Dating the evolutionary origins of wrasse lineages (Labridae) and the rise of trophic novelty on coral reefs

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.

Parrotfishes (Teleostei: Labridae: Scarini) of the Socotra Archipelago: Diversity and distributional biogeography, including a range extension of Scarus zufar Randall & Hoover, 1995

An updated account of the diversity of parrotfishes from the Socotra Archipelago is provided. Fourteen species are positively recorded based on underwater observations, photography and collections, including confirmations of three species which were previously only tentatively recorded: Scarus falcipinnis(Playfair, 1868), Scarus scaber Valenciennes, 1840 and Scarus tricolorBleeker, 1847. The distribution of Scarus zufar Randall & Hoover, 1995, previously known only from coastal waters of southern Oman, Pakistan and Bangladesh, is extended to the Archipelago, with Abd al-Kuri Island representing the westernmost edge of its known range. Visual records of three additional species are yet to be documented. With 1417species the Archipelago approximates the modal richness range of 1518 species for Arabian ecoregions. A species account, accompanied by photographs, provides distinctive characters, distribution details in the Arabian region, and general remarks for each species. The distributional biogeography of the family pertinent to the Socotra Archipelago and the Arabian region is analysed in the context of the Western Indian Ocean. Three main Arabian units are identified: A Red Sea unit spans the combined Red Sea ecoregions and the western Gulf of Aden; a Socotra unit covers south-eastern Arabia including the Archipelago, the eastern Gulf of Aden and southern Oman; and a Gulf unit combines the Arabian/Persian Gulf, the Gulf of Oman, and putatively central Oman. These units form a discrete pan-Arabian cluster within the wider Western Indian Ocean. The Socotra unit resembles more strongly the Gulf unit than the Red Sea unit. Parrotfishes thus contrast overall distributional patterns of reef fishes in Arabia.

Beaks promote rapid morphological diversification along distinct evolutionary trajectories in labrid fishes (Eupercaria: Labridae)

The upper and lower jaws of some wrasses (Eupercaria: Labridae) possess teeth that have been coalesced into a strong durable beak that they use to graze on hard coral skeletons, hard-shelled prey, and algae, allowing many of these species to function as important ecosystem engineers in their respective marine habitats. While the ecological impact of the beak is well understood, questions remain about its evolutionary history and the effects of this innovation on the downstream patterns of morphological evolution. Here we analyze 3D cranial shape data in a phylogenetic comparative framework and use paleoclimate modeling to reconstruct the evolution of the labrid beak across 205 species. We find that wrasses evolved beaks three times independently, once within odacines and twice within parrotfishes in the Pacific and Atlantic Oceans. We find an increase in the rate of shape evolution in the Scarus+Chlorurus+Hipposcarus (SCH) clade of parrotfishes likely driven by the evolution of the intramandibular joint. Paleoclimate modeling shows that the SCH clade of parrotfishes rapidly morphologically diversified during the middle Miocene. We hypothesize that possession of a beak in the SCH clade coupled with favorable environmental conditions allowed these species to rapidly morphologically diversify.

The evolution of fast-growing coral reef fishes

Individual growth is a fundamental life history trait^1-4, yet its macroevolutionary trajectories have rarely been investigated for entire animal assemblages. Here we analyse the evolution of growth in a highly diverse vertebrate assemblage-coral reef fishes. We combine state-of-the-art extreme gradient boosted regression trees with phylogenetic comparative methods to detect the timing, number, location and magnitude of shifts in the adaptive regime of somatic growth. We also explored the evolution of the allometric relationship between body size and growth. Our results show that the evolution of fast growth trajectories in reef fishes has been considerably more common than the evolution of slow growth trajectories. Many reef fish lineages shifted towards faster growth and smaller body size evolutionary optima in the Eocene (56-33.9 million years ago), pointing to a major expansion of life history strategies in this Epoch. Of all lineages examined, the small-bodied, high-turnover cryptobenthic fishes shifted most towards extremely high growth optima, even after accounting for body size allometry. These results suggest that the high global temperatures of the Eocene⁵ and subsequent habitat reconfigurations⁶ might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems.

A marine cleaning mutualism provides new insights in biological market dynamics

Most mutually beneficial social interactions (cooperation within species, mutualism between species) involve some degree of partner choice. In an analogy to economic theory as applied to human trading practices, biological market theory (BMT) focuses on how partner choice affects payoff distributions among non-human traders. BMT has inspired a great diversity of research, including research on the mutualism between cleaner fish Labroides dimidiatus and other marine fish, their 'clients'. In this mutualism, clients have ectoparasites removed and cleaners obtain food in return. We use the available data on L. dimidiatus cleaner-client interactions to identify avenues for future expansion of BMT. We focus on three main topics, namely how partner quality interacts with supply-to-demand ratios to affect service quality, the role of threats and forms of forceful intervention, and the potential role of cognition. We consider it essential to identify the specifics of each biological market as a basis for the development of more sophisticated BMT models. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes

Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (lws) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. Lws is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no lws expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased lws expression) only emerged in association with algivory but never with zooplanktivory. Higher lws expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.

