The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs

Low human interest for the most at-risk reef fishes worldwide

Human interest in biodiversity is essential for effective conservation action but remains poorly quantified at large scales. Here, we investigated human interest for 2408 marine reef fishes using data obtained from online public databases and social media, summarized in two synthetic dimensions, research effort and public attention. Both dimensions are mainly related to geographic range size. Research effort is also linked to fishery importance, while public attention is more related to fish aesthetic value and aquarium trade importance. We also found a strong phylogenetic bias, with certain fish families receiving disproportional research effort and public attention. Most concerningly, species at the highest risk of extinction and those most vulnerable to future climate change tend to receive less research effort and public attention. Our results provide a lens through which examining the societal attention that species garner, with the ultimate goals to improve conservation strategies, research programs, and communication plans.

Quantifying energy and nutrient fluxes in coral reef food webs

The movement of energy and nutrients through ecological communities represents the biological 'pulse' underpinning ecosystem functioning and services. However, energy and nutrient fluxes are inherently difficult to observe, particularly in high-diversity systems such as coral reefs. We review advances in the quantification of fluxes in coral reef fishes, focusing on four key frameworks: demographic modelling, bioenergetics, micronutrients, and compound-specific stable isotope analysis (CSIA). Each framework can be integrated with underwater surveys, enabling researchers to scale organismal processes to ecosystem properties. This has revealed how small fish support biomass turnover, pelagic subsidies sustain fisheries, and fisheries benefit human health. Combining frameworks, closing data gaps, and expansion to other aquatic ecosystems can advance understanding of how fishes contribute to ecosystem functions and services.

Responses of the coral reef cryptobiome to environmental gradients in the Red Sea

An essential component of the coral reef animal diversity is the species hidden in crevices within the reef matrix, referred to as the cryptobiome. These organisms play an important role in nutrient cycling and provide an abundant food source for higher trophic levels, yet they have been largely overlooked. Here, we analyzed the distribution patterns of the mobile cryptobiome (>2000 μm) along the latitudinal gradient of the Saudi Arabian coast of the Red Sea. Analysis was conducted based on 54 Autonomous Reef Monitoring Structures. We retrieved a total of 5273 organisms, from which 2583 DNA sequences from the mitochondrially encoded cytochrome c oxidase I were generated through sanger sequencing. We found that the cryptobiome community is variable over short geographical distances within the basin. Regression tree models identified sea surface temperature (SST), percentage cover of hard coral and turf algae as determinant for the number of operational taxonomic units present per Autonomous Reef Monitoring Structures (ARMS). Our results also show that the community structure of the cryptobiome is associated with the energy available (measured as photosynthetic active radiation), sea surface temperature, and nearby reef habitat characteristics (namely hard corals, turf and macroalgae). Given that temperature and reef benthic characteristics affect the cryptobiome, current scenarios of intensive climate change are likely to modify this fundamental biological component of coral reef functioning. However, the trajectory of change is unknow and can be site specific, as for example, diversity is expected to increase above SST of 28.5°C, and with decreasing hard coral and turf cover. This study provides a baseline of the cryptobenthic community prior to major coastal developments in the Red Sea to be used for future biodiversity studies and monitoring projects. It can also contribute to better understand patterns of reef biodiversity in a period where Marine Protected Areas are being discussed in the region.

Reduced small-scale structural complexity on sponge-dominated areas of Indo-Pacific coral reefs

Corals provide a complex 3D framework that offers habitat to diverse coral reef fauna. However, future reefs are likely to experience reduced coral abundance. Sponges have been proposed as one potential winner on future coral reefs, but little is known of how they contribute to reef 3D structure. Given the ecological importance of structural complexity, it is critical to understand how changes in the abundance of structure-building organisms will affect the three-dimensional properties of coral reefs. To investigate the potentially important functional role of coral reef sponges as providers of structural complexity, we compared the structural complexity of coral- and sponge-dominated areas of an Indonesian coral reef, using 3D photogrammetry at a 4 m2 spatial scale. Structural complexity of 31 4 m2 quadrats was expressed as rugosity indicating reef contour complexity (R), vector dispersion indicating heterogeneity of angles between reef surfaces (1/k), and fractal dimension indicating geometrical complexity at five different spatial scales between 1 and 120 cm (D1-5). Quadrats were identified as high- or low-complexity using hierarchical clustering based on the complexity metrics. At high structural complexity, coral- and sponge-dominated quadrats were similar in terms of R and 1/k. However, smallest-scale refuge spaces (1-5 cm) were more abundant in coral-dominated quadrats, whereas larger scale refuge spaces (30-60 cm) were more abundant in sponge-dominated quadrats. Branching and massive corals contributed the most to structural complexity in coral-dominated quadrats, and barrel sponges in sponge-dominated quadrats. We show that smaller-scale refugia (1-5 cm) are reduced on sponge-dominated reefs at the spatial scale considered here (4 m2), with potential negative implications for smaller reef fauna.

Similar functional composition of fish assemblages despite contrasting levels of habitat degradation on shallow Caribbean coral reefs

Functional trait-based approaches provide an opportunity to assess how changes in habitat affect the structure of associated communities. Global analyses have found a similarity in the composition of reef fish functional traits despite differences in species richness, environmental regimes, and habitat components. These large-scale patterns raised the question of whether this same stability can be observed at smaller spatial scales. Here, we compared the fish trait composition and their functional diversity in two Caribbean shallow coral reefs with contrasting levels of habitat degradation: Limones (>30% cover), constituted mainly by colonies of Acropora palmata and Bonanza, a reef with extensive areas of dead Acropora structures, dominated by algae. To characterize the functional structure of fishes on each reef, we calculated the community-weighted mean trait values (CWM), functional richness, functional evenness, functional dispersion, and functional originality. Despite the differences in habitat quality, reefs exhibited a similar proportion and common structure on fish functional traits. Functional richness and functional evenness differed significantly, but functional dispersion and functional originality did not show differences between reefs. The greater niche complexity driven by the high availability of microhabitats provided by A. palmata may explain the higher functional richness in Limones, whereas the reef degradation in Bonanza may contribute to a higher functional evenness because of a similar distribution of abundance per fish trait combinations. Our results suggest that widespread degradation on Caribbean reefs has limited the type, variety, and range of traits, which could lead to a functional homogenization of fish communities even at local scales.

