Article

A phylogeny reconstruction of the Dendrophylliidae (Cnidaria, Scleractinia) based on molecular and micromorphological criteria, and its ecological implications

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  • Naturalis Biodiversity Center / University of Groningen
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Abstract

Recent molecular phylogenetic studies have shown that most traditional families of zooxanthellate shallow-water scleractinians are polyphyletic, whereas most families mainly composed of deep-sea and azooxanthellate species are monophyletic. In this context, the family Dendrophylliidae (Cnidaria, Scleractinia) has unique features. It shows a remarkable variation of morphological and ecological traits by including species that are either colonial or solitary, zooxanthellate or azooxanthellate, and inhabiting shallow or deep water. Despite this morphological heterogeneity, recent molecular works have confirmed that this family is monophyletic. Nevertheless, what so far is known about the evolutionary relationships within this family, is predominantly based on skeleton macromorphology, while most of its species have remained unstudied from a molecular point of view. Therefore, we analysed 11 dendrophylliid genera, four of which were investigated for the first time, and 30 species at molecular, micromorphological and microstructural levels. We present a robust molecular phylogeny reconstruction based on two mitochondrial markers (COI and the intergenic spacer between COI and 16S) and one nuclear (rDNA), which is used as basis to compare micromorphogical and microstructural character states within the family. The monophyly of the Dendrophylliidae is well supported by molecular data and also by the presence of rapid accretion deposits, which are ca. 5 μm in diameter and arranged in irregular clusters, and fibres that thicken the skeleton organized in small patches of a few micrometres in diameter. However, all genera represented by at least two species are not monophyletic, Tubastraea excluded. They were defined by traditional macromorphological characters that appear affected by convergence, homoplasy and intraspecific variation. Micromorphogical and microstructural analyses do not support the distinction of clades, with the exception of the organization of thickening deposits for the Tubastraea clade.

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... The biogeography of corals has only been studied in the last few decades (Stehli and Wells 1971) with species level comparisons in the last two decades. Corals of the World (CoTW; Veron et al. (2016) recognizes 833 valid zooxanthellate scleractinian species globally and does not include the azooxanthellate dendrophylliid corals (Cairns 2001;Arrigoni et al. 2014) as well as the cave dwelling Leptoseris troglodyta Hoeksema, 2012 (Hoeksema 2012a). The World List of Scleractinia (WLS) reports 1,610 valid species with approximately half of those being zooxanthellate, hermatypic species (Hoeksema and Cairns 2019). ...
... The notation also provides a hyperlink to the factsheet available on the CoTW webpage (http://www.coralsoftheworld.org/page/home/). Veron et al. (2016) is an electronic source that has evolved from the printed worldwide overview of reefdwelling Scleractinia by Veron (2000), while Hoeksema and Cairns (2019) is based on published taxonomic revisions of various scleractinian families and genera, partly based on molecular analyses and/or on the re-examination of type specimens and other museum material (Wallace 1999;Wallace et al. 2007Wallace et al. , 2012Hoeksema 2009Hoeksema , 2012aHoeksema , 2012bHoeksema , 2014Benzoni et al. 2010Benzoni et al. , 2011Benzoni et al. , 2012aBenzoni et al. , 2014Gittenberger et al. 2011;Huang et al. 2011Huang et al. , 2014aHuang et al. , 2014bHuang et al. , 2016Budd et al. 2012;Arrigoni et al. 2014Arrigoni et al. , 2015Arrigoni et al. , 2016aArrigoni et al. , 2016bArrigoni et al. , 2017Arrigoni et al. , 2018aKitano et al. 2014;Schmidt-Roach et al. 2014;Terraneo et al. 2016Terraneo et al. , 2017. ...
... An analysis of the skeletal characteristics is warranted before a firm conclusion on species presence can be made. Arrigoni et al. (2014: fig. 10M-O) provide more information on and illustrations of this species. ...
Article
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An annotated checklist of the stony corals (Scleractinia, Milleporidae, Stylasteridae, and Helioporidae) of American Sāmoa is presented. A total of 377 valid species has been reported from American Sāmoa with 342 species considered either present (251) or possibly present (91). Of these 342 species, 66 have a recorded geographical range extension and 90 have been reported from mesophotic depths (30-150 m). Additionally, four new species records (Acanthastreasubechinata Veron, 2000, Favitesparaflexuosus Veron, 2000, Echinophylliaechinoporoides Veron & Pichon, 1980, Turbinariairregularis Bernard, 1896) are presented. Coral species of concern include species listed under the US Endangered Species Act (ESA) and the International Union for Conservation of Nature's (IUCN) Red List of threatened species. Approximately 17.5% of the species present or possibly present are categorized as threatened by IUCN compared to 27% of the species globally. American Sāmoa has seven ESA-listed or ESA candidate species, including Acroporaglobiceps (Dana, 1846), Acroporajacquelineae Wallace, 1994, Acroporaretusa (Dana, 1846), Acroporaspeciosa (Quelch, 1886), Fimbriaphylliaparadivisa (Veron, 1990), Isoporacrateriformis (Gardiner, 1898), and Pocilloporameandrina Dana, 1846. There are two additional species possibly present, i.e., Pavonadiffluens (Lamarck, 1816) and Poritesnapopora Veron, 2000.
... Such diversity is represented by a wide variety of growth forms (e.g., solitary and colonial), presence or absence of algal symbionts (i.e., zooxanthellate, azooxanthellate and apozooxanthellate), and an extensive geographic and bathymetric ranges, occurring from the tropics to polar regions at depths up to 2,165 m (Cairns, 2001). Although the family was recovered as monophyletic in the light of molecular data (Kitahara et al., 2010;Arrigoni et al., 2014), the generic evolutionary relationships within the family remains unclear, including several poly/paraphyletic genera (Arrigoni et al., 2014;Kitahara et al., 2016). ...
... Such diversity is represented by a wide variety of growth forms (e.g., solitary and colonial), presence or absence of algal symbionts (i.e., zooxanthellate, azooxanthellate and apozooxanthellate), and an extensive geographic and bathymetric ranges, occurring from the tropics to polar regions at depths up to 2,165 m (Cairns, 2001). Although the family was recovered as monophyletic in the light of molecular data (Kitahara et al., 2010;Arrigoni et al., 2014), the generic evolutionary relationships within the family remains unclear, including several poly/paraphyletic genera (Arrigoni et al., 2014;Kitahara et al., 2016). ...
... The classical taxonomy of scleractinian corals relies on skeletal morphological characters, but high intraspecific variation, convergence and homoplasy frequently challenge their identification, especially in shallow-water species (Todd, 2008). Among dendrophylliids, morphological characters used to reconstruct the evolutionary history of the group (i.e., corallum morphology, theca structure, calicular elements, and presence of zooxanthellae) do not seem to be sufficiently informative (Arrigoni et al., 2014). In addition, not all evolutionary changes resulting in speciation, such as changes in reproduction and ecology, are accompanied by detected morphological changes (Paz-García, García-de León & Balart, 2015;Gélin et al., 2017). ...
Article
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Atlantia is described as a new genus pertaining to the family Dendrophylliidae (Anthozoa, Scleractinia) based on specimens from Cape Verde, eastern Atlantic. This taxon was first recognized as Enallopsammia micranthus and later described as a new species, Tubastraea caboverdiana, which then changed the status of the genus Tubastraea as native to the Atlantic Ocean. Here, based on morphological and molecular analyses, we compare fresh material of T. caboverdiana to other dendrophylliid genera and describe it as a new genus named Atlantia in order to better accommodate this species. Evolutionary reconstruction based on two mitochondrial and one nuclear marker for 67 dendrophylliids and one poritid species recovered A. caboverdiana as an isolated clade not related to Tubastraea and more closely related to Dendrophyllia cornigera and Leptopsammia pruvoti. Atlantia differs from Tubastraea by having a phaceloid to dendroid growth form with new corallites budding at an acute angle from the theca of a parent corallite. The genus also has normally arranged septa (not Portualès Plan), poorly developed columella, and a shallow-water distribution all supporting the classification as a new genus. Our results corroborate the monophyly of the genus Tubastraea and reiterate the Atlantic non-indigenous status for the genus. In the light of the results presented herein, we recommend an extensive review of shallow-water dendrophylliids from the Eastern Atlantic.
... In situ species identification of unifacial plating Turbinaria corals is challenging. At a species level, existing studies based on cytochrome oxidase I (COI) and rDNA show that most species are polyphyletic (Shimpi et al., 2019) and there is a high level of genetic overlap amongst morphospecies and particularly between Turbinaria mesenterina and T. reniformis (Arrigoni et al., 2014). With this in mind, we included three general morphotypes in our collections-T. ...
... DNA extractions were used at neat or 1:5 dilutions to amplify two mitochondrial DNA fragments. These were COI and the Intergenomic Repeat area (IGR), previously shown to provide informative signal in this taxon (Arrigoni et al., 2014) (see Appendix S1: (Leigh & Bryant, 2015). The museum vouchered specimens were included in this analysis to assist species identification. ...
... *FIS values significantly greater than zero (p ≤ 0.05). Despite common use of COI for phylogeographic and phylogenetic studies (Arrigoni et al., 2014) neither COI nor IGR data could fully discriminate the six Turbinaria species included in this study. The lack of species monophyly likely indicates that these morphospecies are recently diverged, or that ancestral polymorphisms have been retained due to the unusually slow rate of mitogenome evolution in corals (Romano & Palumbi, 1996). ...
Article
Aim Genetic connectivity is a key component of species resilience to climate change in terms of recovery capacity following disturbance and capacity to disperse to novel locations as the climate warms and isotherms shift poleward. We aimed to strengthen our understanding of resilience in this context by characterizing patterns of connectivity and genetic diversity in a broadcast spawning coral across a tropical–temperate transition zone. We hypothesize genetic differentiation between tropical and temperate populations and decreasing genetic diversity with higher latitudes. Location Western Australia (WA). Taxon Turbinaria species complex. Turbinaria ‘reniformis’ Oken, 1815 (Scleractinia: Dendrophylliidae). Methods A total of 930 target corals were sampled from 10 locations between 13 and 32° latitude spanning a 9°C mean temperature range. In situ species identification of T. reniformis is hindered by morphological plasticity and homoplasy with sister species. We combined Sanger sequencing of two mitochondrial DNA markers and high-throughput genotyping by sequencing (GBS) to isolate a single genetic Turbinaria lineage from our dataset through which patterns of genetic flow and diversity along the WA coastline could be explored using population- and individual-based clustering analyses. Results Mitochondrial DNA sequence variation was low among Turbinaria samples and could not resolve individual species. Using GBS, we identified three genetically distinct lineages. Subsequent analyses within one of these lineages revealed strong spatial subdivision with 2–3 genetic clusters. While temperate populations were genetically diverged from more tropical sites, we did not observe declines in genetic diversity with latitude. Main conclusions Tropical populations of T. ‘reniformis’ in Western Australia exhibit strong genetic connectivity, which extends to a southern limit at sub-tropical Shark Bay. Temperate populations are genetically isolated from their tropical counterparts but have relatively high genetic diversity. While the maintenance of genetic variation in temperate populations may provide some resilience to future climate scenarios, their isolation may increase their vulnerability.
