Functional diversity patterns have been thoroughly described for reef fishes across geographic gradients, but the effect of depth on these patterns remains largely unknown. Using diet, life-history, and behavioral traits, we evaluated the functional diversity of Caribbean reef-fishes from the surface to 450 m depth to test if taxonomically distinct communities along the reef slope are characterized by similar or distinct ecological traits. Core ecological traits found in shallow reef-fish communities were conserved in the upper section of deep reefs (i.e., mesophotic zone) across three taxonomically distinct assemblages. By contrast, the deepest reef communities (i.e., rariphotic zone) displayed a distinct functional structure, mainly driven by trait loss. Functional redundancy was highest in the deepest reef communities and was generated by intrageneric diversification and functional convergence across phylogenetic lineages. The decrease in functional richness and divergence combined with an increase in functional redundancy suggest that environmental filtering is the dominant evolutionary constraint shaping the functional diversity of deep-reef fishes.

Unravelling food web dynamics across biological communities is a central goal of ecology. In size-structured ecosystems, the shape of trophic pyramids is often inferred from their size spectra-the distribution of biomass across body-mass classes. Size-spectrum analysis has become a popular tool to study ecosystem functioning in aquatic ecosystems, including coral reefs. However, the key assumption behind size spectra, that body size directly and positively correlates with trophic position, has rarely been evaluated in these systems. Here, we test this assumption by quantifying body mass, population densities and estimating trophic position from stable isotopes for 325 fish species across four Indo-Pacific locations. Consistent with prior studies, we found a positive relationship between biomass and body mass. However, weak and variable relationships between body mass and trophic position led to higher biomass in primary consumers than in predators, as expected in traditional bottom-heavy or diamond-shaped trophic structures. Our findings thus challenge previous reports of coral reef fish biomass prevalence in higher trophic levels (e.g. inverted biomass pyramids), supporting earlier suggestions that simple size-spectrum models do not adequately represent the trophic structure of reef fish communities.

Abstract The metabolic processes sustaining coral reefs, from carbonate and primary production to secondary production, remain poorly integrated and rarely quantified simultaneously at global scales. This hampers our ability to predict global responses to accelerating human pressures and manage coral reef functioning. Using metabolic scaling and bioenergetic models applied to surveys from 1,100 reefs worldwide, we provide a global, standardized quantification of 14 ecosystem functions spanning benthic (corals and algae) and fish communities. Our analysis reveals a continuous functional spectrum of global coral reefs organized along four dominant axes: 1) primary production, 2) calcification and habitat structure, 3) secondary biomass production and consumption, and 4) biomass turnover. Functions mediated by fish and benthic communities show weak associations at the global scale rather than tight coupling. Climate stressors reduced calcification and local human impacts lowered secondary production. Yet these directional effects unfolded against a backdrop of substantial natural variability in reef functional configurations, such that heavily and minimally impacted reefs overlap substantially in the global functional space. Temporal analyses across three representative reef systems further revealed that functional trajectories following disturbance are context-dependent, with no universal pattern of recovery across locations. This continuous and context-dependent functional spectrum challenges the notion of universal functional benchmarks and supports locally tailored conservation strategies.

Biogenic structural complexity is a key driver of biodiversity and ecosystem functioning, yet its ecological and environmental determinants remain poorly understood across broad biogeographic scales. Here, we conducted standardized 90-day field experiments at 16 coastal sites, spanning a 41-degree latitudinal gradient, using naturally assembled marine fouling communities on settlement panels. We measured rugosity as our metric of biogenic structural complexity and modeled its relationship with species richness, community composition, community growth rates, and abiotic conditions (salinity and temperature). Species richness increased with temperature and salinity and declined with latitude, with more diverse communities exhibiting greater biogenic complexity due to increased morphological variation. At high-latitude sites, low-diversity communities dominated by arborescent bryozoans also had increased complexity. Structural equation models showed that abiotic conditions influenced growth and composition, which in turn shaped complexity. Warmer, saltier sites promoted richness-driven complexity, while colder conditions favored structurally important dominant taxa. We found that biodiversity is important not only as a beneficiary of complexity but also as a contributor to complexity itself within fouling communities. Our results also demonstrate that both species richness and functional group identity regulate biogenic complexity across environmental gradients, underscoring biodiversity's role in supporting ecosystem structure and resilience in the face of increasing global change. Understanding these relationships is essential for biodiversity conservation and the management of marine ecosystems facing increasing anthropogenic pressures.