Blood meal identification reveals extremely broad host range and host-bias in a temporary ectoparasite of coral reef fishes

Appreciation for the role of cryptofauna in ecological systems has increased dramatically over the past decade. The impacts blood-feeding arthropods, such as ticks and mosquitos, have on terrestrial communities are the subject of hundreds of papers annually. However, blood-feeding arthropods have been largely ignored in marine environments. Gnathiid isopods, often referred to as "ticks of the sea", are temporary external parasites of fishes. They are found in all marine environments and have many consequential impacts on host fitness. Because they are highly mobile and only associated with their hosts while obtaining a blood meal, their broader trophic connections are difficult to discern. Conventional methods rely heavily on detecting gnathiids on wild-caught fishes. However, this approach typically yields few gnathiids and does not account for hosts that avoid capture. To overcome this limitation, we sequenced blood meals of free-living gnathiids collected in light traps to assess the host range and community-dependent exploitation of Caribbean gnathiid isopods. Using fish-specific COI (cox1) primers, sequencing individual blood meals from 1060 gnathiids resulted in the identification of 70 host fish species from 27 families. Comparisons of fish assemblages to blood meal identification frequencies at four collection sites indicated that fishes within the families Haemulidae (grunts) and Lutjanidae (snappers) were exploited more frequently than expected based on their biomass, and Labrid parrotfishes were exploited less frequently than expected. The broad host range along with the biased exploitation of diel-migratory species has important implications for the role gnathiid isopods play in Caribbean coral reef communities.

Seq' and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs

Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef-associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardized sampling with 12 units of the Autonomous Reef Monitoring Structure (ARMS) and high-throughput sequencing was utilized to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non-metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger-sized non-coral invertebrates influencing spatial patterns among sites. Our study showed that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.

Two new species of Varicus from Caribbean deep reefs, with comments on the related genus Pinnichthys (Teleostei, Gobiidae, Gobiosomatini, Nes subgroup)

Tropical deep reefs (~40-300 m) are diverse ecosystems that serve as habitats for diverse communities of reef-associated fishes. Deep-reef fish communities are taxonomically and ecologically distinct from those on shallow reefs, but like those on shallow reefs, they are home to a species-rich assemblage of small, cryptobenthic reef fishes, including many species from the family Gobiidae (gobies). Here we describe two new species of deep-reef gobies, Varicusprometheussp. nov. and V.roatanensissp. nov., that were collected using the submersible Idabel from rariphotic reefs off the island of Roatan (Honduras) in the Caribbean. The new species are the 11th and 12th species of the genus Varicus, and their placement in the genus is supported by morphological data and molecular phylogenetic analyses. Additionally, we also collected new specimens of the closely-related genus and species Pinnichthysaimoriensis during submersible collections off the islands of Bonaire and St. Eustatius (Netherland Antilles) and included them in this study to expand the current description of that species and document its range extension from Brazil into the Caribbean. Collectively, the two new species of Varicus and new records of P.aimoriensis add to our growing knowledge of cryptobenthic fish diversity on deep reefs of the Caribbean.

Underwater analysis of the reproductive behaviour and egg development of the jawfish Opistognathus iyonis

Fishes of the jawfish family Opistognathidae are cryptobenthic and distributed in subtropical seas, and new species are still being reported. Opistognathus spp. live alone in burrows and males orally brood their egg clutches. The life cycle of jawfish, including their reproductive behaviour, is poorly understood. Here we describe the natural reproduction and embryonic development of Opistognathus iyonis in Yamaguchi, Japan, based on underwater surveys for 3 years. Spawning was observed as female jawfish came into the male's burrow ~30 min before sunrise. The jawfish had a mean number of 4.4 egg clutches in the burrow through 48.2 days, and the egg took 12 days to hatching. The mean temperature for developmental days was 20.8°C. The mean and cumulative water temperature during development significantly correlated with the number of developmental days. During egg development, male jawfish took care of eggs by holding them for part of the time in their mouths. Hatching was observed ~20 min after sunset. When hatching occurred orally, eggs were pushed out and back repeatedly using the lower jaw; consequently, the egg clutches were let out in an upward direction. To our best knowledge, this is the first report of the reproductive behaviour of O. iyonis in the natural environment in the same area for several years.

Effects of anthropogenic noise and natural soundscape on larval fish behavior in four estuarine species

The larval and post-larval forms of many marine organisms, such as oysters, crabs, lobster, coral, and fish, utilize ambient acoustic cues to orient, settle, or metamorphose. In this study, the effect of anthropogenic and ambient sounds on the orientation behavior of four larval estuarine fishes was examined in a controlled, laboratory experiment. Pre-settlement size red drum Sciaenops ocellatus, southern flounder Paralichthys lethostigma, spotted seatrout Cynoscion nebulosus, and Florida blenny Chasmodes saburrae larvae were exposed to four sound treatments-control, estuarine soundscape, seismic airguns, and large-ship passage-in a linear acoustic chamber. Initial significant (p < 0.05) avoidance of airguns was observed in three of the four species (all but the Florida blenny), but habituation to this sound occurred as the experiment progressed. All species avoided ship passage sounds; however, the avoidance behavior was not significant. Interestingly, none of the species studied were significantly attracted to the acoustic cues alone of the estuarine soundscape; in fact, three of the four species spent less time near the speaker when it was broadcast. These results suggest that larval fish can potentially habituate to anthropogenic noise relatively quickly (<10 min). Understanding how sounds affect larval behavior is necessary because successful recruitment ultimately affects a population's success.

