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Tropical reef fishes are widely regarded as being perhaps the most morphologically diverse vertebrate assemblage on earth, yet much remains to be discovered about the scope and patterns of this diversity. We created a morphospace of 2,939 species spanning 56 families of tropical Indo-Pacific reef fishes and established the primary axes of body shape variation, the phylogenetic consistency of these patterns, and whether dominant patterns of shape change can be accomplished by diverse underlying changes. Principal component analysis showed a major axis of shape variation that contrasts deep-bodied species with slender, elongate forms. Furthermore, using custom methods to compare the elongation vector (axis that maximizes elongation deformation) and the main vector of shape variation (first principal component) for each family in the morphospace, we showed that two thirds of the families diversify along an axis of body elongation. Finally, a comparative analysis using a principal coordinate analysis based on the angles among first principal component vectors of each family shape showed that families accomplish changes in elongation with a wide range of underlying modifications. Some groups such as Pomacentridae and Lethrinidae undergo decreases in body depth with proportional increases in all body regions, while other families show disproportionate changes in the length of the head (e.g., Labridae), the trunk or caudal region in all combinations (e.g., Pempheridae and Pinguipedidae). In conclusion, we found that evolutionary changes in body shape along an axis of elongation dominates diversification in reef fishes. Changes in shape on this axis are thought to have immediate implications for swimming performance, defense from gape limited predators, suction feeding performance and access to some highly specialized habitats. The morphological modifications that underlie changes in elongation are highly diverse, suggesting a role for a range of developmental processes and functional consequences.

Assessing the escalating biodiversity crisis, driven by climate change, habitat destruction, and exploitation, necessitates efficient monitoring strategies to assess species presence and abundance across diverse habitats. Video-based surveys using remote cameras are a promising, non-invasive way to collect valuable data in various environments. Yet, the analysis of recorded videos remains challenging due to time and expertise constraints. Recent advances in deep learning models have enhanced image processing capabilities in both object detection and classification. However, the impacts on models’ performances and usage on assessment of biodiversity metrics on videos is yet to be assessed. This study evaluates the impacts of video processing rates, detection and identification model performance, and post-processing algorithms on the accuracy of biodiversity metrics, using simulated remote videos of fish communities and 14,406 simulated automated processing pipelines. We found that a processing rate of one image per second minimizes errors while ensuring detection of all species. However, even near-perfect detection (both recall and precision of 0.99) and identification (accuracy of 0.99) models resulted in overestimation of total abundance, species richness and species diversity due to false positives. We reveal that post-processing model outputs using a confidence threshold approach (i.e., to discard most erroneous predictions while also discarding a smaller proportion of correct predictions) is the most efficient method to accurately estimate biodiversity from videos.

Background The surface of marine animals is covered by abundant and diversified microbial communities , which have major roles for the health of their host . While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

In the marine environment, fish contribute to key ecological processes such as controlling food‐webs through top‐down impacts, especially on algae. To date, the assessment of fish grazing activity has mostly been performed using short‐term (<1 h) censuses by divers or remote cameras which do not allow estimating the variability of grazing rate within and between days. However, understanding the temporal variation of fish activity and hence contribution of species to ecosystem functioning is of particular interest in the context of biological invasion. Here, using long‐duration remote underwater cameras, we recorded fish abundance and grazing events over three consecutive days in October 2019 in a shallow Mediterranean ecosystem from northern Crete. This novel approach allowed us to assess temporal variation of abundance and grazing activity of the two native (Sarpa salpa and Sparisoma cretense) and the two non‐indigenous fish species (Siganus rivulatus and Siganus luridus). Non‐indigenous Siganus rivulatus was the most common species in the studied coastal habitat, followed by the two native species while the non‐indigenous Siganus luridus was scarce. Overall, the non‐indigenous S. rivulatus and the native S. salpa are responsible for more than 90% of the recorded grazing activity with similar bite rates between the two species. More than 70% of the grazing activity arose in grazing pulses in the afternoon, supporting the diel feeding hypothesis according to which feeding is greater in the afternoon when nutritive quality of macrophytes is the highest. In addition, some of the highest peaks in grazing activity were driven by a few individuals. Hence, surveys of only abundance could not provide accurate estimates of herbivory. Last, Siganus rivulatus presence did not significantly affect grazing activity of the native Sarpa salpa. Our results demonstrate that long‐duration remote underwater videos are a useful tool to accurately assess the contribution of fishes to ecosystem functioning. Using long‐duration remote underwater cameras, we recorded fishes throughout the day during three consecutive days in a shallow Mediterranean ecosystem from northern Crete. This novel approach allowed us to assess temporal variation of abundance and grazing activity of two native (Sarpa salpa and Sparisoma cretense) and two non‐indigenous fish species (Siganus rivulatus and Siganus luridus). Non‐indigenous Siganus rivulatus was the most seen species in the environment, followed by the native species while the non‐indigenous Siganus luridus was quasi‐absent. Overall, the non‐indigenous S. rivulatus and the native S. salpa were responsible for more than 90% of the recorded grazing activity with similar bite rates between the two species. Moreover, more than 70% of the recorded grazing activity arose in grazing pulses in the afternoon, supporting the diel feeding hypothesis. Interestingly, big grazing events were not always led by a high abundance of fish.

