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Three species of nannosquillid mantis shrimps, including two new species, Acanthosquilla ryukyuensis n. sp. and Acanthosquilla shoheii n. sp., are described based on specimens collected from the Ryukyu Islands, Japan. The two new species resemble A. derijardi Manning, 1970, but can be distinguished from A. derijardi by the following features: 1) rostral plate anterolateral corner forms almost a right angle; 2) the distal tip of the antennular somite dorsal process reaches or slightly falls short of proximal half of rostral plate; and 3) eighth thoracic somite (= TS8) posterior margin is black medially. Furthermore, A. ryukyuensis n. sp. and A. shoheii n. sp. are easy to identify by the bifurcated lateral tooth of the telson, and by the posterodorsal pattern of the telson, respectively. In this study, molecular analyses based on partial sequences of mitochondrial 12S and 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and the partial nuclear gene of 28S ribosomal DNA recovers these three species of Acanthosquilla and A. multifasciata (Wood-Mason, 1895) (the type species of the genus) in a single clade. The resulting trees also suggest the polyphyly of Nannosquillidae but with low nodal support. Detailed examinations of the morphological and color features and DNA barcoding results allowed us to delineate intraspecific variations and interspecific differences. The number and shape of setae under the dorsal spine of raptorial claw carpus was found to be useful in distinguishing A. shoheii n. sp. from A. derijardi and A. ryukyuensis n. sp., while combinations of the coloration of the rostral plate, posterior margin of TS8 and posterodorsal surface of telson are useful to distinguish the three species.

Family Xanthidae comprises 15 subfamilies and over 600 accepted species; they are represented well in the foreshore marine environments. Members of family Xanthidae are multi-colored crabs, usually inhabiting rocky coasts, coral reefs, and mud flats, all of which are well represented along the Egyptian coast of the Red Sea. Here, we utilized cytochrome oxidase subunit I (COI) sequences combined with morphology to provide information on some xanthid specimens collected from the Egyptian coast of the Red Sea. Six species within four genera (Leptodius, Etisus, Cyclodius, Chlorodiella) were collected. Genetic distances combined with morphological analyses showed intraspecific variations between two morphotypes of Leptodius exaratus. Two Etisus species were examined, E. laevimanus and E. sp. The latter Etisus sp. was close to E. frontalis, especially with regard to frontal lobe morphology, but different in male's first gonopod, with interspecific genetic distances. We also identified Chlorodiella nigra and C. laevissima. Obtained genetic distances between two morphotypes of Cyclodius granulatus revealed that these morphotypes are also likely cases of intraspecific variation. The results of this study should provide a basis for future work on family Xanthidae along the coasts of the Red Sea, which is needed as data remain scant.

Colour patterns in fish are often used as an important medium for communication. Anemonefish, characterized by specific patterns of white bars, inhabit host anemones and defend the area around an anemone as their territory. The host anemone is used not only by the anemonefish, but also by other fish species that use anemones as temporary shelters. Anemonefish may be able to identify potential competitors by their colour patterns. We first examined the colour patterns of fish using host anemones inhabited by Amphiprion ocellaris as shelter and compared them with the patterns of fish using surrounding scleractinian corals. There were no fish with bars sheltering in host anemones, although many fish with bars were found in surrounding corals. Next, two fish models, one with white bars and the other with white stripes on a black background, were presented to an A. ocellaris colony. The duration of aggressive behaviour towards the bar model was significantly longer than that towards the stripe model. We conclude that differences in aggressive behaviour by the anemonefish possibly select the colour patterns of cohabiting fish. This study indicates that colour patterns may influence not only intraspecific interactions but also interspecific interactions in coral reef ecosystems.