Composition and Long-Term Variation Characteristics of Coral Reef Fish Species in Yongle Atoll, Xisha Islands, China

Yongle Atoll was the largest atoll in the Xisha Islands of the South China Sea, and it was a coral reef ecosystem with important ecological and economic values. In order to better protect and manage the coral reef fish resources in Yongle Atoll, we analyzed field survey data from artisanal fishery, catches, and underwater video from 2020 to 2022 and combined historical research to explore the changes in fish species composition and community structure in Yongle Atoll over the past 50 years. The results showed that a total of 336 species of fish were found on Yongle Atoll, belonging to 17 orders and 60 families. Among them, Perciformes had the most fish species with 259 species accounting for 77.08% of the total number of species. The number of fish species in the coral reef of Yongle Atoll was exponentially correlated with its corresponding maximum length and significantly decreases with its increase. The fish community structure of Yongle Atoll changed, and the proportion of large carnivorous fish decreased significantly, while the proportion of small-sized and medium-sized fish increased. At the same time, Yongle Atoll has 18 species of fish listed on the IUCN Red List, 15 of which are large fish. The average taxonomic distinctness (Delta+, Δ+) and the variation taxonomic distinctness (Lambda+, Λ+) in 2020-2022 were lower than the historical data, and the number of fish orders, families, and genera in Yongle Atoll has decreased significantly, which indicates that the current coral reef fish species in Yongle Atoll have closer relatives and higher fish species uniformity. In addition, the similarity of fish species in Yongle Atoll was relatively low at various time periods, further proving that the fish community structure has undergone significant variation. In general, due to multiple impacts, such as overfishing, fishing methods, environmental changes, and habitat degradation, the fish species composition of Yongle Atoll may have basically evolved from carnivorous to herbivorous, from large fish to small fish, and from complexity to simplicity, leaving Yongle Atoll in an unstable state. Therefore, we need to strengthen the continuous monitoring of the coral reef ecosystem in Yongle Atoll to achieve the protection and restoration of its ecological environment and fishery resources, as well as sustainable utilization and management.

Microhabitat partitioning between sympatric intertidal fish species highlights the importance of sediment composition in gravel beach conservation

Gravel beaches in the Mediterranean ecoregion represent an economically important and unique habitat type. Yet, burgeoning tourism, intensive coastal development and artificial nourishment of beaches may jeopardize their ecological communities. To date, species that reside on gravel beaches and the consequences of beach alterations are poorly understood, which hampers the development of a sustainable coastal tourism industry along the region's shorelines. Using a simple collection method based on dredging buckets through the intertidal section of beaches, we quantified the microhabitat association of two sympatric clingfish species in the genus Gouania at seven natural and an artificial gravel beach based on sediment characteristics. We hypothesized that slender (G. pigra) and stout (G. adriatica) morphotypes would partition interstitial niche space based on sediment size, which may affect the vulnerability of the species to changes in gravel beach composition due to coastal development. We detected substantial differences in gravel composition within and among the sampled beaches which suggests scope for microhabitat partitioning in Gouania. Indeed, we found significant relationships between species identity and the presence/absence and abundance of individuals in hauls based on their positioning on PC1. Our results suggest that modifications of gravel beaches through coastal development, including beach nourishment, intensifying coastal erosion, or artificial beach creation, may have detrimental consequences for the two species if sediment types or sizes are altered. We posit that, given the simplicity and efficacy of our sampling method and the sensitivity of Gouania species to prevailing gravel composition, the genus could serve as an important indicator for gravel beach management in the Mediterranean ecoregion.

Black coral forests enhance taxonomic and functional distinctiveness of mesophotic fishes in an oceanic island: implications for biodiversity conservation

The degradation of shallow ecosystems has called for efforts to understand the biodiversity and functioning of Mesophotic Ecosystems. However, most empirical studies have been restricted to tropical regions and have majorly focused on taxonomic entities (i.e., species), neglecting important dimensions of biodiversity that influence community assembly and ecosystem functioning. Here, using a subtropical oceanic island in the eastern Atlantic Ocean (Lanzarote, Canary Islands), we investigated variation in (a) alpha and (b) beta functional (i.e., trait) diversity across a depth gradient (0-70 m), as a function of the presence of black coral forests (BCFs, order Antipatharian) in the mesophotic strata, a vulnerable but often overlooked 'ecosystem engineer' in regional biodiversity. Despite occupying a similar volume of the functional space (i.e., functional richness) than shallow (< 30 m) reefs, mesophotic fish assemblages inhabiting BCFs differed in their functional structure when accounting for species abundances, with lower evenness and divergence. Similarly, although mesophotic BCFs shared, on average, 90% of the functional entities with shallow reefs, the identity of common and dominant taxonomic and functional entities shifted. Our results suggest BCFs promoted the specialization of reef fishes, likely linked to convergence towards optimal traits to maximize the use of resources and space. Regional biodiversity planning should thus focus on developing specific management and conservation strategies for preserving the unique biodiversity and functionality of mesophotic BCFs.

