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The concept of dominance is frequently used to describe changes in rapidly reconfiguring ecosystems, but the definition of dominance can vary widely among studies. Using coral reefs as a model, we use extensive benthic composition data to explore how variability in applying dominance concepts can shape perceptions. We reveal that coral dominance is sensitive to the exclusion of key algal groups and the categorization of other benthic groups, with ramifications for detecting an ecosystem phase shift. For example, ignoring algal turf inflates the dominance of hard and soft corals in the benthic habitats underpinning reef ecosystems. We need a consensus on how dominance concepts are applied so that we can build a more comprehensive understanding of ecosystem shifts across a broad range of aquatic and terrestrial settings. For reefs, we highlight the benefits of comprehensive and inclusive surveys for evaluating and managing the altered ecosystem states that are emerging in the Anthropocene.

Coral reefs are highly productive ecosystems, in part due to the productivity of planktivorous fishes. The planktivorous fish community contains two distinct groups which target either the gelatinous or the non-gelatinous fractions of the incoming zooplankton. However, the nutritional value of these prey fractions and, consequently, their potential contribution to planktivorous fish productivity are poorly understood. We explored the zooplankton fractions potential contribution to planktivorous fish productivity (our function of interest), by quantifying the nutritional content a key trait of the gelatinous and non-gelatinous prey fractions which are accessible to reef-associated diurnal planktivores. By combining vertical plankton tows with stoichiometric analyses, we found that the three zooplankton community fractions—gelatinous, > 2 mm non-gelatinous and −2 to our study reef over a flood tide was then estimated. The abundant −2 (median: 0.88 gN m−2 6 h−1), which was estimated to be one to two orders of magnitude greater than the delivery from the > 2 mm non-gelatinous (0.06 gN) and gelatinous (0.03 gN) communities, respectively. Overall, our results highlight the quality of both gelatinous and non-gelatinous zooplankton as prey for planktivorous fishes, emphasizing the potential importance of the often-overlooked gelatinous fraction.

Seascape connectivity can facilitate key ecosystem functions in complex ecosystems like coral reefs. Many reef fishes move across the seascape, bridging different ecosystems. However, their role in shaping important functions, such as biomass production and nutrient cycling, is still poorly understood. This study, therefore, assesses the extent of natural movements of cardinalfishes (Apogonidae), one of the major contributors to nocturnal fish biomass production with the potential for a major role in transferring energy and nutrients between sandy ecosystems and adjacent coral reefs. Consistent with previous work, showing their ability to move distances of 100 s to 1000 s of metres when displaced, we reveal that these small fishes undergo major voluntary nocturnal foraging forays extending up to at least 145 m from reef structures. Their estimated daily movement distances are at least 430 times greater than expected based solely on body size-home range expectations. Given their large travel distances and strong homing abilities, apogonids may provide a major conduit for material transfer between lagoonal soft sediment habitats and adjacent coral reefs. These results highlight the potential importance of apogonids in the cross-system or cross-habitat transport of energy and nutrients on coral reefs.

An organism's colouration is often linked to the environment in which it lives. The fishes that inhabit coral reefs are extremely diverse in colouration, but the specific environmental factors that support this extreme diversity remain unclear. Interestingly, much of the aesthetic and intrinsic value humans place on coral reefs (a core ecosystem service they provide) is based on this extreme diversity of colours. However, like many processes on coral reefs, the relationship between colouration and the environment is likely to be impacted by global environmental change. Using a novel community-level measure of fish colouration, as perceived by humans, we explore the potential links between fish community colouration and the environment. We then asked if this relationship is impacted by human-induced environmental disturbances, e.g. mass coral bleaching events, using a community-level dataset spanning 27 years on the Great Barrier Reef. We found that the diversity of colours found within a fish community is directly related to the composition of the local environment. Areas with a higher cover of structurally complex corals contained fish species with more diverse and brighter colourations. Most notably, fish community colouration contracted significantly in the years following the 1998 global coral bleaching event. Fishes with colouration directly appealing to human aesthetics are becoming increasingly rare, with the potential for marked declines in the perceived colour of reef fish communities in the near future. Future reefs may not be the colourful ecosystems we recognize today, representing the loss of a culturally significant ecosystem service.

