish communities. Considered from a functional group approach, we found general agreement in the distribution of simulated and observed predation events, among both predator and prey functional groups. Predation on coral reefs is a process driven by small fish, most of which are neither seen nor quantified.

Habitat type and complexity drive fish assemblages in a tropical seascape

Inshore marine seascapes support a diversity of interconnected habitats and are an important focus for biodiversity conservation. This study examines the importance of habitat attributes to fish assemblages across a mosaic of inshore habitats: coral reefs, rocky reefs, macroalgae beds and sand/rubble beds. Fishes and benthic habitats were surveyed at 34 sites around continental islands of the central Great Barrier Reef using baited remote underwater video stations (BRUVS). Species richness was influenced foremost by habitat type and also by structural complexity within habitat types. The most speciose assemblages occurred in coral and rocky reef habitats with high structural complexity, provided by the presence of coral bommies/overhangs, boulders and rock crevices. Nonetheless, macroalgae and sand/rubble beds also supported unique species, and therefore contributed to the overall richness of fish assemblages in the seascape. Most trophic groups had positive associations with complexity, which was the most important predictor for abundance of piscivorous fishes and mobile planktivores. There was significant differentiation of fish assemblages among habitats, with the notable exception of coral and rocky reefs. Species assemblages overlapped substantially between coral and rocky reefs, which had 60% common species, despite coral cover being lower on rocky reefs. This suggests that, for many species, rocky and coral substrates can provide equivalent habitat structure, emphasizing the importance of complexity in providing habitat refuges, and highlighting the contribution of rocky reefs to habitat provision within tropical seascapes. The results of this study support an emerging recognition of the collective value of habitat mosaics in inshore marine ecosystems.

Natural and anthropogenic-induced stressors affecting the composition of fish communities on the rocky reefs of Ecuador

Natural and human-induced stressors have threatened the sustainability of the fish communities of coral-rocky reefs worldwide in the last decades. The composition of the fish communities on the reefs of Ecuador and the factors affecting spatiotemporal changes are unknown. We studied the influence of the descriptors of structural complexity, the current status of coral and human-induced variables over fish communities. A video transect method was used to assess fish communities in three zones (slope, crest, and bottom) of two reefs during two seasons (rainy and dry). The structure of fish communities was highly influenced by the zones and season; rugosity and live coral affected the fish composition on the crest and slope zones. The fractured coral and derelict fishing gear on coral produced an adverse effect on fish composition over the crest. A multifactorial process causing loss of structural complexity and affecting fish composition was identified, however, periodical assessment is required for a greater understanding of this process.

Spatial drivers of instability in marine size-spectrum ecosystems

Size-spectrum models are a recent class of models describing the dynamics of a whole community based on a description of individual organisms. The models are motivated by marine ecosystems where they cover the size range from multicellular plankton to the largest fish. We propose to extend the size-spectrum model with spatial components. The spatial dynamics is governed by a random motion and a directed movement in the direction of increased fitness, which we call 'fitness-taxis'. We use the model to explore whether spatial irregularities of marine communities can occur due to the internal dynamics of predator-prey interactions and spatial movements. This corresponds to a pattern-formation analysis generalized to an entire ecosystem but is not limited to one prey and one predator population. The analyses take the form of Fourier analysis and numerical experiments. Results show that diffusion always stabilizes the equilibrium but fitness-taxis destabilizes it, leading to non-stationary spatially inhomogeneous population densities, which are travelling in size. However, there is a strong asymmetry between fitness-induced destabilizing effects and diffusion-induced stabilizing effects with the latter dominating over the former. These findings reveal that fitness taxis acts as a possible mechanism behind pattern formations in ecosystems with high diversity of organism sizes, which can drive the emergence of spatial heterogeneity even in a spatially homogeneous environment.