Emigration patterns of motile cryptofauna and their implications for trophic functioning in coral reefs

Patterns of movement of marine species can reflect strategies of reproduction and dispersal, species' interactions, trophodynamics, and susceptibility to change, and thus critically inform how we manage populations and ecosystems. On coral reefs, the density and diversity of metazoan taxa are greatest in dead coral and rubble, which are suggested to fuel food webs from the bottom up. Yet, biomass and secondary productivity in rubble is predominantly available in some of the smallest individuals, limiting how accessible this energy is to higher trophic levels. We address the bioavailability of motile coral reef cryptofauna based on small-scale patterns of emigration in rubble. We deployed modified RUbble Biodiversity Samplers (RUBS) and emergence traps in a shallow rubble patch at Heron Island, Great Barrier Reef, to detect community-level differences in the directional influx of motile cryptofauna under five habitat accessibility regimes. The mean density (0.13-4.5 ind cm^-3) and biomass (0.14-5.2 mg cm^-3) of cryptofauna were high and varied depending on microhabitat accessibility. Emergent zooplankton represented a distinct community (dominated by the Appendicularia and Calanoida) with the lowest density and biomass, indicating constraints on nocturnal resource availability. Mean cryptofauna density and biomass were greatest when interstitial access within rubble was blocked, driven by the rapid proliferation of small harpacticoid copepods from the rubble surface, leading to trophic simplification. Individuals with high biomass (e.g., decapods, gobies, and echinoderms) were greatest when interstitial access within rubble was unrestricted. Treatments with a closed rubble surface did not differ from those completely open, suggesting that top-down predation does not diminish rubble-derived resources. Our results show that conspecific cues and species' interactions (e.g., competition and predation) within rubble are most critical in shaping ecological outcomes within the cryptobiome. These findings have implications for prey accessibility through trophic and community size structuring in rubble, which may become increasingly relevant as benthic reef complexity shifts in the Anthropocene.

New insights into the diversity of cryptobenthic Cirripectes blennies in the Mascarene Archipelago sampled using Autonomous Reef Monitoring Structures (ARMS)

Autonomous Reef Monitoring Structures (ARMS) are artificial mini-reefs designed for standardized sampling of sessile and small motile cryptobenthic organisms. ARMS are also effective for collecting small cryptobenthic fishes, such as the combtooth blennies of the genus Cirripectes. Recent studies discovered several Cirripectes species endemic to islands or archipelagos, in spite of the generally broad distributions of tropical and subtropical blennies. Thus, to evaluate the diversity and distribution of Cirripectes species in the Mascarene Archipelago, a little-studied region but an important biodiversity hotspot, complete mitochondrial genomes, and nuclear rhodopsin genes were sequenced for 39 specimens collected with ARMS deployed on outer reef slopes at Reunion and Rodrigues islands. Mitochondrial COI sequences were analyzed to integrate these specimens within the largest dataset of publicly available sequences. Three species were found in the Mascarene Archipelago, Cirripectes castaneus, Cirripectes randalli, and Cirripectes stigmaticus. C. castaneus and C. stigmaticus both have an Indo-Pacific distribution with several haplotypes shared among distant localities. In agreement with the literature, C. randalli shows a small-range endemism restricted to the Mascarenes. We confirmed the presence of C. castaneus, C. randalli, and C. stigmaticus in Rodrigues, and the presence of C. stigmaticus in Reunion. This study contributes to filling the gaps in taxonomic and molecular knowledge of the reef cryptobiome in the South-West Indian Ocean, and provides the first complete mitogenomes for the genus, a crucial step for future molecular-based inventories (e.g., eDNA).

The global depth range of marine fishes and their genetic coverage for environmental DNA metabarcoding

The bathymetric and geographical distribution of marine species represent a key information in biodiversity conservation. Yet, deep-sea ecosystems are among the least explored on Earth and are increasingly impacted by human activities. Environmental DNA (eDNA) metabarcoding has emerged as a promising method to study fish biodiversity but applications to the deep-sea are still scarce. A major limitation in the application of eDNA metabarcoding is the incompleteness of species sequences available in public genetic databases which reduces the extent of detected species. This incompleteness by depth is still unknown. Here, we built the global bathymetric and geographical distribution of 10,826 actinopterygian and 960 chondrichthyan fish species. We assessed their genetic coverage by depth and by ocean for three main metabarcoding markers used in the literature: teleo and MiFish-U/E. We also estimated the number of primer mismatches per species amplified by in silico polymerase chain reaction which influence the probability of species detection. Actinopterygians show a stronger decrease in species richness with depth than Chondrichthyans. These richness gradients are accompanied by a continuous species turnover between depths. Fish species coverage with the MiFish-U/E markers is higher than with teleo while threatened species are more sequenced than the others. "Deep-endemic" species, those not ascending to the shallow depth layer, are less sequenced than not threatened species. The number of primer mismatches is not higher for deep-sea species than for shallower ones. eDNA metabarcoding is promising for species detection in the deep-sea to better account for the 3-dimensional structure of the ocean in marine biodiversity monitoring and conservation. However, we argue that sequencing efforts on "deep-endemic" species are needed.

Habitat configurations shape the trophic and energetic dynamics of reef fishes in a tropical-temperate transition zone: implications under a warming future

Understanding the extent to which species' traits mediate patterns of community assembly is key to predict the effect of natural and anthropogenic disturbances on ecosystem functioning. Here, we apply a trait-based community assembly framework to understand how four different habitat configurations (kelp forests, Sargassum spp. beds, hard corals, and turfs) shape the trophic and energetic dynamics of reef fish assemblages in a tropical-temperate transition zone. Specifically, we tested (i) the degree of trait divergence and convergence in each habitat, (ii) which traits explained variation in species' abundances, and (iii) differences in standing biomass (kg ha-1), secondary productivity (kg ha-1 day-1) and turnover (% day-1). Fish assemblages in coral and kelp habitats displayed greater evidence of trait convergence, while turf and Sargassum spp. habitats displayed a higher degree of trait divergence, a pattern that was mostly driven by traits related to resource use and thermal affinity. This filtering effect had an imprint on the trophic and energetic dynamics of reef fishes, with turf habitats supporting higher fish biomass and productivity. However, these gains were strongly dependent on trophic guild, with herbivores/detritivores disproportionately contributing to among-habitat differences. Despite these perceived overall gains, turnover was decoupled for fishes that act as conduit of energy to higher trophic levels (i.e. microinvertivores), with coral habitats displaying higher rates of fish biomass replenishment than turf despite their lower productivity. This has important implications for biodiversity conservation and fisheries management, questioning the long-term sustainability of ecological processes and fisheries yields in increasingly altered marine habitats.