... A study inferring interfamily relationships confirmed it as a well-supported monophyletic scleractinian family composed of shallow to deep-water azooxanthellate and zooxanthellate species (Kitahara et al. 2010). Yet, further examination of the systematics within the Dendrophylliidae (Arrigoni et al. 2014) revealed polyphyletic relationships in some of the dendrophylliid genera, including Balanophyllia Wood, 1844, Cladopsammia Lacaze-Duthiers, 1897, Dendrophyllia de Blainville, 1830, Rhizopsammia Verrill, 1870and Turbinaria Oken,1815. They also noted that the morphological characters used by Cairns (2001) to distinguish dendrophylliid taxa may be insufficient in inferring the evolutionary changes and speciation in this family. ...
... Among the 11 genera examined by Arrigoni et al. (2014), Tubastraea Lesson, 1830 represented a monophyletic clade. The genus is characterized by six characters: 1), colonial coralla firmly attached and encrusting; 2), septa cycles hexamerally arranged and typically inserted with spongy columella; 3), septa not arranged in a Pourtalès plan; 4), corallum with a rough texture; 5), colony developing from a common basal coenosteum by budding, with clear connection among polyps; 6), columella small to moderate in size and lacks an epitheca (Cairns 2001;Cairns & Kitahara 2012). ...
... Photographs of the specimens were taken using an Olympus OM-D EM1markII with a M. Zuiko Digital ED 60mm f2.8 Macro lens. Morphological characters defined by Cairns (2001); Cairns & Kitahara (2012) and Arrigoni et al. (2014) were used for species identification. They included whole colony size, corallite size, fossa depth, intercorallite distance and septa arrangement. ...
Article
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Tubastraea, commonly known as sun coral, is a genus of brightly coloured azooxanthellate corals in the family Dendrophylliidae. The diversity of this genus is low, with only seven recognized species. Herein, we describe Tubastraea megacorallita sp. nov. from Hong Kong based on morphological and molecular analyses. This new species exhibits several characteristics of the genus including being colonial, having a rough texture of corallum and no epitheca. It can be distinguished from its congenerics by bigger corallites, and the Pourtalès plan arrangement of its septa. The rDNA gene sequences (consisting of ITS1, 5.8S, ITS2, 18S and 28S) showed 2.45–5.18% divergence from those of its closest relatives, T. coccinea and T. micranthus.
... All subclades were highly supported in both BI and ML analyses, resulting in a stable phylogenetic definition of all genera. Therefore, the obtained results continued to demonstrate the phylogenetic utility of mitochondrial and nuclear barcodes, such as COI, histone H3 and ITS, for defining boundaries and phylogenetic relationships among scleractinian genera Arrigoni, Kitano, et al., 2014;Fukami et al., 2008;Kitahara et al., 2010). At the species level, we recovered only O. bennettae as a monophyletic species, whereas the other eight analysed species belonging to Astraeosmilia, Caulastraea and Oulophyllia were not resolved from a molecular perspective. ...
... The most likely explanation for the unresolved species relationships is that the four molecular markers chosen in this study were not variable enough to define species boundaries. The challenges of using relatively conserved markers to reconstruct evolutionary relationships have been discussed in several studies on reef corals (Arrigoni, Kitano, et al., 2014;Arrigoni, Richards, et al., 2014;Forsman et al., 2009;Huang, Benzoni, Arrigoni, et al., 2014;Prada et al., 2014;Terraneo et al., 2016Terraneo et al., , 2019. A lack of genetic differentiation can be the result of both slow evolution rate of coral mitochondrial genome and a lack of intragenomic variation of rDNA (Hellberg, 2006;Huang et al., 2008;Kitahara et al., 2016). ...
... The revised genus consists of four species that represent a wide degree of corallite organization, including cerioid, flabello-meandroid and phaceloid. More generally, as illustrated in previous studies (Arrigoni, Kitano, et al., 2014;Arrigoni et al., 2018;Arrigoni, Richards, et al., 2014;Benzoni et al., 2012;Budd et al., 2012;Forsman et al., 2009;Fukami et al., 2004;Huang et al., 2016;Huang, Benzoni, Arrigoni, et al., 2014;, our work clearly confirmed that colony growth form is regularly similar among lineages due to homoplasy. Taxonomic considerations based exclusively on this trait should be cautioned. ...
Article
Modern systematics integrating molecular and morphological data has greatly improved our understanding of coral evolutionary relationships during the last two decades and led to a deeply revised taxonomy of the order Scleractinia. The family Merulinidae (Cnidaria: Scleractinia) was recently subjected to a series of revisions following this integrated approach but the phylogenetic affinities of several genera ascribed to it remain unknown. Here, we partially fill this gap through the study of 89 specimens belonging to all 10 valid species from four genera (Caulastraea, Erythrastrea, Oulophyllia and Dipsastraea) collected from 14 localities across the Indo‐Pacific realm. Four molecular loci (histone H3, COI, ITS and IGR) were sequenced, and a total of 44 skeletal morphological characters (macromorphology, micromorphology and microstructure) were analysed. Molecular phylogenetic analyses revealed that the phaceloid Caulastraea species are split into two distinct lineages. A species previously ascribed to the genus Dipsastraea, Dipsastraea maxima, is also recovered in one on these lineages. Furthermore, Erythrastrea is nested within Oulophyllia. The molecular reconstructions of evolutionary relationships are further corroborated by multiscale morphological evidence. To resolve the taxonomy of these genera, Astraeosmilia is resurrected to accommodate Astraeosmilia connata, Astraeosmilia curvata, Astraeosmilia tumida and Astraeosmilia maxima, with Caulastraea retaining Caulastraea furcata and Caulastraea echinulata. Based on the examination of type material, Erythrastrea flabellata is considered an objective synonym of Lobophyllia wellsi, which is transferred to Oulophyllia following the obtained morpho‐molecular results. This work further confirms that an integrated morpho‐molecular approach based on a rigorous phylogenetic framework is fundamental for an objective classification that reflects the evolutionary history of scleractinian corals.
... phylogram, constructed using a COI alignment of 601 bp, yielded three clades and a distinct branch with GoK Turbinaria sequence (Fig. 4). T. peltata, which ought to be moved to genus Duncanopsammia (Arrigoni et al., 2014), formed a distinct well-supported clade (I). The other clades (II and III) formed discrete groups and included some unidentified species. ...
... G20 from the GoK grouped separately (branch sister to Clades II-III). Clade I was composed of T. peltata, whereas Clade II was comprised of T. reniformis, T. horenensis, and two unidentified species from the south-west Pacific (Arrigoni et al., 2014). Clade III was formed of five species including two unidentified, two T. patula, two T. reniformis, and two T. mesenterina. ...
... Turbinaria (Oken, 1815) is an important shallowwater, reef-building genus in the Indo-Pacific. Species boundaries are typically obscured and troublesome (Arrigoni et al., 2014). Only two species of the genus Turbinaria are known from the GoK, i.e., T. peltata, T. mesenterina (Venkataraman, Satyanarayana, Alfred, & Wolstenholme, 2003). ...
Article
Knowledge of extant biodiversity with accurate species boundaries is one of the crucial prerequisites for guiding conservation priorities in the face of global climate change. DNA taxonomy promises to provide a rapid and reliable tool for species delimitation of morphologically challenging taxa, such as reef-building corals. Despite harbouring diverse coral assemblages, molecular studies of hard corals occurring in the seas around India are lacking. The Gulf of Kutch (GoK), located in the north-western part of India, is one such region. Information on coral species inhabiting this unique ecosystem is limited to morphology, which is often highly variable and phenotypically plastic, obscuring species boundaries. Here, we present the first exploration of molecular divergence of hard corals of the GoK in order to identify evolutionarily distinct lineages. Nuclear ribosomal ITS and mitochondrial COI markers were sequenced for samples of dominant genera, Porites and Turbinaria for phylogenetic comparisons with available data from other ecosystems of the world. Five molecular species delimitation methods were applied to the datasets and their performance was evaluated. Our analyses clearly suggest the occurrence of unique genotypes of both these genera in the GoK, unequivocally discerned by all the five methods as well as microskeletal features. This first integrative assessment provides implications for the phylogeny of these genera and identifies previously unrecognized scleractinian species hidden in the GoK ecoregion.
... Ocaña et al. (2015) recently described a new species, T. caboverdiana Ocaña & Brito based on morphological characteristics. Many of these morpho-species have yet to be confirmed by molecular methods although recently Arrigoni et al. (2014) used molecular techniques and recognised seven species of Tubastraea. ...
... For example as well as issues previously discussed for Tubastraea in the Eastern Atlantic (ex. Fig. 7); (Arrigoni et al. 2014) presented molecular evidence for at least seven Tubastraea species, two of which are undescribed, as well as separating some species synonymised by Wells (Wells 1982). In the case of T. tagusensis it seems possible that the few records outside the Galapagos Islands are misidentifications. ...
Article
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In this review, we describe the history, pathways and vectors of the biological invasion of the azooxanthellate coral Tubastraea (Scleractinia: Dendrophylliidae) throughout the world. In order to do so we consulted previous reports in the literature and also compiled new unpublished information on the distribution of the three species of Tubastraea which have been reported as non indigenous species, both within their native and non-native ranges and also on vectors, and where cryptogenic. We combine these data with historical aspects of marine vectors in order to get insights into how Tubastraea species have successfully spread around the world, established and invaded and where future studies would be best focused. T. coccinea and T. tagusensis are recognized as being highly invasive and are causing significant environmental, economic, and social impacts requiring management actions. The third species, T. micranthus so far only reported outside its native range on oil platforms, may have similar potential for negative impact. The vectors of introduction of Tubastraea may have changed throughout history and the biological invasion of these invasive corals may reflect changing practices, demands and legislation in shipping activities over the years. Today it is clear that these corals are fouling organisms strongly associated with oil and gas platforms worldwide which are thus primary vectors for new introductions.
... 1 and 2). The genus Astroides is monotypic and phylogenetically most closely related to Tubastraea, which also consists of azooxanthellate corals (Arrigoni et al. 2014). It is endemic to the western Mediterranean Sea and adjacent Atlantic coasts of Spain and Morocco (Zibrowius 1995;Bianchi 2007;Terrón-Sigler et al. 2016a). ...
... Further studies have documented this asexual dispersal mechanism in Seriatopora hystrix Dana, 1846(Sammarco 1982, Pocillopora damicornis (Linnaeus, 1758) (Sin et al. 2012;Kvitt et al. 2015;Shapiro et al. 2016), Acropora tenuis (Dana, 1846) (Yuyama et al. 2012;Kariyazono and Hatta 2015), Cladocora caespitosa (Linnaeus, 1767) (Kružić 2007), and Tubastraea coccinea Lesson, 1829 (Capel et al. 2014). The latter is phylogenetically most closely related to A. calycularis (Arrigoni et al. 2014). In these studies, the release of single polyps devoid of skeleton was associated to an escape response to environmental stress (i.e., enclosed seawater and low food availability in mesocosm experiments, seawater acidification , and thermal, salinity and/or chemical stresses) or biotic interactions (i.e., competition with macroalgae). ...
