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Live corals are the key habitat forming organisms on coral reefs, contributing to both biological and physical structure. Understanding the importance of corals for reef fishes is, however, restricted to a few key families of fishes, whereas it is likely that a vast number of fish species will be adversely affected by the loss of live corals. This study used data from published literature together with independent field based surveys to quantify the range of reef fish species that use live coral habitats. A total of 320 species from 39 families use live coral habitats, accounting for approximately 8 % of all reef fishes. Many of the fishes reported to use live corals are from the families Pomacentridae (68 spp.) and Gobiidae (44 spp.) and most (66 %) are either planktivores or omnivores. 126 species of fish associate with corals as juveniles, although many of these fishes have no apparent affiliation with coral as adults, suggesting an ontogenetic shift in coral reliance. Collectively, reef fishes have been reported to use at least 93 species of coral, mainly from the genus Acropora and Porities and associate predominantly with branching growth forms. Some fish associate with a single coral species, whilst others can be found on more than 20 different species of coral indicating there is considerable variation in habitat specialisation among coral associated fish species. The large number of fishes that rely on coral highlights that habitat degradation and coral loss will have significant consequences for biodiversity and productivity of reef fish assemblages.

Marine vegetated habitats such as seagrass, mangroves, and macroalgae are common along tropical coastlines globally and provide habitats for a diversity of fishes, including juvenile fish and species found on coral reefs. Understanding the use of these habitats by different fish species and life stages is fundamental to spatial planning, fisheries management, and conservation. While previous studies have focused on the habitat potential of seagrass, macroalgae, or mangroves for coral reef fish independently, it is important to consider their combined roles, as tropical seascapes are often mosaics of such habitats. In this study, we evaluated habitat associations across life stages for fish species in coral reefs, seagrasses, macroalgae, and mangroves in Saudi Arabia’s central Red Sea. Through in situ visual surveys, we documented 36% of local coral reef fish species in one or more vegetated habitats, with the fraction of coral reef species utilizing macroalgae or seagrass much greater than that of mangroves (29%, 18%, and 6%, respectively). Mangroves hosted mainly juvenile fish (83% of observed population) and macroalgae hosted the largest proportion of herbivores (39% of observed population), suggesting that each environment offers different combinations of resources (food and shelter), and a mix of these habitats could support biological connectivity across a seascape. Species targeted by local fisheries made up 37% of the species documented in vegetated habitats. The use of multiple habitat types by juvenile and commercially important fishes in the Red Sea underscores the need for a holistic approach to habitat protection.

Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.

Al Wajh Bank in the northern Red Sea contains an extensive coral reef system that potentially supports a novel fish community. The large (1500km2) and shallow (< 40m depth) lagoon experiences greater temperature and salinity fluctuations, as well as higher turbidity, than most other Red Sea reefs. Since these conditions often influence coral community structure and introduce physiological challenges to its resident organisms, changes in reef-associated fishes are expected. We present critical baseline data on fish biodiversity and benthic composition for the Al Wajh Bank. Underwater visual census of conspicuous fishes and standardized collections of cryptobenthic fishes were combined to provide a comprehensive assessment of these fish communities. We documented 153 fish species and operational taxonomic units, including undescribed species, within 24 families on reefs largely dominated by hard coral and soft sediment (39% and 32% respectively). The families Pomacentridae and Gobiidae contributed the most towards fish diversity and abundance. Bray-Curtis dissimilarity distances among sampled sites suggest a distinctive fish community within the lagoon, and coefficients of variation for each species show high variation in their distribution across the lagoon. Species accumulation curves predict that additional sampling would document many more species throughout Al Wajh. Our findings provide the most extensive biodiversity survey of fishes from this region to date and record the condition of the reef prior to major coastal development planned to occur in the near future.