Abstract Predation is a critical ecosystem process that shapes the structure and functioning of biological communities. However, due to its intermittent nature, fast pace and general unpredictability, predation is difficult to observe and quantify. Therefore, we commonly rely on indirect metrics or proxies of predation, which reflect the outcome of predation events but do not allow for inference about the predator's decision‐making process or predation rates. In terrestrial ecosystems, lifelike prey replicas have allowed ecologists to gain a broad understanding of predator choice, predation intensity and their drivers. Yet in aquatic ecosystems, few scalable, interactive predation assays have been developed. We introduce Goby Gummies, a customizable, edible prey model developed for aquatic ecology. Gummies are constructed using an inert, edible medium that can be cast into any desired shape (in our case, a goby fish), dyed various colours and supplemented with edible material to introduce variation in nutritional profiles. As such, goby gummies are a cheap, sustainable, high‐throughput assay that can be tailored to a variety of aquatic ecosystems. We performed two pilot studies to test goby gummies in a natural setting on coral reefs in Belize during which gummies were reliably consumed by a range of predatory fishes. First, we show that gummies supplemented with fishmeal were preferred by predators over agar‐only gummies, but the strength of this preference was dependent on their coloration, suggesting an intriguing interplay between external appearance and internal composition. Second, we compared fish‐supplemented gummies to squidpops, a previously developed predation assay for marine systems. Goby gummies were consumed first more frequently and eaten at quicker rates than squidpops and consistently attracted carnivorous predators, whereas squidpops were frequently consumed by herbivorous parrotfishes. Our results highlight that goby gummies provide a new predation assay tool in aquatic ecosystems that permits the exploration of many exciting questions surrounding prey and predator traits and their interplay. We envision goby gummies to kindle a diverse range of impactful studies across disciplines that mirror those conducted in terrestrial ecosystems.

Nutrients moving across ecosystems can propagate through food webs via distinct trophic pathways. Their integration into food webs is often mediated by small, abundant taxa that channel subsidies from primary producers to higher trophic levels. On coral reefs, cryptobenthic fishes and invertebrates can fill these roles, yet their responses to allochthonous nutrients are poorly understood. We compared cryptofaunal communities and associated trophic dynamics across nutrient-rich islands with intact seabird populations and nutrient-poor rat-infested islands in the Chagos Archipelago, Indian Ocean. Specifically, we evaluated how the presence of seabird colonies influenced cryptofaunal nutrient assimilation, biomass, structure, and isotopic niche dynamics, and how these shifts propagated to mesopredators and higher order piscivorous and invertivorous fishes. Most cryptobenthic fishes and some invertebrates showed nutrient enrichment near seabird colonies. Although the isotopic niches of cryptobenthic fishes and invertebrates overlapped, niche widths diverged in nutrient-rich environments, with invertebrates exhibiting broader niches and cryptobenthic fishes remaining comparatively constrained, reflecting differential access to shared resources. Mixing models also reflected a shift toward cryptobenthic fishes in the diet of a mixed carnivore near seabird colonies. Community patterns revealed strong asymmetries: Nutrient-rich reefs supported twice the amount of cryptobenthic fish biomass and a 10-fold increase in larger piscivorous fish productivity, while reefs near rat-infested islands were characterized by relatively greater cryptic invertebrate biomass and higher invertivore productivity. Taken together, these results suggest that cryptobenthic fishes' capacity to capitalize on seabird nutrients may allow them to exert competitive dominance and top-down control over invertebrates in nutrient-rich environments, thereby amplifying piscivorous pathways, while nutrient-poor environments appear to favor invertebrates and their consumers. Rather than reflecting uniform biomass loss under rat invasion, these patterns indicate a shift in trophic routing from fish-mediated to invertebrate-mediated energy channels. Our findings demonstrate that cross-ecosystem nutrient vectors do not simply enhance reef productivity but reorganize trophic structure. Therefore, invasive species that sever these linkages can drive the emergence of alternative food-web configurations with distinct energetic pathways.