Article
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Knowledge of reproductive biology is essential for ecological studies on coral population dynamics. The azooxanthellate colonial coral Astroides calycularis is endemic to the western Mediterranean Sea and adjacent Atlantic coasts. Specimens of this species in artificial conditions, an aquarium with enclosed seawater and low food availability, appeared to show an asexual dispersal mechanism. This mechanism consisted of the detachment and release of single, skeletonless polyps from the underlying colony skeleton (i.e., polyp bail-out). While the released free-living polyps regularly showed extended tentacles and most of them survived, they did not show re-attachment to the substrate or any skeleton formation until the end of the experiment, ∼2–3 months after bail-out. Formation of new reproductive colonies, thereby the eventual completion of asexual reproduction through polyp bail-out in A. calycularis, still needs to be confirmed. In addition to sexual reproduction, polyp bail-out may constitute an alternative propagation mechanism during periods of environmental stress, thereby potentially increasing the survival rate of the parental genotype and the dispersal by drifting soft polyps.
... (6). Most of these sequences were from a study by Arrigoni et al. (2014) who targeted a 750 bp region of mtCOI. Our sequences only overlapped 421 bp of this targeted region. ...
... Whether this group is a new species of Tubastraea, a subspecies of T. coccinea, or a hybrid of T. coccinea and T. tagusensis will require detailed morphological analyses of all Tubastraea species combined with a comprehensive phylogenetic analyses that in addition to mitochondrial genes also uses nuclear genes. Arrigoni et al. (2014) did such an analysis for species of the family Dendrophylliidae, which include Tubastraea. Their analysis included four species of Tubastraea (T. ...
Article
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Our research presents the first record of Tubastraea tagusensis (Wells, Notes on Indo-Pacific scleractinian corals. Part 9. New corals from the Galápagos Islands, 1982) in the Gulf of Mexico. Specimens of Tubastraea were collected from various artificial reefs. Morphological analyses of these specimens show that there are three distinct lineages of Tubastraea that have remained cryptic due to similar morphology in the field: Tubastraea coccinea (Lesson, 1829), T. tagusensis, and a third clade containing a mix of characters of the former two. These results based on morphology are corroborated by phylogenetic and haplotype analyses using a partial sequence of the mitochondrial genes ATP8 and cytochrome oxidase I (mtCOI). The negative effects on natural habitats by invasive species of Tubastraea have been documented worldwide. Therefore, it is imperative to implement management policies that will help prevent the expansion of these species into natural habitats in the Gulf of Mexico. The essential first step is accurate identification to determine possible sources, vectors, and current expansion rates. We present a clear set of morphological characters and a genetic marker to help distinguish between these three cryptic lineages.
... The genus Astroides is monospecific. Distinct microstructural features and 28S rRNA sequences 41,42 have revealed that A. calycularis, and species of Balanophyllia and Tubastraea form a monophyletic group 41 , highlighting the special phylogenetic position occupied by the orange coral within the Dendrophylliidae. ...
... Large polyps may generally offer better opportunities for capturing large prey 48 , including sea slugs 49 , especially in azooxanthellate species that depend exclusively on food intake for their nutrition, which is in fact a common feature among the Dendrophylliidae 38 . Thus, the possible advantage of having many (relatively) small polyps, in a colonial azooxanthellate species such as A. calycularis remains elusive 42 . However, recent evidence suggests that A. calycularis preys on large gelatinous plankton using a protocooperative strategy involving polyps of several colonies 50 . ...
Article
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Abstract Shallow-water marine organisms are among the first to suffer from combined effects of natural and anthropogenic drivers. The orange coral Astroides calycularis is a shallow-water bioconstructor species endemic to the Mediterranean Sea. Although raising conservation interest, also given its special position within the Dendrophylliidae, information about the threats to its health is scant. We investigated the health status of A. calycularis at five locations in northwestern Sicily along a gradient of cumulative human impact and the most probable origin of the threats to this species, including anthropogenic land-based and sea-based threats. Cumulative human impact appeared inversely related to the performance of A. calycularis at population, colony, and polyp levels. Sea-based human impacts appeared among the most likely causes of the variation observed. The reduction in polyp length can limit the reproductive performance of A. calycularis, while the decrease of percent cover and colony area is expected to impair its peculiar feeding behaviour by limiting the exploitable dimensional range of prey and, ultimately, reef functioning. This endangered habitat-forming species appeared susceptible to anthropogenic pressures, suggesting the need to re-assess its vulnerability status. Creating microprotected areas with specific restrictions to sea-based human impacts could be the best practice preserve these bioconstructions.
... A growing volume of work dealing with taxonomy and systematics of scleractinian corals have demonstrated that the use of both genetic and morphological analyses is an indispensable approach to understand and clarify the evolution of these invertebrates (Benzoni et al., 2007(Benzoni et al., , 2012aBudd et al., 2010Budd et al., , 2012Gittenberger et al., 2011;Kitahara et al., 2012aKitahara et al., , 2012bSchmidt-Roach et al., 2014;Huang et al., 2014b;Arrigoni et al., 2014c;Terraneo et al., 2014). In this study we combine robust molecular analyses based on multiple DNA regions with detailed observations of morphology at colony, corallite, and sub-corallite scales. ...
... We strongly encourage the examination of specimens from multiple localities, ideally including the entire geographic distribution range of a species and above all the type locality, in order to define the intraspecific morphological variation and evaluate the possible presence of cryptic or previously overlooked species. Finally, we recommend also the inclusion of microstructural data to the presented molecular and micromorphological observations in future works as they were demonstrated to be useful and diagnostic in previous systematic revisions (Budd et al., 2012;Kitahara et al., 2012b;Huang et al., 2014a: Arrigoni et al., 2014cJaniszewska et al., 2015). S6. ...
... In fact, Campoy and colleagues 16 used four markers (18S rDNA, 28S rDNA, 16S rDNA and cox1) and 513 scleractinian coral species from almost all extant families and hypothesized that the first scleractinian would have been azooxanthellate and solitary. Nonetheless, symbiosis with zooxanthellae was widespread in Triassic corals 65 and there is some degree of disagreement about it being lost and reappearing a few times 64,66 or being gained only once during scleractinian evolution 16 . In contrast, it appears that coloniality was the first one to be gained and there is an agreement that it was lost and gained more than once 16,64 and even the presence of multiple mouths in one polyp seems to be a labile trait in some families of this order as well (e.g. ...
... In contrast, it appears that coloniality was the first one to be gained and there is an agreement that it was lost and gained more than once 16,64 and even the presence of multiple mouths in one polyp seems to be a labile trait in some families of this order as well (e.g. Dendrophylliidae 66 and Fungiidae 67,68 ). ...
Article
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Abstract Evolutionary reconstructions of scleractinian corals have a discrepant proportion of zooxanthellate reef-building species in relation to their azooxanthellate deep-sea counterparts. In particular, the earliest diverging “Basal” lineage remains poorly studied compared to “Robust” and “Complex” corals. The lack of data from corals other than reef-building species impairs a broader understanding of scleractinian evolution. Here, based on complete mitogenomes, the early onset of azooxanthellate corals is explored focusing on one of the most morphologically distinct families, Micrabaciidae. Sequenced on both Illumina and Sanger platforms, mitogenomes of four micrabaciids range from 19,048 to 19,542 bp and have gene content and order similar to the majority of scleractinians. Phylogenies containing all mitochondrial genes confirm the monophyly of Micrabaciidae as a sister group to the rest of Scleractinia. This topology not only corroborates the hypothesis of a solitary and azooxanthellate ancestor for the order, but also agrees with the unique skeletal microstructure previously found in the family. Moreover, the early-diverging position of micrabaciids followed by gardineriids reinforces the previously observed macromorphological similarities between micrabaciids and Corallimorpharia as well as its microstructural differences with Gardineriidae. The fact that both families share features with family Kilbuchophylliidae ultimately points towards a Middle Ordovician origin for Scleractinia.
... The taxonomy of scleractinian corals based on macromorphological characters has been challenged because of their large intraspecific variation, morphological similarity among species, and phenotypic variation due to various environmental factors (Hoeksema and Moka, 1989;Gittenberger and Hoeksema, 2006;Todd, 2008;Mondal et al., 2013). Recent comprehensive approaches have overcome these problems by applying both morphological and molecular analyses, revising major taxa in the scleractinian corals at the family and genus levels (e.g., Budd et al., 2012;Arrigoni et al., 2014Arrigoni et al., , 2016Huang et al., 2014aHuang et al., , b, 2016Kitano et al., 2014;Kitahara et al., 2016). ...
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Mushroom corals are reef corals of the family Fungiidae, which live in the tropical and subtropical Indo-Pacific region. Recently, most species of this family have been revised taxonomically based on morphological and molecular analyses. However, the phylogenetic position of Cycloseris hexagonalis (Milne Edwards and Haime, 1848) has not been analyzed and remains unclear. This species is believed to show allometric growth by changing its corallum shape from hexagonal in juveniles to irregularly circular with an undulated corallum margin in mature individuals. However, these morphological changes have not been monitored and their genetic basis has not been confirmed. In the present study morphological and molecular phylogenetic analyses were performed to evaluate the identity of the morpho-types in C. hexagonalis and to clarify the phylogenetic and taxonomic position of the species. In the morphological analysis, we used 20 specimens of C. hexagonalis collected from around Iriomote Island, Okinawa, Japan, and identified four morphotypes. Moreover, the molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers showed that all morpho-types of C. hexagonalis together form an independent clade, indicating that they are all conspecific. Molecular phylogenetic comparison between this species and other fungiids revealed that the clade of C. hexagonalis is clearly distant from the Cycloseris clade as well as from clades representing other genera in the Fungiidae. Considering these data, we establish a monotypic new genus, Sinuorota, to accommodate C. hexagonalis.
... Molecular phylogenetic techniques have improved the taxonomy and systematics of cnidarian taxa such as jellyfishes, octocorals, and hexacorals (Fukami et al., 2004;McFadden et al., 2006;Miranda et al., 2016), and are powerful tools to reveal cryptic hexacorallian species that have few diagnostic characteristics (e.g., Kise and Reimer, 2016;Arrigoni et al., 2018). Additionally, molecular phylogeny can aid in our understanding of the evolutionary history of morphological and ecological traits in marine invertebrates and other organisms (e.g., Hoeksema, 2012;Arrigoni et al., 2014). ...
Article
The Family Hydrozoanthidae are macrocnemic zoantharians, however their phylogenetic position is closer to brachycnemic zoantharians than to other macrocnemic zoantharians. Previous studies have indicated the presence of undescribed Hydrozoanthidae species from various locations in the Indo-Pacific Ocean. In this study, two new Hydrozoanthidae species, Aenigmanthus segoi gen. n., sp. n. and Hydrozoanthus sils sp. n., are described from Japanese and Palauan waters based on combined morphological and molecular phylogenetic analyses utilizing multiple genetic markers. Additionally, Hydrozoanthidae consists of species with an obligate epizoic relationship with hydroids (Hydrozoanthus) and of species with facultative epizoic relationships (Aenigmanthus gen. n. and Terrazoanthus). Results of ancestral state reconstruction analyses indicate that Hydrozoanthus gained obligate epizoic relationships in their evolutionary history perhaps due to structural differences of host invertebrates.
... Here we describe how several small colonies of a polystomatous coral with tiny mouths and small gapes cooperate to do so analogously. Indeed, the ecological and evolutionary advantage for some Dendrophylliidae of having many small polyps has remained elusive (Arrigoni et al. 2014). Collective predation among relatively small polyps allows A. calycularis to access food resources well beyond its gape, thereby exploiting ephemeral, highly abundant patches of large prey. ...