Understanding species-specific resource requirements is paramount in managing and protecting biodiversity in a world where environmental quality is in decline. Dietary data can inform predator–prey relationships and how changes in prey availability impact different species. However, for many coral reef fishes, prey and predatory events can be difficult to observe and identify, both in situ and within examined stomach samples. Here we applied DNA metabarcoding of stomach content samples for 11 Red Sea butterflyfish species to identify the diversity of dietary components that these primarily benthic feeding fish consume across coral reefs. Detections based on 18S and COI sequences from partially digested stomach contents significantly increased the resolution and diversity of the known diet for this group of fish, which included cryptic prey that are difficult to visually document due to soft parts or morphological ambiguity. In addition to scleractinian corals and other Cnidaria, the obligate corallivore species fed on a wide range of benthic organisms, whereas facultative species displayed a broader diet with crustaceans, tunicates, and worms contributing to samples. While a number of individuals contained DNA that could not be confidently identified using this method, the proportion of unidentifiable sequences was relatively low across butterflyfish species. The COI marker identified the importance of soft corals in the diet for two hard coral specialists; Chaetodonmelannotus and Chaetodonsemilarvatus, with soft coral detected in over half of the individuals and contributing significantly to the number of DNA sequence reads within their gut. Notably, five prey items identified to the species level were detected that are currently not documented in the Red Sea. Our analysis revealed that the diet of different species of butterflyfish significantly overlaps, with all species deriving most of their diet from the phylum Cnidaria (hard and soft coral, anemones) and symbiotic Symbiodiniaceae algae. Furthermore, accumulation curves suggest that all study species may feed on an even greater fraction of the benthos, likely driven by the availability and diversity of each individual/pair’s territory. This approach increases the known dietary resolution and diversity of these key reef fishes and further enhances our understanding of the relationship between butterflyfish and benthic organisms.

Surveys to document coral-reef fish assemblages are often limited to visually conspicuous species, thus excluding a significant proportion of the biodiversity. Through standardized collections of cryptobenthic reef fishes in the central and southern Red Sea, a total of 238 species and operational taxonomic units (OTUs) from 35 families were collected. Abundance and species richness increased by 60 and 30%, respectively, from north to south, and fish community composition differed between the two regions and with proximity to shore in the central region. Models suggest regional influences in fish communities, with latitudinal patterns influenced by key coral groups (Acropora, Pocilloporidae) and variation in environmental parameters (chlorophyll a, sea surface temperature, salinity). This study illustrates the limited taxonomic resolution in this group and in this region, and the need to expand baseline data for this under-studied assemblage. To assist in advancing this initiative, we have produced a catalogue of specimens, archived photographs, and established a DNA sequence library based on cytochrome-c oxidase subunit-I barcodes for all OTUs.

For many animals, affiliative relationships such as pair bonds form the foundation of society and are highly adaptive. Animal systems amenable for comparatively studying pair bonding are important for identifying underlying biological mechanisms, but mostly exist in mammals. Better establishing fish systems will enable comparison of pair bonding mechanisms across taxonomically distant lineages that may reveal general underlying mechanistic principles. We examined the utility of wild butterflyfishes (f: Chaetodontidae; g: Chaetodon) for comparatively studying pair bonding. Using stochastic character mapping, we provide the first analysis of the evolutionary history of butterflyfish sociality, revealing that pairing is ancestral, with at least seven independent transitions to gregarious grouping and solitary behavior since the late Miocene. We then formally verified social systems in six sympatric and wide-spread species representing a clade with one ancestrally reconstructed transition from paired to solitary grouping at Lizard Island, Australia. In situ observations of the size, selective affiliation and aggression, fidelity, and sex composition of social groups confirmed that Chaetodon baronessa, C. lunulatus, and C. vagabundus are predominantly pair bonding, whereas C. rainfordi, C. plebeius, and C. trifascialis are predominantly solitary. Even in the predominantly pair bonding species, C. lunulatus, a proportion of adults (15%) are solitary. Importantly, inter- and intra-specific differences in social systems do not co-vary with other previously established attributes, including parental care. Hence, the proposed butterflyfish populations are promising for inter- and intra-species comparative analyses of pair bonding and its mechanistic underpinnings. Avenues for further developing the system are proposed, including determining whether the aforementioned utility of these species applies across their geographic disruptions.