Small predators dominate fish predation in coral reef communities

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

Functional and phylogenetic responses of motile cryptofauna to habitat degradation

Biodiversity of terrestrial and marine ecosystems, including coral reefs, is dominated by small, often cryptic, invertebrate taxa that play important roles in ecosystem structure and functioning. While cryptofauna community structure is determined by strong small-scale microhabitat associations, the extent to which ecological and environmental factors shape these communities are largely unknown, as is the relative importance of particular microhabitats in supporting reef trophodynamics from the bottom up. The goal of this study was to address these knowledge gaps, provided coral reefs are increasingly exposed to multiple disturbances and environmental gradients that influence habitat complexity, condition and ecosystem functioning. We compared the density, biomass, size range, phylogenetic diversity and functional roles of motile cryptofauna in Palau, Western Micronesia, among four coral-derived microhabitats representing various states of degradation (live coral [Acropora and Pocillopora], dead coral and coral rubble) from reefs along a gradient of effluent exposure. In total, 122 families across ten phyla were identified, dominated by the Arthropoda (Crustacea) and Mollusca. Cryptofauna biomass was greatest in live Pocillopora, while coral rubble contained the greatest density and diversity. Size ranges were broader in live corals than both dead coral and rubble. From a bottom-up perspective, effluent exposure had mixed effects on cryptic communities including a decline in total biomass in rubble. From a top-down perspective, cryptofauna were generally unaffected by predator biomass. Our data show that, as coral reef ecosystems continue to decline in response to more frequent and severe disturbances, habitats other than live coral may become increasingly important in supporting coral reef biodiversity and food webs.

Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes

The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.

Coral diversity matches marine park zonation but not economic value of coral reef sites at St. Eustatius, eastern Caribbean

Stony corals play a key role in the marine biodiversity of many tropical coastal areas as suppliers of substrate, food and shelter for other reef organisms. Therefore, it is remarkable that coral diversity usually does not play a role in the planning of protected areas in coral reef areas. In the present study we examine how stony coral diversity patterns relate to marine park zonation and the economic value of reefs around St. Eustatius, a small island in the eastern Caribbean, with fisheries and tourism as important sources of income. The marine park contains two no-take reserves. A biodiversity survey was performed at 39 sites, 24 inside the reserves and 15 outside; 22 had a maximum depth >18 m and 17 were shallower. Data on economic value per site were obtained from the literature. Corals were photographed for the verification of identifications made in the field. Coral species richness (n = 49) was highest in the no-take reserves and species composition was mainly affected by maximum depth. No distinct relation is observed between coral diversity and fishery value or total economic value. Based on the outcome of this study we suggest that in future designs of marine park zonation in reef areas, coral diversity should be taken into consideration. This is best served by including reef areas with a continuous depth gradient from shallow flats to deep slopes.

Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient

The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.

Life-history constraints, short adult life span and reproductive strategies in coral reef gobies of the genus Trimma

Body size influences many life-history traits, with small-bodied animals tending to have short life spans, high mortality and greater reproductive effort early in life. In this study, the authors investigated the life-history traits and reproductive strategies of three small-bodied coral reef gobies of the genus Trimma: Trimma benjamini, Trimma capostriatum and Trimma yanoi. The authors found all Trimma species studied attained a small body size of <25 mm, had a short life span of <140 days and experienced high estimated daily mortality of 3.0%-6.7%. Furthermore, the pelagic larval phase accounted for 25.3%-28.5% of the maximum life span, and maturation occurred between 74.1 and 82.1 days at 15.2-15.8 mm, leaving only 35%-43% of the total life span as a reproductively viable adult. All mature individuals had gonad structures consistent with bidirectional sex change, with bisexual gonads including both ovarian and testicular portions separated by a thin wall of connective tissue. In the female and male phases, only ovaries or testes were mature, whereas gonadal tissue of the non-active sex remained. One T. benjamini individual and one T. yanoi individual had ovarian and testicular tissue active simultaneously. The results of this study highlight the life-history challenges small CRFs face on their path to reproduction and reproductive strategies that could be beneficial in fishes with high and unpredictable mortality and short reproductive life spans.

Paternal care regulates the timing, synchrony and success of hatching in a coral reef fish

In oviparous species, the timing of hatching is a crucial decision, but for developing embryos, assessing cues that indicate the optimal time to hatch is challenging. In species with pre-hatching parental care, parents can assess environmental conditions and induce their offspring to hatch. We provide the first documentation of parental hatching regulation in a coral reef fish, demonstrating that male neon gobies (Elacatinus colini) directly regulate hatching by removing embryos from the clutch and spitting hatchlings into the water column. All male gobies synchronized hatching within 2 h of sunrise, regardless of when eggs were laid. Paternally incubated embryos hatched later in development, more synchronously, and had higher hatching success than artificially incubated embryos that were shaken to provide a vibrational stimulus or not stimulated. Artificially incubated embryos displayed substantial plasticity in hatching times (range: 80-224 h post-fertilization), suggesting that males could respond to environmental heterogeneity by modifying the hatching time of their offspring. Finally, paternally incubated embryos hatched with smaller yolk sacs and larger propulsive areas than artificially incubated embryos, suggesting that paternal effects on hatchling phenotypes may influence larval dispersal and fitness. These findings highlight the complexity of fish parental care behaviour and may have important, and currently unstudied, consequences for fish population dynamics.