... Environment-induced phenotypic plasticity (Todd, 2008) and intraspecific morphological variation caused by genotype (Carlon and Budd, 2002) are typical attributes of these animals and further contribute to the confusion of coral identification. In the last decade, genetic data have revealed molecular lineages that do not correspond to taxa defined by traditional taxonomy, suggesting that evolutionary convergence of morphological structures (Fukami et al., 2004b;Gittenberger et al., 2011;Budd et al., 2012a;Arrigoni et al., 2014c), morphological stasis over long periods (Flot et al., 2011;Arrigoni et al., 2016a) and genetic exchange through introgression (Combosch and Vollmer, 2015;Suzuki et al., 2016) occur in corals. Moreover, large geographical samplings across the Indo-Pacific have demonstrated the occurrence of genetic structure, demographic isolation, and cryptic lineages within taxa that were traditionally considered to be widespread and common in the Indo-Pacific. ...
Article
Extant biodiversity can easily be underestimated owing to the presence of cryptic taxa, even among commonly observed species. Scleractinian corals are challenging to identify because of their ecophenotypic variation and morphological plasticity. In addition, molecular analyses have revealed the occurrence of cryptic speciation. Here, we describe a new cryptic lobophylliid genus and species Paraechinophyllia variabilis gen. nov., sp. nov., which is morphologically similar to Echinophyllia aspera and E. orpheensis. The new taxon occurs in Mayotte Island, Madagascar, the Gulf of Aden and the Red Sea. Six molecular markers (COI, 12S, ATP6‐NAD4, NAD3‐NAD5, histone H3 and ITS) and 46 morphological characters at three different levels (macromorphology, micromorphology and microstructure) were examined. The resulting molecular phylogenetic reconstruction showed that Paraechinophyllia gen. nov. represents a distinct group within the Lobophylliidae that diverged from the lineage leading to Echinophyllia and Oxypora in the Early Miocene, approximately 21.5 Ma. The morphological phylogenetic reconstruction clustered Paraechinophyllia gen. nov., Echinophyllia and Oxypora together in a single clade. A sole morphological character, calice relief, discriminated Paraechinophyllia gen. nov. from the latter two genera, suggesting that limited morphological variation has occurred over a long period. These results highlight the importance of cryptic taxa in reef corals, with implications for population genetics, ecological studies and conservation.
... The currently accepted names for these species were then determined using either the World Register of Marine Species (Hoeksema 2018) or the most recent peer-reviewed research (e.g. Arrigoni et al. 2014). ...
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Research on coral reproduction has increased dramatically in recent times; however, there remain significant regions, in particular high latitude reefs, where research is limited. For example, the reproductive biology of species in the coral assemblage at Hall Bank, a high latitude site (32° S) in southern Western Australia, remain unknown. Here, reproductive traits and the likely time of spawning for 12 of the approximately 16 species that occur at Hall Bank were established using histology between March 2009 and March 2011 at 7 discrete time points. Peak reproductive activity most likely occurs in February, as 7 of the 10 species sampled in this month had colonies with mature gametes. The sexuality, mode of larval development and transmission of symbionts were, as expected, consistent with previous work. The reproductive biology of the corals at Hall Bank is consistent with other regions of the Indo-Pacific, supporting the hypothesis that reproductive traits such as sexuality and mode of larval development are evolutionarily conserved and do not vary biogeographically.
... It is found at depths from 0 to 50 m (Zibrowius 1980). From a phylogenetic perspective, it shows a unique set of character traits within the family Dendrophylliidae (Arrigoni et al. 2014). Even though recent investigations of Turkish scleractinian fauna in the Dardanelles report B. europaea as one of the dominant shallow-water scleractinians, with peaks of around 400 individuals m -2 (Ö zalp and Alparslan 2016), no information is available on skeletal growth rate and parameters at this location. ...
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Studying coral populations along depth gradients is important to find out if deeper habitats can act as microrefugia from bleaching and/or mortality events associated with high temperature and irradiance. Skeletal biometry, growth, and parameters of the solitary, zooxanthellate, Mediterranean endemic scleractinian Balanophyllia europaea were determined at depths of 1, 11, and 21 m in the Dardanelles (Turkey), to (1) compare the population parameters in the Eastern Mediterranean Sea with the well-characterized populations in the NW Mediterranean Sea, that are threatened by ocean warming and acidification; and (2) assess the variation of studied parameters along a depth gradient in the Dardanelles. Biometric relationships were similar to those previously described on Italian coasts. At shallow depths, average coral height decreased, likely because of (1) the higher current velocity and wave action that is expected to limit vertical skeletal growth and/or (2) the need to increase photoprotection in high light conditions. Only a very slight increase of skeletal bulk density with depth (and consequent slight decrease of porosity) was detected, while age–length relationship, linear extension rate and net calcification rate were homogeneous among depths. The homogeneous net calcification rate with depth may depend on the balance between the response of zooxanthellae photosynthesis to temperature and light. In fact, shallow depths are likely to experience higher temperatures that negatively affect photosynthetic efficiency of B. europaea, thus reducing available energy for calcification. On the other hand, lower light availability with depth is expected to decrease photosynthesis and these two effects may compensate each other. Unexpectedly, the observed net calcification rate in the Dardanelles was almost double than the higher value reported in the northwestern Mediterranean Sea. Further analyses are required to analyse if energetic trade-offs between skeletal growth and reproduction differ in the two regions.
... The second deviation showed that paraphyly was found in 11 traditional families of the Scleractinia ( Fukami et al., 2008;Huang et al., 2009;Huang et al., 2011;Huang et al., 2014a;Huang et al., 2014b;Arrigoni et al., 2012). These findings further suggested that skeletal features (colony formation, corallite diameter, and characteristics of the septa and costae) that are widely used in identifying species of corals are not fully reflective of evolutionary relationships within families and even between conspecific populations from the Atlantic, Pacific, and Indian Oceans ( Chen et al., 1995;Romano & Palumbi, 1996;Romano & Palumbi, 1997;Romano & Cairns, 2000;Fukami et al., 2004;Fukami et al., 2008;Budd & Stolarski, 2009;Kitahara et al., 2010;Kerr, 2005;Arrigoni et al., 2012;Arrigoni et al., 2014a;Arrigoni et al., 2014b;Arrigoni et al., 2016). These deviations have challenged systematists to reexamine phylogenetic groupings in contrast with the traditional families and to discern and propose characteristics, apart from the skeleton or other aspects of the skeleton, that are systematically informative and diagnostic of species in the new groupings. ...
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Background The corallum is crucial in building coral reefs and in diagnosing systematic relationships in the order Scleractinia. However, molecular phylogenetic analyses revealed a paraphyly in a majority of traditional families and genera among Scleractinia showing that other biological attributes of the coral, such as polyp morphology and reproductive traits, are underutilized. Among scleractinian genera, the Euphyllia , with nine nominal species in the Indo-Pacific region, is one of the groups that await phylogenetic resolution. Multiple genetic markers were used to construct the phylogeny of six Euphyllia species, namely E. ancora, E. divisa, E. glabrescens, E. paraancora, E. paradivisa, and E. yaeyamaensis. The phylogeny guided the inferences on the contributions of the colony structure, polyp morphology, and life history traits to the systematics of the largest genus in Euphyllidae (clade V) and, by extension, to the rest of clade V. Results Analyses of cytochrome oxidase 1 ( cox1 ), cytochrome b ( cytb ), and β-tubulin genes of 36 colonies representing Euphyllia and a confamilial species, Galaxea fascicularis, reveal two distinct groups in the Euphyllia that originated from different ancestors. Euphyllia glabrescens formed a separate group. Euphyllia ancora, E. divisa, E. paraancora, E. paradivisa, and E. yaeyamaensis clustered together and diverged from the same ancestor as G. fascicularis. The 3′-end of the cox1 gene of Euphyllia was able to distinguish morphospecies. Discussion Species of Euphyllia were traditionally classified into two subgenera, Euphyllia and Fimbriaphyllia, which represented a dichotomy on colony structure. The paraphyletic groups retained the original members of the subgenera providing a strong basis for recognizing Fimbriaphyllia as a genus. However, colony structure was found to be a convergent trait between Euphyllia and Fimbriaphyllia, while polyp shape and length, sexuality, and reproductive mode defined the dichotomy better. Species in a genus are distinguished by combining polyp morphology and colony form. The cluster of E. glabrescens of the Euphyllia group is a hermaphroditic brooder with long, tubular tentacles with knob-like tips, and a phaceloid colony structure. The Fimbriaphyllia group, with F. paraancora, F. paradivisa, F. ancora, F. divisa, and F. yaeyamaensis, are gonochoric broadcast spawners with short polyps, mixed types of tentacle shapes, and a phaceloid or flabello-meandroid skeleton. Soft-tissue morphology of G. fascicularis and Ctenella chagius were found to be consistent with the dichotomy. Conclusions The paraphyly of the original members of the previous subgenera justify recognizing Fimbriaphyllia as a genus. The integrated approach demonstrates that combining polyp features, reproductive traits, and skeletal morphology is of high systematic value not just to Euphyllia and Fimbriaphyllia but also to clade V; thus, laying the groundwork for resolving the phylogeny of clade V.
... Instances of octocoral genera having both zooxanthellate and azooxanthellate species are rare but have been documented in a few genera, including Muricea (Sánchez 2016), Eunicella (Gori 2011), Junceella (Williams et al. 2010), and Briareum and Euplexaura (van Oppen et al. 2005). Additional examples are also known from other anthozoan genera, such as some among zoantharians (i.e., Palythoa spp. in Irei et al. 2015) and scleractinians, such as Balanophyllia (Arrigoni et al. 2014), Leptoseris (Hoeksema 2012), and Madracis (Santodomingo et al. 2007). ...
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The octocoral Nanipora kamurai is the fifth species of octocoral described with an aragonite skeleton. So far, it has only been known from a single location in Okinawa, Japan. Here, we report on the second recorded location of the genus Nanipora, in the Gulf of Thailand, where its colonies were found in relatively high densities. A total of 143 separate Nanipora colonies were counted in transects on a coral reef at Koh Tao, Thailand. They were found living on dead coral skeletons and on the shell of a living Tridacna squamosa clam. Phylogenetic analyses of cytochrome oxidase subunit 1 (COI) and mitochondrial mismatch repair protein (mtMutS) sequences showed that they belong to N. kamurai or to a close relative of this species. Additionally, a symbiotic relationship with Symbiodinium was observed for the first time in Nanipora, confirmed by sequences of the internal transcribed spacer region of ribosomal DNA (ITS-rDNA) of the dinoflagellate.
... However, even within monophyletic groups, the coloniality seems to have evolved at multiple times, suggesting that distinct selective pressures can promote it (Jackson 1977;Sebens 1987). Among anthozoans, separate lineages showing the development from one polyp or one mouth to more than one are well known among scleractinians, such as in the families Dendrophylliidae (Arrigoni et al. 2014), Fungiidae (Benzoni et al. 2012), and Faviidae, which were formerly known as Mussidae (Budd et al. 2012). ...