Nanipora Miyazaki and Reimer, 2015 is a recently described monotypic octocoral genus belonging to the family Helioporidae (class Octocorallia). Nanipora kamurai Miyazaki & Reimer, 2015 was formally described from shallow coral reefs around Zamami Island, within Kerama-shoto National Park, in Okinawa, southern Japan. To date, Nanipora has been reported from two other locations in Japan: N. aff. kamurai from a shallow inner lagoon at Iriomote Island, and N. cf. kamurai from the coral reef surrounding a shallow CO2 vent at Iotorishima Island, both in Okinawa. Additionally, N. cf. kamurai has been reported from two locations outside Japan; in shallow seagrass meadows at Dongsha Atoll in the South China Sea, and on coral reefs at Kho Tao in Thailand. Finally, N. kamurai has been detected in environmental DNA samples from the Rowley Shoals off north western Australia. As a ‘living fossil’ and also apparently common in the low pH environment of Iotorishima I., a clearer understanding of the distribution of the genus should aid in better understanding its ecology. Here, we report three new additional records from the Ryukyu Archipelago where Nanipora colonies were found, resulting in nine total records of Nanipora. However, as Nanipora has been reported as N. kamurai (= azooxanthellate), and as zooxanthellate N. aff. kamurai and N. cf. kamurai across different environments, these findings suggest that the genus Nanipora contains more than one species, and might be a more common and widespread genus across the western Pacific than has been believed until now.

Marine community datasets are key to the effective management and conservation of marine ecosystems, including coral reefs, which are increasingly threatened by a myriad of stressors. Although community information exists for many comparatively well-studied taxa, other common groups remain to be examined for even such basic information. In this study, we report on the zoantharian communities (Cnidaria: Anthozoa: Hexacorallia: Zoantharia) on the reefs of Bonaire in the southern Caribbean, and compare current results from 30, 20, 10, and 5 m depths to recent similar surveys from nearby Curaçao. The surveys revealed a total of 17 zoantharian species and epibiotic associations on the reefs of Bonaire. Additionally, results showed that while zoantharian assemblages around Bonaire at shallow 5 and 10 m depths, dominated by Palythoa spp., were similar to those found on Curaçao, diversity and numbers of zoantharians were higher at 20 and 30 m due to more abundant epibiotic Parazoanthidae species associated with sponges. Differences in assemblage structure were seen in deeper 20 and 30 m depths between the two islands, implying that conservation of deeper reef slopes, or along depth gradients, may need to be independently considered and addressed for each location. Analyses with environmental parameters on the Bonaire dataset indicate the potential importance of coral reef rugosity and physical structure in shaping these zoantharian communities, aspects that should be focused on in more detail in future research.

We present the complete genome sequences of 7 species of the zoantharian genus Epizoanthus. Illumina sequencing was performed on genetic material from single wild-collected individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank.

Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 Ma, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae subfam. nov. is designated for the clade comprising Tectus, Cittarium, and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models versus concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent (MSC) model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the MSC might be necessary to resolve these and other recalcitrant nodes in the Tree of Life. [Fissurellidae; Haliotidae; likelihood mapping; multispecies coalescent; phylogenetic signal; phylogenomic conflict; site heterogeneity; Trochoidea.]

Ankistromeces Nolan & Cribb, 2004 and Phthinomita Nolan & Cribb, 2006 are sister genera of threadlike blood flukes (Trematoda: Aporocotylidae) infecting teleost fishes of the tropical Indo-west Pacific. Here, we report new collections of these genera from Australia, Indonesia, and Japan. A new species of Ankistromeces, Ankistromeces kawamurai n. sp., is described from Siganus spinus (Linnaeus) off Okinawa, Japan, and a new species of Phthinomita, Phthinomita abdita n. sp., from Choerodon cephalotes (Castelnau), in Moreton Bay, Australia; the new species are morphologically cryptic within their respective genera and are delineated by molecular and ecological data. Ankistromeces olsoni Nolan & Cribb, 2006 is reported from Siganus fuscescens (Houttuyn) off Heron Island (southern Great Barrier Reef), Lizard Island (northern Great Barrier Reef), and Okinawa and Wakayama Prefectures, Japan and from Siganus spinus (Linnaeus) from off Bali, Indonesia. Ankistromeces mariae Nolan & Cribb, 2004 is re-reported from the type-host, Meuschenia freycineti (Quoy & Gaimard), from a new location, Gypsy Bay, Tasmania. Phthinomita poulini Nolan & Cribb, 2006 is re-reported from its type-locality, Lizard Island, from a range of mullids, including five new host species, and its range is extended to include Moreton Bay. Phthinomita symplocos Nolan & Cribb, 2006 is reported from Bali and P. hallae Nolan & Cribb, 2006, P. jonesi Nolan & Cribb, 2006, P. littlewoodi Nolan & Cribb, 2006, and P. munozae Nolan & Cribb, 2006 are each re-reported from their type-host and type-localities. New cox1 mtDNA data were generated for all known species of these two genera from new and archival material. Analyses of these data enabled an evaluation of all known Phthinomita species; P. robertsthomsoni Nolan & Cribb, 2006 is synonymised with P. adlardi Nolan & Cribb, 2006, and P. brooksi Nolan & Cribb, 2006 is synonymised with P. sasali Nolan & Cribb, 2006. We highlight the failure of ITS2 data to delineate closely related aporocotylid species. In contrast, cox1 sequence data are proving reliable and effective in this context and we recommend their incorporation in future studies of blood fluke taxonomy.