Rising from the Ashes: The Biogeographic Origins of Modern Coral Reef Fishes

During the excavation of Mayan tombs, little did the archaeologists know that the fossils they discovered in the tomb stones would fundamentally alter our understanding of the earliest origins of coral reef fishes. Located just 500 kilometers from the point where an asteroid impact reconfigured the world's biological systems 66 million years ago, we find the earliest origins of three typical reef fish groups. Their presence in Mexico just 3 million years after this impact finally reconciles the conflict between the fossil and phylogenetic evidence for the earliest origins of reef fishes. The incorporation of these fossils into a global reconstruction of fish evolutionary history reveals a new picture of the early biogeography of reef fishes, with strong Atlantic links. From locations associated with biological destruction and societal collapse, we see evidence of the origins of one of the world's most diverse and spectacular marine ecosystems: coral reefs.

Complete mitochondrial genome of the six-line wrasse Pseudocheilinus hexataenia (Labriformes, Labridae)

Here, we report the complete mitogenome information of the six-line wrasse Pseudocheilinus hexataenia (Bleeker, 1857). Genome sequencing using the Illumina HiSeq platform allowed the assembly of a circular mitochondrial genome of 17,111 bp from P. hexataenia, consisting of 54% AT nucleotides, 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a putative control region in the typical Labriformes gene composition. The gene order of the P. hexataenia mitochondrion was identical to that of the Labridae mitogenomes. Phylogenetic reconstruction places P. hexataenia with a close relationship with the mitogenome of the goldsinny wrasse, Ctenolabrus rupestris.

Redescription of Conniella apterygia Allen and its reassignment in the genus Cirrhilabrus Temminck and Schlegel (Teleostei: Labridae), with comments on cirrhilabrin pelvic morphology

Conniella apterygia is redescribed from re-examination of the holotype, two paratypes, and six additional specimens. The genus is closely allied to Cirrhilabrus, sharing similarities in general morphological and meristic details, but is separated from Cirrhilabrus and most other labrid fishes in lacking pelvic fins and a pelvic girdle. Recent molecular phylogenetic studies have provided strong evidence for the deep nesting of Conniella within Cirrhilabrus, contradicting its generic validity and suggesting that the loss of pelvic elements is autapomorphic. Consequently, the species is redescribed and assigned to the genus Cirrhilabrus, as Cirrhilabrus apterygia new combination. The pelvic morphologies of related cirrhilabrin labrids are discussed, and a new synapomorphy is identified for Paracheilinus.

Phylogeny, body morphology, and trophic level shape intestinal traits in coral reef fishes

Trait-based approaches are increasingly used to study species assemblages and understand ecosystem functioning. The strength of these approaches lies in the appropriate choice of functional traits that relate to the functions of interest. However, trait-function relationships are often supported by weak empirical evidence.Processes related to digestion and nutrient assimilation are particularly challenging to integrate into trait-based approaches. In fishes, intestinal length is commonly used to describe these functions. Although there is broad consensus concerning the relationship between fish intestinal length and diet, evolutionary and environmental forces have shaped a diversity of intestinal morphologies that is not captured by length alone.Focusing on coral reef fishes, we investigate how evolutionary history and ecology shape intestinal morphology. Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area.We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles.Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.

Chromosome-level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes

Wrasses are dominant components of major coral reef systems. Among wrasses, Cheilinus undulatus is an endangered species with high economic and ecological value that exhibits sex reversal of females to males, while sexual selection occurs in breeding aggregations. However, the molecular-associated mechanism underlying this remains unclear. Opsin gene diversification is regarded as a potent force in sexual selection. Here we present a genome assembly of C. undulatus, using Illumina, Nanopore and Hi-C sequencing. The 1.17 Gb genome was generated from 328 contigs with an N50 length of 16.5 Mb and anchored to 24 chromosomes. In total, 22,218 genes were functionally annotated, and 96.36% of BUSCO genes were fully represented. Transcriptomic analyses showed that 96.79% of the predicted genes were expressed. Transposons were most abundant, accounting for 39.88% of the genome, with low divergence, owing to their evolution with close species ~60.53 million years ago. In total, 567/1,826 gene families were expanded and contracted in the reconstructed phylogeny, respectively. Forty-six genes were under positive selection. Comparative genomic analyses with other fish revealed expansion of opsin SWS2B, LWS1 and Rh2. The elevated duplicates of SWS2B were generated by gene conversions via transposition of transposons followed by nonallelic homologous recombination. Amino acid substitutions of opsin paralogues occurred at key tuning sites, causing a spectral shift in maximal absorbance of visual pigment to capture functional changes. Among these opsin genes, SWS2B-3 and 4 and Rh1 are expressed in the retina. The genome sequence of C. undulatus provides valuable resources for future investigation of the conservation, evolution and behaviour of fishes.

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences

The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.

