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The concept of dominance is frequently used to describe changes in rapidly reconfiguring ecosystems, but the definition of dominance can vary widely among studies. Using coral reefs as a model, we use extensive benthic composition data to explore how variability in applying dominance concepts can shape perceptions. We reveal that coral dominance is sensitive to the exclusion of key algal groups and the categorization of other benthic groups, with ramifications for detecting an ecosystem phase shift. For example, ignoring algal turf inflates the dominance of hard and soft corals in the benthic habitats underpinning reef ecosystems. We need a consensus on how dominance concepts are applied so that we can build a more comprehensive understanding of ecosystem shifts across a broad range of aquatic and terrestrial settings. For reefs, we highlight the benefits of comprehensive and inclusive surveys for evaluating and managing the altered ecosystem states that are emerging in the Anthropocene.

The Great Barrier Reef (GBR)—the largest coral reef ecosystem in the world—supports over 1,200 fish species with some of the highest population densities and diversities observed in vertebrates, offering a high potential for virus transmission among species. As such, the GBR represents an exceptional natural ecosystem to determine the impact of host community diversity on virus evolution and emergence. In recent decades, the GBR has also experienced significant threats of extinction, making it one of the most vulnerable ecosystems on the planet. Despite the global importance of the GBR, our understanding of virus diversity and connectivity in tropical reef fishes remains poor. Here, we employed metatranscriptomic sequencing to reveal the viromes of sixty-one reef fish species. This identified transcripts representing 132 putative viral sequences, 38 of which exhibited strong phylogenetic relationships with known vertebrate-associated viral genera, including a novel Santee-Cooper ranavirus (Iridoviridae). We found little evidence for virus transmission between fish species living within a very restricted geographical space—a 100-m2 coral reef ecosystem—suggesting that there might be important host barriers to successful cross-species transmission despite regular exposure. We also identified differences in virome composition among reef fish families, such that cryptobenthic reef fishes—characterized by small body sizes and short life spans—exhibited greater virome richness compared to large reef fishes. This study suggests that there are important barriers to cross-species virus transmission and that successful emergence in a reef fish community likely requires active host adaptation, even among closely related host species.

In complex, diverse ecosystems, one is faced with an exceptionally challenging decision: which species to examine first and why? This raises the question: Is there evidence of subconscious biases in study species selection? Likewise, is there evidence of this bias in selecting methods, locations, and times? We addressed these questions by surveying the literature on the most diverse group of vertebrates (fishes) in an iconic high-diversity ecosystem (coral reefs). The evidence suggests that we select study species that are predominantly yellow. Reef fish studies also selectively examine fishes that are behaviorally bold and in warm, calm, attractive locations. Our findings call for a reevaluation of study species selection and methodological approaches, recognizing the potential for subconscious biases to drive selection for species that are attractive rather than important and for methods that give only a partial view of ecosystems. Given the challenges faced by high-diversity ecosystems, we may need to question our decision-making processes.

SynopsisTeeth facilitate the acquisition and processing of food in most vertebrates. However, relatively little is known about the functions of the diverse tooth morphologies observed in fishes. Piscivorous fishes (fish-eating fish) are crucial in shaping community structure and rely on their oral teeth to capture and/or process prey. However, how teeth are utilized in capturing and/or processing prey remains unclear. Most studies have determined the function of teeth by assessing morphological traits. The behavior during feeding, however, is seldom quantified. Here, we describe the function of teeth within piscivorous fishes by considering how morphological and behavioral traits interact during prey capture and processing. This was achieved through aquarium-based performance experiments, where prey fish were fed to 12 species of piscivorous fishes. Building on techniques in forensic odontology, we incorporate a novel approach to quantify and categorize bite damage on prey fish that were extracted from the piscivore’s stomachs immediately after being ingested. We then assess the significance of morphological and behavioral traits in determining the extent and severity of damage inflicted on prey fish. Results show that engulfing piscivores capture their prey whole and head-first. Grabbing piscivores capture prey tail-first using their teeth, process them using multiple headshakes and bites, before spitting them out, and then re-capturing prey head-first for ingestion. Prey from engulfers sustained minimal damage, whereas prey from grabbers sustained significant damage to the epaxial musculature. Within grabbers, headshakes were significantly associated with more severe damage categories. Headshaking behavior damages the locomotive muscles of prey, presumably to prevent escape. Compared to non-pharyngognaths, pharyngognath piscivores inflict significantly greater damage to prey. Overall, when present, oral jaw teeth appear to be crucial for both prey capture and processing (immobilization) in piscivorous fishes.

Revealing the determinants of virome composition is central to placing disease emergence in a broader evolutionary context. Fish are the most species-rich group of vertebrates and so provide an ideal model system to study the factors that shape virome compositions and their evolution. We characterized the viromes of nineteen wild-caught species of marine fish using total RNA sequencing (meta-transcriptomics) combined with analyses of sequence and protein structural homology to identify divergent viruses that often evade characterization. From this, we identified twenty-five new vertebrate-associated viruses and a further twenty-two viruses likely associated with fish diet or their microbiomes. The vertebrate-associated viruses identified here included the first fish virus in the

The Labridae (including wrasses, the Odacidae and the Scaridae) is a species-rich group of perciform fishes whose members are prominent inhabitants of warm-temperate and tropical reefs worldwide. We analyse functionally relevant morphometrics for the feeding apparatus of 130 labrid species found on the Great Barrier Reef and use these data to explore the morphological and mechanical basis of trophic diversity found in this assemblage. Morphological measurements were made that characterize the functional and mechanical properties of the oral jaws that are used in prey capture and handling, the hyoid apparatus that is used in expanding the buccal cavity during suction feeding, and the pharyngeal jaw apparatus that is used in breaking through the defences of shelled prey, winnowing edible matter from sand and other debris, and pulverizing the algae, detritus and rock mixture eaten by scarids (parrotfishes). A Principal Components Analysis on the correlation matrix of a reduced set of ten variables revealed complete separation of scarids from wrasses on the basis of the former having a small mouth with limited jaw protrusion, high mechanical advantage in jaw closing, and a small sternohyoideus muscle and high kinematic transmission in the hyoid four-bar linkage. Some scarids also exhibit a novel four-bar linkage conformation in the oral jaw apparatus. Within wrasses a striking lack of strong associations was found among the mechanical elements of the feeding apparatus. These weak associations resulted in a highly diverse system in which functional properties occur in many different combinations and reflect variation in feeding ecology. Among putatively monophyletic groups of labrids, the cheilines showed the highest functional diversity and scarids were moderately diverse, in spite of their reputation for being trophically monomorphic and specialized. We hypothesize that the functional and ecological diversity of labrids is due in part to a history of decoupled evolution of major components of the feeding system (i.e. oral jaws, hyoid and pharyngeal jaw apparatus) as well as among the muscular and skeletal elements of each component.

The fossil record of the Pomacentridae has been based on species from six genera. The status of these taxa is reviewed. Only two are tentatively accepted as belonging to the Pomacentridae: Chromis savornini from the Miocene of Algeria and Izuus nakamurai from the Miocene of Japan. In addition, a new genus and species Palaeopomacentrus orphae is described from the lower Middle Eocene of Monte Bolca, Northern Italy. This is the first substantiated record of a pomacentrid from the Eocene, and represents the oldest record of the family.