Zoantharians (Cnidaria: Hexacorallia: Zoantharia) of the genus Palythoa are ubiquitous species that occupy reef habitats in every tropical ocean. Disagreements among classifications based on morphology, reproductive traits, and molecular techniques have generated taxonomic challenges within this group. Molecular studies provide limited phylogenetic resolution between species, and discordance is frequently attributed to slow mitochondrial rates and lack of resolution among molecular markers. Here we conducted the first phylogenomic survey of Palythoa, using a reduced representation genomic approach (ezRAD) to resolve relationships among eight described and four putative Palythoa species (N = 22 plus two outgroups) across the Pacific and Atlantic Oceans. We constructed nearly complete mitochondrial genomes and assembled transcriptome loci datasets by reference mapping. A de novo assembly was performed for the holobiont dataset, and we compared a range of filtering strategies from unfiltered data down to 136 unlinked high-quality biallelic SNPs shared by all samples to resolve evolutionary lineages within Palythoa. Across all these datasets, the resulting Bayesian and ML trees revealed six highly concordant and well-supported clades, however, the phylogenomic data were inconclusive in resolving species relationships within the clades. We detected putative species complexes within two well sampled Palythoa clades (clades I and II), but species delimitation results were inconsistent in whether these clades contain multiple nominal species or represent a single variable species. Polyphyly in the broadly distributed species Palythoa tuberculosa and P. mutuki highlight the need for additional study. Consistency among nuclear and mitogenomic datasets points to a lack of biological understanding of species boundaries among these zoantharians rather than limitations of the molecular markers. More complete taxonomic sampling of nominal species across the geographic ranges of distribution is necessary to resolve species boundaries and evolutionary histories among members of this genus.

The diversity of symbiotic dinoflagellate Symbiodiniaceae hosted by anthozoans is known to be driven by the environment where the hosts are found. This study examined how environmental variations (Palythoa tuberculosa. We monitored the dominant Symbiodiniaceae lineages within tagged P. tuberculosa colonies near the Hija River mouth and adjacent coastal reefs at Mizugama, Okinawa, Japan, between July 2016 and April 2018. Seven sites were chosen based on depth and distance from the river mouth, with 5 tagged colonies at each site. Water parameters of tidal pools (TPs) at the river mouth, especially temperature, were significantly different from other sites. Surprisingly, P. tuberculosa colonies at TPs were more resilient to bleaching during summers compared to colonies at other shallow sites. We observed different Cladocopium psbAncr lineages hosted by the tagged P. tuberculosa, with TPs colonies usually hosting one Cladocopium lineage (designated as lineage 4). Colonies from the deep sites and other shallow sites hosted mostly Cladocopium lineages 1 (generalist) and 2 (riverine specialist). Throughout the study period, the shallow colonies (included TPs) recorded higher rates of switching dominant Cladocopium lineages (mostly to lineage 1), whereas most deep colonies did not switch their dominant Cladocopium lineages. Our results show that Cladocopium lineage 1, previously reported as a generalist lineage in terms of environmental parameters, could also be an opportunist lineage during periods of host stress. Our study confirms that Cladocopium lineage flexibility likely helps the resilience of P. tuberculosa in such variable environments.