Phylogenomic Analysis of Concatenated Ultraconserved Elements Reveals the Recent Evolutionary Radiation of the Fairy Wrasses (Teleostei: Labridae: Cirrhilabrus)

The fairy wrasses (genus Cirrhilabrus) are among the most successful of the extant wrasse lineages (Teleostei: Labridae), with their 61 species accounting for nearly 10% of the family. Although species complexes within the genus have been diagnosed on the basis of coloration patterns and synapomorphies, attempts to resolve evolutionary relationships among these groups using molecular and morphological data have largely been unsuccessful. Here we use a phylogenomic approach with a data set comprising 991 ultraconserved elements (UCEs) and mitochondrial COI to uncover the evolutionary history and patterns of temporal and spatial diversification of the fairy wrasses. Our analyses of phylogenetic signal suggest that most gene-tree incongruence is caused by estimation error, leading to poor resolution in a summary-coalescent analysis of the data. In contrast, analyses of concatenated sequences are able to resolve the major relationships of Cirrhilabrus. We determine the placements of species that were previously regarded as incertae sedis and find evidence for the nesting of Conniella, an unusual, monotypic genus, within Cirrhilabrus. Our relaxed-clock dating analysis indicates that the major divergences within the genus occurred around the Miocene-Pliocene boundary, followed by extensive cladogenesis of species complexes in the Pliocene-Pleistocene. Biogeographic reconstruction suggests that the fairy wrasses emerged within the Coral Triangle, with episodic fluctuations of sea levels during glacial cycles coinciding with shallow divergence events but providing few opportunities for more widespread dispersal. Our study demonstrates both the resolving power and limitations of UCEs across shallow timescales where there is substantial estimation error in individual gene trees.

Evolutionary determinism and convergence associated with water-column transitions in marine fishes

Repeatable, convergent outcomes are prima facie evidence for determinism in evolutionary processes. Among fishes, well-known examples include microevolutionary habitat transitions into the water column, where freshwater populations (e.g., sticklebacks, cichlids, and whitefishes) recurrently diverge toward slender-bodied pelagic forms and deep-bodied benthic forms. However, the consequences of such processes at deeper macroevolutionary scales in the marine environment are less clear. We applied a phylogenomics-based integrative, comparative approach to test hypotheses about the scope and strength of convergence in a marine fish clade with a worldwide distribution (snappers and fusiliers, family Lutjanidae) featuring multiple water-column transitions over the past 45 million years. We collected genome-wide exon data for 110 (∼80%) species in the group and aggregated data layers for body shape, habitat occupancy, geographic distribution, and paleontological and geological information. We also implemented approaches using genomic subsets to account for phylogenetic uncertainty in comparative analyses. Our results show independent incursions into the water column by ancestral benthic lineages in all major oceanic basins. These evolutionary transitions are persistently associated with convergent phenotypes, where deep-bodied benthic forms with truncate caudal fins repeatedly evolve into slender midwater species with furcate caudal fins. Lineage diversification and transition dynamics vary asymmetrically between habitats, with benthic lineages diversifying faster and colonizing midwater habitats more often than the reverse. Convergent ecological and functional phenotypes along the benthic-pelagic axis are pervasive among different lineages and across vastly different evolutionary scales, achieving predictable high-fitness solutions for similar environmental challenges, ultimately demonstrating strong determinism in fish body-shape evolution.

Complete mitochondrial genome of Iniistius trivittatus and unique variation in two observed inserts between rRNA and tRNA genes in wrasses

BACKGROUND

The family Labridae made up of 519 species in the world. The functional evolution of the feeding-related jaws leaded to differentiation of species, and the pharyngeal jaw apparatus evolved independently, but evolutionary mechanism still remain unaddressed in wrasses. Mitogenomes data can be used to infer genetic diversification and investigate evolutionary history of wrasses, whereas only eight complete mitogenomes in this family have been sequenced to date. Here, we sequenced the complete mitogenomes of Iniistius trivittatus to investigate genetic differentiation among wrasse species.

RESULTS

We sequenced the complete mitogenomes of I. trivittatus using a novel PCR strategy. The I. trivittatus mitogenomes is 16,820 bp in length and includes 13 protein -coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. Compared to eight known mitochondrial genome, 2 additional noncoding regions (lengths of 121 and 107 bp), or so-called inserts, are found in the intergenic regions 12S rRNA - tRNAVal - 16S rRNA. The presumed origin of the two rare inserts is from tRNA- related retrotransposons. Compared with cytochrome b gene, the two insert sequences are highly conserved at the intraspecies level, but they showed significant variation and low similarity (< 70%) at the interspecies level. The insert events were only observed in I. trivittatus by checking the phylogenetic trees based on the complete mitogenomes of Labrida species. This finding provides evidence that in the mitogenomes, retrotransposon inserts result in intraspecific homoplasmy and interspecific heteroplasmy by natural selection and adaptation to various environments.

CONCLUSIONS

This study found additional mitogenome inserts limited in wrasse species. The rRNA genes with inserts might have experienced a selective pressure for adaptation to feeding modes. Such knowledge can enable a better understanding of molecular mechanism underlying morphological evolution in wrasses.