Nearly a billion people depend on tropical seascapes. The need to ensure sustainable use of these vital areas is recognised, as one of 17 policy commitments made by world leaders, in Sustainable Development Goal (SDG) 14 (‘Life below Water’) of the United Nations. SDG 14 seeks to secure marine sustainability by 2030. In a time of increasing social-ecological unpredictability and risk, scientists and policymakers working towards SDG 14 in the Asia–Pacific region need to know: (1) How are seascapes changing? (2) What can global society do about these changes? and (3) How can science and society together achieve sustainable seascape futures? Through a horizon scan, we identified nine emerging research priorities that clarify potential research contributions to marine sustainability in locations with high coral reef abundance. They include research on seascape geological and biological evolution and adaptation; elucidating drivers and mechanisms of change; understanding how seascape functions and services are produced, and how people depend on them; costs, benefits, and trade-offs to people in changing seascapes; improving seascape technologies and practices; learning to govern and manage seascapes for all; sustainable use, justice, and human well-being; bridging communities and epistemologies for innovative, equitable, and scale-crossing solutions; and informing resilient seascape futures through modelling and synthesis. Researchers can contribute to the sustainability of tropical seascapes by co-developing transdisciplinary understandings of people and ecosystems, emphasising the importance of equity and justice, and improving knowledge of key cross-scale and cross-level processes, feedbacks, and thresholds.

Herbivorous fishes are a key functional group in coral reef ecosystems and have been the focus of a vast body of research. While substantial progress has been made in research, challenges persist, especially in respect to quantifying patterns versus processes. Despite this challenge being recognised over 40 years ago. To help clarify such challenges, and work towards solutions, in this perspective we explore how the definition of ‘herbivorous reef fishes’ precludes an easy translation between patterns of herbivore abundance and the process of herbivory. Indeed, if herbivorous fishes are defined as, a fish in which the diet is predominantly based on plant material, then this encompasses a diverse suite of fishes which all remove primary producers to varying extents and have markedly different impacts on reef functioning. Given this situation, we explore how our approaches to directly quantifying herbivory on reefs have progressed. We highlight how lessons learnt from macroalgal assays could be applied to the direct quantification of herbivory from algal turfs in the epilithic algal matrix (EAM); a community of primary producers that are invariably difficult to work with and quantify. Nevertheless, given the abundance of turfs on coral reefs, and their relative importance in herbivore dynamics, widespread process-based assessment of EAM herbivory represents an avenue for expanding future research. Recognising the difficulty of translating patterns in herbivore abundance to the process of herbivory, and an enhanced focus on EAM herbivory, will be necessary to comprehensively quantify the process of herbivory on Anthropocene coral reefs.

Cryptobenthic fishes are abundant on coral reefs, and their larvae dominate the ichthyoplankton in near reef waters. However, we have a limited understanding of how pelagic and on-reef processes are linked, especially how late-stage cryptobenthic fish larvae use near reef waters. We therefore used depth-stratified light trap sampling from 2 to 27 m at Lizard Island, Great Barrier Reef. This revealed clear depth variation in late-stage larval fish assemblages. Gobiidae larvae characterised mid-depth (13 m) samples. By contrast, larval Apogonidae were only abundant in shallow samples. Deep samples were typified by (non-target) adult apogonids. Contrary to expectations that poor-swimming cryptobenthic larvae would be flow-sheltering in deeper water, our results suggest that late-stage cryptobenthic larvae use large portions of the water column, although their preferred positions may be taxon-specific.

The Great Barrier Reef (GBR)—the largest coral reef ecosystem in the world—supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space—a 100-m2 coral reef ecosystem—suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes—characterized by small body sizes and short life spans—exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.