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Ceriantharians or tube-dwelling sea anemones are known for synthesizing soft and flexible tubes made of mucus, cnidae filaments (ptychocysts), and sediments found on the soft bottom. These tubes are used to house and protect them from danger, although many species of marine invertebrates use ceriantharian tubes as alternative substrates. Little is known about the organizational structure of ceriantharians in their own tubes. Although ceriantharians are always considered solitary animals, this study presents the first record of a ceriantharian colony of Botrucnidifer norvegicus Carlgren, 1912. Future studies regarding the population structure in ceriantharian aggregations may help to clarify this unusual habit for Ceriantharia.
... Our results support Verrill's qualitative observations and indicate that neither colony shape nor the arrangement and size of pores are diagnostic morphological characters distinguishing either species (Figs. 2, 3). Among scleractinian corals, recent work has shown that macro-morphological characters are usually homoplastic (Fukami et al. 2004;Gittenberger et al. 2011;Benzoni et al. 2012;Huang et al. 2014a), but that micromorphology and microstructure provide additional informative characters for taxonomy Stolarski 2009, Budd et al. 2012;Arrigoni et al. 2014;Huang et al. 2014b). The data presented here indicate that M. braziliensis and M. nitida can only be distinguished with molecular data. ...
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Fire corals are the only branching corals in the South Atlantic and provide an important ecological role as habitat-builders in the region. With three endemic species (Millepora brazilensis, M. nitida and M. laboreli) and one amphi-Atlantic species (M. alcicornis), fire coral diversity in the Brazilian Province rivals that of the Caribbean Province. Phylogenetic relationships and patterns of population genetic structure and diversity were investigated in all four fire coral species occurring in the Brazilian Province to understand patterns of speciation and biogeography in the genus. A total of 273 colonies from the four species were collected from 17 locations spanning their geographic ranges. Sequences from the 16S ribosomal DNA (rDNA) were used to evaluate phylogenetic relationships. Patterns in genetic diversity and connectivity were inferred by measures of molecular diversity, analyses of molecular variance, pairwise differentiation, and by spatial analyses of molecular variance. Morphometrics of the endemic species M. braziliensis and M. nitida were evaluated by discriminant function analysis; macro-morphological characters were not sufficient to distinguish the two species. Genetic analyses showed that, although they are closely related, each species forms a well-supported clade. Furthermore, the endemic species characterized a distinct biogeographic barrier: M. braziliensis is restricted to the north of the São Francisco River, whereas M. nitida occurs only to the south. Millepora laboreli is restricted to a single location and has low genetic diversity. In contrast, the amphi-Atlantic species M. alcicornis shows high genetic connectivity within the Brazilian Province, and within the Caribbean Province (including Bermuda), despite low levels of gene flow between these populations and across the tropical Atlantic. These patterns reflect the importance of the Amazon–Orinoco Plume and the Mid-Atlantic Barrier as biogeographic barriers, and suggest that, while M. alcicornis is capable of long-distance dispersal, the three endemics have restricted ranges and more limited dispersal capabilities.
... Based on a literature comparison, the South African Rhizopsammia verrilli differs from the previously reported Indo-Pacific representatives by having four complete cycles instead of five, the last incomplete. Striking similarities between R. verrilli and R. wettsteini Scheel & Pillai, 1983 have been highlighted (Arrigoni et al 2014), however specimens of the latter have not been examined and thus a comparison is not detailed herein. Specimens reported here are new records for the South African region, but not for the southwest Indian Ocean, as this R. verrilli has been recorded off Mozambique by MacNae and Kalk (1958). ...
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Globally, South Africa ranks in the top five countries regarding marine species richness per unit area. Given the high diversity, it is not surprising that many invertebrate taxa in the region are poorly characterised. The South African azooxanthellate Scleractinia (Anthozoa) is one such taxonomic group, and was last reviewed by Boshoff in 1980. Although more recent regional publications have reported on some species, there has not been a faunistic review that accounts for the country’s species diversity since then. Moreover, numerous unidentified specimens representing more than three decades of sampling effort have accumulated. In this study the authors update the state of knowledge of South African azooxanthellate coral species. Specimens, particularly those within the extensive collections of the Iziko South African and Smithsonian museums, were morphologically examined and identified. Other data considered included historic data represented as imagery data, associated species data from recent research surveys, and the scientific literature. To date, the study has increased the total number of known species from 77 to 108 across eleven families, 28 new South African records, and three are new species with one new genus.
... The identity of T. tagusensis (Fig. 1c) was determined based on morphological characters (De Paula and Creed 2004). However, considering the taxonomic difficulties posed by Tubastraea species (Cairns 2001;Arrigoni et al. 2014;Capel et al. 2016), further analyses, particularly employing DNA data, may also reveal the presence of invasive T. coccinea in the region, since both species are frequently found co-occurring (De Paula and Creed 2004;Creed and De Paula 2007). ...
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Invasive species are recognized as a major threat to marine biodiversity. The scleractinian coral Tubastraea tagusensis has been expanding its range into the southwest Atlantic Ocean, causing negative impacts on marine ecosystems. In 2016, the species was recorded on a shipwreck located 40 km off the Brazilian coast of Ceará State (latitude 2°30′ S), at densities ranging from 16 to 872 colonies × m⁻². This is the first documented occurrence and density of T. tagusensis in the northern region of Brazilian coral reefs (NBR), expanding the range of the genus along the Brazilian coastline to ca. 3850 km. Here it may form a threat to marine environments such as coral reefs, rocky shores, mussel beds, and fouling communities on manmade structures. Considering that the NBR contains vulnerable marine ecosystems, such as the reef system off the Amazon River, and that it is connected by both the North Brazil Current and shipping lanes associated with oil and gas platforms, a monitoring programme is needed to study the population dynamics of this invasive species.
... families or clades identified by Fukami et al. (2008) (Fig. S5, Supporting information). In some cases, genera or the same molecular lineages identified by previous molecular analyses were recovered, such as in Dendrophylliidae (Arrigoni et al. 2014a), Poritidae (Kitano et al. 2014), Pocilloporidae , Lobophylliidae (Arrigoni et al. 2014b;Huang et al. 2016) and clade XIV ), but congeneric species were not resolved. In Agariciidae, Fungiidae, Psammocoridae, Coscinaraeidae and Merulinidae, species Fig. 6 Phylogenetic relationships between all the complete SSU rRNA gene sequences, as obtained by two combined run of 100 000 000 generations each with BEAST 1.8.2. ...
Article
Scleractinian corals (i.e. hard corals) play a fundamental role in building and maintaining coral reefs, one of the most diverse ecosystems on Earth. Nevertheless, their phylogenies remain largely unresolved and little is known about dispersal and survival of their planktonic larval phase. The small subunit ribosomal RNA (SSU rRNA) is a commonly-used gene for DNA barcoding in several metazoans, and small variable regions of SSU rRNA are largely adopted as barcode marker to investigate marine plankton community structure worldwide. Here, we provide a large sequence dataset of the complete SSU rRNA gene from 298 specimens, representing all reef coral families and a total of 106 genera. The secondary structure was extremely conserved within the order with few exceptions due to insertions or deletions occurring in the variable regions. Remarkable differences in SSU rRNA length and base composition were detected between and within acroporids (Acropora, Montipora, Isopora, and Alveopora) compared to the other corals. V4 and V9 regions seem to be promising barcode loci because variation at commonly used barcode primer binding sites was extremely low and their levels of divergence allowed to distinguish families and genera. A time-calibrated phylogeny of Scleractinia is provided and mutation rate heterogeneity is demonstrated across main lineages. The use of this dataset as a valuable reference resource to investigate aspects of ecology, biology, molecular taxonomy, and evolution of scleractinian corals is discussed. This article is protected by copyright. All rights reserved.
... zooxanthellate) corals is underway, supported by various molecular and morphological approaches (e.g. Gittenberger, Reijnen & Hoeksema, 2011;Benzoni et al., 2012a,b;Arrigoni et al., 2014a;Kitano et al., 2014). The present study is the third in a series of monographs that considers species traditionally placed in the suborder Faviina sensu Vaughan & Wells (1943) and Wells (1956), or Faviina + Meandriina sensu Veron (1995). ...
Article
Lobophylliidae is a family-level clade of corals within the ‘robust’ lineage of Scleractinia. It comprises species traditionally classified as Indo-Pacific ‘mussids’, ‘faviids’, and ‘pectiniids’. Following detailed revisions of the closely related families Merulinidae, Mussidae, Montastraeidae, and Diploastraeidae, this monograph focuses on the taxonomy of Lobophylliidae. Specifically, we studied 44 of a total of 54 living lobophylliid species from all 11 genera based on an integrative analysis of colony, corallite, and subcorallite morphology with molecular sequence data. By examining coral skeletal features at three distinct levels – macromorphology, micromorphology, and microstructure – we built a morphological matrix comprising 46 characters. Data were analysed via maximum parsimony and transformed onto a robust molecular phylogeny inferred using two nuclear (histone H3 and internal transcribed spacers) and one mitochondrial (cytochrome c oxidase subunit I) DNA loci. The results suggest that micromorphological characters exhibit the lowest level of homoplasy within Lobophylliidae. Molecular and morphological trees show that Symphyllia, Parascolymia, and Australomussa should be considered junior synonyms of Lobophyllia, whereas Lobophyllia pachysepta needs to be transferred to Acanthastrea. Our analyses also lend strong support to recent revisions of Acanthastrea, which has been reorganized into five separate genera (Lobophyllia, Acanthastrea, Homophyllia, Sclerophyllia, and Micromussa), and to the establishment of Australophyllia. Cynarina and the monotypic Moseleya remain unchanged, and there are insufficient data to redefine Oxypora, Echinophyllia, and Echinomorpha. Finally, all lobophylliid genera are diagnosed under the phylogenetic classification system proposed here, which will facilitate the placement of extinct taxa on the scleractinian tree of life.
... A total of 3%, N = 27 of H. cochlea showed even more than two polyps. Budding is a feature common in this F I G U R E 1 Map showing (a) the location of the study area in the Zanzibar Archipelago; and (b) the study sites (black squares indicate study sites)species and is usually developed by elongation and later bipartition of the main corallite(Arrigoni et al., 2014). ...
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Marine symbioses are integral to the persistence of ecosystem functioning in coral reefs. Solitary corals of the species Heteropsammia cochlea and Heterocyathus aequicostatus have been observed to live in symbiosis with the sipunculan worm Aspidosiphon muelleri muelleri, which inhabits a cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these photosymbiotic corals enables the coral holobiont to move, in fine to coarse unconsolidated substrata, a process termed as “walking.” This allows the coral to escape sediment cover in turbid conditions which is crucial for these light‐dependent species. An additional commensalistic symbiosis of this coral‐worm holobiont is found between the Aspidosiphon worm and the cryptoendolithic bivalve Jousseaumiella sp., which resides within the cavity of the coral skeleton. To understand the morphological alterations caused by these symbioses, interspecific relationships, with respect to the carbonate structures between these three organisms, are documented using high‐resolution imaging techniques (scanning electron microscopy and µCT scanning). Documenting multi‐layered symbioses can shed light on how morphological plasticity interacts with environmental conditions to contribute to species persistence. The photosymbiotic solitary corals Heteropsammia cochlea and Heterocyathus aequicostatus live in symbiosis with the sipunculid worm Aspidosiphon muelleri muelleri, and the cryptoendolithic bivalve Jousseaumiella sp., which reside within the cavity of the coral skeleton. The symbiosis enables the coral holobiont to escape sediment cover in turbid conditions. High‐resolution imaging reveals morphological alterations caused by these symbioses, and allows to better understand the interspecific relationships.
