Pachyseris inattesa sp. n. (Cnidaria, Anthozoa, Scleractinia): a new reef coral species from the Red Sea and its phylogenetic relationships

Molecular diversity of black corals from the Saudi Arabian Red Sea: a first assessment

Black corals occur as part of benthic assemblages from shallow to deep waters in all oceans. Despite the importance in many benthic ecosystems, where these act as biodiversity aggregators, antipatharians remain poorly studied, with 75% of the known species occurring below recreational SCUBA diving depth limits. Currently, information regarding the diversity and evolutionary history is limited, with most studies focusing on Hawaii and the South Pacific Ocean. Other regions of the world have received less attention, such as the Red Sea, where only two black coral families and four genera have been recorded. We provide the first analysis of the molecular diversity of black corals in the eastern Gulf of Aqaba and the northern and central Saudi Arabian Red Sea, based on a dataset of 161 antipatharian colonies collected down to 627 m deep. Based on specimen morphology, we ascribed our material to 11 genera belonging to 4 of the 7 known Antipatharia families, i.e. Antipathidae, Aphanipathidae, Myriopathidae and Schizopathidae. The genus level phylogeny of three intergenic mitochondrial regions, the trnW-IGR-nad2 (IgrW ), nad5-IGR-nad1 (IgrN ) and cox3-IGR-cox1 was reconstructed including previously published material. Overall, we recovered six molecular clades that included exclusively Red Sea sequences, with the highest diversity occurring at mesophotic depths. This study highlights that diversity of black corals in the Red Sea is much higher than previously known, with seven new generic records, suggesting that this basin may be a hotspot for antipatharian diversity as is known for other taxa. Our results recovered unresolved relationships within the order at the familial and generic levels. This emphasises the urgent need for an integration of genomic-wide data with a re-examination of informative morphological features necessary to revise the systematics of the order at all taxonomic levels.

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

BACKGROUND

Mesophotic coral communities are increasingly gaining attention for the unique biological diversity they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies on corals have rarely included mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers.

RESULTS

Here, we used reduced-representation genome sequencing to conduct a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed deep divergences within the two genera and undescribed diversity across the current taxonomic species. Five of the eight focal species consisted of at least two sympatric and genetically distinct lineages, which were consistently detected across different methods.

CONCLUSIONS

The repeated observation of genetically divergent lineages associated with mesophotic depths highlights that there may be many more mesophotic-specialist coral species than currently acknowledged and that an urgent assessment of this largely unstudied biological diversity is warranted.

A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia)

A well-supported evolutionary tree representing most major lineages of scleractinian corals is in sight with the development and application of phylogenomic approaches. Specifically, hybrid-capture techniques are shedding light on the evolution and systematics of corals. Here, we reconstructed a broad phylogeny of Scleractinia to test previous phylogenetic hypotheses inferred from a few molecular markers, in particular, the relationships among major scleractinian families and genera, and to identify clades that require further research. We analysed 449 nuclear loci from 422 corals, comprising 266 species spanning 26 families, combining data across whole genomes, transcriptomes, hybrid capture and low-coverage sequencing to reconstruct the largest phylogenomic tree of scleractinians to date. Due to the large number of loci and data completeness (<38% missing data), node supports were high across shallow and deep nodes with incongruences observed in only a few shallow nodes. The "Robust" and "Complex" clades were recovered unequivocally, and our analyses confirmed that Micrabaciidae Vaughan, 1905 is sister to the "Robust" clade, transforming our understanding of the "Basal" clade. Several families remain polyphyletic in our phylogeny, including Deltocyathiidae Kitahara, Cairns, Stolarski & Miller, 2012, Caryophylliidae Dana, 1846, and Coscinaraeidae Benzoni, Arrigoni, Stefani & Stolarski, 2012, and we hereby formally proposed the family name Pachyseridae Benzoni & Hoeksema to accommodate Pachyseris Milne Edwards & Haime, 1849, which is phylogenetically distinct from Agariciidae Gray, 1847. Results also revealed species misidentifications and inconsistencies within morphologically complex clades, such as Acropora Oken, 1815 and Platygyra Ehrenberg, 1834, underscoring the need for reference skeletal material and topotypes, as well as the importance of detailed taxonomic work. The approach and findings here provide much promise for further stabilising the topology of the scleractinian tree of life and advancing our understanding of coral evolution.