Trophic innovations fuel reef fish diversification

Reef fishes are an exceptionally speciose vertebrate assemblage, yet the main drivers of their diversification remain unclear. It has been suggested that Miocene reef rearrangements promoted opportunities for lineage diversification, however, the specific mechanisms are not well understood. Here, we assemble near-complete reef fish phylogenies to assess the importance of ecological and geographical factors in explaining lineage origination patterns. We reveal that reef fish diversification is strongly associated with species' trophic identity and body size. Large-bodied herbivorous fishes outpace all other trophic groups in recent diversification rates, a pattern that is consistent through time. Additionally, we show that omnivory acts as an intermediate evolutionary step between higher and lower trophic levels, while planktivory represents a common transition destination. Overall, these results suggest that Miocene changes in reef configurations were likely driven by, and subsequently promoted, trophic innovations. This highlights trophic evolution as a key element in enhancing reef fish diversification.

Weak Relationships Between Swimming Morphology and Water Depth in Wrasses and Parrotfish Belie Multiple Selective Demands on Form-Function Evolution

Mechanical tradeoffs in performance are predicted to sculpt macroevolutionary patterns of morphological diversity across environmental gradients. Water depth shapes the amount of wave energy organisms' experience, which should result in evolutionary tradeoffs between speed and maneuverability in fish swimming morphology. Here, we tested whether morphological evolution would reflect functional tradeoffs in swimming performance in 131 species of wrasses and parrotfish (Family: Labridae) across a water depth gradient. We found that maximum water depth predicts variation in pectoral fin aspect ratio (AR) in wrasses, but not in parrotfish. Shallow-water wrasses exhibit wing-like pectoral fins that help with "flapping," which allows more efficient swimming at faster speeds. Deeper water species, in contrast, exhibit more paddle-like pectoral fins associated with enhanced maneuverability at slower speeds. Functional morphology responds to a number of different, potentially contrasting selective pressures. Furthermore, many-to-one mapping may release some traits from selection on performance at the expense of others. As such, deciphering the signatures of mechanical tradeoffs on phenotypic evolution will require integrating multiple aspects of ecological and morphological variation. As the field of evolutionary biomechanics moves into the era of big data, we will be uniquely poised to disentangle the intrinsic and extrinsic predictors of functional diversity.

Chromosomal Evolution and Cytotaxonomy in Wrasses (Perciformes; Labridae)

The wrasses (family Labridae) represent a suitable model to understand chromosomal evolution and to test the efficacy of cytotaxonomy since they display a remarkable karyotypic variation, rarely reported in marine Perciformes, as well as a high number of species and complex systematics. Therefore, we provided new chromosomal data in 5 labrids from South Atlantic (Doratonotus megalepis, Halichoeres dimidiatus, Halichoeres penrosei, Thalassoma noronhanum, and Xyrichtys novacula) and carried out a detailed comparative analysis of karyotypic data in Labridae using multivariate approaches. Basal diploid values (2n = 48) were observed in most of species studied in the present work but D. megalepis (2n = 46), along with distinct karyotype formulae. Single 18S rDNA sites interspersed with GC-rich heterochromatin were also commonly reported except for both Halichoeres species (2 18S rDNA-bearing pairs), following a species-specific pattern. These data show the high rates of chromosomal evolution in wrasses, ranging from microstructural rearrangements to centric fusions. A revision of chromosomal data in Labridae based on multivariate analysis of 74 taxa allowed inferring karyoevolutionary trends within tribes and genera of wrasses. The dendrogram obtained was in agreement with recent systematic hypotheses. In spite of the independent occurrence of some chromosomal rearrangements, karyoevolutionary trends could be identified within tribes of Labridae. Moreover, the karyotypic features are also suitable as cytotaxonomic markers of wrasses.

Trophic separation in planktivorous reef fishes: a new role for mucus?

The feeding apparatus directly influences a species' trophic ecology. In fishes, our understanding of feeding modes is largely derived from studies of rigid structures (i.e. bones, teeth, gill rakers). A recently described lip innovation, however, highlighted the role of soft anatomy in enabling specialized feeding modes. In this study, we explore whether similar diversification may also occur in the soft anatomy of the buccal cavity. Using four key anatomical traits to classify 19 species (14 genera) of wrasses, we evaluated the relationship between anatomical specialization of the buccal cavity and diet. Our data revealed a previously undocumented anatomical adaptation in the mouths of fairy wrasses (Cirrhilabrus): the mucosa throughout the buccal cavity (i.e. anterior to the pharynx) is packed with goblet cells, enabling it to secrete large quantities of mucus in this region; a new trait that, until now, had not been documented in wrasses. This disparity reflects diet differences, with mucus secretion found only in planktivorous Cirrhilabrus that feed predominantly on amorphous organic material (potentially gelatinous organisms). This suggests a cryptic mucus-based resource partitioning in planktivorous wrasses.

The Role of Symbioses in the Adaptation and Stress Responses of Marine Organisms

Ocean ecosystems are experiencing unprecedented rates of climate and anthropogenic change, which can often initiate stress in marine organisms. Symbioses, or associations between different organisms, are plentiful in the ocean and could play a significant role in facilitating organismal adaptations to stressful ocean conditions. This article reviews current knowledge about the role of symbiosis in marine organismal acclimation and adaptation. It discusses stress and adaptations in symbioses from coral reef ecosystems, which are among the most affected environments in the ocean, including the relationships between corals and microalgae, corals and bacteria, anemones and clownfish, and cleaner fish and client fish. Despite the importance of this subject, knowledge of how marine organisms adapt to stress is still limited, and there are vast opportunities for research and technological development in this area. Attention to this subject will enhance our understanding of the capacity of symbioses to alleviate organismal stress in the oceans.