A new species of zoantharian within the genus Antipathozoanthus is described based on specimens collected from the coast of mainland Japan, northwest Pacific Ocean. Antipathozoanthus tubussp. nov. is characterized by its substrate (epibiotic on polychaete tube) and habitat (exposed rock). As well, the results of molecular phylogenetic analyses using concatenated multiple genetic markers also support the distinction between A. tubussp. nov. and its congenerics. Antipathozoanthus tubussp. nov. is the first species of Antipathozoanthus species reported to be epibiotic on polychaete tubes, and is the second species in the genus that is not associated with antipatharians.

This paper reviews all currently known records of copepod crustaceans of the family Lamippidae (Cyclopoida). The lamippids are highly modified endosymbionts found only on octocorals in the channels of mesoglea and gall-like proliferations of the host tissues. 54 species and 11 genera of copepods have been reported associated with 42 species, 33 genera and 18 families of the octocoral orders Alcyonacea and Pennatulacea. The highest numbers of records of lamippids living on octocorals have been reported among the diverse and common octocoral families Alcyoniidae, Gorgoniidae, Nephtheidae, Pennatulidae, and Plexauridae. Lamippids are better studied on more common octocorals from shallow depths and still comparatively poorly studied on octocorals from bathyal and abyssal depths. Lamippids have been recorded from 62 sites in 12 realms of the World Ocean and are comparatively better studied in the Northern Atlantic, Central Indo-Pacific and Tropic Atlantic; no lamippids have been reported so far from the Tropical Eastern Pacific, Temperate South America, South Africa, or Australasia. The data show that only approximately 1% of potential octocoral hosts have been explored thus far, showing a clear need for further integrative studies on this unusual group of symbiotic crustaceans.

Benthic cnidarians are suspension feeders that ingest items ranging from particulate organic matter to macrozooplankton. Additionally, many species receive photosynthetic products from associated endosymbiotic microalgae (Symbiodiniaceae). Although benthic cnidarians are ubiquitous to reef ecosystems, variation in their nutrition acquisition strategy across distinct environments is poorly understood. In this study, we evaluated the trophic niche and symbiotic interactions of the widespread species Palythoa tuberculosa (Hexacorallia: Zoantharia) inhabiting depths ranging from the intertidal to 35 m across three Indo-Pacific regions, using carbon and nitrogen stable isotope ratios and isotopic niche metrics. Our results revealed that populations in shallow (0-8 m) and deep zones (down to 35 m) had distinct niche placements and overlap with the endosymbionts’ niches across all regions. Associated Symbiodiniaceae were identified as Cladocopium. Contradicting the paradigm of a more productive endosymbiosis in shallower waters, P. tuberculosa had less isotopic niche overlap with its endosymbionts in shallow reefs (0–9%) but a higher niche overlap in deep waters (up to 70%). Among regions, this was most evident in Dongsha Atoll, South China Sea, which has comparatively high influence of internal waves and, thus, high concentrations of plankton. The low niche overlap with endosymbionts in shallow waters indicated that P. tuberculosa may have a high heterotrophic performance, which partially explains the species’ resilience during bleaching events. Regarding the distinct niche placements across depths, lower δ13C in the shallower zone could be due to light-driven effects on fixation by the endosymbionts. Additional non-exclusive explanations include that water flow regimes and nocturnal feeding behavior could enable P. tuberculosa populations to ingest more/distinct prey items, with lower δ13C, in the shallow compared to the deep zone. The nutritional plasticity of P. tuberculosa likely contributes to its widespread distribution and provides an advantage under a warming climate that will affect cnidarian-endosymbiont relationships.

Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.

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.