The First Deep-Sea Stylasterid (Hydrozoa, Stylasteridae) of the Red Sea

The Stylasteridae, commonly known as lace corals, is a family of colonial calcifying hydrozoans mostly inhabiting deep waters. Stylasterids show a cosmopolitan distribution but, in some areas, they are characterized by low species diversity, such as in the Red Sea, where only a shallow-water species has been reported so far. With this work, we provide the first evidence of a deep-sea stylasterid inhabiting the NEOM region in the northern Saudi Arabian Red Sea, at depths ranging between 166 and 492 m. Morphological examinations revealed that this species was previously unknown and belonging to the genus Stylaster. We, therefore, describe Stylaster tritoni sp. nov., representing the first record of the genus in the Red Sea. Lastly, the phylogenetic position of the species within the Stylasteridae was evaluated, revealing a close relationship with shallow-water Indo-Pacific and Western Atlantic Stylaster species and confirming the polyphyletic nature of the genus Stylaster.

Morphological stasis masks ecologically divergent coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

Spatial variation in coral reef fish and benthic communities in the central Saudi Arabian Red Sea

Local-scale ecological information is critical as a sound basis for spatial management and conservation and as support for ongoing research in relatively unstudied areas. We conducted visual surveys of fish and benthic communities on nine reefs (3–24 km from shore) in the Thuwal area of the central Saudi Arabian Red Sea. Fish biomass increased with increasing distance from shore, but was generally low compared to reefs experiencing minimal human influence around the world. All reefs had a herbivore-dominated trophic structure and few top predators, such as sharks, jacks, or large groupers. Coral cover was considerably lower on inshore reefs, likely due to a 2010 bleaching event. Community analyses showed inshore reefs to be characterized by turf algae, slower-growing corals, lower herbivore diversity, and highly abundant turf-farming damselfishes. Offshore reefs had more planktivorous fishes, a more diverse herbivore assemblage, and faster-growing corals. All reefs appear to be impacted by overfishing, and inshore reefs seem more vulnerable to thermal bleaching. The study provides a description of the spatial variation in biomass and community structure in the central Saudi Arabian Red Sea and provides a basis for spatial prioritization and subsequent marine protected area design in Thuwal.

Cross shelf benthic biodiversity patterns in the Southern Red Sea

The diversity of coral reef and soft sediment ecosystems in the Red Sea has to date received limited scientific attention. This study investigates changes in the community composition of both reef and macrobenthic communities along a cross shelf gradient. Coral reef assemblages differed significantly in species composition and structure with location and depth. Inner shelf reefs harbored less abundant and less diverse coral assemblages with higher percentage macroalgae cover. Nutrient availability and distance from the shoreline were significantly related to changes in coral composition and structure. This study also observed a clear inshore offshore pattern for soft sediment communities. In contrast to the coral reef patterns the highest diversity and abundance of soft sediment communities were recorded at the inshore sites, which were characterized by a higher number of opportunistic polychaete species and bivalves indicative of mild disturbance. Sediment grain size and nutrient enrichment were important variables explaining the variability. This study aims to contribute to our understanding of ecosystem processes and biodiversity in the Red Sea region in an area that also has the potential to provide insight into pressing topics, such as the capacity of reef systems and benthic macrofaunal organisms to adapt to global climate change.

Cyphastrea (Cnidaria : Scleractinia : Merulinidae) in the Red Sea: phylogeny and a new reef coral species

The scleractinian coral Cyphastrea is a common and widespread genus throughout the coral reefs of the Indo-Pacific. Little is known about the phylogenetic relationships within this taxon and species identification is based mainly on traditional skeletal characters, such as the number of septa, septa cycles, growth form and corallite dimensions. Here we present the first focussed reconstruction of phylogenetic relationships among Cyphastrea species, analysing 57 colonies from the Red Sea, where five morphospecies live in sympatry. Analyses based on three loci (nuclear histone H3, 28S rDNA and a mitochondrial intergenic region) reveal the existence of three well-supported molecular lineages. None of the five previously defined morphospecies are monophyletic and they cluster into two clades, suggesting the need of a systematic revision in Cyphastrea. The third lineage is described as C. magna Benzoni &amp; Arrigoni, sp. nov., a new reef coral species collected from the northern and central Red Sea. Cyphastrea magna Benzoni &amp; Arrigoni, sp. nov. is characterised by the largest corallite diameter among known Cyphastrea species, a wide trabecular columella &gt;1/4 of calice width, and 12 equal primary septa. This study suggests that morphology-based taxonomy in Cyphastrea may not identify monophyletic units and strengthens the application of genetics in coral systematics.

Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea

Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic. We investigated Stylophora species boundaries from the Red Sea and the associated Symbiodinium by sequencing seven DNA loci. Stylophora morphospecies from the Red Sea were not resolved based on mitochondrial phylogenies and showed nuclear allele sharing. Low genetic differentiation, weak isolation, and strong gene flow were found among morphospecies although no signals of genetic recombination were evident among them. Stylophora mamillata harboured Symbiodinium clade C whereas the other two Stylophora morphospecies hosted either Symbiodinium clade A or C. These evolutionary patterns suggest that either gene exchange occurs through reticulate evolution or that multiple ecomorphs of a phenotypically plastic species occur in the Red Sea. The recent origin of the lineage leading to the Red Sea Stylophora may indicate an ongoing speciation driven by environmental changes and incomplete lineage sorting.

Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species

Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals.

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

Endangered New Caledonian endemic mushroom coral Cantharellus noumeae in turbid, metal-rich, natural and artificial environments

Since its description in 1984, little attention has been paid to the New Caledonian endemic mushroom coral Cantharellus noumeae (Fungiidae), an IUCN Red-listed, endangered coral species. Our study presents the first ever quantitative assessment conducted on C. noumeae populations for two contrasting sites in the same turbid bay. Sites differed by their substrates of artificial or natural origins. Metal concentrations of superficial sediment were measured. C. noumeae was found in high densities in metal-rich and turbid environments at both locations, reaching up to 288 individuals per 50m(2). It was 3.5 times more abundant on natural rock than on artificial substrates. Recruitment was also higher proportionally on rock (47% vs 7-14%). The composition of the associated coral communities included 30-37 species occurring in low densities. Our findings clarify the environmental niche of this species and its colonization potential, in order to eventually better characterize its conservation status.

Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavonamaldivensis (Gardiner, 1905)

Layang-Layang is a small island part of an oceanic atoll in the Spratly Islands off Sabah, Malaysia. As the reef coral fauna in this part of the South China Sea is poorly known, a survey was carried out in 2013 to study the species composition of the scleractinian coral families Fungiidae, Agariciidae and Euphylliidae. A total of 56 species was recorded. The addition of three previously reported coral species brings the total to 59, consisting of 32 Fungiidae, 22 Agariciidae, and five Euphylliidae. Of these, 32 species are new records for Layang-Layang, which include five rarely reported species, i.e., the fungiids Lithophyllonranjithi, Podabaciasinai, Sandalolithaboucheti, and the agariciids Leptoseriskalayaanensis and Leptoseristroglodyta. The coral fauna of Layang-Layang is poor compared to other areas in Sabah, which may be related to its recovery from a crown-of-thorns seastar outbreak in 2010, and its low habitat diversity, which is dominated by reef slopes consisting of steep outer walls. Based on integrative molecular and morphological analyses, a Pavona variety with small and extremely thin coralla was revealed as Pavonamaldivensis. Since specimens from Sabah previously identified as Pavonamaldivensis were found to belong to Pavonaexplanulata, the affinities and distinctions of Pavonamaldivensis and Pavonaexplanulata are discussed.

Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community

The composition, ecology and environmental conditions of mesophotic coral ecosystems near the lower limits of their bathymetric distributions remain poorly understood. Here we provide the first in-depth assessment of a lower mesophotic coral community (60–100 m) in the Southern Caribbean through visual submersible surveys, genotyping of coral host-endosymbiont assemblages, temperature monitoring and a growth experiment. The lower mesophotic zone harbored a specialized coral community consisting of predominantly Agaricia grahamae, Agaricia undata and a “deep-water” lineage of Madracis pharensis, with large colonies of these species observed close to their lower distribution limit of ~90 m depth. All three species associated with “deep-specialist” photosynthetic endosymbionts (Symbiodinium). Fragments of A. grahamae exhibited growth rates at 60 m similar to those observed for shallow Agaricia colonies (~2–3 cm yr⁻¹), but showed bleaching and (partial) mortality when transplanted to 100 m. We propose that the strong reduction of temperature over depth (Δ5°C from 40 to 100 m depth) may play an important contributing role in determining lower depth limits of mesophotic coral communities in this region. Rather than a marginal extension of the reef slope, the lower mesophotic represents a specialized community, and as such warrants specific consideration from science and management.