A new species of the gobiid genus Trimma is described from the Farasan Banks in the southeastern Red Sea. The new species is characterized by having a predorsal midline with 7–8 scales, the fifth pelvic-fin ray unbranched, cheek and opercle scaleless, all pectoral-fin rays unbranched, and a dorsal fin VI + I,7, without elongate spines. In life, the species is bright yellow throughout, with a distinctive yellow-green longitudinal band in the central third of the dorsal fins. The new species inhabits caves on exposed offshore reefs at depths between 15 and 30 m where it occurs in small groups of up to 10 individuals. The new species appears to be sister to T. winchi from the western Indian Ocean. We also present a multilocus phylogeny (COI, 16S, Ptr, S7I1), including all known Red Sea Trimma and 21 non-Red Sea species, and an expanded supermatrix tree with 93 species to place Red Sea endemism in broader context. This brings the total number of Trimma species known from the Red Sea to 10, with eight appearing to be endemic to the region. The high proportion of endemism in the genus is noteworthy, even for the Red Sea, which has one of the highest proportions of endemic reef fishes in the Indo-Pacific. Moreover, K2P distances in the two widespread species suggest they may also represent cryptic endemic species, but further analyses are needed. The new species is currently known only from the Farasan Banks region despite extensive sampling along the Saudi Arabian Red Sea coast.

Identifying relationships between fishes and their environment is an integral part of understanding coral reef ecosystems. However, this information is lacking for many species, particularly in understudied and remote regions. With coral reefs continuing to face environmental pressures, insight into abundance and distribution patterns along with resource use of fish communities will aid in advancing our ecological understanding and management processes. Based on ecological surveys of hawkfish assemblages (Family: Cirrhitidae) in the Red Sea, we reveal distinct patterns in the distribution and abundance across the continental shelf, wave exposure, and with depth, particularly in the four colour morphs of Paracirrhites forsteri. Distinct patterns were observed among hawkfishes, with higher abundance of all species recorded on reefs farther from shore and on wave exposed reef zones. Cirrhitus spilotoceps was only recorded on the exposed crest, but unlike the other species, did not associate with live coral colonies. Overall, the most abundant species was P. forsteri. This species exploited a variety of habitats but showed an affinity for complex habitats provided by live and dead coral colonies. No difference in habitat use was observed among the four colour morphs, but distinct patterns were apparent in distribution and abundance with depth. This study suggests that in addition to P. forsteri exhibiting diverse colour morphologies, these various morphotypes appear to have corresponding ecological differences in the Red Sea. To better understand this, further studies are needed to identify what these differences extend to and the mechanisms involved.

Tropical seagrass meadows are highly productive ecosystems that thrive in oligotrophic environments. The Red Sea is characterized by strong N-S latitudinal nutrient and temperature gradients, which constrain pelagic productivity. To date, the influence of these natural gradients have not been assessed in metabolic rates for local seagrass communities. Here we report metabolic rates (gross primary production, respiration, and net community production) in four common species of seagrass (Halodule uninervis, Halophila ovalis, Halophila stipulacea, and Thalassia hemprichii) along latitudinal and thermal gradients in the Red Sea. In addition, we quantified leaf nutrient concentration (nitrogen, phosphorous, and iron), and correlate this with latitude. Our results show that average metabolic rates and aboveground biomass of seagrass meadows in the Red Sea were generally in the lower range when compared to global values reported for the same species forming meadows. The optimum temperature of Red Sea seagrass meadows varied among species with declines along the sequence: H. stipulacea > T. hemprichii > H. uninervis ~ H. ovalis. Gross primary production for H. uninervis – a seagrass thermophile – was lowest in higher latitudes and increased toward lower latitudes during the summer months. While temperature was identified as a strong driver of metabolic rates across seagrass meadows, leaf concentration of phosphorous and iron (but not nitrogen), were below nutrient sufficiency thresholds, indicating these two elements might be limiting for seagrass meadows in the Red Sea.