Tropicalization is rapidly restructuring subtropical marine communities. A key driver for tropicalization is changes in herbivory pressure that are linked with degrading ecosystem stability. Consequently, subtropical algal beds are being displaced by climate-mediated colonisation of coral communities. This process is thought to be aided by the elevated herbivory resulting from tropicalization, but the relative contribution to herbivory by different taxa is not fully understood. Evaluating herbivory pressure and its effect on coral cover and rugosity across a subtropical latitudinal gradient will help predict how these processes may change with further tropicalization and ocean warming. Herbivory pressure exerted by fishes and urchins across this subtropical latitudinal gradient remains unquantified. Using in-situ feeding observations, we quantify fish and urchin herbivory pressure at seven sites across non-accreting coral communities, and warmer accreting coral reefs in southern Japan. We then relate herbivory pressure to respective fish and urchin community structure and coral cover and rugosity. Urchin herbivory is greater on non-accreting coral communities than on true coral accreting reefs; a result which is reversed for fish herbivory. Overall, herbivory pressure is greater on accreting coral reefs than on coral non-accreting communities, but is dependent on reef characteristics as community structures differ more strongly among reefs than between regions. These factors are linked to coral cover and rugosity that differ between reefs, but not between climatic regions, further emphasising the influence of local factors on the benthic cover and the associated fish and urchin community, and thus herbivory pressure. Our findings provide a foundation for understanding how non-accreting coral communities may respond to ongoing tropicalization, given the fish and invertebrate herbivores they host.

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 the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.]

Identifying how past environmental conditions shaped the evolution of corals and their skeletal traits provides a framework for predicting their persistence and that of their non-calcifying relatives under impending global warming and ocean acidification. Here we show that ocean geochemistry, particularly aragonite-calcite seas, drives patterns of morphological evolution in anthozoans (corals, sea anemones) by examining skeletal traits in the context of a robust, time-calibrated phylogeny. The lability of skeletal composition among octocorals suggests a greater ability to adapt to changes in ocean chemistry compared with the homogeneity of the aragonitic skeleton of scleractinian corals. Pulses of diversification in anthozoans follow mass extinctions and reef crises, with sea anemones and proteinaceous corals filling empty niches as tropical reef builders went extinct. Changing environmental conditions will likely diminish aragonitic reef-building scleractinians, but the evolutionary history of the Anthozoa suggests other groups will persist and diversify in their wake.

Sea surface temperatures (SST) and chlorophyll a concentrations (Chl a) in the southern Red Sea have wide variations based on distance from the coast. To understand how these variations can affect the diversity of symbionts hosted by reef-associated organisms, we conducted a study in the central and southern Red Sea to examine the diversity of Symbiodiniaceae hosted by the zooxanthellate zoantharian Palythoa tuberculosa at different distances from the coast: offshore (FBO), midshelf (FBM) and inshore (FBI) of Farasan Banks, and inshore at Thuwal (TI). Genomic DNA was extracted from 198 specimens, followed by amplification of the ribosomal DNA internal transcribed spacer 2 (ITS-2) and noncoding region of the chloroplast plastid minicircle (psbAncr). Durusdinium and six lineages of Cladocopium (Pt-1-a, Pt-1-b, Pt-1-c, Pt-1-d, Pt-3-a, Pt-3-b) were identified based on sequences of the two marker regions. Changes in composition of Symbiodiniaceae lineages were observed from FBI (high SST, high Chl a) to FBO (low SST, low Chl a). Molecular variance analyses showed that distance from coast was the most likely predictor of differences in Cladocopium lineages. Multinomial logistic regression analysis showed a transition among different Cladocopium lineages as SST increased. One Cladocopium lineage, Pt-1-b, demonstrated higher prevalences at high SSTs and increased in prevalences at the same rate as thermotolerant Durusdinium. Additionally, Cladocopium lineage Pt-3-a had a high affinity to low Chl a concentrations. This study demonstrates that environmental variations in SSTs and Chl a concentrations are significant predictors for the diversity of dominant Symbiodiniaceae within individual host P. tuberculosa colonies. We theorize that flexibility with different lineages of Symbiodiniaceae allows generalist P. tuberculosa to live across a wide range of environments in the southern Red Sea.