Planktivorous reef-associated fishes provide a significant nutrient input to the reef, linking pelagic and reef environments. Highly mobile and relatively large body-sized fusiliers (Lutjanidae) often dominate reef fish biomass, but their role in ecosystem processes is poorly understood. We therefore combined fish counts and behavioural observations at Lizard Island, Great Barrier Reef, to investigate: (1) the spatial distribution and biology of fusiliers on a lagoonal coral reef system, and (2) how does fusilier behaviour and size distribution change from exposed to sheltered locations. We found higher abundances of large-sized fusiliers (≥ 20 cm total length) on exposed reef sites. Sheltered sites had almost exclusively small individuals (

During the excavation of Mayan tombs, little did the archaeologists know that the fossils they discovered in the tomb stones would fundamentally alter our understanding of the earliest origins of coral reef fishes. Located just 500 kilometers from the point where an asteroid impact reconfigured the world's biological systems 66 million years ago, we find the earliest origins of three typical reef fish groups. Their presence in Mexico just 3 million years after this impact finally reconciles the conflict between the fossil and phylogenetic evidence for the earliest origins of reef fishes. The incorporation of these fossils into a global reconstruction of fish evolutionary history reveals a new picture of the early biogeography of reef fishes, with strong Atlantic links. From locations associated with biological destruction and societal collapse, we see evidence of the origins of one of the world's most diverse and spectacular marine ecosystems: coral reefs.

Black and white or fleur-de-lis high comb morions are distinctive helmets of the late 16th century and early 17th century. We constructed a typology of black and white high comb morions, identifyin...

Efforts to understand and protect ecosystem functioning have put considerable emphasis on classifying species according to the functions they perform. However, coarse classifications based on diet or feeding mode often oversimplify species' contributions to ecological processes. Behavioral variation among superficially similar species is easily missed but could indicate important differences in competitive interactions and the spatial scale at which species deliver their functions. To test the extent to which behavior can vary within existing functional classifications, we investigate the diversity of foraging movements in three herbivorous coral reef fishes across two functional groups. We find significant variation in foraging movements and spatial scales of operation between species, both within and across existing functional groups. Specifically, we show that movements and space use range from low frequency foraging bouts separated by short distances and tight turns across a small area, to high frequency, far‐ranging forays separated by wide sweeping turns. Overall, we add to the burgeoning evidence that nuanced behavioral differences can underpin considerable complementarity within existing functional classifications, and that species assemblages may be considerably less redundant than previously thought., Broad functional groupings may mask important behavioral nuances that could affect competitive interactions and the spatial scale at which species deliver their functions. We find considerable variation in foraging patterns and spatial scales of operation both within and across traditional functional groups (grazers and scrapers). This highlights substantial complementarity within the grazer group, indicating that together these species may contribute more strongly to algal grazing than any could alone.

As habitats change, highly specialised species may die or be forced to relocate. However, some obligate coral-dwelling damselfishes appear to survive the localized extinction of their primary habitat, branching coral, caused by coral bleaching. To address this apparent paradox, we documented the spatial behaviour of obligate coral-dwellers in relation to habitat quality. Focussing on two obligate coral-dwelling damselfishes (Pomacentrus moluccensis and Chromis viridis), we used KUDs (Kernel Utilisation Distributions) to quantify fishes’ short-term space use (daily 5 min observations across 6 days) and related it to live coral cover and structural complexity derived from 3D photogrammetry. Specifically, we calculated movement extent (95% KUD), core areas (50% KUD) and the temporal consistency of occupied areas across consecutive days. Structural complexity had no effect on space use. The effect of live coral cover was significant but weak and dependent on fish body-size: core areas increased with decreasing live coral cover for large fishes; smaller fishes showed little response. In contrast to weak habitat effects, there were strong differences across sites. At one site, average core areas increased three-fold to 1.1 m2 for P. moluccensis and over 60-fold for C. viridis, from 1.14 m2 to an average core area of 92.34 m2 and a maximum recorded extent of 1471.4 m2. These findings may help explain these fishes’ apparent, unexpected resilience to habitat loss. Obligate coral-dwelling fishes may prefer branching live coral, but their ‘obligate’ dependence may be more flexible and context dependent. As ecosystems reconfigure, plasticity in fine-scale spatial behaviour may be critical for the persistence of fish populations.

