Diversity, phylogeography and taxonomy of hard corals in the genus Porites

Tullia Terraneo studied the species richness, taxonomy and historical biogeography of Porites, one of the most important reef corals in the tropics. She found that Porites diversity needs to be reconsidered and the taxonomy of the genus revised. Finally, she found several species new to taxonomy that are awaiting description. This work increases our knowledge regarding coral reef biodiversity and will help guide future conservation strategies

Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (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 Lithophyllon ranjithi, Podabacia sinai, Sandalolitha boucheti, and the agariciids Leptoseris kalayaanensis and L. troglodyta. 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 P. maldivensis. Since specimens from Sabah previously identified as P. maldivensis were found to belong to P. explanulata, the affinities and distinctions of P. maldivensis and P. explanulata are discussed

Environmental latitudinal gradients and host specificity shape Symbiodiniaceae distribution in Red Sea Porites corals

AimTo assess the diversity of algal symbionts of the family Symbiodiniaceae associated with the coral genus Porites in the Red Sea, and to test for host-specificity and environmental variables driving biogeographical patterns of algal symbiont distribution.LocationSaudi Arabian Red SeaTaxonEndosymbiotic dinoflagellates of the family Symbiodiniaceae in association with the reef-building coral genus Porites.MethodsEighty Porites coral specimens were collected along the Saudi Arabian Red Sea coast. Species boundaries were assessed morphologically and genetically (putative Control Region - mtCR; ITS region – ITS). Community composition of symbiotic dinoflagellates of the family Symbiodiniaceae was also assessed. Using the ITS2 marker with the SymPortal framework, Symbiodiniaceae data at the genus, majority ITS2 sequence, and ITS2 type profile were used to assess symbiont diversity and distribution patterns. These were analyzed in relation to coral host diversity, geographic location, and environmental variables.ResultsAmong the 80 Porites samples, 10 morphologies were identified. These corals were clustered into five lineages (clades I to V) by each of the markers independently. Clades I, II, and III each comprised of a single Porites morphology, while clades IV and V contained up to five distinct morphologies. The diversity of Symbiodiniaceae associated with Porites was high and latitudinal differentiation was observed. In particular, a shift from a Cladocopium- to a Durusdinium-dominated community was found along the north-south gradient. Symbiont diversity showed patterns of geographic-specific association at Symbiodiniaceae genus, majority ITS2 sequence, and ITS2 type profile level. Specific associations with host-genotypes (but not morphological species) were also recovered when considering Symbiodiniaceae majority ITS2 sequence and ITS2 type profiles.Main conclusionsThis study provides the first large scale molecular characterization of Symbiodiniaceae communities associated with Porites corals from the Saudi Arabian Red Sea. The use of intragenomic diversity data enabled the resolution of host-symbiont specificity and biogeographical patterns of distribution, previously unachievable with the ITS2 marker alone. Finally, correlation among symbiont diversity and Red Sea environmental gradients was documented

Supplementary material 5 from: Waheed Z, Benzoni F, van der Meij SET, Terraneo TI, Hoeksema BW (2015) Scleractinian corals (Fungiidae, Agariciidae and Euphylliidae) of Pulau Layang-Layang, Spratly Islands, with a note on Pavona maldivensis (Gardiner, 1905). ZooKeys 517: 1-37. https://doi.org/10.3897/zookeys.517.9308

Figure S2: Explanation note: Variation of corallite form and structure in Pavona maldivensis (a, c, e), and Pavona explanulata (b, d, f). a specimen LAC23 from Layang-Layang, b specimen BAN01 from Banggi, North Borneo, c specimen LOY12 from Loyalty Islands, d specimen BAN02 from Banggi, North Borneo, e specimen MAL from the Maldives, and f specimen TER28 from Ternate, Indonesia

A new species of Bathypathes (Cnidaria, Anthozoa, Antipatharia, Schizopathidae) from the Red Sea and its phylogenetic position