Co-evolution of cleaning and feeding morphology in western Atlantic and eastern Pacific gobies

Cleaning symbioses are mutualistic relationships where cleaners remove and consume ectoparasites from their clients. Cleaning behavior is rare in fishes and is a highly specialized feeding strategy only observed in around 200 species. Cleaner fishes vary in their degree of specialization, ranging from species that clean as juveniles or facultatively as adults, to nearly obligate or dedicated cleaners. Here, we investigate whether these different levels of trophic specialization correspond with similar changes in feeding morphology. Specifically, we model the evolution of cleaning behavior across the family Gobiidae, which contains the most speciose radiation of dedicated and facultative cleaner fishes. We compared the cranial morphology and dentition of cleaners and non-cleaners across the phylogeny of cleaning gobies and found that facultative cleaners independently evolved four times and have converged on an intermediate morphology relative to that of dedicated cleaners and non-cleaning generalists. This is consistent with their more flexible feeding habits. Cleaner gobies also possess a distinct tooth morphology, which suggests they are adapted for scraping parasites off their clients and show little similarity to other cleaner clades. We propose that evolutionary history and pre-adaptation underlie the morphological and ecological diversification of cleaner fishes.

Characterization of the complete mitochondrial genome of the coral reef fish, Hemigymnus melapterus (Pisces: Labridae) and its phylogenetic implications

Hemigymnus melapterus belongs to the family Labridae, which inhabit in coastal and continental shelf waters. The entire mitochondrial genome of H. melapterus is 16,527 base pairs (bp) in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The overall base composition is 27.56% A, 25.58% T, 30.02% C, and 16.85% G, showing AT-rich feature (53.14%). Phylogenetic analysis based on 13 protein-coding genes shows the H. melapterus has the closest evolutionary relationship with Stethojulis strigiventer. This work provides valuable genome variation information, which will be useful for phylogenetic analysis and population genetics research.

Do Coral Reefs Promote Morphological Diversification? Exploration of Habitat Effects on Labrid Pharyngeal Jaw Evolution in the Era of Big Data

Coral reefs are complex marine habitats that have been hypothesized to facilitate functional specialization and increased rates of functional and morphological evolution. Wrasses (Labridae: Percomorpha) in particular, have diversified extensively in these coral reef environments and have evolved adaptations to further exploit reef-specific resources. Prior studies have found that reef-dwelling wrasses exhibit higher rates of functional evolution, leading to higher functional variation than in non-reef dwelling wrasses. Here, we examine this hypothesis in the lower pharyngeal tooth plate of 134 species of reef and non-reef-associated labrid fishes using high-resolution morphological data in the form of micro-computed tomography scans and employing three-dimensional geometric morphometrics to quantify shape differences. We find that reef-dwelling wrasses do not differ from non-reef-associated wrasses in morphological disparity or rates of shape evolution. However, we find that some reef-associated species (e.g., parrotfishes and tubelips) exhibit elevated rates of pharyngeal jaw shape evolution and have colonized unique regions of morphospace. These results suggest that while coral reef association may provide the opportunity for specialization and morphological diversification, species must still be able to capitalize on the ecological opportunities to invade novel niche space, and that these novel invasions may prompt rapid rates of morphological evolution in the associated traits that allow them to capitalize on new resources.

Conservation and diversity in expression of candidate genes regulating socially-induced female-male sex change in wrasses

Fishes exhibit remarkably diverse, and plastic, patterns of sexual development, most striking of which is sequential hermaphroditism, where individuals readily reverse sex in adulthood. How this stunning example of phenotypic plasticity is controlled at a genetic level remains poorly understood. Several genes have been implicated in regulating sex change, yet the degree to which a conserved genetic machinery orchestrates this process has not yet been addressed. Using captive and in-the-field social manipulations to initiate sex change, combined with a comparative qPCR approach, we compared expression patterns of four candidate regulatory genes among three species of wrasses (Labridae)-a large and diverse teleost family where female-to-male sex change is pervasive, socially-cued, and likely ancestral. Expression in brain and gonadal tissues were compared among the iconic tropical bluehead wrasse (Thalassoma bifasciatum) and the temperate spotty (Notolabrus celidotus) and kyusen (Parajulus poecilepterus) wrasses. In all three species, gonadal sex change was preceded by downregulation of cyp19a1a (encoding gonadal aromatase that converts androgens to oestrogens) and accompanied by upregulation of amh (encoding anti-müllerian hormone that primarily regulates male germ cell development), and these genes may act concurrently to orchestrate ovary-testis transformation. In the brain, our data argue against a role for brain aromatase (cyp19a1b) in initiating behavioural sex change, as its expression trailed behavioural changes. However, we find that isotocin (it, that regulates teleost socio-sexual behaviours) expression correlated with dominant male-specific behaviours in the bluehead wrasse, suggesting it upregulation mediates the rapid behavioural sex change characteristic of blueheads and other tropical wrasses. However, it expression was not sex-biased in temperate spotty and kyusen wrasses, where sex change is more protracted and social groups may be less tightly-structured. Together, these findings suggest that while key components of the molecular machinery controlling gonadal sex change are phylogenetically conserved among wrasses, neural pathways governing behavioural sex change may be more variable.