Context Dependence: A Conceptual Approach for Understanding the Habitat Relationships of Coastal Marine Fauna

Coastal habitats, such as seagrasses, mangroves, rocky and coral reefs, salt marshes, and kelp forests, sustain many key fish and invertebrate populations around the globe. Our understanding of how animals use these broadly defined habitat types is typically derived from a few well-studied regions and is often extrapolated to similar habitats elsewhere. As a result, a working understanding of their habitat importance is often based on information derived from other regions and environmental contexts. Contexts such as tidal range, rainfall, and local geomorphology may fundamentally alter animal–habitat relationships, and there is growing evidence that broadly defined habitat types such as “mangroves” or “salt marsh” may show predictable spatial and temporal variation in habitat function in relation to these environmental drivers. In the present article, we develop a framework for systematically examining contextual predictability to define the geographic transferability of animal–habitat relationships, to guide ongoing research, conservation, and management actions in these systems.

Habitat zonation on coral reefs: Structural complexity, nutritional resources and herbivorous fish distributions

Distinct zonation of community assemblages among habitats is a ubiquitous feature of coral reefs. The distribution of roving herbivorous fishes (parrotfishes, surgeonfishes and rabbitfishes) is a particularly clear example, with the abundance of these fishes generally peaking in shallow-water, high-energy habitats, regardless of the biogeographic realm. Yet, our understanding of the factors which structure this habitat partitioning, especially with regards to different facets of structural complexity and nutritional resource availability, is limited. To address this issue, we used three-dimensional photogrammetry and structure-from-motion technologies to describe five components of structural complexity (rugosity, coral cover, verticality, refuge density and field-of-view) and nutritional resource availability (grazing surface area) among habitats and considered how these factors are related to herbivorous fish distributions. All complexity metrics (including coral cover) were highest on the slope and crest. Nutritional resource availability differed from this general pattern and peaked on the outer-flat. Unexpectedly, when compared to the distribution of herbivorous fishes, none of the complexity metrics had a marked influence in the models. However, grazing surface area was a strong predictor of both the abundance and biomass of herbivorous fishes. The strong relationship between grazing surface area and herbivorous fish distributions indicates that nutritional resource availability may be one of the primary factors driving the distribution of roving herbivorous fishes. The lack of a relationship between complexity and herbivorous fishes, and a strong affinity of herbivorous fishes for low-complexity, algal turf-dominated outer-flat habitats, offers some cautious optimism that herbivory may be sustained on future, low-complexity, algal turf-dominated reef configurations.

Capturing complexity: field-testing the use of 'structure from motion' derived virtual models to replicate standard measures of reef physical structure

Reef structural complexity provides important refuge habitat for a range of marine organisms, and is a useful indicator of the health and resilience of reefs as a whole. Marine scientists have recently begun to use 'Structure from Motion' (SfM) photogrammetry in order to accurately and repeatably capture the 3D structure of physical objects underwater, including reefs. There has however been limited research on the comparability of this new method with existing analogue methods already used widely for measuring and monitoring 3D structure, such as 'tape and chain rugosity index (RI)' and graded visual assessments. Our findings show that analogue and SfM RI can be reliably converted over a standard 10-m reef section (SfM RI = 1.348 × chain RI-0.359, r 2 = 0.82; and Chain RI = 0.606 × SfM RI + 0.465) for RI values up to 2.0; however, SfM RI values above this number become increasingly divergent from traditional tape and chain measurements. Additionally, we found SfM RI correlates well with visual assessment grades of coral reefs over a 10 × 10 m area (SfM RI = 0.1461 × visual grade + 1.117; r 2 = 0.83). The SfM method is shown to be affordable and non-destructive whilst also allowing the data collected to be archival, less biased by the observer, and broader in its scope of applications than standard methods. This work allows researchers to easily transition from analogue to digital structural assessment techniques, facilitating continued long-term monitoring, whilst also improving the quality and additional research value of the data collected.