A black coral, Bathypathes thermophila Chimienti, sp. nov. is described from the Saudi Arabian coasts of the Gulf of Aqaba and north Red Sea (Neom area) using an integrated taxonomic approach. The morphological distinctiveness of the new species is confirmed by molecular analyses. The species thrives in warm and high salinity waters typical of the Red Sea at bathyal depths. It can form colony aggregations on muddy bottoms with scattered, small hard substrates. Colonies are monopodial, feather-like, and attached to a hard substrate through a thorny basal plate. Pinnules are simple, arranged biserially and alternately, and all the same length (up to approximately 20 cm) except for few, proximal ones. Spines are triangular, laterally compressed, subequal, smooth, and simple or rarely bifurcated. Polyps are elongated transversely, 1.5–2.0 mm in transverse diameter. Large colonies can have one or few branches, whose origin is discussed. The phylogenetic position of B. thermophila sp. nov. within the order Antipatharia, recovered using three mitochondrial markers, shows that it is nested within the family Schizopathidae. It is close to species in the genera Parantipathes, Lillipathes, Alternatipathes, and Umbellapathes rather than to the other available representatives of the genus Bathypathes, as currently defined based on morphology. In agreement with previous findings, our results question the evolutionary significance of morphological characters traditionally used to discriminate Antipatharia at higher taxonomic level

An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea

Fire corals of the hydrocoral genus Millepora provide an important ecological role as framework builders of coral reefs in the Indo-Pacific and the Atlantic. Recent works have demonstrated the incongruence between molecular data and the traditional taxonomy of Millepora spp. based on overall skeleton growth form and pores. In an attempt to establish a reliable and standardized approach for defining species boundaries in Millepora, we focused on those from the Red Sea. In this region, three species are currently recognized: the fan-shaped branching M. dichotoma, the blade-like M. platyphylla, and the massive/encrusting M. exaesa. A total of 412 colonies were collected from six localities. Two mitochondrial marker genes (COI and 16S rDNA) were sequenced to obtain phylogeny reconstructions and haplotype networks. Eight morphological traits of pores and the nematocysts of both polyp and eumedusoid stages were measured to determine whether significant morphological differences occur among the three species. Both markers clearly resolved M. dichotoma, M. platyphylla, and M. exaesa as distinct, monophyletic lineages in the Red Sea. Nevertheless, they also revealed deep genetic breaks with Southwestern Indian Ocean populations of the three species. In the Red Sea, the three species were further distinguished based on their pore and nematocyst features. A discriminant analysis revealed dactylopore density, number of dactylopores per gastropore, dactylopore distance, and gastropore diameter as the most informative discriminative characters. The heteronemes, the large and small stenoteles of polyps, and the distribution of mastigophores of eumedusoids also showed significant interspecific differences. An integrated morpho-molecular approach proved to be decisive in defining species boundaries of Millepora supported by a combination of pore and nematocyst characters, which may be phylogenetically informative

Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific

Accurate delimitation of species and their relationships is a fundamental issue in evolutionary biology and taxonomy and provides essential implications for conservation management. Scleractinian corals are difficult to identify because of their ecophenotypic and geographic variation and their morphological plasticity. Furthermore, phylogenies based on traditional loci are often unresolved at the species level because of uninformative loci. Here, we attempted to resolve these issues and proposed a consistent species definition method for corals by applying the genome-wide technique Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species delimitation within the genus Leptastrea. We collected 77 colonies from nine localities of the Indo-Pacific and subjected them to genomic analyses. Based on de novo clustering, we obtained 44,162 SNPs (3701 loci) from the holobiont dataset and 62,728 SNPs (9573 loci) from the reads that map to coral transcriptome to reconstruct a robust phylogenetic hypothesis of the genus. Moreover, nearly complete mitochondrial genomes and ribosomal DNA arrays were retrieved by reference mapping. We combined concatenation-based phylogenetic analyses with coalescent-based species tree and species delimitation methods. Phylogenies suggest the presence of six distinct species, three corresponding to known taxa, namely Leptastrea bottae, Leptastrea inaequalis, Leptastrea transversa, one characterized by a remarkable skeletal variability encompassing the typical morphologies of Leptastrea purpurea and Leptastrea pruinosa, and two distinct and currently undescribed species. Therefore, based on the combination of genomic, morphological, morphometric, and distributional data, we herein described Leptastrea gibbosa sp. n. from the Pacific Ocean and Leptastrea magaloni sp. n. from the southwestern Indian Ocean and formally considered L. pruinosa as a junior synonym of L. purpurea. Notably, mitogenomes and rDNA yielded a concordant yet less resolved phylogeny reconstruction compared to the ones based on SNPs. This aspect demonstrates the strength and utility of RADseq technology for disentangling species boundaries in closely related species and in a challenging group such as scleractinian corals