An integrative phylogenetic approach for inferring relationships of fossil gobioids (Teleostei: Gobiiformes)

The suborder Gobioidei is among the most diverse groups of vertebrates, comprising about 2310 species. In the fossil record gobioids date back to the early Eocene (c. 50 m.y. ago), and a considerable increase in numbers of described species is evident since the middle Miocene (c. 16 m.y. ago). About 40 skeleton-based gobioid species and > 100 otolith-based species have been described until to date. However, assignment of a fossil gobioid species to specific families has often remained tentative, even if well preserved complete specimens are available. The reasons are that synapomorphies that can be recognized in a fossil skeleton are rare (or absent) and that no phylogenetic framework applicable to gobioid fossils exists. Here we aim to overcome this problem by developing a phylogenetic total evidence framework that is suitable to place a fossil skeleton-based gobioid at family level. Using both literature and newly collected data we assembled a morphological character matrix (48 characters) for 29 extant species, representing all extant gobioid families, and ten fossil gobioid species, and we compiled a multi-gene concatenated alignment (supermatrix; 6271 bp) of published molecular sequence data for the extant species. Bayesian and Maximum Parsimony analyses revealed that our selection of extant species was sufficient to achieve a molecular ‘backbone’ that fully conforms to previous molecular work. Our data revealed that inclusion of all fossil species simultaneously produced very poorly resolved trees, even for some extant taxa. In contrast, addition of a single fossil species to the total evidence data set of the extant species provided new insight in its possible placement at family level, especially in a Bayesian framework. Five out of the ten fossil species were recovered in the same family as had been suggested in previous works based on comparative morphology. The remaining five fossil species had hitherto been left as family incertae sedis. Now, based on our phylogenetic framework, new and mostly well supported hypotheses to which clades they could belong can be presented. We conclude that the total evidence framework presented here will be beneficial for all future work dealing with the phylogenetic placement of a fossil skeleton-based gobioid and thus will help to improve our understanding of the evolutionary history of these fascinating fishes. Moreover, our data highlight that increased sampling of fossil taxa in a total-evidence context is not universally beneficial, as might be expected, but strongly depends on the study group and peculiarities of the morphological data.

A 3D perspective on sediment turnover and feeding selectivity in blennies

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.

Clarifying the taxonomy of some cryptic blennies (Blenniidae) in their native and introduced range

Omobranchus punctatus is native to the Indo-Pacific region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identified to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the first genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least five distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confirmed that O. punctatus sensu stricto, O. dispar and O. sewalli correspond to different species that started to diverge about 2.6 Mya. Furthermore, O. sewalli was identified as the invasive species colonizing Atlantic shores. The existence of historical oceanographic barriers, such as the emergence of the Sunda Shelf in the Eastern Indian Ocean during the Pleistocene, and the biological traits of these blennies are the most likely factors responsible for their genetic differentiation and subsequent speciation.

An updated, illustrated inventory of the marine fishes of the US Virgin Islands

The US Virgin Islands (USVI) include St. John and St. Thomas on the Puerto Rican Platform (PRP) and St. Croix, isolated by 2000 m deep water 45 km south of that platform. Previous inventories of the marine fishes of these islands include a comprehensive 2014 checklist of the fishes of St. Croix and a list of the fishes of the PRP produced in 2000. The latter list noted the locations of many records of the plateau's fishes, allowing the construction of a combined inventory for St. John and St. Thomas. Those two islands are treated here as a single faunal unit because they are only 3.5 km apart on a shared shallow shelf with various islets and reefs in between. Here we provide updated information on those two USVI (St. Croix and St. John-Thomas) marine fish faunas. The additions to the St. Croix and St. John-Thomas inventories presented here are based on a combination of information from the two sources indicated above, more recent publications dealing with those faunas, a review of location records on various online sources of biogeographic data, and voucher photographs taken of fishes in the field by authors of this paper and other citizen scientists. This assessment increased the known fauna of St. Croix by 7.5% to 585 species. The inventory for St. John-Thomas increased by 39.9% from 401 species on the 2000 PRP list to 561 with the inclusion of records from other sources. On-site mtDNA (COI) barcodes are available for approximately one-third of the species of the St. John-Thomas fauna, but for only one species collected at St. Croix. A set of underwater photographs of 372 species (34 of them representing the sole record of a species) from St. John-Thomas and of 11 shallow-water species added to the St. Croix fauna is included. These represent occurrence vouchers and also are intended to facilitate future work that builds on the present compendium.

Comparative trophic ecology of microhabitat-associated guilds of reef fishes in the Adriatic Sea

Reef ecosystems are characterized by highly heterogenous habitats and functionally diverse fish communities. Few studies have examined how functional diversity differs among habitats within these communities, i.e., species associated with a specific habitat may have similar trophic ecologies meaning that the functional diversity within the community is driven by habitat diversity or, conversely, high functional diversity within each habitat would indicate that resource segregation also occurs at the habitat level. We used stable isotope ratios of carbon and nitrogen to estimate trophic position, resource use and ontogenetic niche shifts of 15 reef fishes associated with four distinct habitat types (cryptobenthic, epibenthic sand, epibenthic rock and hyperbenthic) on the Croatian coast of the Adriatic Sea. Trophic ecology was quite similar across fish assemblages, but there was strong evidence of niche segregation among fish species within each assemblage showing high functional diversity within each microhabitat. The sampled fish community contained benthic and pelagic resource users, along with multiple intermediate generalists. Consumer stable isotope ratios revealed considerable interspecific variation in resource use among fishes within each habitat type. The cryptobenthic fishes were a notable exception to this trend with the narrow range of resource use values, indicating reliance of these species on a single resource. The greatest diversity of trophic positions within a guild was observed in cryptobenthic and rock-associated epibenthic fishes. The majority of observed ontogenetic variation in studied fish species reflected an increase in benthic resource use and trophic position. However, the degree of ontogenetic variation in trophic ecology of studied species, if present, was generally low, showing no dramatic change in the ecology of any species. The size structuring among guilds was considerable, with cryptobenthic fishes the smallest on average and hyperbenthic fishes the largest, despite guilds having similar ranges of trophic positions.