Cross-shelf Heterogeneity of Coral Assemblages in Northwest Australia

Understanding the spatial and temporal distribution of coral assemblages and the processes structuring those patterns is fundamental to managing reef assemblages. Cross-shelf marine systems exhibit pronounced and persistent gradients in environmental conditions; however, these gradients are not always reliable predictors of coral distribution or the degree of stress that corals are experiencing. This study used information from government, industry and scientific datasets spanning 1980–2017, to explore temporal trends in coral cover in the geographically complex system of the Dampier Archipelago, northwest Australia. Coral composition at 15 sites surveyed in 2017 was also modelled against environmental and spatial variables (including turbidity, degree heat weeks, wave exposure, and distance to land/mainland/isobath) to assess their relative importance in structuring coral assemblages. High spatial and temporal heterogeneity was observed in coral cover and recovery trajectories, with reefs located an intermediate distance from the shore maintaining high cover over the past 20 years. The abundance of some prominent genera in 2017 (Acropora, Porites, and Turbinaria spp.) decreased with the distance from the mainland, suggesting that inshore processes play an important role in dictating the distribution of these genera. The atypical distributions of these key reef-building corals and spatial heterogeneity of historical recovery trajectories highlight the risks in making assumptions regarding cross-shelf patterns in geographically complex systems.

Do spatial scale and life history affect fish-habitat relationships?

Understanding how animals interact with their environment is a fundamental ecological question with important implications for conservation and management. The relationships between animals and their habitat, however, can be scale-dependent. If ecologists work at suboptimal spatial scales, they will gain an incomplete picture of how animals respond to the landscape. Identifying the scale at which animal-landscape relationships are strongest (the "scale of effect") will improve our ability to better plan management and conservation activities. Several recent studies have greatly enhanced our knowledge about the scale of effect, and the potential drivers of interspecific variability, in particular life-history traits. However, while many marine systems are inherently multiscalar, research into the scale of effect has been mainly focussed on terrestrial taxa. As the scales of observation in fish-habitat association studies are often selected based on convention rather than biological reasoning, they may provide an incomplete picture of the scales where these associations are strongest. We examined fish-habitat associations across four nested spatial scales in a temperate reef system to ask: (a) at what scale are fish-habitat associations the strongest, (b) are habitat elements consistently important across scales, and (c) do scale-dependent fish-habitat associations vary in relation to either body size, geographic range size or trophic level? We found that: (a) the strongest fish-habitat associations were observed when these relationships were examined at considerably larger spatial scales than usually investigated; (b) the importance of environmental predictors varied across spatial scales, indicating that conclusions about the importance of habitat elements will depend on the scales at which studies are undertaken; and (c) scale-dependent fish-habitat associations were consistent across all life-history traits. Our results highlight the importance of considering how animals relate to their environment and suggest the small scales often chosen to examine fish-habitat associations are likely to be suboptimal. Developing a more mechanistic understanding of animal-habitat associations will greatly aid in predicting and managing responses to future anthropogenic disturbances.

Early Warnings for State Transitions

New concepts have emerged in theoretical ecology with the intent to quantify complexities in ecological change that are unaccounted for in state-and-transition models and to provide applied ecologists with statistical early warning metrics able to predict and prevent state transitions. With its rich history of furthering ecological theory and its robust and broad-scale monitoring frameworks, the rangeland discipline is poised to empirically assess these newly proposed ideas while also serving as early adopters of novel statistical metrics that provide advanced warning of a pending shift to an alternative ecological regime. Were view multivariate early warning and regime shift detection metrics, identify situations where various metrics will be most useful for rangeland science, and then highlight known shortcomings. Our review of a suite of multivariate-based regime shift/early warning indicators provides a broad range of metrics applicable to a wide variety of data types or contexts, from situations where a great deal is known about the key system drivers and a regime shift is hypothesized a priori, to situations where the key drivers and the possibility of a regime shift are both unknown. These metrics can be used to answer ecological state-and-transition questions, inform policymakers, and provide quantitative decision-making tools for managers.

Enhancing quantitative approaches for assessing community resilience

Scholars from many different intellectual disciplines have attempted to measure, estimate, or quantify resilience. However, there is growing concern that lack of clarity on the operationalization of the concept will limit its application. In this paper, we discuss the theory, research development and quantitative approaches in ecological and community resilience. Upon noting the lack of methods that quantify the complexities of the linked human and natural aspects of community resilience, we identify several promising approaches within the ecological resilience tradition that may be useful in filling these gaps. Further, we discuss the challenges for consolidating these approaches into a more integrated perspective for managing social-ecological systems.