Mesophotic foraminiferal-algal nodules play a role in the Red Sea carbonate budget

Abstract During two scientific expeditions between 2020 and 2022, direct surveys led to the discovery of free-living mesophotic foraminiferal-algal nodules along the coast of the NEOM region (northern Saudi Arabian Red Sea) where they form an unexpected benthic ecosystem in mesophotic water depths on the continental shelf. Being mostly spheroidal, the nodules are transported en masse down slope, into the deep water of the basin, where they stop accreting. Radiometric dating informs that these nodules can be more than two thousand years old and that they collectively contribute up to 66 g m−2 year−1 to the mesophotic benthic carbonate budget and account for at least 980 megatons of calcium carbonate, a substantial contribution considering the depauperate production of carbonate by other means in this light-limited environment. Our findings advance the knowledge of mesophotic biodiversity and carbonate production, and provide data that will inform conservation policies in the Saudi Arabian Red Sea

Amphistegina lobifera foraminifera are excellent bioindicators of heat stress on high latitude red sea reefs

Coral reefs are in global decline and anomalously hot temperatures shoulder the blame. Foraminferal bioindicators are important because they record historical reef stress over periods of centuries to millennia, as compared to the few decades offered by diver surveys. For a region lacking systematic long-term reef monitoring programs, the use of bioindicators in the Red Sea is compelling. Whereas foraminfera-based indices exist to reconstruct histories of nutrient stress on reefs, there is a paucity of equivalent bioindicators that respond to temperature. Capitalizing on a portfolio of surficial sediment samples collected along the eastern margin of the N. Red Sea and Gulf of Aqaba, this study shows that the relative abundance of Amphisteginidae foraminifera—specifically Amphistegina lobifera—closely track heat stress, as has recently been reported for this family in the S. Pacific. This result is consequential for at least three reasons. First, the Red Sea hosts some of the most northerly coral reefs on Earth. Establishment of a thermal bioindicator here confirms the strategy can be deployed on high latitudes reefs, which are disproportionally afflicted with heat extremes. Second, the considered reefs, and the foraminifera they host, are famed for their thermal resilience. Foraminiferal bioindicators have not previously been trialed on reefs that have adapted in this way. Finally, as a restricted offshoot of the Indian Ocean, the level of endemism in the Red Sea is especially high. The bioindicator that we propose is apparently not compromised by endemism. Our findings advocate for an expanded deployment of Amphistegina-based reef bioindicators.This work was supported by the National Science Foundation (NSF) under Grant No. EAR-2035135. We extend our thanks to Francesca Benzoni for her assistance gathering benthic samples. We owe a debt of gratitude to our Saudi Arabian partners, NEOM, and to Paul Marshall, in particular, for facilitating the Deep Blue Expedition. We thank the crew of OceanXplorer for their operational and logistical support for the duration of this expedition. In particular, we acknowledge the ship and small boat teams for data acquisition, sample collection and support of scientific operations on board OceanXplorer. We also thank OceanX Media, for documenting and communicating this work with the public. Finally, we are indebted to two anonymous reviewers whose comments greatly improved the quality of our work