Are fish communities on coral reefs becoming less colourful?

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.

A, Pouyaud L, Stuart-Smith RD, Sugeha HY, Valentini A, Vigliola L, Vimono IB, Pellissier L, Manel S. Cross-ocean patterns and processes in fish biodiversity on coral reefs through the lens of eDNA metabarcoding

Increasing speed and magnitude of global change threaten the world's biodiversity and particularly coral reef fishes. A better understanding of large-scale patterns and processes on coral reefs is essential to prevent fish biodiversity decline but it requires new monitoring approaches. Here, we use environmental DNA metabarcoding to reconstruct well-known patterns of fish biodiversity on coral reefs and uncover hidden patterns on these highly diverse and threatened ecosystems. We analysed 226 environmental DNA (eDNA) seawater samples from 100 stations in five tropical regions (Caribbean, Central and Southwest Pacific, Coral Triangle and Western Indian Ocean) and compared those to 2047 underwater visual censuses from the Reef Life Survey in 1224 stations. Environmental DNA reveals a higher (16%) fish biodiversity, with 2650 taxa, and 25% more families than underwater visual surveys. By identifying more pelagic, reef-associated and crypto-benthic species, eDNA offers a fresh view on assembly rules across spatial scales. Nevertheless, the reef life survey identified more species than eDNA in 47 shared families, which can be due to incomplete sequence assignment, possibly combined with incomplete detection in the environment, for some species. Combining eDNA metabarcoding and extensive visual census offers novel insights on the spatial organization of the richest marine ecosystems.

Protecting connectivity promotes successful biodiversity and fisheries conservation

The global decline of coral reefs has led to calls for strategies that reconcile biodiversity conservation and fisheries benefits. Still, considerable gaps in our understanding of the spatial ecology of ecosystem services remain. We combined spatial information on larval dispersal networks and estimates of human pressure to test the importance of connectivity for ecosystem service provision. We found that reefs receiving larvae from highly connected dispersal corridors were associated with high fish species richness. Generally, larval "sinks" contained twice as much fish biomass as "sources" and exhibited greater resilience to human pressure when protected. Despite their potential to support biodiversity persistence and sustainable fisheries, up to 70% of important dispersal corridors, sinks, and source reefs remain unprotected, emphasizing the need for increased protection of networks of well-connected reefs.

Recent dispersal and diversification within the clingfish genus Acyrtus (Actinopterygii: Gobiesocidae), with the description of a new western Atlantic species

Abstract The genus Acyrtus (Gobiesocidae) is represented by four valid species distributed in the western Atlantic, and a recently described fifth species from the eastern Pacific. Here, we describe a new species endemic to Trindade Island, Brazil, and provide the first phylogenetic inference for the genus including all representatives. The new species can be distinguished from all its congeners by meristic and morphometric characters, as well as genetic differences. It presents low genetic diversity and, contrarily to other Trindade Island endemic fishes, shows no evidence of recent population growth. Our phylogeny reveals cryptic species and the paraphyletic nature of Acyrtus, which included Arcos nudus (western Atlantic) in a clade that separated from Arcos erythrops (tropical eastern Pacific) around 20 Mya. The three species found in the Brazilian Province, including one that remains undescribed, form a monophyletic clade which colonized the western South Atlantic around 2.6 Mya. Our study suggests that Arcos nudus should be placed in Acyrtus, and that the relationships among the closely-related Gobiesocidae genera Acyrtus (mostly from the Atlantic Ocean) and Arcos (from the Pacific Ocean) need further investigation.

Gonad morphology of Rhyacichthys aspro (Valenciennes, 1837), and the diagnostic reproductive morphology of gobioid fishes

Rhyacichthys aspro is a “basal” taxon in the Suborder Gobioidei of the teleost order Gobiiformes. We provide detailed descriptions of the reproductive morphology of adult males and females to assess the diagnostic reproductive morphological characters of this speciose clade of bony fishes. Female R. aspro are asynchronous spawners: they are able to spawn more than once in a breeding season. Oocytes are inferred to have short attachment filaments. A conspicuous feature of the external anatomy of the reproductive system (RSy) of female R. aspro is an ornate fimbriate pad upon which the urogenital papilla rests. The male reproductive system is characterized by an intralobar collection system in both the testicular and secretory lobes, termed the “sperm‐collecting canal” and “milt‐collecting canal,” respectively. These may provide additional storage for sperm and milt. The spermatogenic lobe, or testis, is that portion of the male gobioid RSy comprising seminiferous lobules and separate from other RSy components. The secretory lobe is that portion of the male gobioid reproductive system that consists of secretory lobules and is separated from other components of the male RSy. The secretory lobe has also been called, in English, the sperm‐duct gland, accessory gonadal structure, or seminal vesicle, and is endorsed as a synapomorphy of gobioid fishes.