Life on Earth has evolved into a staggering diversity of species, most of which still remain undiscovered, unrecognized, or unmonitored. As our ocean's richest biodiversity hotspot, coral reefs harbor more than one third of marine biodiversity, but many reef species are small and cryptic and, therefore, difficult to identify and study. Among these, tiny bottom-dwelling ('cryptobenthic') fishes have been highlighted as a highly diverse (>3,000 species), understudied, and ecologically important group. However, the classification and monitoring of these fishes depend almost exclusively on the knowledge of few expert scientists, which has resulted in limited knowledge concerning the taxonomy, distribution, and population trends of these fishes. Deep learning-driven image classification-known for its ability to learn complex patterns in visual data-is an ideal candidate for automating taxonomic image classification and therefore broaden participation in ecological monitoring and biodiversity science. We developed CryptoVision, a new taxonomy-aware convolutional neural network with three output heads that explicitly considers taxonomic hierarchies (family, genus, species) and their biological constraints. Built on ResNet50v2 and enhanced with Squeeze-and-Excitation modules, CryptoVision employs a custom taxonomy-focal cross-entropy loss and four hierarchical fusion strategies (standard, concatenation, gating, attention) to assess the algorithm's performance. Trained on a unique dataset of ~7,600 laboratory-standard and ~18,800 web-sourced images covering 113 species of small reef fishes, our tool highlights the power of integrating deep learning with innovative, taxonomically-informed design and high-resolution imagery. Indeed, CryptoVision achieved a ~ 25% improvement across all metrics when lab-standard imagery was incorporated and among the fusion variants, the gating approach delivered the best calibration (expected calibration error ≈ 0.01) and 90.5% average precision. Finally, guided saliency map analyses of species in the dwarfgoby genus Eviota illustrate that model attention can align with expert-defined morphological traits that represent critical features for species delimitation. Our results demonstrate that taxonomy-aware, multi-output deep learning on curated imagery provides a robust, interpretable framework for scalable biodiversity monitoring, ecological research, and streamlined taxonomic workflows that is particularly well-suited for the many taxa that are typically understudied due to their small size, cryptic nature, or ambiguous taxonomy.

Cross-ecosystem nutrient transfer can enhance coral reef functioning in an otherwise oligotrophic environment. While the influence of seabird-derived nutrients on coral reef organisms is increasingly recognized, how they are integrated into reef food webs remains unclear. Cryptobenthic reef fishes are crucial for energy transfer on coral reefs, and their fast life histories imply that they respond strongly to seabird-derived nutrients. Here, we investigate how variation in nearshore seabird nutrient subsidies affects coral reef fish communities. By comparing fish communities across locations differing in seabird nutrient inputs and using stable isotope analysis, we explore nutrient integration across depth, their influence on cryptobenthic and associated larger reef fishes and investigated the relative reliance of cryptobenthic fishes on seabird-enriched benthic and non-enriched pelagic pathways. We find that, near seabird colonies, cryptobenthic fishes' diets can transition from pelagic to benthic dominance; cryptobenthic fish communities are larger; herbivores and all feeding groups comprising potential cryptobenthic fish predators have higher biomass. Collectively, our results stress the importance of seabirds in shaping energy pathways and suggest that, even in dynamic, ocean-swept reef systems, cryptobenthic fishes can mobilize seabird subsidies and potentially act as a nutritional bridge to higher trophic levels.

Understanding how humans have altered coral reef food webs remains challenging due to the absence of prehistoric baselines. Here, we use fish remains preserved in fossil and archaeological deposits from Panamá and the Dominican Republic to explore how Caribbean reef fish mortality patterns have changed over millennia. By quantifying accumulation rates of shark dermal denticles (scales) and bony fish otoliths (ear stones) in reef sediments, we assess relative fish abundance, while otolith size serves as a proxy for body size at death. Comparisons of these death assemblages suggest a 75% decline in shark-derived material and a 22% reduction in the sizes of human-targeted fishes—consistent with historical exploitation. This evidence of decline in large-bodied, higher trophic level fish remains coincided with a doubling in prey fish otolith accumulation and a 17% increase in their reconstructed body sizes. These patterns in time-averaged death assemblages align with effects of release from predation, documenting an often assumed (but rarely shown) cascading effect. In contrast, otoliths of predator-sheltered cryptobenthic fishes showed no change in either accumulation or size, suggesting that ‘‘bottom–up”environmental factors were not responsible for the observed changes. Together, these data indicate that pre-exploitation predator communities strongly controlled exposed prey fishes, but this “top–down” effect diminishes rapidly toward the food chain base, especially in predator-resistant groups. Understanding trophic cascades on Caribbean reefs requires studying systems before predator depletion.