Species of the genus

1. Urbanized coral reefs experience anthropogenic disturbances caused by coastal development, pollution, and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity. 2. There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional levels. As such, it is unclear how they will respond to future disturbance events. 3. Here, we examine the patterns of coral reef community change and determine whether ecosystem functions provided by specialist species are lost post-disturbance. We present a comparison of community and functional trait-based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975–1976 and 2018, in Nakagusuku Bay, Okinawa, Japan. 4. We observed an increase in fish habitat generalists, a dominance shift from branching to massive/sub-massive corals and increasing site-based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait-based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (8 m) coral genera shifting towards the mid-depths (5–8 m). 5. We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.

Among family Zoanthidae (Anthozoa: Hexacorallia: Zoantharia)

The Indo-Pacific zooxanthellate scleractinian coral genus Montipora is the host of many coral diseases. Among these are cyanobacterial Black Band Disease (BBD) and Skeletal Growth Anomalies (GAs), but in general data on both diseases are lacking from many regions of the Indo-Pacific, including from Okinawa, southern Japan. In this study, we collected annual prevalence data of Black Band Disease (BBD) and Skeletal Growth Anomalies (GAs) affecting the encrusting form of genus Montipora within the shallow reefs of the subtropical Sesoko Island (off the central west coast of Okinawajima Island) from summer to autumn for four years (2017 to 2020). In 2020 Montipora percent coverage and colony count were also assessed. Generalized Linear Models (GLM) were used to understand the spatial and temporal variation of both BBD and GAs in the nearshore (NE) and reef edge (RE) sites, which revealed higher probability of BBD occurrence in RE sites. BBD prevalence was significantly higher in 2017 in some sites than all other years with site S12 having significant higher probability during all four surveyed years. In terms of GAs, certain sites in 2020 had higher probability of occurrence than during the other years. While the general trend of GAs increased from 2017 to 2020, it was observed to be non-fatal to colonies. In both diseases, the interaction between sites and years was significant. We also observed certain BBD-infected colonies escaping complete mortality. BBD progression rates were monitored in 2020 at site S4, and progression was related to seawater temperatures and was suppressed during periods of heavy rain and large strong typhoons. Our results suggest that higher BBD progression rates are linked with high sea water temperatures (SST > bleaching threshold SST) and higher light levels (>1400 µmol m−2 s−1), indicating the need for further controlled laboratory experiments. The current research will help form the basis for continued future research into these diseases and their causes in Okinawa and the Indo-Pacific Ocean.

Hexactinellid sponges are important members of deep-sea benthic ecosystems because they provide available hard substrate habitats for filter-feeding invertebrates. However, symbioses between hexactinellid sponges and their symbionts are poorly known. Zoantharians associated with hexactinellid sponges have been reported widely from deep-sea marine ecosystems, either on the bodies or stalks of hexactinellid sponges. Despite these records, there has been a lack of research on their diversity and phylogenetic relationships. In this study, 20 specimens associated with amphidiscophoran and hexasterophoran sponges were collected from the waters of Australia and Japan in the Pacific, and from Curaçao in the southern Caribbean, and these were examined in addition to museum specimens. Based on molecular phylogenetic analyses and morphological observations, we formally describe two new genera and three new species of Zoantharia and report several previously described species. The results suggest at least two independent origins for the symbioses between hexactinellid sponges and zoantharians. Our results demonstrate that the diversity of hexactinellid sponge-associated zoantharians is much higher than has been previously thought. The new taxa described in this work further reconfirm that the deep-sea harbours high levels of undescribed zoantharian diversity.

Savalia savaglia is an Atlantic-Mediterranean zoantharian species with a patchy geographic and bathymetric distribution. Due to its longevity, S. savaglia may form large-sized colonies which play a crucial role in the ecosystem as habitat formers. Despite its ecological importance, little is known about the population structure and intraspecific genetic diversity of this species. Using ddRAD-Seq genotyping, we obtained genome-wide single nucleotide polymorphisms (SNPs) from 50 S. savaglia individuals collected at different depths (8–60 m) and localities across the Mediterranean Sea (Marseille, Sardinia, Puglia and Montenegro) and eastern Atlantic (Portugal). Our molecular observations were discussed with the reproductive behaviour of the species to understand the observed patterns of connectivity and gene flow. These results highlight the presence of three main genetic clusters (Marseille; Sardinia; and Montenegro + Portugal + Puglia), with some of the Mediterranean individuals being genetically closer to the Atlantic population rather than to other Mediterranean populations. The strong linkage disequilibrium recorded across loci and the detection of clonal individuals in the shallow populations suggest that asexual reproduction seems to be the dominant reproductive strategy among the S. savaglia populations sampled at lower depths. Our work highlights the potential of genome-wide SNP data to study the reproductive behaviour in species such as S. savaglia that are difficult to investigate in the field. The genetic connectivity data obtained in this study can be used in the future to better guide the development of effective management and conservation plans.