... Molecular data have therefore become increasingly important in recent years to overcome the limitations of morphological analyses among scleractinians (e.g. Benzoni et al. 2011Benzoni et al. , 2012aBenzoni et al. , 2014Gittenberger et al. 2011;Huang et al. 2011Huang et al. , 2014aHuang et al. , 2014bBudd et al. 2012;Arrigoni et al. 2014aArrigoni et al. , 2017Kitano et al. 2014;Schmidt-Roach et al. 2014;Terraneo et al. 2016aTerraneo et al. , 2017. In particular, the family Lobophylliidae has received much attention recently with regard to its phylogeny (Arrigoni et al. 2014b(Arrigoni et al. , 2015Huang et al. 2016). ...
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Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coral Echinophylliaaspera (Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows that E.aspera clustered closely with Sclerophylliamaxima (Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome of E.aspera provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.
... The Tubastraea species recorded in this study also showed high dispersion abilities, with specimens widely distributed along the Santa Cruz de Tenerife harbor. Although taxonomy of Tubastraea genus is complex, to the point that molecular studies now question the validity of certain species (Arrigoni et al., 2014;Brito et al., 2017), we have assigned the specific names of the two species present in the Canary Islands, T. coccinea and T. tagusensis, based on the criteria of the most recent studies (Silva et al., 2011;Creed et al., 2017). ...
Article
Zooxanthellate zoantharians (Cnidaria: Anthozoa) are commonly found in tropical and subtropical marine regions around the world. However, due to the low genetic variability of commonly used DNA markers combined with high levels of intraspecific morphological variation, misidentifications and species synonyms are commonly found in the literature. In this study, zoantharians from the suborder Brachycnemina collected in the Macaronesia and Cape Verde ecoregions were studied combining morphological, molecular and ecological data, in order to comprehensively assess the species diversity of the region. Moreover, molecular analyses of endosymbiotic Symbiodiniaceae zooxanthellae were also performed to provide more information on each holobiont. Our integrative results demonstrate that Brachycnemina species diversity increases as seawater temperature rises toward the tropics with a total of nine species recorded: one from waters around northern Madeira, five in the Canary Islands and seven in the southernmost Cape Verde Archipelago. All species were seen to host either Symbiodiniaceae of the genera Symbiodinium (former Symbiodinium ‘Clade A’) or Cladocopium (former Symbiodinium ‘Clade C’). Moreover, this study records for the first time the presence of Palythoa grandis, P. aff. clavata, P. grandiflora, an unknown Zoanthus species and Z. pulchellus in the East Atlantic Ocean. These results show no endemic zooxanthellate zoantharians in the East Atlantic, with all species shared with the West Atlantic.
... Although the ecological role of Dendrophylliidae is well known, our current knowledge about the phylogenetic relationships of the family remains scarce. Most taxa in fact have been predominately investigated morphologically or with few genes (Arrigoni et al. 2014;Kitahara et al. 2016;Capel et al. 2020). Reduced-representation genome approaches, such as RAD sequencing, are shedding light into coral evolution by providing a fast and efficient way to reconstruct mitochondrial genomes (hereafter mitogenome) (Forsman et al. 2017;Terraneo et al. 2018aTerraneo et al. , 2018b. ...
Article
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The scleractinian coral family Dendrophylliidae is a major component of shallow and deep-water coral ecosystems worldwide, but our knowledge on the evolutionary history of the family remains scarce. Here, we used ezRAD coupled with Illumina sequencing technology and reconstructed the complete mitochondrial genome of Dendrophyllia minuscula (GenBank accession number OL634845), from mesophotic depths in the Red Sea NEOM area. The mitochondrial genome of D. minuscula consisted of 19,054 bp, organized in 13 protein-coding genes, 2 rRNA genes, and 2 tRNA genes, in agreement with the Scleractinia typical mitogenome organization. This complete mitochondrial genome contributes toward a better knowledge of mesophotic and deep-water coral diversity and evolutionary history.
... In dead polyps (Fig. 2b), septa of the new species show a bifurcating pattern according to the Pourtal es plan (Cairns 1994), which does not occur in Tubastraea (Fig. 2c). The septal pattern and the presence of stolons indicate that this species belongs to either the genus Cladopsammia or Rhizopsammia, which are both phylogenetically closely related to Tubastraea (Cairns 2001, Arrigoni et al. 2014. Genetic information on Atlantic Cladopsammia and Rhizopsammia is currently not available, but a preliminary molecular analysis based on the mitochondrial marker cytochrome c oxidase subunit I (COI) revealed that the species found on Curac ßao is very closely related to both Cladopsammia gracilis (Milne Edwards & Haime, 1848) and Rhizopsammia wettsteini (Scheer & Pillai, 1983) from the Red Sea (A.-F. ...
Article
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In contrast with a general decline of Caribbean reef corals, a previously rare sun coral is increasing in abundance within shallow coral communities on Curac ßao. This azooxanthellate scleractinian was identified as Cladopsammia manuelensis, which has an amphi-Atlantic distribution. Over the last decade , C. manuelensis has increased abundance along the leeward coast of Curac ßao (southern Caribbean) between depths of 4 and 30 m. This species was initially not noticed because it resembles the invasive coral Tubastraea coccinea, which was introduced to Curac ßao from the Indo-Pacific around 1940. However, in contrast to T. coccinea, C. manuelensis was previously only present on deeper reef sections (>70 m) of Caribbean reefs. Our observations illustrate how the sudden increase in abundance of a previously unnoticed, apparently cryptogenic species could result from natural dynamics on present-day reefs, but also could easily be mistaken for an invasive species. The finding that deep reef sections can harbor species capable of colonizing shallower reef zones highlights the importance of thorough inventories of reef communities across large depth ranges, which can help us to discriminate between range increases of native species and the arrival of invasives.
... More than 5 replications of the process from extraction to amplification were conducted to ensure that the final sequencing accuracy is more than 99%. The QIAGEN Multiplex PCR Kit (Qiagen, Hilden, Germany) was used to perform the polymerized chain reaction for the amplification of mitochondrial region 16S 39 and IGR 40 . The PCR cycling parameters used are as follows: initial 95 °C denaturation for 15 min. ...
Article
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Abstract This paper reports a deep-water coral framework (a single colonial bush or a larger bioconstruction of coral covering the sea bottom), formed entirely by the scleractinian coral Eguchipsammia fistula (Alcock, 1902) (Dendrophylliidae), in the northern Red Sea waters of Saudi Arabia at a depth of about 640 m. The framework consists of mostly live corals with a total area of about 10 m2 and the length of the individual coral branches range from 12 to 30 cm. Although E. fistula is ubiquitous, this discovery is the second record of a framework formed by this species and the first discovery of a large living reef in the Red Sea. The results of the genetic study indicate the potential existence of a genetic variation of E. fistula in the Red Sea. This discovery implies that the Red Sea has favorable habitats for framework-forming DWC species and highlights the need for conducting more systematic surveys for understanding their distribution, abundance, and ecology.
... The Tubastraea species recorded in this study also showed high dispersion abilities, with specimens widely distributed along the Santa Cruz de Tenerife harbor. Although taxonomy of Tubastraea genus is complex, to the point that molecular studies now question the validity of certain species (Arrigoni et al., 2014;Brito et al., 2017), we have assigned the specific names of the two species present in the Canary Islands, T. coccinea and T. tagusensis, based on the criteria of the most recent studies (Silva et al., 2011;Creed et al., 2017). ...
Article
In this study the presence, distribution and density of several species of Scleractinia corals introduced in the Canary Islands and settled in artificial substrata (marina pontoons and port docks) of the Santa Cruz de Tenerife harbor were studied. Tubastraea spp. and Oculina patagonica densities in such locations were assessed owing to their potential as invasive species, and the abundance of other introduced and native corals was also estimated. O. patagonica showed a high frequency of occurrence (28.8%), reaching densities of 0.25 colonies/m² and was exclusively located in the marina pontoons, found opposite the anchoring spots of oil platforms, mainly in shaded environments. Tubastraea spp. were also found in said area, where they showed very high densities (44.6% of frequency and 2.0 colonies/m²) regardless of light availability, as well as in the inner wall of another port dock where oil platforms berth. Other species were only recorded in the pontoon areas of the marina, with the occurrence of the Culicia genus especially remarkable (15.9%), whose only previous record in the Atlantic was in the Cape of Good Hope (South Africa). Tubastraea tagusensis was also recorded for the first time in the eastern Atlantic. Results confirm that oil platforms have been the introductory vector of non-native corals and the introduction process, the expansion and invasion risks, as well as the need for a control plan are discussed.
... Molecular systematics resolved these biogeographically separated elkhorn corals as highly divergent lineages and distinct species . Molecular data has also helped identify evolutionary convergence in at least five other scleractinian coral families (Dendrophyllidae: Arrigoni et al., 2014;Fungiidae: Benzoni et al., 2012;Gittenberger et al., 2011;and Mussidae: Merulinidae, and Lobophylliidae, Budd et al., 2012;Fukami et al., 2004). ...
Article
Scleractinian corals are a diverse group of ecologically important yet highly threatened marine invertebrates, which can be challenging to identify to the species level. An influx of molecular studies has transformed scleractinian systematics, highlighting that cryptic species may be more common than previously understood. In this study, we test the hypothesis that Plesiastrea versipora (Lamarck, 1816), a species currently considered to occur throughout the Indo-Pacific in tropical, sub-tropical and temperate waters, is a single species. Molecular and morphological analyses were conducted on 80 samples collected from 31 sites spanning the majority of the species putative range and twelve mitogenomes were assembled to identify informative regions for phylogenetic reconstruction. Congruent genetic data across three gene regions supports the existence of two monophyletic clades aligning with distinct tropical and temperate provenances. Multivariate macromorphological analyses based on 13 corallite characters provided additional support for the phylogeographic split, with the number of septa and corallite density varying across this biogeographic divide. Furthermore, micromorphological and microstructural analyses identified that the temperate representatives typically develop sub-cerioid corallites with sparse or absent coenosteal features and smooth septal faces. In contrast, tropical representatives typically develop plocoid corallites separated by a porous dissepimental coenosteum and have granulated septal faces. These data suggest that at least two species exist within the genus Plesiastrea Milne Edwards & Haime, 1848. Based on examination of type material, we retain the name Plesiastrea versipora (Lamarck, 1816) for the temperate representatives of the genus and resurrect the name Plesiastrea peroni Milne Edwards & Haime, 1857 for the tropical members. This study highlights how broadly distributed hard coral taxa still need careful re-examination through an integrated systematics approach to better understand their phylogeographic patterns. Furthermore, it demonstrates the utility of integrating micro-, macro-morphological and genetic datasets, and the importance of type specimens when dealing with taxonomic revisions of scleractinian taxa.
... The other Mediterranean species included in the dataset, P. pulchellus, was sister to Polycyathus muellerae, a shallow-water coral occurring also in the Mediterranean Sea. Although the majority of shallow-water scleractinian families are polyphyletic, Arrigoni et al. (2014) confirmed the monophyly of Dendrophylliidae using molecular phylogeny, micromorphology and skeleton microstructure. In their study, sequences of five Mediterranean species were included, two of which Dendrophyllia cornigera and L. pruvoti occur in deep waters, although the latter is of predominant shallow-water occurrence. ...