Local habitat availability can strongly affect animal communities. On coral reefs, the biodiversity of small, bottom-dwelling (‘cryptobenthic’) reef fishes and drivers of their community assembly have yet to be explored in many locations. Here, we investigate how local and regional factors shape the structure and composition of cryptobenthic reef fish communities in the Veracruz Reef System National Park (VRS) in the Gulf of Mexico (GoM). Focusing on five reefs in the VRS, we surveyed cryptobenthic reef fish communities at scales of reef outcrops ( 3–5 m2) and isolated microhabitats, while also quantifying the benthic composition of each reef to determine microhabitat availability. We found no significant differences in species richness or abundance across park regions and reef zones, but community composition differed qualitatively across reef zones. Furthermore, we discovered strong differences in cryptobenthic reef fishes’ preferences for various microhabitats, which are likely to drive community assembly and provide evidence for species-specific vulnerabilities to reef degradation. Caves harbored the highest biodiversity and abundance of cryptobenthic fishes, while gorgonian soft corals and algae supported the fewest species and individuals. The endemic gobies Tigrigobius redimiculus and Elacatinus jarocho both showed high abundance and occurrence but displayed opposite patterns of microhabitat specialization; T. redimiculus was categorized as a microhabitat generalist, while E. jarocho was revealed as a cave-dwelling specialist species. Overall, our quantitative exploration of the cryptobenthic reef fish community in the southwest GoM provides a crucial baseline for habitat and biodiversity monitoring in the region and highlights E. jarocho as an emblematic, endemic indicator species that will be vulnerable to extinction if further reduction of habitat complexity occurs.

Biogeochemical fluxes through ecological communities underpin the functioning of ecosystems worldwide. These fluxes are often heavily influenced by small-bodied consumers, such as insects, worms, mollusks, or small vertebrates, which transfer energy and nutrients from autotrophic sources to larger animals. Although coral reefs are one of the most productive ecosystems in the world, we know relatively little about how small consumers make energy available to larger predators and how their roles may vary across reefs. Here, we use community-scale collections of small, bottom-dwelling ("cryptobenthic") reef fishes along with size spectrum analyses, stable isotopes, and demographic modeling to examine their role in harnessing and transferring carbon in two distinct coral reef habitats. Using a comprehensive dataset from Mo'orea (French Polynesia), we demonstrate that, despite only being separated by a narrow reef crest, forereef and backreef habitats harbor distinct communities of cryptobenthic fishes that play vastly divergent roles in carbon transfer. Forereef communities in Mo'orea are depauperate, largely consisting of predatory and planktivorous species that have comparatively high standing biomass (both individually and collectively). In these communities, the combination of size spectra and isotope values suggests important contributions of pelagic subsidies, but the rate of biomass production and turnover (i.e., the rate at which biomass is replenished) is relatively low. In contrast, cryptobenthic fish communities in the backreef are characterized by high abundances of the smallest bodied species, forming a traditional bottom-heavy trophic pyramid that is fueled by benthic autotrophs. In these communities, benthic productivity fuels rapid production and turnover of fish biomass, while pelagic energy channels are notably less productive. Our integrative approach demonstrates the utility of combining multiple methods (e.g., isotopically informed demographic models) to trace energy fluxes through small consumer communities in complex ecosystems. Furthermore, our results highlight that coral reef productivity dynamics are highly habitat-dependent and the role of the smallest coral reef consumers may be most pronounced in shallow systems with limited connectivity to the open ocean.

Introductions of nonnative species are known to negatively impact coral reef ecosystems. The planktivorous Indo-Pacific damselfish Neopomacentrus cyanomos has spread throughout the Gulf of Mexico (GoM) over the past decade. However, its population dynamics and potential adverse effects on native reef-fish communities have not been assessed. Here, we examined temporal change in the occurrence, density, and social-group size of N. cyanomos on reefs in the southern GoM and assessed its possible impact on native species by (i) modeling the occurrence and densities of N. cyanomos and syntopic native fish species and (ii) evaluating differences in the species composition of the broader reef-fish community on the Veracruz reef system (PNSAV) before and after N. cyanomos established there. Neopomacentrus cyanomos became more widely dispersed and abundant on PNSAV reefs from 2014 to 2021. Between 2006 and 2013 seven native fishes (four planktivores and three nonplanktivores) on PNSAV reefs experienced varying population trends. However, from 2014 onwards, populations of those seven species declined, although the 162-species PNSAV reef-fish community did not exhibit notable shifts in species composition. Our results indicate that while N. cyanomos has become an increasingly common inhabitant of reefs in the southwestern GoM, it has had no measurable impact on native planktivorous fishes. Instead, changes in the populations of native species are likely related to the increasing habitat degradation of reefs immediately adjacent to a large city experiencing expanding industrial development. Detailed and mechanistic explorations are required to determine if N. cyanomos has negative ecological effects on wider Caribbean reefs.