The current exposure of species assemblages to high environmental variability may grant them resilience to future increases in climatic variability. In globally threatened coral reef ecosystems, management seeks to protect resilient reefs within variable environments. Yet, our lack of understanding for the determinants of coral population performance within variable environments hinders forecasting the future reassembly of coral communities. Here, using Integral Projection Models, we compare the short- (i.e., transient) and long-term (i.e., asymptotic) demographic characteristics of tropical and subtropical coral assemblages to evaluate how thermal variability influences the structural composition of coral communities over time. Exploring spatial variation across the dynamics of functionally different competitive, stress-tolerant, and weedy coral assemblages in Australia and Japan, we show that coral assemblages trade-off long-term performance for transient potential in response to thermal variability. We illustrate how coral assemblages can reduce their susceptibility towards environmental variation by exploiting volatile short-term demographic strategies, thus enhancing their persistence within variable environments. However, we also reveal considerable variation across the vulnerability of competitive, stress-tolerant, and weedy coral assemblages towards future increases in thermal variability. In particular, stress-tolerant and weedy corals possess an enhanced capacity for elevating their transient potential in response to environmental variability. Accordingly, despite their current exposure to high thermal variability, future climatic shifts threaten the structural complexity of coral assemblages, derived mostly from competitive coral taxa within highly variable subtropical environments, emulating the degradation expected across global coral communities.

Recently, sea cucumbers (Echinodermata: Holothuroidea) have been over-exploited in many areas of the world, including in the Ryukyu Islands, southern Japan, due to increases in their economic importance. Nevertheless, management and protection of sea cucumbers are insufficient worldwide. The black sea cucumber Holothuria (Halodeima) atra Jaeger, 1833, inhabits a large range across the Indo-West Pacific Ocean and is a widely harvested species. Here we conducted population genetic analyses on H. atra using partial mitochondrial DNA sequences of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S) to examine 11 different populations around three island groups in the middle Ryukyus; Okinawajima Island, the Kerama Islands, and the Sakishima Islands, all within Okinawa Prefecture. We found 27 haplotypes for COI and 16 haplotypes for 16S. Locations within national and quasi-national parks (Zamami Island, Keramas, and Manza, Okinawajima; managed by the national Ministry of Environment and Okinawa Prefecture, respectively) had the highest number of haplotypes, whereas locations with less management and more anthropogenic pressure had lower numbers The mean of all samples' genetic diversity indices was moderate with regards to both haplotype and nucleotide diversity. According to our results, Zamami Ama was the most genetically diverse location based on both markers used, likely because it is located within Kerama-Shoto National Park with comparatively stricter regulations than most other locations. Based on our COI sequences, three-quarters of the locations with the highest haplotype diversity were found to be distant from Okinawajima Island, indicating that the genetic diversity of H. atra was reduced around Okinawajima Island. Our results possibly reflect negative impacts from anthropogenic pressures such as over-harvesting and coastal development, although future comprehensive research including sequences of nuclear loci is needed to confirm this hypothesis.