Ecological Complexity in Plant Virus Host Range Evolution

The host range of a plant virus is the number of species in which it can reproduce. Most studies of plant virus host range evolution have focused on the genetics of host-pathogen interactions. However, the distribution and abundance of plant viruses and their hosts do not always overlap, and these spatial and temporal discontinuities in plant virus-host interactions can result in various ecological processes that shape host range evolution. Recent work shows that the distributions of pathogenic and resistant genotypes, vectors, and other resources supporting transmission vary widely in the environment, producing both expected and unanticipated patterns. The distributions of all of these factors are influenced further by competitive effects, natural enemies, anthropogenic disturbance, the abiotic environment, and herbivory to mention some. We suggest the need for further development of approaches that (i) explicitly consider resource use and the abiotic and biotic factors that affect the strategies by which viruses exploit resources; and (ii) are sensitive across scales. Host range and habitat specificity will largely determine which phyla are most likely to be new hosts, but predicting which host and when it is likely to be infected is enormously challenging because it is unclear how environmental heterogeneity affects the interactions of viruses and hosts.

Ecosystem regime shifts disrupt trophic structure

Regime shifts between alternative stable ecosystem states are becoming commonplace due to the combined effects of local stressors and global climate change. Alternative states are characterized as substantially different in form and function from pre-disturbance states, disrupting the delivery of ecosystem services and functions. On coral reefs, regime shifts are typically characterized by a change in the benthic composition from coral to macroalgal dominance. Such fundamental shifts in the benthos are anticipated to impact associated fish communities that are reliant on the reef for food and shelter, yet there is limited understanding of how regime shifts propagate through the fish community over time, relative to initial or recovery conditions. This study addresses this knowledge gap using long-term data of coral reef regime shifts and recovery on Seychelles reefs following the 1998 mass bleaching event. It shows how trophic structure of the reef fish community becomes increasingly dissimilar between alternative reef ecosystem states (regime-shifted vs. recovering) with time since disturbance. Regime-shifted reefs developed a concave trophic structure, with increased biomass in base trophic levels as herbivorous species benefitted from increased algal resources. Mid trophic level species, including specialists such as corallivores, declined with loss of coral habitat, while biomass was retained in upper trophic levels by large-bodied, generalist invertivores. Recovering reefs also experienced an initial decline in mid trophic level biomass, but moved toward a bottom-heavy pyramid shape, with a wide range of feeding groups (e.g., planktivores, corallivores, omnivores) represented at mid trophic levels. Given the importance of coral reef fishes in maintaining the ecological function of coral reef ecosystems and their associated fisheries, understanding the effects of regime shifts on these communities is essential to inform decisions that enhance ecological resilience and economic sustainability.

Comparing two remote video survey methods for spatial predictions of the distribution and environmental niche suitability of demersal fishes

Information on habitat associations from survey data, combined with spatial modelling, allow the development of more refined species distribution modelling which may identify areas of high conservation/fisheries value and consequentially improve conservation efforts. Generalised additive models were used to model the probability of occurrence of six focal species after surveys that utilised two remote underwater video sampling methods (i.e. baited and towed video). Models developed for the towed video method had consistently better predictive performance for all but one study species although only three models had a good to fair fit, and the rest were poor fits, highlighting the challenges associated with modelling habitat associations of marine species in highly homogenous, low relief environments. Models based on baited video dataset regularly included large-scale measures of structural complexity, suggesting fish attraction to a single focus point by bait. Conversely, models based on the towed video data often incorporated small-scale measures of habitat complexity and were more likely to reflect true species-habitat relationships. The cost associated with use of the towed video systems for surveying low-relief seascapes was also relatively low providing additional support for considering this method for marine spatial ecological modelling.