Chapter
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Within the Mediterranean basin there are 82 species of deep-sea corals belonging to six orders of the phylum Cnidaria (Antipatharia, Scleractinia, Zoantharia, Alcyonacea, Pennatulacea and Anthoathecata), with the Alcyonacea (40) and the Scleractinia (25) being the most speciose. Thirteen species have a pronounced habitat-building ability at depths >200 m. Remarkable sites characterised by rich coral frameworks and gardens have been found in biodiversity surveys during the last years, revealing that some species are more abundant than previously thought. However, in terms of species richness, the Mediterranean deep-sea coral fauna is less diverse when compared with the nearby Atlantic areas. This discrepancy is probably in part due to unfavourable environmental conditions of the deep Mediterranean Sea, and to differences in sampling efforts between both areas. In this respect, considerable efforts have been recently done in terms of deep-sea fauna inventories. Nevertheless, updates made to the Mediterranean inventory of deep-sea corals since the beginning of the twenty-first century are few except for the octocorals. Therefore, ten species were included to the Mediterranean inventory, among which two have been newly described. The species concerned belong to the orders Scleractinia (1), Pennatulacea (1) and Alcyonacea (8).
... Phylogenetic reconstructions and species delimitation of scleractinian corals have long been hampered by a disagreement between genetic data and colony-level morphology [43][44][45][46][47]. This challenge is particularly difficult among genera in which colony morphology is known to be highly variable, such as the Hawaiian Montipora. ...
Article
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Background: Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results: All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05-2.6] Myr) or assuming rate homogeneity (0.4 [0.14-0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions: Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.
... Our analysis supports several subsequent losses of coloniality in scleractinians but no secondary gains. This result is also likely to change with increased taxon sampling, as molecular phylogenetic analyses of scleractinian families that include colonial and solitary forms have found evidence for both evolutionary transitions (Gittenberger et al. 2011;Arrigoni et al. 2014). ...
Article
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648–894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for interpretation of the Precambrian environment and the early evolution of metazoans.
... Dendrophylliidae : Arrigoni et al. (2014a) and Cairns (2001). ...
Book
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Volume 2 presents the last part of coral studies carried out by late Hans Ditlev (HD). We have revised the nomenclature to be in accordance with WoRMS. In case of recent changes, we have also shown the names applied by Hans Ditlev (HD id as). We have not changed his descriptions but we have supplemented texts where HD had photos but no text. Such places are marked by an asterisk and source ofcitation. The following taxa are illustrated: Agariciidae (5 genera, 33 sp.), Caryophylliidae (1 genus, 1 sp.), Coscinaraeidae (3 genera, 6 sp.), Dendrophylliidae (5 genera, 17 sp.), Diploastreidae (1 genus, 1 sp.), Fungiidae (15 genera, 108 sp.), Lobophylliidae (9 genera, 32 sp.), Merulinidae (21 genera, 108 sp.), Mussidae, (1 genus, 1 sp.), Psammocoridae (1 genus, 7 sp.), Siderastreidae (2 genera, 2 sp.), Familia incertae sedis (5 genera, 15 sp.). Technical terms are explained and the original identification keys by HD are rewritten and expanded considering the many changes coral taxonomy has gone through in recent years. An overview of coral literature is compiled and listed by author, year and title of publication. A substantial part ofthe publications can be downloaded from the Internet.
... Our analysis supports several subsequent losses of coloniality in scleractinians but no secondary gains. This result is also likely to change with increased taxon sampling, as molecular phylogenetic analyses of scleractinian families that include colonial and solitary forms have found evidence for both evolutionary transitions (Gittenberger et al. 2011;Arrigoni et al. 2014). ...
Article
Full-text available
Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648–894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for interpretation of the Precambrian environment and the early evolution of metazoans.
Article
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As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia , as exemplary case studies. We designed an updated bait set (29,181 baits) to target‐capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species‐level phylogenies were highly supported for both genera. Clustering methods based on filtered SNPs delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using Restriction Site Associated DNA Sequencing. Both case studies demonstrate the utility of target‐enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow time scales in corals.
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Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some species like Tubastraea coccinea and T. tagusensis have been spreading very fast replacing the native ones which affect the local environment and decrease biodiversity of corals and other organisms associated with them. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for both conservation and management of invasive species. In this circumstance, it is expected that genome sequencing would provide powerful insights that could lead to better strategies for prevention, management, and control of this and other invasive species. Here, we present three genomes of Tubastraea spp. in one of the most comprehensive biological studies of corals, that includes flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The genome of T. tagusensis is organized in 23 chromosomes pairs and has 1.1 Gb, the T. coccinea genome is organized in 22 chromosome pairs and has 806 Mb, and the Tubastraea sp. genome is organized in 21 chromosome pairs and has 795 Mb. The hybrid assembly of T. tagusensis using short and long-reads has a N50 of 227,978 bp, 7,996 contigs and high completeness estimated as 91.6% of BUSCO complete genes, of T. coccinea has a N50 of 66,396 bp, 17,214 contigs and 88.1% of completeness, and of Tubastraea sp. has a N50 of 82,672 bp, 12,922 contigs and also 88.1% of completeness. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. We provide evidence for exclusive Scleractinia and Tubastraea gene content related to adhesion and immunity. The Tubastraea spp. genomes are a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral genus, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of coral species, whether invasive or threatened.
Article
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Comparative lists of species’ extinction risk are increasingly being used to prioritise conservation resources. Extinction risk is most rigorously assessed using quantitative data on species’ population trajectories, but in the absence of such data, assessments often rely on qualitative estimates based on expert opinion of species abundances, distributions and threats. For example, one-third of coral species are classified as threatened and another third as near threatened on the IUCN Red List, despite a lack of data at the population level for the vast majority of species. Since many taxa show a strong correlation between species traits and extinction risk, an alternate approach is to identify traits associated with extinction in other groups and apply them to the taxon of interest. Here, we examine whether life-history traits associated with stress tolerance, fecundity and habitat specialisation are correlated with Red List conservation status in reef corals. We found no relationship between conservation status and life-history traits, suggesting that either traits identified as important predictors of extinction risk in other taxa are not important in corals, or that conservation status does not accurately reflect species’ relative extinction risk. Therefore, using global-scale extinction risk assessments to inform conservation of coral reefs presents a high risk of ‘silent extinctions’ of undescribed species. We argue that the conservation status for the vast majority of coral species should be ‘data deficient’ and is likely to remain so for the foreseeable future, and that the status and trends of coral populations can only be reliably assessed at relatively small scales.
Article
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Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lin-eage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and ge-nus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.
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Scleractinian corals provide habitats for a broad variety of cryptofauna, which in turn may contribute to the overall functioning of coral symbiomes. Among these invertebrates, hydrozoans belonging to the genus Zanclea represent an increasingly known and ecologically important group of coral symbionts. In this study, we analysed 321 Zanclea colonies associated with 31 coral genera collected from 11 localities across the Indo-Pacific and Caribbean regions, and used a multi-disciplinary approach to shed light on the evolution and biogeography of the group. Overall, we found high genetic diversity of hydrozoans that spans nine clades corresponding to cryptic or pseudo-cryptic species. All but two clades are associated with one or two coral genera belonging to the Complex clade, whereas the remaining ones are generalists associated with both Complex and Robust corals. Despite the observed specificity patterns, no congruence between Zanclea and coral phylogenies was observed, suggesting a lack of coevolutionary events. Most Zanclea clades have a wide distribution across the Indo-Pacific, including a generalist group extending also into the Caribbean, while two host-specific clades are possibly found exclusively in the Red Sea, confirming the importance of this peripheral region as an endemicity hotspot. Ancestral state reconstruction suggests that the most recent common ancestor of all extant coral-associated Zanclea was a specialist species with a perisarc, occurring in what is now known as the Indo-Pacific. Ultimately, a mixture of geography- and host-related diversification processes is likely responsible for the observed enigmatic phylogenetic structure of coral-associated Zanclea.
Article
The diversity in the skeletal features of coral species is an outcome of their evolution, distribution and habitat. Here, we explored, from macro- to nano-scale, the skeletal structural and compositional characteristics of three coral species belonging to the genus Balanophyllia having different trophic strategies. The goal is to address whether the onset of mixotrophy influenced the skeletal features of B. elegans, B. regia, and B. europaea. The macroscale data suggest that the presence of symbiotic algae in B. europaea can lead to a surplus of energy input that increases its growth rate and skeletal bulk density, leading to larger and denser corals compared to the azooxanthellate ones, B. regia and B. elegans. The symbiosis would also explain the higher intra-skeletal organic matrix (OM) content, which is constituted by macromolecules promoting the calcification, in B. europaea compared to the azooxanthellate species. The characterization of the soluble OM also revealed differences between B. europaea and the azooxanthellate species, which may be linked to diverse macromolecular machineries responsible for skeletal biosynthesis and final morphology. Differently, the crystallographic features were homogenous among species, suggesting that the basic building blocks of skeletons remained a conserved trait in these related species, regardless of the trophic strategy. These results show changes in skeletal phenotype that could be triggered by the onset of mixotrophy, as a consequence of the symbiotic association, displaying remarkable plasticity of coral skeletons which repeatedly allowed this coral group to adapt to a range of changing environments throughout its geological history.
Article
Across the tree of life, phylogenetic analysis is increasingly being performed using transcriptome data. As a result of heterogeneous gene expression within individual organisms and unequal sequencing depth between samples, coverage of homologous loci in such datasets is typically inhomogeneous. Consequently, missing data are a common feature of phylotranscriptomic inference, but their impact on phylogenetic analysis remains poorly characterised empirically. Considering the complexity of the evolutionary history of stony corals (Cnidaria: Anthozoa: Scleractinia), transcriptome data hold great promise for resolving their phylogeny, particularly if there is a good understanding of missing data and data type (either amino acid or DNA) effects. Here, we reconstructed a broad phylogenetic tree of 39 scleractinian species with 3 corallimorpharians as outgroups, including 15 transcriptomes that were newly sequenced and assembled in this study. Between 63 and 505 loci were used to analyse the scleractinian phylogeny, and we quantified differences in tree topology, tree shape, bootstrap support and effects of conflicting gene trees among datasets of varying completeness for both amino acid and DNA sequences. Even with almost 70% missing data, tree topologies appear to be mostly unaffected, although there are higher incongruence levels in the less complete datasets. Furthermore, DNA trees outperform amino acid trees in bootstrap support and robustness against incongruent loci. Overall, our findings indicate that high levels of missing data can still produce expected tree topologies, but identifying and omitting incongruent loci can lead to more consistent branch length estimates.
