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Aim To investigate biotic and abiotic correlates of reef‐fish species richness across multiple spatial scales. Location Tropical reefs around the globe, including 485 sites in 109 sub‐provinces spread across 14 biogeographic provinces. Time period Present. Major taxa studied 2,523 species of reef fish. Methods We compiled a database encompassing 13,050 visual transects. We used hierarchical linear Bayesian models to investigate whether fish body size, reef area, isolation, temperature, and anthropogenic impacts correlate with reef‐fish species richness at each spatial scale (i.e., sites, sub‐provinces, provinces). Richness was estimated using coverage‐based rarefaction. We also tested whether species packing (i.e., transect‐level species richness/m2) is correlated with province‐level richness. Results Body size had the strongest effect on species richness across all three spatial scales. Reef area and temperature were both positively correlated with richness at all spatial scales. At the site scale only, richness decreased with reef isolation. Species richness was not correlated with proxies of human impacts. Species packing was correlated with species richness at the province level following a sub‐linear power function. Province‐level differences in species richness were also mirrored by patterns of body size distribution at the site scale. Species‐rich provinces exhibited heterogeneous assemblages of small‐bodied species with small range sizes, whereas species‐poor provinces encompassed homogeneous assemblages composed by larger species with greater dispersal capacity. Main conclusions Our findings suggest that body size distribution, reef area and temperature are major predictors of species richness and accumulation across scales, consistent with recent theories linking home range to species–area relationships as well as metabolic effects on speciation rates. Based on our results, we hypothesize that in less diverse areas, species are larger and likely more dispersive, leading to larger range sizes and less turnover between sites. Our results indicate that changes in province‐level (i.e., regional) richness should leave a tractable fingerprint in local assemblages, and that detailed studies on local‐scale assemblage composition may be informative of responses occurring at larger scales.

In the marine realm, the tropics host an extraordinary diversity of taxa but the drivers underlying the global distribution of marine organisms are still under scrutiny and we still lack an accurate global predictive model. Using a spatial database for 6336 tropical reef fishes, we attempted to predict species richness according to geometric, biogeographical and environmental explanatory variables. In particular, we aimed to evaluate and disentangle the predictive performances of temperature, habitat area, connectivity, mid-domain effect and biogeographical region on reef fish species richness. We used boosted regression trees, a flexible machine-learning technique, to build our predictive model and structural equation modeling to test for potential ‘mediation effects’ among predictors. Our model proved to be accurate, explaining 80% of the total deviance in fish richness using a cross-validated procedure. Coral reef area and biogeographical region were the primary predictors of reef fish species richness, followed by coast length, connectivity, mid-domain effect and sea surface temperature, with interactions between the region and other predictors. Important indirect effects of water temperature on reef fish richness, mediated by coral reef area, were also identified. The relationship between environmental predictors and species richness varied markedly among biogeographical regions. Our analysis revealed that a few easily accessible variables can accurately predict reef fish species richness. They also highlight concerns regarding ongoing environmental declines, with region-specific responses to variation in environmental conditions predicting a variable response to anthropogenic impacts.

Coral reefs are among the most species-rich and threatened ecosystems on Earth, yet the extent to which human stressors determine species occurrences, compared with biogeography or environmental conditions, remains largely unknown. With ever-increasing human-mediated disturbances on these ecosystems, an important question is not only how many species can inhabit local communities, but also which biological traits determine species that can persist (or not) above particular disturbance thresholds. Here we show that human pressure and seasonal climate variability are disproportionately and negatively associated with the occurrence of large-bodied and geographically small-ranging fishes within local coral reef communities. These species are 67% less likely to occur where human impact and temperature seasonality exceed critical thresholds, such as in the marine biodiversity hotspot: the Coral Triangle. Our results identify the most sensitive species and critical thresholds of human and climatic stressors, providing opportunity for targeted conservation intervention to prevent local extinctions. Knowing which species traits may confer resilience to human-mediated stressors will help predict future impacts on biodiversity. Here, Mellin et al . show that large bodied fish with small geographic ranges are disproportionately affected by the negative impacts of human disturbance and climate variability.

Coral reefs are increasingly being altered by a myriad of anthropogenic activities and natural disturbances. Long-term studies offer unique opportunities to understand how multiple and recurrent disturbances can influence coral reef resilience and long-term dynamics. While the long-term dynamics of coral assemblages have been extensively documented, the long-term dynamics of coral reef fish assemblages have received less attention. Here, we describe the changes in fish assemblages on Tiahura reef, Moorea, from 1979 to 2011. During this 33-yr period, Tiahura was exposed to multiple disturbances (crown-of-thorns seastar outbreaks and cyclones) that caused recurrent declines and recoveries of coral cover and changes in the dominant coral genera. These shifts in coral composition were associated with long-term cascading effects on fish assemblages. The composition and trophic structure of fish assemblages continuously shifted without returning to their initial composition, whereas fish species richness remained stable, albeit with a small increase over time. We detected nonlinear responses of fish density when corals were most degraded. When coral cover dropped below 10 % following a severe crown-of-thorns sea star outbreak, the density of most fish trophic groups sharply decreased. Our study shows that historical contingency may potentially be an important but largely underestimated factor explaining the contemporary structure of reef fish assemblages and suggests that temporal stability in their structure and function should not necessarily be the target of management strategies that aim at increasing or maintaining coral reef resilience.