Sediments are ubiquitous on coral reefs. However, studies of reef sediments have largely focused on isolated reservoirs, or processes, and rarely consider hydrodynamic drivers. We therefore provide a quantitative snapshot of sediment dynamics on a coral reef. Across a depth profile, we simultaneously examined: suspended sediments, sediment deposition and accumulation, and hydrodynamic and biological movement processes. We reveal the marked potential for the water column to deliver sediments. Currents carried 12.6 t of sediment over the 2,314 m

Traits are measurable features of organisms. Functional traits aspire to more. They quantify an organism's ecology and, ultimately, predict ecosystem functions based on local communities. Such predictions are useful, but only if 'functional' really means 'ecologically relevant'. Unfortunately, many 'functional' traits seem to be characterized primarily by availability and implied importance - not by their ecological information content. Better traits are needed, but a prevailing trend is to 'functionalize' existing traits. The key may be to invert the process, that is, to identify functions of interest first and then identify traits as quantifiable proxies. We propose two distinct, yet complementary, perspectives on traits and provide a 'taxonomy of traits', a conceptual compass to navigate the diverse applications of traits in ecology.

The Great Barrier Reef (GBR) – the largest coral reef ecosystem in the world – supports over 1200 fish species with some of the highest population densities and diversities seen in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. However, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of 61 reef fish species. This identified a total of 132 viruses, 38 of which were vertebrate-associated and therefore likely infecting the fish, including a novel isolate of Santee-cooper ranavirus (Iridoviridae). Notably, we found little evidence for virus transmission between fish species living within a very restricted geographical space – a 100 m2 coral reef ecosystem – suggesting that there might be important host genetic barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition between reef fish families, such that cryptobenthic reef fishes – characterized by small body sizes and short life-spans – exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species transmission, and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.

Cryptobenthic reef fishes (small, camouflaged, benthic-dwelling fishes) face exceptionally high mortality rates, yet they are the most abundant fishes on coral reefs. To maintain local adult populations in the face of these mortality rates, larval cryptobenthics may have adaptations that limit dispersal. However, the basis for this larval retention is unknown. Here, we compared the body shapes of adult and larval cryptobenthics with those of adult and larval large reef fishes to explore how morphological adaptations may enable cryptobenthic larvae to stay near their natal reefs. We found that while adults and larvae of large reef fishes and adult cryptobenthics display different ‘average’ morphological characteristics (i.e. different locations of the morphospace centroid), they all display a similar range of body shapes (i.e. similar morphospace sizes around their centroids). Larval cryptobenthics, however, exhibit a greatly constrained range of morphologies (occupying less than 20% of the morphospace of any other category). Larval cryptobenthics appear to be limited to a simple body plan, with elongate bodies and small fins. This simple body shape is likely to result in relatively poor swimming abilities, which may limit the ability of cryptobenthic larvae to maintain their position against prevailing currents in the pelagic zone. As such, limited dispersal in cryptobenthic larvae is likely to depend upon behavioural adaptations, such as flow-refuging, to avoid being washed away from their natal reefs.

In complex, diverse ecosystems, one is faced with an exceptionally challenging decision: which species to examine first and why? This raises the question: Is there evidence of subconscious biases in study species selection? Likewise, is there evidence of this bias in selecting methods, locations, and times? We addressed these questions by surveying the literature on the most diverse group of vertebrates (fishes) in an iconic high-diversity ecosystem (coral reefs). The evidence suggests that we select study species that are predominantly yellow. Reef fish studies also selectively examine fishes that are behaviorally bold and in warm, calm, attractive locations. Our findings call for a reevaluation of study species selection and methodological approaches, recognizing the potential for subconscious biases to drive selection for species that are attractive rather than important and for methods that give only a partial view of ecosystems. Given the challenges faced by high-diversity ecosystems, we may need to question our decision-making processes.

