Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

Short-wavelength-sensitive 1 (SWS1) opsin gene duplications and parallel visual pigment tuning support ultraviolet communication in damselfishes (Pomacentridae)

Damselfishes (Pomacentridae) are one of the most behaviourally diverse, colourful and species-rich reef fish families. One remarkable characteristic of damselfishes is their communication in ultraviolet (UV) light. Not only are they sensitive to UV, they are also prone to have UV-reflective colours and patterns enabling social signalling. Using more than 50 species, we aimed to uncover the evolutionary history of UV colour and UV vision in damselfishes. All damselfishes had UV-transmitting lenses, expressed the UV-sensitive SWS1 opsin gene, and most displayed UV-reflective patterns and colours. We find evidence for several tuning events across the radiation, and while SWS1 gene duplications are generally very rare among teleosts, our phylogenetic reconstructions uncovered two independent duplication events: one close to the base of the most species-rich clade in the subfamily Pomacentrinae, and one in a single Chromis species. Using amino acid comparisons, we found that known spectral tuning sites were altered several times in parallel across the damselfish radiation (through sequence change and duplication followed by sequence change), causing repeated shifts in peak spectral absorbance of around 10 nm. Pomacentrinae damselfishes expressed either one or both copies of SWS1, likely to further finetune UV-signal detection and differentiation. This highly advanced and modified UV vision among damselfishes, in particular the duplication of SWS1 among Pomacentrinae, might be seen as a key evolutionary innovation that facilitated the evolution of the exuberant variety of UV-reflectance traits and the diversification of this coral reef fish lineage.

DNA barcoding of marine teleost fishes (Teleostei) in Cebu, the Philippines, a biodiversity hotspot of the coral triangle

A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.

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.

Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure, and speciation (Dascyllus). The genus Dascyllus includes a group of small-bodied species, and a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex that is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus, is a widespread and common coral reef fish species found across the tropical Indo-Pacific. Here, we present the first-genome assembly of this species. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the Benchmarking Universal Single-Copy Orthologs score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. We also find that the D. trimaculatus chromosomes are each homologous with single chromosomes of the closely related clownfish species, Amphiprion percula. This assembly will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade.

Species delimitation, molecular phylogeny and historical biogeography of the sweetlips fish (Perciformes, Haemulidae)

The subfamily Plectorhinchinae (sweetlips) is composed of poorly-known species with high commercially and ecologically values that exhibit phenotypic plasticity and various morphologies. Few studies have assessed the validity of sweetlips, intergeneric relationships and evolutionary survey in this subfamily, which have not yet been resolved. This study investigated the DNA sequences of (1) the mitochondrial COI gene to delimit species, and (2) two mitochondrial (COI and Cyt b), and one nuclear (RAG1) markers to infer phylogenetic relationships and evolutionary and biogeographic history. The molecular results could differentiate Diagramma punctatum from the other species, but failed to distinguish D. labiosum as a distinct species with considerably lower genetic distances for the COI (0.53%) and Cyt b (0.51%) markers. However, additional taxonomic investigations are required to shed light on this issue. All previously described nominal species of sweetlips in the northwest Indian Ocean were found to be well supported. The monophyly of Plectorhinchus is not supported and Diagramma pictum and D. punctatum should be assigned to the genus Plectorhinchus. The biogeographic history of Plectorhinchinae likely originated in the Indo-Pacific ca. 34 Ma (30–39 Ma; late Eocene/ middle Oligocene) and subsequently colonised the Western Indian Ocean and the Central Indo-Pacific. Maximum diversification within the subfamily occurred from the middle Miocene to Pliocene, coinciding with dispersal and vicariance events. Diversification was probably driven by both biological and geographical factors.

Divergence in metabolomic profile in clownfish and damselfish skin mucus

Introduction

The clownfish - sea anemone mutualism was suggested to have triggered the adaptive radiation of clownfishes, but the origin of clownfish resistance to stinging tentacles of host anemones remains unclear. The presence of specific compounds in the mucus of clownfishes conferring them the unique ability to prevent nematocyst discharge from their hosts has been the most supported hypothesis. Yet the mystery regarding the types of compounds found in clownfish skin mucus remains unsolved.

Methods

We analyzed the chemical composition of clownfish and damselfish mucus using an untargeted metabolomics (HILIC-HRMS) and lipidomics (RPLC-HRMS) approach.