Coral reefs are under increasing threat, and the loss of reef‐associated fishes providing valuable ecosystem services is accelerating. The monitoring of such rapid changes has become a challenge for ecologists and ecosystems managers using traditional approaches like scuba divers performing underwater visual censuses (UVC) or diver operated video recording (DOV). However, the use of small, low‐cost robots could help tackle the challenge of such monitoring, provided that they perform at least as well as diver‐based methods. To address this question, tropical fish assemblages from 13 fringing reefs around Mayotte Island (Indian Ocean) were monitored along 50 m‐long transects using stereo videos recorded by a semi‐autonomous underwater vehicle (SAUV) and by a scuba diver (Diver Operated stereo Video system, DOV). Differences between the methods were tested for complementary fish assemblage metrics (species richness, total biomass, total density, Shannon diversity and Pielou evenness) and for the number and size of nine targeted species. SAUV recorded on average 35% higher biomass than DOV which in turn recorded on average 12% higher species richness. Biomass differences were found to be due to SAUV monitoring larger fishes than DOV, a potential marker of human‐related fish avoidance behaviour. This study demonstrates that SAUV provides accurate metrics of coral reef fish biodiversity compared to diver‐based procedures. Given their ability to conduct video transects at high frequency, 100 m depth range and at a moderate cost, SAUV is a promising tool for monitoring fish assemblages in coral reef ecosystems. New tools are needed in light of exosystemic global change monitoring, therefore we tested the possibility to use robots to perform coral reef fishes monitoring surveys. Thirteen fringing reefs around Mayotte Island (Indian Ocean) were surveyed along 50 m‐long transects using stereo videos recorded by a semi‐autonomous underwater vehicle (SAUV) and by the standard approach using a scuba‐diver operated stereo video system (DOV). SAUV recorded on average 35% higher biomass than DOV which recorded on average 12% higher species richness. The biomass differences were found to be due to SAUV monitoring larger fishes than DOV, a potential marker of human‐related fish wariness.

Tropical reef fishes exhibit a large disparity of organismal morphologies contributing to their astonishing biodiversity. Morphological disparity, scaling from differences among individuals within populations to differences among species, is governed by ecological and evolutionary processes. Here, we examined the relationship between intra- and interspecific disparity in 1111 individuals from 17 tropical reef fish species, representing 10 families with different dispersal abilities, across four Indian Ocean regions. We compared intraspecific measurements with species-level measures from a database of 1061 reef fish species. Species with high morphological disparity among individuals from distinct regions are found to be nested in families that display a high disparity among their genera. We show an association between the morphological disparity at the intra- and interspecific levels for several morphological ratios such as the caudal peduncle elongation. We evaluated the link between morphological disparity and genetic diversity with species dispersal ability. A structural equation model indicates that dispersal ability correlates positively with species genetic diversity, which is associated with morphological disparity. Our results suggest that traits associated with dispersal may foster gene flow and morphological evolution. Future works combining genomic, morphological and environmental data across more species is necessary to generalize these findings to other regions. Morphological disparity in tropical reef fishes links intra- and interspecific variation, shaped by ecological and evolutionary processes. Dispersal traits promote genetic diversity and disparity, highlighting their role in gene flow and morphological evolution.

The squat lobster Munida rugosa has an unusual chela dimorphism exhibited mainly by large males. Some individuals have 'arched' chelae in which there is a gap between the dactylus and the pollex when closed, and others have a 'straight' morphology in which the dactylus and pollex oppose along most of their length. Geometric morphometric analysis indicated that, compared with males, the arched morphology does not develop fully in females, so further investigation was confined to males. In males, the distal part of the chela was similar in both the forms and seemed to be adapted to hold and shred prey items. Both morphologies had a major cylindrical tooth on the inner proximal part of the dactylus, but the arched morphology had a higher and wider propodus, a greater major tooth-pollex distance and a greater force generation than the straight morphology. The findings suggest that the arched chela morphology in M. rugosa is a sexually selected trait adapted to inflict puncture wounds on opponents during agonistic interactions. The arched morphology, therefore, appears to have evolved in males by means of sexual selection because it enhanced the function of the chela as a weapon, while retaining functionality for feeding.