Effects of low pH on the coral reef cryptic invertebrate communities near CO2 vents in Papua New Guinea

Small cryptic invertebrates (the cryptofauna) are extremely abundant, ecologically important, and species rich on coral reefs. Ongoing ocean acidification is likely to have both direct effects on the biology of these organisms, as well as indirect effects through cascading impacts on their habitats and trophic relationships. Naturally acidified habitats have been important model systems for studying these complex interactions because entire communities that are adapted to these environmental conditions can be analyzed. However, few studies have examined the cryptofauna because they are difficult to census quantitatively in topographically complex habitats and are challenging to identify. We addressed these challenges by using Autonomous Reef Monitoring Structures (ARMS) for sampling reef-dwelling invertebrates >2 mm in size and by using DNA barcoding for taxonomic identifications. The study took place in Papua New Guinea at two reef localities, each with three sites at varying distances from carbon dioxide seeps, thereby sampling across a natural gradient in acidification. We observed sharp overall declines in both the abundance (34-56%) and diversity (42-45%) of organisms in ARMS under the lowest pH conditions sampled (7.64-7.75). However, the overall abundance of gastropods increased slightly in lower pH conditions, and crustacean and gastropod families exhibited varying patterns. There was also variability in response between the two localities, despite their close proximity, as one control pH site displayed unusually low diversity and abundances for all invertebrate groups. The data illustrate the complexity of responses of the reef fauna to pH conditions, and the role of additional factors that influence the diversity and abundance of cryptic reef invertebrates.

Range expansion and complete mitochondrial genome of the highfin blenny (Lupinoblennius nicholsi)

BACKGROUND

The highfin blenny, Lupinoblennius nicholsi, is a marine fish species reported in reef and rocky inshore habitats with a disjunct distribution in the southern Gulf of Mexico. Overall, there are very few studies on this species and there is a scarcity of molecular resources for genetic comparisons. We set out to report the first mitochondrial genome for L. nicholsi and report a range expansion for the species.

METHODS AND RESULTS

An individual of L. nicholsi was collected from the coast of Dauphin Island, Alabama. The mitochondrial genome was sequenced, assembled, and annotated. The fragment corresponding to cytochrome oxidase I (COI) was used to compare this sample to other cryptobenthic species of the Atlantic. Finding a mature individual in the coast of Alabama implies this species has a continuous distribution throughout the northern Gulf of Mexico. The mitochondrial genome of L. nicholsi is 16,416 bp in length and comprised of 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding D-loop. Comparisons using COI support the species is L. nicholsi and separate it from other cryptobenthic fishes found in the area.

CONCLUSIONS

This study represents the first mitochondrial genome for this L. nicholsi, serving as a reference for future comparative studies with marine fishes. By reporting the range expansion of this species, this study provides insights on the fish diversity of the Gulf of Mexico.

Coral reef fishes reveal strong divergence in the prevalence of traits along the global diversity gradient

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 re-organization if the ongoing climate-induced reef fragmentation is not halted.

A multi-locus approach to elucidating the evolutionary history of the clingfish Tomicodon petersii (Gobiesocidae) in the Tropical Eastern Pacific

Marine species that are widely distributed in the Tropical Eastern Pacific (TEP) has served as a model for studying biogeographic patterns resulting from the effects of intraregional habitat discontinuities and oceanographic processes on the diversification and evolution of cryptobenthic reef fishes. Tomicodon petersii, a clingfish (Gobiesocidae) endemic to the TEP, is found on very shallow rocky reefs from central Mexico to northern Peru, and in the Cocos and Galapagos islands. We evaluated the effect of likely biogeographic barriers in different parts of the TEP on the diversification process of this species. We used one mitochondrial and three nuclear DNA markers from 112 individuals collected across the distribution range of T. petersii. Our phylogenetic results showed the samples constituted a monophyletic group, with three well-supported, allopatric subgroups: in the Mexican province, the Panamic province (from El Salvador to Ecuador), and the Galapagos Islands. The split between the Mexican and more southerly clades was estimated to occur at the end of the Miocene ca. 5.74 Mya, and the subsequent cladogenetic event separating the Galapagos population from the Panamic population at the junction of the Pliocene and Pleistocene, ca. 2.85 Mya. The species tree, Bayesian species delimitation tests (BPP), STACEY, and substantial genetic distances separating these three populations indicate that these three independent evolutionary units likely include two unnamed species. The cladogenetic events that promoted the formation of those genetically differentiated groups are consistent with disruptive effects on gene flow of habitat discontinuities and oceanographic processes along the mainland shoreline in the TEP and of ocean-island isolation, in conjunction with the species intrinsic life-history characteristics.

Regional heterogeneity in coral species richness and hue reveals novel global predictors of reef fish intra-family diversity

Habitat heterogeneity shapes biological communities, a well-known process in terrestrial ecosystems but substantially unresolved within coral reef ecosystems. We investigated the extent to which coral richness predicts intra-family fish richness, while simultaneously integrating a striking aspect of reef ecosystems-coral hue. To do so, we quantified the coral richness, coral hue diversity, and species richness within 25 fish families in 74 global ecoregions. We then expanded this to an analysis of all reef fishes (4465 species). Considering coral bleaching as a natural experiment, we subsequently examined hue's contribution to fish communities. Coral species and hue diversity significantly predict each family's fish richness, with the highest correlations (> 80%) occurring in damselfish, butterflyfish, emperors and rabbitfish, lower (60-80%) in substrate-bound and mid-water taxa such as blennies, seahorses, and parrotfish, and lowest (40-60%) in sharks, morays, grunts and triggerfish. The observed trends persisted globally. Coral bleaching's homogenization of reef colouration revealed hue's contribution to maintaining fish richness, abundance, and recruit survivorship. We propose that each additional coral species and associated hue provide added ecological opportunities (e.g. camouflage, background contrast for intraspecific display), facilitating the evolution and co-existence of diverse fish assemblages.