Body size and mortality rates in coral reef fishes: a three-phase relationship

Body size is closely linked to mortality rates in many animals, although the overarching patterns in this relationship have rarely been considered for multiple species. A meta-analysis of published size-specific mortality rates for coral reef fishes revealed an exponential decline in mortality rate with increasing body size, however, within this broad relationship there are three distinct phases. Phase one is characterized by naive fishes recruiting to reefs, which suffer extremely high mortality rates. In this well-studied phase, fishes must learn quickly to survive the many predation risks. After just a few days, the surviving fishes enter phase two, in which small increases in body size result in pronounced increases in lifespan (estimated 11 d mm^-1). Remarkably, approximately 50% of reef fish individuals remain in phase two throughout their lives. Once fishes reach a size threshold of about 43 mm total length (TL) they enter phase three, where mortality rates are relatively low and the pressure to grow is presumably, significantly reduced. These phases provide a clearer understanding of the impact of body size on mortality rates in coral reef fishes and begin to reveal critical insights into the energetic and trophic dynamics of coral reefs.

Body size distributions signal a regime shift in a lake ecosystem

Communities of organisms, from mammals to microorganisms, have discontinuous distributions of body size. This pattern of size structuring is a conservative trait of community organization and is a product of processes that occur at multiple spatial and temporal scales. In this study, we assessed whether body size patterns serve as an indicator of a threshold between alternative regimes. Over the past 7000 years, the biological communities of Foy Lake (Montana, USA) have undergone a major regime shift owing to climate change. We used a palaeoecological record of diatom communities to estimate diatom sizes, and then analysed the discontinuous distribution of organism sizes over time. We used Bayesian classification and regression tree models to determine that all time intervals exhibited aggregations of sizes separated by gaps in the distribution and found a significant change in diatom body size distributions approximately 150 years before the identified ecosystem regime shift. We suggest that discontinuity analysis is a useful addition to the suite of tools for the detection of early warning signals of regime shifts.

Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology

Structural complexity strongly influences biodiversity and ecosystem productivity. On coral reefs, structural complexity is typically measured using a single and small-scale metric (‘rugosity’) that represents multiple spatial attributes differentially exploited by species, thus limiting a complete understanding of how fish associate with reef structure. We used a novel approach to compare relationships between fishes and previously unavailable components of reef complexity, and contrasted the results against the traditional rugosity index. This study focused on damselfish to explore relationships between fishes and reef structure. Three territorial species, with contrasting trophic habits and expected use of the reef structure, were examined to infer the potential species-specific mechanisms associated with how complexity influences habitat selection. Three-dimensional reef reconstructions from photogrammetry quantified the following metrics of habitat quality: 1) visual exposure to predators and competitors, 2) density of predation refuges and 3) substrate-related food availability. These metrics explained the species distribution better than the traditional measure of rugosity, and each species responded to different complexity components. Given that a critical effect of reef degradation is loss of structure, adopting three-dimensional technologies potentially offers a new tool to both understand species-habitat association and help forecast how fishes will be affected by the flattening of reefs.

Characterizing ontogenetic habitat shifts in marine fishes: advancing nascent methods for marine spatial management

Niche requirements and habitat resource partitioning by conspecific fishes of different sizes are significant knowledge gaps in the species distribution modelling domain. Management actions and operations are typically concentrated on static habitats, or specific areas of interest, without considering movement patterns of species associated with ontogenetic shifts in habitat usage. Generalized additive models were used to model the body-length-habitat relationships of six fish species. These models were used to identify subsets of environmental parameters that drive and explain the continuous length-habitat relationships for each of the study species, which vary in their degree of ecological and/or commercial importance. Continuous predictive maps of the length distributions for each of the six study species across approximately 200 km² of the study area were created from these models. The spatial patterns in habitat partitioning by individuals of different body lengths for all six study species provide strong evidence for ontogenetic shifts. This highlights the importance of considering ontogenetic processes for marine spatial management. Importantly, predictive hotspot maps were created that identify potential areas that accumulate individuals of similar life stages of multiple species (e.g., multispecies nursery areas). In circumstances where limited resources are available for monitoring and management of fish resources, predictive modelling is a valuable tool for studying previously overlooked processes such as ontogenetic habitat shifts. Predictive modelling provides crucial information that elucidates spatial patterns in community composition across mosaics of benthic habitats. This novel technique can contribute to the spatial management of coastal fish and fisheries by identifying areas that are important for different life history stages of multiple fish species.