Results and Discussion

The polar and lipid metabolome signatures were highly specific and allowed to discriminate between the clownfish and damselfish clades. The most discriminative part of the signature was the sphingolipid profile, displaying a broader diversity of ceramides present in significantly higher levels in clownfish mucus. Importantly, the inter-specific variability of metabolic signature was significantly higher in clownfishes, although their diversification is evolutionarily more recent, thus implying the impact of symbiosis on metabolic variability and adaptation. Furthermore, specialists and generalists clownfish species displayed distinctive metabolite signature. Two strict clownfish specialists, which are phylogenetically distant but share the same host species, clustered together based on their molecular signature, suggesting a link with their mutualistic nature. Overall, comparative analyses of metabolic signatures highlight differences in chemical composition of clownfish mucus and provide insight into biochemical pathways potentially implicated in clownfish adaptation to inhabit sea anemones and consequently diversify.

Extraoral Taste Buds on the Paired Fins of Damselfishes

Some fish species have taste buds on the surface of their bodies and fins, as well as in the oral cavity. The extraoral taste system of fish has traditionally been studied in species that inhabit environments and/or employ feeding strategies where vision is limited. Here we examined taste sensation in a new ecological context by investigating the paired fins of damselfish (Pomacentridae), a group of diurnal midwater fishes that inhabit the light-rich waters of coral reefs. Immunohistochemistry demonstrated the presence of taste buds on the paired fins of Chromis viridis, including on the distal tips of elongate leading-edge pelvic fin rays, where they are particularly densely packed, suggesting specialization for chemosensation. Similar anatomical results were also recorded from two other species, Pomacentrus amboinensis and Pomacentrus coelestis. We found that afferent pectoral fin nerves of C. viridis responded to a food-derived stimulus. By investigating the extraoral taste system in a new phylogenetic and ecological context, these results show that taste buds on fins are more widespread amongst fish than previously known and are present even in highly visual environments.

Phylogenomics and body shape morphometrics reveal recent diversification in the goatfishes (Syngnatharia: Mullidae)

Clades of marine fishes exhibit many patterns of diversification, ranging from relatively constant throughout time to rapid changes in the rates of speciation and extinction. The goatfishes (Syngnatharia: Mullidae) are a family of marine, reef associated fishes with a relatively recent origin, distributed globally in tropical and temperate waters. Despite their abundance and economic importance, the goatfishes remain one of the few coral reef families for which the species level relationships have not been examined using genomic techniques. Here we use phylogenomic analysis of ultra-conserved elements (UCE) and exon data to resolve a well-supported, time-calibrated phylogeny for 72 species of goatfishes, supporting a recent crown age of the goatfishes at 21.9 million years ago. We used this framework to test hypotheses about the associations among body shape morphometrics, taxonomy, and phylogeny, as well as to explore relative diversification rates across the phylogeny. Body shape was strongly associated with generic-level taxonomy of goatfishes, with morphometric analyses showing evidence for high phylogenetic signal across all morphotypes. Rates of diversification in this clade reveal a recent sharp increase in lineage accumulation, with 92% of the goatfish species sampled across all clades and major body plans having originated in just the past 5 million years. We suggest that habitat diversity in the early Pliocene oceans and the generalist ecology of goatfishes are key factors in the unusual evolutionary tempo of the family Mullidae.

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.

Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific

Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.

Rapid evolution fuels transcriptional plasticity to ocean acidification

Ocean acidification (OA) is postulated to affect the physiology, behavior, and life-history of marine species, but potential for acclimation or adaptation to elevated pCO₂ in wild populations remains largely untested. We measured brain transcriptomes of six coral reef fish species at a natural volcanic CO₂  seep and an adjacent control reef in Papua New Guinea. We show that elevated pCO₂ induced common molecular responses related to circadian rhythm and immune system but different magnitudes of molecular response across the six species. Notably, elevated transcriptional plasticity was associated with core circadian genes affecting the regulation of intracellular pH and neural activity in Acanthochromis polyacanthus. Gene expression patterns were reversible in this species as evidenced upon reduction of CO₂ following a natural storm-event. Compared with other species, Ac. polyacanthus has a more rapid evolutionary rate and more positively selected genes in key functions under the influence of elevated CO₂ , thus fueling increased transcriptional plasticity. Our study reveals the basis to variable gene expression changes across species, with some species possessing evolved molecular toolkits to cope with future OA.