The exceptional diversity of shallow‐water marine fishes contributes to the nutrition of millions of people worldwide through coastal wild‐capture fisheries, with different species having diverse nutritional profiles. Fishes in ecosystems are reservoirs of micronutrients with benefits to human health. Yet, the amount of micronutrients contained in fish species on coral reefs and in shallow tropical waters is challenging to estimate, and the micronutrients caught by fisheries remain uncertain. To assess whether micronutrient deficiencies could be addressed through specific fisheries management actions, we first require a quantification of the potentially available micronutrients contained in biodiverse reef fish assemblages. Here, we therefore undertake a broad heuristic assessment of available micronutrients on tropical reefs using ensemble species distribution modelling and identify potential mismatches with micronutrients derived from summarising coastal fisheries landings data. We find a mismatch between modelled estimates of micronutrients available in the ecosystem on the one hand and the micronutrients in small‐scale fisheries landings data. Fisheries had lower micronutrients than expected from fishes in the modelled assemblage. Further, fisheries were selective for vitamin A, thus resulting in a trade‐off with other micronutrients. Our results remained unchanged after accounting for the under‐sampling of fish communities and under‐reporting of small‐scale fisheries catches—two major sources of uncertainty. This reported mismatch indicates that current estimates of fished micronutrients are not adequate to fully assess micronutrient inventories. However, small‐scale fisheries in some countries were already selective towards micronutrient mass, indicating policies that target improved access, distribution and consumption of fish could leverage this existing high micronutrient mass. Enhanced taxonomic resolution of catches and biodiversity inventories using localised species consumption surveys could improve understanding of nature‐people linkages. Improving fisheries reporting and monitoring of reef fish assemblages will advance the understanding of micronutrient mismatches, which overall indicate a weak uptake of nutritional goals in fisheries practices. The decoupling between micronutrients in ecosystems and in fisheries catches indicates that social, economic, and biodiversity management goals are not shaped around nutritional targets—but this is key to achieve a sustainable and healthy planet for both people and nature. Read the free Plain Language Summary for this article on the Journal blog. Read the free Plain Language Summary for this article on the Journal blog.

Feeding activities by fishes are among the key ecological processes that sustain coral reef functioning. Those trophic-based processes are known to vary across space and across seasons or years. However, there is still little knowledge about their variability within and between days as well as whether these processes are dominated by the same species across time. Using remote underwater cameras, we quantified rates of three feeding activities (corallivory, herbivory and invertivory) for three one-hour time slots (morning, midday, afternoon) over two days on two coral reefs around Mayotte Island (Western Indian Ocean). Feeding activities were highly variable at within and between-day scales and concentrated in a few pulses. Herbivory was the highest in the afternoon which aligns with previous findings regarding activity of herbivorous fishes. Corallivory was the highest in the morning, which highlights the advantage of long-duration benthic remote underwater videos to accurately assess all trophic activities. Trophic-related processes were dominated by the same few species in both sites and across time of the day. This study pinpoints the importance of including within-day and between-day variations when studying ecological processes, as neglecting these variations may introduce biases into our understanding of these processes.

Functional diversity (FD), the diversity of organism attributes that relates to their interactions with the abiotic and biotic environment, has been increasingly used for the last two decades in ecology, biogeography and conservation. Yet, FD has many facets and their estimations are not standardized nor embedded in a single tool. mFD (multifaceted functional diversity) is an R package that uses matrices of species assemblages and species trait values as building blocks to compute most FD indices. mFD is firstly based on two functions allowing the user to summarize trait and assemblage data. Then it calculates trait-based distances between species pairs, informs the user whether species have to be clustered into functional entities and finally computes multidimensional functional space. To let the user choose the most appropriate functional space for computing multidimensional functional diversity indices, two mFD functions allow assessing and illustrating the quality of each functional space. Next, mFD provides 6 core functions to calculate 16 existing FD indices based on trait-based distances, functional entities or species position in a functional space. The mFD package also provides graphical functions based on the ggplot library to illustrate FD values through customizable and high-resolution plots of species distribution among functional entities or in a multidimensional space. All functions include internal validation processes to check for errors in data formatting which return detailed error messages. To facilitate the use of mFD framework, we built an associated website hosting five tutorials illustrating the use of all the functions step by step.