Coral reefs are experiencing declines due to climate change and local human impacts. While at a local scale these impacts induce biodiversity loss and shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggests that regional communities represent a random subset of the global species and traits pool, whatever their species richness. Using distributional data on 3586 fish species and latest advances in species distribution models, we show marked gradients in the prevalence of size classes and diet categories across the biodiversity gradient. This divergence in trait structure is best explained by reef isolation during past unfavourable climatic conditions, with large and piscivore fishes better represented in isolated areas. These results suggest the risk of a global community reorganization if the ongoing climate-induced reef fragmentation is not halted.

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction.

Indo-West Pacific coral reef fishes form speciose ecological communities. A biogeographically meaningful interpretation of diversity patterns in this region requires accurate inventories of species. Previous studies have suggested that biogeographic scenarios for Indo-West Pacific coral reef fishes are compromised by an unacknowledged yet substantial amount of cryptic diversity. DNA barcoding, the use of a mitochondrial gene as an internal species tag for species identification, has opened new perspectives on global biodiversity. The present study, based on the largest DNA barcode reference library produced to date for Indo-West Pacific coral reef fishes, sheds new light on the extent of cryptic diversity and its evolutionary origin. We analyzed 3174 DNA barcodes for 805 species of coral reef fishes sampled at 3 different locations across the Indo-West Pacific (including 538 new DNA barcodes for 270 species sampled from New Caledonia). Among the 183 species with Indo-West Pacific distribution and multiple specimens analyzed, 78 (42.6%) were represented by 2 or more monophyletic lineages alternatively sorted between the sampling sites in the Indian and Pacific oceans and another 73 (40%) showed evidence of phylogeographic structure. Spatial analyses pointed to a detectable impact of geographic isolation on the emergence of cryptic diversity. The significant correlation of several life history traits to the maximum intraspecific genetic distances suggests that genetic divergence among geographically isolated cryptic lineages accumulated though mutation and genetic drift.

Aim: We applied a multicomponent approach based on the decomposition of taxonomic (both presence-absence and abundance) and functional beta diversity to determine the influence of ecological factors in shaping spatial distribution diversity of coral reef fishes, and the implications for conservation decisions. Location: Lagoons of ten atolls characterized by low human pressure but with contrasted geomorphology in the Tuamotu Archipelago, French Polynesia. Methods: We computed beta diversities and their partitioning components, both at local (inter-transect, from 200 m to 10 km) and large (among atolls, from 22 to 350 km) spatial scales. Null models were applied to test whether the observed beta diversity differed from random expectation. Multiple generalized dissimilarity models were run to test which environmental factors were the best predictors of observed beta diversities. Results: Beta diversity was indistinguishable from randomness at both spatial scales. Species remained generally interchangeable among transects within an atoll and to some extent among atolls. However, strong deviance explained by models showed that the number of species, the number of individuals and functional traits present in transects and atolls were determined by deterministic factors (i.e. environmental factors). Modelling each beta diversity component separately also revealed partial mismatch among atolls and among species and functional dissimilarities. The influence of environmental variables strongly varied among atolls, species and functional dissimilarities. Main conclusions: By revealing the spatial scaling of ecological factors and partial congruence among species and functional diversity, assessment of beta diversity provides insight into conservation planning. Our results support the idea that conservation planning applied to protect taxonomic diversity cannot be fully extended to functional diversity. We have addressed the dilemma of which diversity component should be favoured in conservation strategies.

Aim We applied a multicomponent approach based on the decomposition of taxonomic (both presence-absence and abundance) and functional beta diversity to determine the influence of ecological factors in shaping spatial distribution diversity of coral reef fishes, and the implications for conservation decisions. Location Lagoons of ten atolls characterized by low human pressure but with contrasted geomorphology in the Tuamotu Archipelago, French Polynesia. Methods We computed beta diversities and their partitioning components, both at local (inter-transect, from 200 m to 10 km) and large (among atolls, from 22 to 350 km) spatial scales. Null models were applied to test whether the observed beta diversity differed from random expectation. Multiple generalized dissimilarity models were run to test which environmental factors were the best predictors of observed beta diversities. Results Beta diversity was indistinguishable from randomness at both spatial scales. Species remained generally interchangeable among transects within an atoll and to some extent among atolls. However, strong deviance explained by models showed that the number of species, the number of individuals and functional traits present in transects and atolls were determined by deterministic factors (i.e. environmental factors). Modelling each beta diversity component separately also revealed partial mismatch among atolls and among species and functional dissimilarities. The influence of environmental variables strongly varied among atolls, species and functional dissimilarities. Main conclusions By revealing the spatial scaling of ecological factors and partial congruence among species and functional diversity, assessment of beta diversity provides insight into conservation planning. Our results support the idea that conservation planning applied to protect taxonomic diversity cannot be fully extended to functional diversity. We have addressed the dilemma of which diversity component should be favoured in conservation strategies.

Despite intensive sampling efforts in coral reefs, densities and species richness of anguilliform fishes (eels) are difficult to quantify because these fishes evade classical sampling methods such as underwater visual census and rotenone poisoning. An alternative method revealed that in New Caledonia, eels are far more abundant and diverse than previously suspected. We analysed the stomach contents of two species of sea snakes that feed on eels (Laticauda laticaudata and L. saintgironsi). This technique is feasible because the snakes return to land to digest their prey, and (since they swallow their prey whole) undigested food items are identifiable. The snakes’ diet consisted almost entirely (99.6%) of eels and included 14 species previously unrecorded from the area. Very large populations of snakes occur in the study area (e.g. at least 1,500 individuals on a small coral islet). The snakes capture approximately 36,000 eels (972 kg) per year, suggesting that eels and snakes play key roles in the functioning of this reef ecosystem.