Article
Understanding evolutionary transitions in scleractinian corals is fundamental to predicting responses of coral reefs to climate change. We examine transitions between solitary and colonial corals in the fossil record, focusing on the Caribbean solitary reef coral Scolymia and members of the subfamily Mussinae. Fossil specimens are selected from a large well-documented collection of Neogene Caribbean corals, and a total of 23 species are distinguished using 15 morphological features. Ten of the 23 species are extant Caribbean species, seven are previously described extinct Neogene species, and six other extinct species are formally described as new. The 7 + 6 extinct species are added to a morphological data set consisting of 30 extant molecularly characterized species plus seven additional extinct (five Eocene, two Neogene) species. In addition to the Caribbean subfamily Mussinae, the extant species include the Indo-Pacific families Merulinidae and Lobophylliidae, and the Caribbean subfamily Faviinae. Phylogenetic analysis was performed on the data using maximum parsimony, and the results reveal four clades, which correspond with previously reported molecular clades. Solitary corals group most closely with Caribbean Mussinae and Indo-Pacific Lobophylliidae, whereas colonial corals are present in all four clades. Within Caribbean Mussinae, members of the colonial genera Mycetophyllia and Isophyllia form distinct subclades, as do the extinct solitary genera Antillia and Antillophyllia. The relationships within Scolymia are less well defined but its members appear more closely related to extinct solitary genera dating back to the Eocene. These results indicate that evolutionary transitions between solitary and colonial corals have been rare within the Mussinae. Except Antillophyllia, most Mussinae genera are restricted to the Caribbean. During the late Miocene, Mycetophyllia diversified and three other modern Mussinae genera (Mussa, Scolymia, Isophyllia) originated in association with increased Caribbean productivity. Mussinae that were more likely to survive Plio–Pleistocene extinction may have taken refuge in deep forereef habitats.
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This World list of Scleractinia ever described is part of the World Register of Marine Species (WoRMS), a global initiative to provide an online register of scientific names of all marine organisms. In this continuously updated list, users can find the taxonomic classification of scleractinians, with valid and invalid names of families, genera and species.
Article
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Traditionally and for practical reasons, skeleton structure has been the main source of taxonomic characters for scleractinian systematics, whereas information from soft tissues has been comparatively neglected. However, skeleton variability may leave species identification uncertain. The use of characters from soft tissues (e.g. polyp anatomy, cnidae size) is routine in the study of other (“soft”) hexacorallian orders. This contribution aims to determine whether cnidae characters are useful in taxonomic studies of scleractinians. The cnidae composition of two congeneric species—Balanophyllia europaea (Risso, 1826) and Balanophyllia regia Gosse, 1860—have been studied throughout a wide geographical area. The data obtained show consistent qualitative and quantitative differences between the two species. This study shows that the cnidae characters can be useful taxonomic criteria for distinguishing congeneric species.
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Three Indonesian species of Heterocyathus and two of Heteropsammia are briefly diagnosed. Remarks are given on their synonymy, phenotypic variation, and ecology. All five species are found on soft substrata in the proximity of coral reefs and live in association with a sipunculan worm. This interspecific assocation is discussed with regard to whether it is mutualistic or parasitic.
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An update of the phylogeny and biogeography of mushroom coral species belonging to Fungia (Pleuractis) is presented. Among the five species of this monophyletic group, one is described as new to science. This species, Fungia seychellensis spec, nov., was discovered during the Netherlands Seychelles Expedition (1992-1993) in the framework of the Netherlands Indian Ocean Programme 1990/1995.
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A phylogenetically based comparative analysis of onshore-off-shore distribution patterns of mushroom coral species (Sclerac-tinia: Fungiidae) was made to reconstruct an evolutionary sce-nario for differentiation in fungiid shelf habitats. This phylo-ecological study integrates data on fungiid distribution patterns along environmental gradients on the Spermonde Shelf, SW Sulawesi, with a recently published phylogeny reconstruction of the Fungiidae. A mushroom coral fauna of 34 species was used to compare their distributions by use of 50-m 2 belt quadrats in transects (1) from the mainland to the shelf edge, (2) around reefs with regard to predominant wind directions, and (3) over bathymetrical reef zones. Species association ordinations were made for each of the four shelf zones using both abundance and incidence data to examine whether closely related species co-occurred. Some closely related species or even sister species appeared to show very similar distribution patterns and to co-exist in high abundances. These results indicate that there may not be community saturation and competitive exclusion among mushroom corals species, most of which are free-living. In re-constructions of fungiid habitat evolution, offshore reef slopes appear to be original (ancestral), whereas onshore habitats, shallow reef flats, and deep sandy reef bases seem to be derived. The latter is in contrast with an earlier hypothesis, in which deep sandy substrates were considered ancestral mushroom coral habitats.
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The focus of this paper is to provide an overview of historical and modern accounts of scleractinian evolutionary relationships and classification. Scleractinian evolutionary relationships proposed in the 19th and the beginning of the 20th centuries were based mainly on skeletal data. More in-depth observations of the coral skeleton showed that the gross-morphology could be highly confusing. Profound differences in microstructural and microarchitectural characters of e.g., Mesozoic microsolenine, pachythecaliine, stylophylline, stylinine, and rhipidogyrine corals compared with nominotypic representatives of higher-rank units in which they were classified suggest their separate (?subordinal) taxonomic status. Recent application of molecular techniques resulted in hypotheses of evolutionary relationships that differed from traditional ones. The emergence of new and promising research methods such as high-resolution morphometrics, analysis of biochemical skeletal data, and refined microstructural observations may still increase resolution of the “skeletal” approach. Achieving a more reliable and comprehensive scheme of evolutionary relationships and classification framework for the Scleractinia will require close cooperation between coral biologists, ecologists, geologists, geochemists, and paleontologists.
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Bleaching was studied in populations of phylogenetically closely related species (n = 21) of mushroom corals (Scleractinia:Fungiidae) around Pari Island (Java Sea) during a period of excessive seawater warming in 1983. The interspecific variation in the proportions of affected individuals was significant. Spatial variation in the degree of bleaching among fungiid assemblages depended much on relative species abundances. Mushroom corals in relatively stagnant water of lagoons and on the inner reef flat showed little bleaching. Many of the outer reef mushroom corals at less-than-or-equal-to 9 m depth were affected, but only a few at greater depths (greater-than-or-equal-to 15 m). In most affected fungiids, the bleached part was pale (associated with pigment loss) instead of white (assumedly caused by zooxanthellae expulsion). The difference between the proportions of paled and whitened corals was not clearly depth-related, but most probably species-related. Most bleached fungiids were affected over their whole upper surface, whereas others showed a mosaic pattern. Entire bleaching was most common at depths < 6 m and partial bleaching at 9 m. One species with a predominantly shallow distribution (mainly less-than-or-equal-to 9 m) showed a significant majority of entirely bleached individuals. The smallest mushroom corals (empty set(max) less-than-or-equal-to 5 cm) on the outer reef, usually in sheltered positions, and the largest ones (empty set(max) > 20 cm), usually occurring deep, were the least affected. The latter may have escaped bleaching by recurrent downward migration.
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The Fungiidae are mushroom corals that live in sublittoral habitats in the tropical Indo-Pacific. Their habitats are part of coral reefs or other marine substrata, which usually can be found in the proximity of the reefs. In the present taxonomic revision, the family is divided into 11 genera; one of which, Fungia, is subdivided into seven subgenera. A total of 40 species is described and figured, three of which are new to science. One species is renamed. The stratigraphic distribution is given for all the species recorded in fossil state. A tentative phylogenetic reconstruction down to the species level is given. The cladogram that is provided should be considered a working hypothesis and not a sound basis for a completely revised classification and nomenclature of the Fungiidae. For each species the presently known geographic range is mapped. The pattern of species richness in the Indo-Pacific is compared with that of some other taxa and discussed with respect to their distributional patterns. The ranges of the Fungiidae are analyzed with the use of approaches from both historical and ecological biogeography.
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Until coral molecular phylogenies were published, the genus Plesiastrea was traditionally part of the family Faviidae and considered by several authors to be closely related to the genus Montastraea. However, genetic data has shown that Plesiastrea versipora, the genus type species, is evolutionarily distinct within the Robust clade of the Scleractinia and does not belong to the large clade grouping most representatives of the families Faviidae, including Montastraea, Mussidae, Merulinidae. Trachyphylliidae, and Pectiniidae. Instead, P. versipora is closely related to non reef-dwelling taxa currently ascribed to the Oculinidae (Cyathelia axillaris) and Caryophylliidae (Trochocyathus efateensis). However, no discussion on the morphologic features of P. versipora compared to other taxa has been published yet. Moreover, no information is available about the phylogenetic placement of Plesiastrea devantieri, the only other species in the genus. The phylogeny of both Plesiastrea species was addressed through molecular analyses (COI and rDNA) and morphological analysis. Morphological differences between the two species included number of septa, cycles of vertical structures in front of the septa and septal micromorphology. On the basis of these data and nuclear and mitochondrial markers. P. devantieri belongs to the Faviidae-Merulinidae-Pectiniidae-Trachyphylliidae clade (Clade XVII sensu Fukami et al., 2008) and is most closely related to Goniastrea aspera and G. palauensis. The type species of the genus Goniastrea, G. retiformis, however, is not closely related to either G. aspera and G. palauensis, or to P. devantieri. Taxonomic implications of these findings and morphologic affinities between the two species and closely related taxa are discussed.
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The scleractinian species Psammocora explanulata and Coscinaraea wellsi were originally classified in the family Siderastreidae, but in a recent morpho-molecular study it appeared that they are more closely related to each other and to the Fungiidae than to any siderastreid taxon. A subsequent morpho-molecular study of the Fungiidae provided new insights regarding the phylogenetic relationships within that family. In the present study existing molecular data sets of both families were analyzed jointly with those of new specimens and sequences of P. explanulata and C. wellsi. The results indicate that both species actually belong to the Cycloseris clade within the family Fungiidae. A reappraisal of their morphologic characters based on museum specimens and recently collected material substantiate the molecular results. Consequently, they are renamed Cycloseris explanulata and C. wellsi. They are polystomatous and encrusting like C. mokai, another species recently added to the genus, whereas all Cycloseris species were initially thought to be monostomatous and free-living. In the light of the new findings, the taxonomy and distribution data of C. explanulata and C. wellsi have been updated and revised. Finally, the ecological implications of the evolutionary history of the three encrusting polystomatous Cycloseris species and their free-living monostomatous congeners are discussed.
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Dactylotrochus cervicornis (= Tridacophyllia cervicornis Moseley, 1881), which occurs in Indo-Pacific waters between 73 and 852 m, was originally described as an astraeid but was later transferred to the Caryophylliidae. Assumed to be solitary, this species has no stolons and only one elongated fossa, and is unique among azooxanthellate scleractinians in often displaying extremely long thecal extensions that are septate and digitiform. Based on both molecular phylogenetic analyses (partial mitochondrial CO1 and 16S rDNA, and partial nuclear 28S rDNA) and morphological characteristics, we propose the transfer of D. cervicornis from the Caryophylliidae to the Agariciidae, making it the first extant representative of the latter family that is solitary and from deep water (azooxanthellate). The basal position of D. cervicornis within the agariciids implied by our analyses strengthens the case for inclusion of fossil species that were solitary, such as Trochoseris, in this family and suggests that the ancestor of this scleractinian family, extant members of which are predominantly colonial and zooxanthellate, may have been solitary and azooxanthellate.
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The monotypic genus Craterastrea was assigned to the family Siderastreidae owing to the similarity of its septal micromorphology to that of Coscinaraea. Subsequently, it was synonymized with Leptoseris, family Agariciidae, based on corallum macromorphology. Since then, it has remained poorly studied and has been known only from a small number of specimens from relatively deep reef environments in the Red Sea and the Chagos archipelago, northern Indian Ocean. Access to museum collections enabled examination of type material and the reco