The evolution of traits and functions in herbivorous coral reef fishes through space and time

Herbivory by fishes has been identified as a key ecological process shaping coral reefs through time. Although taxonomically limited, herbivorous reef fishes display a wide range of traits, which results in varied ecosystem functions on reefs around the world. Yet, we understand little about how these trait combinations and functions in ecosystems changed through time and across biogeographic realms. Here, we used fossils and phylogenies in a functional ecological framework to reveal temporal changes in nominally herbivorous fish assemblages among oceanic basins in both trait space and lineage richness among functions. We show that the trait space occupied by extant herbivorous fishes in the Indo-Pacific resulted from an expansion of traits from the ancestral Tethyan assemblages. By contrast, trait space in the Atlantic is the result of lineage turnover, with relatively recent colonization by lineages that arose in the east Tethys/Indo-Pacific. From an ecosystem function perspective, the Atlantic supports a depauperate fauna, with few extant herbivorous reef fish lineages performing each function. Indo-Pacific fishes support both more functions and more lineages within each function, with a marked Miocene to Pleistocene expansion. These disparities highlight the importance of history in explaining global variation in fish functional composition on coral reefs.

On Intraspecific and Interspecific Variation in Teleost Scleral Ossification

Scleral ossicles are bony elements found along the eyes of many fishes, amphibians, and reptiles. These bones provide a superficial layer of support to the eye and may facilitate visual acuity. Previous research has shown that scleral ossicle diversity is generally limited among teleosts, but that scleral ossicles have been lost numerous times among teleosts inhabiting benthopelagic habitats (Franz-Odendaal. Anat Rec 291 (2008) 161-168). In this study, we further investigate these patterns of intraspecific and interspecific variation by examining eyes from multiple individuals of 10 riverine teleosts native to Kentucky as well as one population of the Mexican blind cavefish, Astyanax mexicanus, and by re-analyzing a quantitative database of scleral ossicle number and depth preference from over 100 teleosts using newly resolved teleost phylogenies. Consistent with the limited diversity of most teleost families, we find that intraspecific variation in scleral ossicle number and size is virtually nonexistent among the species sampled, although we do find evidence of additional interspecific variation among the Cyprinodontiformes, as well as dramatic intrapopulation variation among cavefish from Chica Cave. Although our data replicates the negative relationship between scleral ossicle number and the depth preference previously found among teleosts (Franz-Odendaal. Anat Rec 291 (2008) 161-168), even when accounting for phylogenetic relationships, our results further reveal that this relationship is relatively weak. We conclude that further sampling may reveal additional interspecific and even intraspecific variation among some groups of teleosts, and that depth could serve as a proxy for other life history traits that more directly influence teleost scleral ossicle diversity such as prey-capture strategies. Anat Rec, 302:1238-1249, 2019. © 2019 Wiley Periodicals, Inc.

Integration and modularity of teleostean pectoral fin shape and its role in the diversification of acanthomorph fishes

Phenotypic integration and modularity describe the strength and pattern of interdependencies between traits. Integration and modularity have been proposed to influence the trajectory of evolution, either acting as constraints or facilitators. Here, we examine trends in the integration and modularity of pectoral fin morphology in teleost fishes using geometric morphometrics. We compare the fin shapes of the highly diverse radiation of acanthomorph fishes to lower teleosts. Integration and modularity are measured using two-block partial least squares analysis and the covariance ratio coefficient between the radial bones and lepidotrichia of the pectoral fins. We show that the fins of acanthomorph fishes are more tightly integrated but also more morphologically diverse and faster evolving compared to nonacanthomorph fishes. The main pattern of shape covariation in nonacanthomorphs is concordant with the main trajectory of evolution between nonacanthomorphs and acanthomorphs. Our findings support a facilitating role for integration during the acanthomorph diversification. Potential functional consequences and developmental mechanisms of fin integration are discussed.

Functional links on coral reefs: Urchins and triggerfishes, a cautionary tale

Urchins are ubiquitous components of coral reefs ecosystems, with significant roles in bioerosion and herbivory. By controlling urchin densities, triggerfishes have been identified as keystone predators. However, the functional linkages between urchins and triggerfishes, in terms of distributional patterns and concomitant effects on ecosystem processes, are not well understood, especially in relatively unexploited systems. To address this we censused urchins and triggerfishes on two cross-shelf surveys on the Great Barrier Reef (GBR) at the same times and locations. We also evaluated the role of urchins in bioerosion. Although urchin abundance and triggerfish biomass varied by 80% and nearly 900% across sites, respectively, this variability was driven primarily by shelf position with no evidence of top-down control on urchins by triggerfishes. Low urchin abundances meant urchins only played a minor role in bioerosion. We highlight the potential variability in functional links, and contributions to ecosystem processes, among regions.