Cross-scale habitat structure driven by coral species composition on tropical reefs

The availability of habitat structure across spatial scales can determine ecological organization and resilience. However, anthropogenic disturbances are altering the abundance and composition of habitat-forming organisms. How such shifts in the composition of these organisms alter the physical structure of habitats across ecologically important scales remains unclear. At a time of unprecedented coral loss and homogenization of coral assemblages globally, we investigate the inherent structural complexity of taxonomically distinct reefs, across five ecologically relevant scales of measurement (4–64 cm). We show that structural complexity was influenced by coral species composition, and was not a simple function of coral cover on the studied reefs. However, inter-habitat variation in structural complexity changed with scale. Importantly, the scales at which habitat structure was available also varied among habitats. Complexity at the smallest, most vulnerable scale (4 cm) varied the most among habitats, which could have inferences for as much as half of all reef fishes which are small-bodied and refuge dependent for much of their lives. As disturbances continue and species shifts persist, the future of these ecosystems may rely on a greater concern for the composition of habitat-building species and prioritization of particular configurations for protection of maximal cross-scale habitat structural complexity.

Coral reef mesopredators switch prey, shortening food chains, in response to habitat degradation

Diet specificity is likely to be the key predictor of a predator's vulnerability to changing habitat and prey conditions. Understanding the degree to which predatory coral reef fishes adjust or maintain prey choice, in response to declines in coral cover and changes in prey availability, is critical for predicting how they may respond to reef habitat degradation. Here, we use stable isotope analyses to characterize the trophic structure of predator-prey interactions on coral reefs of the Keppel Island Group on the southern Great Barrier Reef, Australia. These reefs, previously typified by exceptionally high coral cover, have recently lost much of their coral cover due to coral bleaching and frequent inundation by sediment-laden, freshwater flood plumes associated with increased rainfall patterns. Long-term monitoring of these reefs demonstrates that, as coral cover declined, there has been a decrease in prey biomass, and a shift in dominant prey species from pelagic plankton-feeding damselfishes to territorial benthic algal-feeding damselfishes, resulting in differences in the principal carbon pathways in the food web. Using isotopes, we tested whether this changing prey availability could be detected in the diet of a mesopredator (coral grouper, Plectropomus maculatus). The δ¹³C signature in grouper tissue in the Keppel Islands shifted from a more pelagic to a more benthic signal, demonstrating a change in carbon sources aligning with the change in prey availability due to habitat degradation. Grouper with a more benthic carbon signature were also feeding at a lower trophic level, indicating a shortening in food chains. Further, we found a decline in the coral grouper population accompanying a decrease in total available prey biomass. Thus, while the ability to adapt diets could ameliorate the short-term impacts of habitat degradation on mesopredators, long-term effects may negatively impact mesopredator populations and alter the trophic structure of coral reef food webs.

Colony geometry and structural complexity of the endangered species Acropora cervicornis partly explains the structure of their associated fish assemblage

In the past decade, significant efforts have been made to describe fish-habitat associations. However, most studies have oversimplified actual connections between fish assemblages and their habitats by using univariate correlations. The purpose of this study was to identify the features of habitat forming corals that facilitate and influences assemblages of associated species such as fishes. For this we developed three-dimensional models of colonies of Acropora cervicornis to estimate geometry (length and height), structural complexity (i.e., volume, density of branches, etc.) and biological features of the colonies (i.e., live coral tissue, algae). We then correlated these colony characteristics with the associated fish assemblage using multivariate analyses. We found that geometry and complexity were better predictors of the structure of fish community, compared to other variables such as percentage of live coral tissue or algae. Combined, the geometry of each colony explained 40% of the variability of the fish assemblage structure associated with this coral species; 61% of the abundance and 69% of fish richness, respectively. Our study shows that three-dimensional reconstructions of discrete colonies of Acropora cervicornis provides a useful description of the colonial structural complexity and may explain a great deal of the variance in the structure of the associated coral reef fish community. This demonstration of the strongly trait-dependent ecosystem role of this threatened species has important implications for restoration and conservation efforts.