In the past 20 years, there has been a sharp rise in the establishment of coral reef restoration programs, which generally aim to restore key services provided by healthy, natural reefs. However, the effect of restoration on arguably more important metrics related to ecosystem functioning is rarely considered, with most programs focusing their monitoring on static variables (e.g. coral cover) only. With crucial metrics related to ecosystem functioning left largely unmonitored, it is difficult to assess the outcomes of reef restoration through a truly ecological lens. We therefore propose that ecosystem functioning should be placed at the forefront of reef restoration, and suggest the following focus points for improvements in the field: (1) Implement a set of standardized methods to monitor key functional processes on restored reefs (and neighboring natural reefs), (2) better understand how reef restoration will support ecosystem functioning in a changing ocean, and the identity of organisms that carry most of the "functionality load" on reefs, and (3) adopt a function-centric approach that implements techniques specifically targeted at protecting the respective species and processes of interest.

Animal body size distributions result from interactions of growth, mortality and recruitment. In ecology and fisheries science, theoretical models of fish body size distributions are widely used but rely on life-history parameters-growth coefficient (K) and natural mortality rate (M)-that remain unknown for most species and are challenging to estimate. Analysing data from underwater visual surveys and exhaustive sampling, representing 3068 populations across 797 species of shallow-water, mostly unfished marine fishes, we demonstrate that post-recruitment body length distributions exhibit a consistent unimodal shape across species and populations. When scaled to the mean body length, these distributions are strikingly similar across all teleost and elasmobranch species, with diverse life histories and maximum body sizes ranging from 1 cm to 3 m. Observed size structure can be approximated by a truncated normal distribution with a coefficient of variation of similar to 0.34 (SE = 0.002). Such consistent observed body size distributions could be aligned with Beverton-Holt population dynamics theory, if assuming an M/K ratio of similar to 1.5 and logistic observational selectivity with 50% detectability at similar to 40% of maximum body length. Alternatively, observed distributions could reflect deviations from theoretical expectations, and reconciling the unimodal distributions with theory may require relaxing some model assumptions, such as continuous recruitment, constant density-independent growth or constant natural mortality. Overall, the consistency of population- and species-level body length distributions means that unfished size structure could be predicted from a single body size parameter. It also suggests evolutionary convergence of diverse growth and mortality processes towards a narrow range of viable outcomes.

Coral reefs are frequently described as "oases in marine deserts" for thriving in nutrient-depleted oceans.1,2,3,4 This contrast is often termed "Darwin's paradox,"5,6,7,8 which allegedly originates from Charles Darwin's coral reef work.9 Decades of research exploring these paradoxical dynamics led to groundbreaking findings in ecophysiology,5,10 ecology,2,11 oceanography, and biogeochemistry.4,12,13 However, the historical foundations and scientific generality of the paradox remain unevaluated. Here, we demonstrate that Darwin's paradox is a misnomer. Indeed, the fundamental knowledge required to formulate this idea did not exist at the time of Darwin's 1842 coral reef treatise: its earliest references date, instead, to the 1940s-1950s. Given the frequent use of the term, and the "marine oasis" analogy, which implies high productivity despite nutrient-poor waters as a hallmark of reefs worldwide, we (1) compare reef productivity across ecosystems and (2) assess how globally widespread oligotrophic, low-nutrient reef conditions are. Our findings support earlier work placing coral reefs among the most productive ecosystems on Earth. However, relatively few coral reefs exist in oligotrophic waters; 80% of them occur in more productive mesotrophic and eutrophic conditions. Globally, median chlorophyll-a near reefs is 0.19 mg m-3, twice the median for tropical oceans and double the upper oligotrophic threshold. Reefs range across the tropical ocean spectrum of phosphate, nitrate, iron, and silicate concentrations but are disproportionally common in moderate levels of these vital nutrients. Thus, coral reefs as oases in marine deserts are not the norm, highlighting the need to recognize environmental variability and both intrinsic and extrinsic pathways sustaining reef productivity.