The role of the reef flat in coral reef trophodynamics: Past, present, and future

The reef flat is one of the largest and most distinctive habitats on coral reefs, yet its role in reef trophodynamics is poorly understood. Evolutionary evidence suggests that reef flat colonization by grazing fishes was a major innovation that permitted the exploitation of new space and trophic resources. However, the reef flat is hydrodynamically challenging, subject to high predation risks and covered with sediments that inhibit feeding by grazers. To explore these opposing influences, we examine the Great Barrier Reef (GBR) as a model system. We focus on grazing herbivores that directly access algal primary productivity in the epilithic algal matrix (EAM). By assessing abundance, biomass, and potential fish productivity, we explore the potential of the reef flat to support key ecosystem processes and its ability to maintain fisheries yields. On the GBR, the reef flat is, by far, the most important habitat for turf-grazing fishes, supporting an estimated 79% of individuals and 58% of the total biomass of grazing surgeonfishes, parrotfishes, and rabbitfishes. Approximately 59% of all (reef-wide) turf algal productivity is removed by reef flat grazers. The flat also supports approximately 75% of all grazer biomass growth. Our results highlight the evolutionary and ecological benefits of occupying shallow-water habitats (permitting a ninefold population increase). The acquisition of key locomotor and feeding traits has enabled fishes to access the trophic benefits of the reef flat, outweighing the costs imposed by water movement, predation, and sediments. Benthic assemblages on reefs in the future may increasingly resemble those seen on reef flats today, with low coral cover, limited topographic complexity, and extensive EAM. Reef flat grazing fishes may therefore play an increasingly important role in key ecosystem processes and in sustaining future fisheries yields.

Community assembly of coral reef fishes along the Melanesian biodiversity gradient

The Indo-Pacific is home to Earth’s most biodiverse coral reefs. Diversity on these reefs decreases from the Coral Triangle east through the islands of Melanesia. Despite this pattern having been identified during the early 20^th century, our knowledge about the interaction between pattern and process remains incomplete. To evaluate the structure of coral reef fish communities across Melanesia, we obtained distributional records for 396 reef fish species in five taxa across seven countries. We used hierarchical clustering, nestedness, and multiple linear regression analyses to evaluate the community structure. We also compiled data on life history traits (pelagic larval duration, body size and schooling behavior) to help elucidate the ecological mechanisms behind community structure. Species richness for these taxa along the gradient was significantly related to longitude but not habitat area. Communities are significantly nested, indicating that species-poor communities are largely composed of subsets of the species found on species rich reefs. These trends are robust across taxonomic groups except for the Pomacentridae, which exhibit an anti-nested pattern, perhaps due to a large number of endemic species. Correlations between life history traits and the number of reefs on which species occurred indicate that dispersal and survival ability contribute to determining community structure. We conclude that distance from the Coral Triangle dominates community structure in reef fish; however, conservation of the most species-rich areas will not be sufficient alone to conserve the vivid splendor of this region.

Revision of Eocene electric rays (Torpediniformes, Batomorphii) from the Bolca Konservat-Lagerstätte, Italy, reveals the first fossil embryo in situ in marine batoids and provides new insights into the origin of trophic novelties in coral reef fishes

The Eocene electric ray †Titanonarke Carvalho, 2010 from the Bolca Konservat-Lagerstätte, north-eastern Italy, is redescribed in detail based upon new material from recent excavations. This taxon exhibits a combination of features (large voids between the pectoral and the axial skeleton filled in life by electric organs, anteriorly directed fan-shaped antorbital cartilages, lack of dermal denticles, long prepelvic processes, and rounded basibranchial copula with a small caudal tab) that clearly supports its assignment to the order Torpediniformes. The analysis of new material also demonstrates that the previous apparent absence of typical narcinoid characters used to diagnose †Titanonarke was the result of taphonomic biases. †Titanonarke shares at least three synapomorphies (presence of a rostral fontanelle, low number of ribs, and rostral cartilage connected to the antorbital cartilage through lateral appendices) with the extant genera Benthobatis, Diplobatis, Discopyge and Narcine, with which it forms a clade (family Narcinidae) recognized herein as unquestionably monophyletic. Moreover, based upon a single specimen of †Titanonarke that exhibits a unique combination of morphometric and meristic features, a new species of Eocene numbfish †T. megapterygia sp. nov., is recognized. The presence of several specimens representing different ontogenetic stages of at least two species of numbfishes suggests a close association of this taxon with shallow-water habitats corresponding to coral reefs as hypothesized for the Monte Postale palaeoenvironment. The occurrence of a fossilized marine batoid embryo is reported here for the first time. Moreover, the analysis of the gut contents suggests that the dietary adaptations of †Titanonarke can be related, at least in part, to an opportunistic strategy in the context of abundant larger foraminifera in the Monte Postale palaeobiotope, suggesting that this kind of feeding mode, known to occur in present-day reefs, already was realized 50 million years ago.

Phylogenetic perspectives on reef fish functional traits

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.