Habitat complexity: coral structural loss leads to fisheries declines

Direct human impacts and global climate change are altering the composition and structure of coral reef habitats. These changes are simplifying size-abundance relationships of reef fish communities, reducing productivity through the system and ultimately threatening fisheries yields.

The dynamics of architectural complexity on coral reefs under climate change

One striking feature of coral reef ecosystems is the complex benthic architecture which supports diverse and abundant fauna, particularly of reef fish. Reef-building corals are in decline worldwide, with a corresponding loss of live coral cover resulting in a loss of architectural complexity. Understanding the dynamics of the reef architecture is therefore important to envision the ability of corals to maintain functional habitats in an era of climate change. Here, we develop a mechanistic model of reef topographical complexity for contemporary Caribbean reefs. The model describes the dynamics of corals and other benthic taxa under climate-driven disturbances (hurricanes and coral bleaching). Corals have a simplified shape with explicit diameter and height, allowing species-specific calculation of their colony surface and volume. Growth and the mechanical (hurricanes) and biological erosion (parrotfish) of carbonate skeletons are important in driving the pace of extension/reduction in the upper reef surface, the net outcome being quantified by a simple surface roughness index (reef rugosity). The model accurately simulated the decadal changes of coral cover observed in Cozumel (Mexico) between 1984 and 2008, and provided a realistic hindcast of coral colony-scale (1-10 m) changing rugosity over the same period. We then projected future changes of Caribbean reef rugosity in response to global warming. Under severe and frequent thermal stress, the model predicted a dramatic loss of rugosity over the next two or three decades. Critically, reefs with managed parrotfish populations were able to delay the general loss of architectural complexity, as the benefits of grazing in maintaining living coral outweighed the bioerosion of dead coral skeletons. Overall, this model provides the first explicit projections of reef rugosity in a warming climate, and highlights the need of combining local (protecting and restoring high grazing) to global (mitigation of greenhouse gas emissions) interventions for the persistence of functional reef habitats.

Mapping reef fish and the seascape: using acoustics and spatial modeling to guide coastal management

Reef fish distributions are patchy in time and space with some coral reef habitats supporting higher densities (i.e., aggregations) of fish than others. Identifying and quantifying fish aggregations (particularly during spawning events) are often top priorities for coastal managers. However, the rapid mapping of these aggregations using conventional survey methods (e.g., non-technical SCUBA diving and remotely operated cameras) are limited by depth, visibility and time. Acoustic sensors (i.e., splitbeam and multibeam echosounders) are not constrained by these same limitations, and were used to concurrently map and quantify the location, density and size of reef fish along with seafloor structure in two, separate locations in the U.S. Virgin Islands. Reef fish aggregations were documented along the shelf edge, an ecologically important ecotone in the region. Fish were grouped into three classes according to body size, and relationships with the benthic seascape were modeled in one area using Boosted Regression Trees. These models were validated in a second area to test their predictive performance in locations where fish have not been mapped. Models predicting the density of large fish (≥ 29 cm) performed well (i.e., AUC = 0.77). Water depth and standard deviation of depth were the most influential predictors at two spatial scales (100 and 300 m). Models of small (≤ 11 cm) and medium (12-28 cm) fish performed poorly (i.e., AUC = 0.49 to 0.68) due to the high prevalence (45-79%) of smaller fish in both locations, and the unequal prevalence of smaller fish in the training and validation areas. Integrating acoustic sensors with spatial modeling offers a new and reliable approach to rapidly identify fish aggregations and to predict the density large fish in un-surveyed locations. This integrative approach will help coastal managers to prioritize sites, and focus their limited resources on areas that may be of higher conservation value.