Coral reefs harbor 30% of oceanic biodiversity, but many species remain undiscovered. Indeed, coral reef taxonomic inventories are heavily skewed toward large, conspicuous organisms, leaving numerous smaller, cryptic species undescribed. Cryptobenthic reef fishes, such as gobies, can speciate rapidly due to short lifespans and limited dispersal, and ecological specialization may facilitate their diversification. Here, we examine whether habitat specialization correlates with genetic and phenotypic divergence in Risor ruber , a sponge-dwelling goby distributed across the western Atlantic Ocean. By integrating phylogenetic evidence, morphometrics, and network analysis, we identify seven distinct genetic lineages within Risor and reveal concordant patterns of Risor –sponge specialization. Despite the absence of lineage-specific morphologies, morphological traits are associated with sponge hosts, indicating high phenotypic plasticity within lineages. Two Risor lineages specialize on a single host sponge across the Caribbean, while five lineages are generalists. Finally, high modularity across Risor –sponge networks provides further evidence that ecological specialization contributes to Risor diversification. Given the rapid changes in coral reef benthic communities, habitat specialists are more likely to lose their primary habitat and face extinction. Documenting and understanding genetic diversification is imperative, especially in understudied, vulnerable organisms such as cryptobenthic reef fishes.

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

AimEcological state shifts that alter the structure and function of entire ecosystems are a concerning consequence of human impact. Yet, when, where and why discrete ecological states emerge remains difficult to predict and monitor, especially in high-diversity systems. We sought to quantify state shifts and their drivers through space and time in the most ecologically complex marine ecosystem: tropical coral reefs.LocationWorldwide.Time Period1987-2019.Major Taxa StudiedCoral reef communities.MethodsUsing a global dataset of 3375 coral reef surveys, along with 13 time series datasets ranging between 1987 and 2019, we applied a novel double-dichotomy approach to classify coral reefs into four simplified and discrete states based on the relative contributions of corals versus algae to benthic cover and small-bodied versus large-bodied fishes to fish standing stock. We then examined state shifts considering a range of spatial predictors and tested whether states have shifted directionally over time, and the nature of the most common transitions.ResultsWe show that geographic, environmental and anthropogenic context fundamentally shapes coral reef states at the local scale, which explains disparities among case studies, and stakes out critical baseline expectations for regional management efforts. We also reveal clear multi-decadal state shifts on coral reefs: over time, systems dominated by reef-building corals and small-bodied, planktivorous fishes tend to have been replaced with reefs characterised by algae and larger-bodied fishes.Main ConclusionsOur results suggest a previously unrecognised transition from systems that harness external subsidies through small-bodied consumers associated with structurally complex live corals, to herbivore-dominated systems with stronger bottom-up dynamics. Overall, the partitioning of complex reef ecosystems into a small suite of discrete ecological states suggests that spatial context-dependency, shifting baselines and changes in reef functioning are crucial considerations for coral reef management in the 21st century.

During ontogeny, animals often undergo significant shape and size changes, coinciding with ecological shifts. This is evident in parrotfishes (Eupercaria: Labridae), which experience notable ecological shifts during development, transitioning from carnivorous diets as larvae and juveniles to herbivorous and omnivorous diets as adults, using robust beaks and skulls for feeding on coral skeletons and other hard substrates. These ontogenetic shifts mirror their evolutionary history, as parrotfishes are known to have evolved from carnivorous wrasse ancestors. Parallel shifts at ontogenetic and phylogenetic levels may have resulted in similar evolutionary and ontogenetic allometric trajectories within parrotfishes. To test this hypothesis, using micro-computed tomography (μCT) scanning and three-dimensional geometric morphometrics, we analyse the effects of size on the skull shape of the striped parrotfish Scarus iseri and compare its ontogenetic allometry to the evolutionary allometries of 57 parrotfishes and 162 non-parrotfish wrasses. The young S. iseri have skull shapes resembling non-parrotfish wrasses and grow towards typical adult parrotfish forms as they mature. There was a significant relationship between size and skull shapes and strong evidence for parallel ontogenetic and evolutionary slopes in parrotfishes. Our findings suggest that morphological changes associated with the ecological shift characterizing interspecific parrotfish evolution are conserved in their intraspecific ontogenies.