Coral reefs provide major nutritional inputs to humans through fish production. Yet, our capacity to adequately assess fish productivity in these and other high-diversity aquatic systems is hampered by a lack of computationally accessible methods with realistic data requirements. Standing stock biomass is often assumed to reflect biomass productivity, yet theoretical and empirical evidence question this assumption. These methodological hurdles have stymied progress in managing this critical coral reef function, potentially jeopardising the future of many small-scale tropical fisheries struggling to respond to global changes. Here, we summarise the physiological and ecological processes that lead to the production of fish biomass. We outline principles and present a robust framework for quantifying fish productivity in high-diversity ecosystems that overcomes these shortcomings by integrating readily accessible individual-level data (e.g. from visual counts) with growth trajectories and predicted mortality rates. This framework provides fisheries-independent estimates of multispecies fish productivity without the need to specify often unknown detailed trophic relationships. We delineate five simple steps and provide a critical user-friendly interface (an easy-to-use R package) to make the calculation of fish productivity a readily accessible tool for coral reef scientists and managers.

Australian Research Council; Lizard Island Reef Research Foundation, Grant/Award Number: Lizard Island Doctoral Fellowships to RAM and CJF; James Cook Univeristy, Grant/Award Number: James Cook University Postgraduate Research Schola

The feeding apparatus directly influences a species' trophic ecology. In fishes, our understanding of feeding modes is largely derived from studies of rigid structures (i.e. bones, teeth, gill rakers). A recently described lip innovation, however, highlighted the role of soft anatomy in enabling specialized feeding modes. In this study, we explore whether similar diversification may also occur in the soft anatomy of the buccal cavity. Using four key anatomical traits to classify 19 species (14 genera) of wrasses, we evaluated the relationship between anatomical specialization of the buccal cavity and diet. Our data revealed a previously undocumented anatomical adaptation in the mouths of fairy wrasses (Cirrhilabrus): the mucosa throughout the buccal cavity (i.e. anterior to the pharynx) is packed with goblet cells, enabling it to secrete large quantities of mucus in this region; a new trait that, until now, had not been documented in wrasses. This disparity reflects diet differences, with mucus secretion found only in planktivorous Cirrhilabrus that feed predominantly on amorphous organic material (potentially gelatinous organisms). This suggests a cryptic mucus-based resource partitioning in planktivorous wrasses.

Algal turfs are the most abundant benthic covering on reefs in many shallow-water marine ecosystems. The particulates and sediments bound within algal turfs can influence a multitude of functions within these ecosystems. Despite the global abundance and importance of algal turfs, comparison of algal turf-bound sediments is problematic due to a lack of standardisation across collection methods. Here we provide an overview of three methods (vacuum sampling, airlift sampling, and TurfPods), and the necessary equipment (including construction suggestions), commonly employed to quantify sediments from algal turfs. We review the purposes of these methods (e.g. quantification of standing stock versus net accumulation) and how methods can vary depending on the research question or monitoring protocol. By providing these details in a readily accessible format we hope to encourage a standardised set of approaches for marine benthic ecologists, geologists and managers, that facilitates further quantification and global comparisons of algal turf sediments.

Sediments in algal turfs can modify a wide variety of key ecological processes on coral reefs. While some larger reef fishes can remove these turf-bound sediments, the role of small, yet abundant, cryptobenthic fishes is currently unclear. To address this knowledge gap, we explored the extent to which the blenny, Ecsenius stictus, can shape sediment dynamics on coral reefs by quantifying their sediment ingestion and space use. Per unit body mass, E. stictus process sediments at comparable rates to key parrotfish and surgeonfish species. However, in absolute terms, E. stictus has a negligible influence on net sediment dynamics, despite their abundance. Behavioural observations and 3D photogrammetry reveal that E. stictus preferentially feed and rest on elevated surfaces; potentially because of low sediment loads on these surfaces. Overall, E. stictus may be responding to sediment loads rather than manipulating them; it is a passenger rather than a driver in reef processes.