Mutualistic cleaner fish maintains high escape performance despite privileged relationship with predators

Predatory reef fishes regularly visit mutualistic cleaner fish (Labroides dimidiatus) to get their ectoparasites removed but show no interest in eating them. The concept of compensated trait loss posits that characters can be lost if a mutualistic relationship reduces the need for a given trait. Thus, selective pressures on escape performance might have relaxed in L. dimidiatus due to its privileged relationship with predators. However, the cost of failing to escape a predatory strike is extreme even if predation events on cleaners are exceptionally rare. Additionally, cleaners must escape from non-predatory clients that regularly punish them for eating mucus instead of parasites. Therefore, strong escape capabilities might instead be maintained in cleaner fish because they must be able to flee when in close proximity to predators or dissatisfied clients. We compared the fast-start escape performance of L. dimidiatus with that of five closely related wrasse species and found that the mutualistic relationship that cleaners entertain with predators has not led to reduced escape performance. Instead, conflicts in cleaning interactions appear to have maintained selective pressures on this trait, suggesting that compensated trait loss might only evolve in cases of high interdependence between mutualistic partners that are not tempted to cheat.

Global ecological success of Thalassoma fishes in extreme coral reef habitats

Phenotypic adaptations can allow organisms to relax abiotic selection and facilitate their ecological success in challenging habitats, yet we have relatively little data for the prevalence of this phenomenon at macroecological scales. Using data on the relative abundance of coral reef wrasses and parrotfishes (f. Labridae) spread across three ocean basins and the Red Sea, we reveal the consistent global dominance of extreme wave‐swept habitats by fishes in the genus Thalassoma, with abundances up to 15 times higher than any other labrid. A key locomotor modification—a winged pectoral fin that facilitates efficient underwater flight in high‐flow environments—is likely to have underpinned this global success, as numerical dominance by Thalassoma was contingent upon the presence of high‐intensity wave energy. The ecological success of the most abundant species also varied with species richness and the presence of congeneric competitors. While several fish taxa have independently evolved winged pectoral fins, Thalassoma appears to have combined efficient high‐speed swimming (to relax abiotic selection) with trophic versatility (to maximize exploitation of rich resources) to exploit and dominate extreme coral reef habitats around the world.

The evolution of fishes and corals on reefs: form, function and interdependence

Coral reefs are renowned for their spectacular biodiversity and the close links between fishes and corals. Despite extensive fossil records and common biogeographic histories, the evolution of these two key groups has rarely been considered together. We therefore examine recent advances in molecular phylogenetics and palaeoecology, and place the evolution of fishes and corals in a functional context. In critically reviewing the available fossil and phylogenetic evidence, we reveal a marked congruence in the evolution of the two groups. Despite one group consisting of swimming vertebrates and the other colonial symbiotic invertebrates, fishes and corals have remarkably similar evolutionary histories. In the Paleocene and Eocene [66-34 million years ago (Ma)] most modern fish and coral families were present, and both were represented by a wide range of functional morphotypes. However, there is little evidence of diversification at this time. By contrast, in the Oligocene and Miocene (34-5.3 Ma), both groups exhibited rapid lineage diversification. There is also evidence of increasing reef area, occupation of new habitats, increasing coral cover, and potentially, increasing fish abundance. Functionally, the Oligocene-Miocene is marked by the appearance of new fish and coral taxa associated with high-turnover fast-growth ecosystems and the colonization of reef flats. It is in this period that the functional characteristics of modern coral reefs were established. Most species, however, only arose in the last 5.3 million years (Myr; Plio-Pleistocene), with the average age of fish species being 5.3 Myr, and corals just 1.9 Myr. While these species are genetically distinct, phenotypic differences are often limited to variation in colour or minor morphological features. This suggests that the rapid increase in biodiversity during the last 5.3 Myr was not matched by changes in ecosystem function. For reef fishes, colour appears to be central to recent diversification. However, the presence of pigment patterns in the Eocene suggests that colour may not have driven recent diversification. Furthermore, the lack of functional changes in fishes or corals over the last 5 Myr raises questions over the role and importance of biodiversity in shaping the future of coral reefs.

Evolution of long-toothed fishes and the changing nature of fish-benthos interactions on coral reefs

Interactions between fishes and the benthos have shaped the development of marine ecosystems since at least the early Mesozoic. Here, using the morphology of fish teeth as an indicator of feeding abilities, we quantify changes over the last 240 million years of reef fish evolution. Fossil and extant coral reef fish assemblages reveal exceptional stasis in tooth design over time, with one notable exception, a distinct long-toothed form. Arising only in the last 40 million years, these long-toothed fishes have bypassed the invertebrate link in the food chain, feeding directly on benthic particulate material. With the appearance of elongated teeth, these specialized detritivores have moved from eating invertebrates to eating the food of invertebrates. Over evolutionary time, fishes have slid back down the food chain.

Tool use by a temperate wrasse, California sheephead Semicossyphus pulcher

Multiple individuals of a temperate reef fish species (California sheephead Semicossyphus pulcher) were observed using an anvil to crush hard-bodied invertebrate prey. Potential implications for this behaviour extend from individuals, which may experience reduced likelihood of injury and increased reproduction, to communities, which could see changes in prey abundance and size-distribution, with particularly important consequences for communities regulated by top-down processes. Until relatively recently, the use of simple tools by fishes was overlooked compared with observations of tool use by primates and birds; however, observations of tool use, and interesting foraging behaviours in general, by aquatic organisms should increase with improved underwater monitoring technology.