Symbioses between invertebrates are common in the ocean although usually the diversity and specificity of their interactions are not well understood. Parazoanthidae (Cnidaria: Anthozoa: Zoantharia) is one of the most diverse zoantharian families in terms of numbers of genera and species. Species in this family are commonly associated with various other invertebrates that they utilize as their substrate. Previous studies have re-organized the taxonomy of Parazoanthidae and revealed a strong specificity between many parazoanthid species and genera and their substrates. However, our understanding of the species diversity of Parazoanthidae is far from complete, as parazoanthids are often overlooked in sampling surveys. In this study, we establish three subgenera under the genus Umimayanthus Montenegro, Sinniger, and Reimer, 2015; the nominotypical Umimayanthus, Paraumimayanthus subgen nov., and Gorgoniazoanthus subgen. nov., based on the finding of a new species, Umimayanthus (Gorgoniazoanthus) kanabou sp. nov., associated with the sea-whip gorgonian Ellisella sp. from approximately 30 m depth in shallow mesophotic coral reef communities in Oura Bay on Okinawajima Island and in Oshima Strait near Amami-Oshima Island, in the Ryukyu Islands, southern Japan. We additionally report on gastropods and crustaceans observed in association with U. kanabou, and these species are thought to potentially prey upon the zoantharians or on gorgonian polyps. Umimayanthus kanabou is phylogenetically closely related to congeneric sponge-associated Umimayanthus spp., further supporting the recent hypothesis that substrate preferences may change during the evolutionary history of zoantharians.

Ocean warming and acidification caused by increases of atmospheric carbon dioxide are now thought to be major threats to coral reefs on a global scale. Here we evaluated the environmental conditions and benthic community structures in semi-closed Nikko Bay at the inner reef area in Palau, which has high pCO

Artificial barriers for coastal protection have been deployed across numerous tropical and subtropical islands in the Pacific, including Okinawa Island, southern Japan, where artificial defences have been installed along a large part of the coastline. Although artificial barriers can lead to beach narrowing or loss and can exacerbate erosion, their effects on coral reef ecosystems remain understudied. This study investigated the impact of a tetrapod breakwater in Ogimi Village, Okinawa Island, Japan, comparing the area affected by the presence of the barrier with a nearby natural coastline, and examining differences in physical parameters (depth profiles, sediment granulometry, and erosion on plaster balls) and benthic community composition. Significant differences in depth profiles, sediment granulometry, and erosion were found, suggestive of alterations in water energy levels (lower than controls on the landward side of the barrier, and higher on the seaward side). The benthic community was also clearly affected, with almost no living corals growing over the blocks or in their proximity. Overall, the data show how breakwaters can affect the physical environment and benthic communities in a subtropical coral reef ecosystem, with negative consequences for coral survival.

Many cnidarians have been reported in association with hermit crabs from shallow waters to the deep sea. Some of these actiniarians and zoantharians produce a carcinoecium, a chitin-like pseudo-she...

Despite being one of the world’s leading countries in coral reef conservation and management, very little data exist for coral reef-associated species in the island nation of Palau, hampering managers’ ability to more effectively protect coral reef ecosystems. Here we examine populations of the vermetid Ceraesignum maximum, a common species on coral reefs, with short or absent pelagic larval stage, in order to elucidate patterns of gene flow within Palauan reefs. We collected specimens (n = 582) from 20 sites across Palau. Cytochrome oxidase subunit I analyses show private haplotypes at all sites examined, with a clear separation between outer and inner reef locations, and a unique population within isolated Nikko Bay. Oceanographic isolation between the waters of Nikko Bay, inner and outer reefs may contribute to our observed genetic differentiation. Our results indicate past demographic expansion of C. maximum across the region and also indicate that multiple sites of both inner and outer reef locations would need to be protected to conserve this species’ genetic diversity, including unique Nikko Bay. These results demonstrate the utility of C. maximum as a good species to investigate gene flow across small scales (

Sabah, Malaysia, is well known for its extensive and diverse coral reefs. It is located on the northwestern edge of the Coral Triangle, the region with the highest marine biodiversity. Much of the marine fauna here is still unknown, especially inconspicuous animals, such as small stoloniferous octocorals, which are common on coral reefs. Here, we describe two new monospecific genera of the family Arulidae found off the coast of Kota Kinabalu, Sabah, East Malaysia; Bunga payunggen. nov. et sp. nov. and Laeta waheedaegen. nov. et sp. nov. As well, the stoloniferan genus Phenganax Alderslade & McFadden, 2011 belonging to the family Clavulariidae is expanded with three new species, P. marumisp. nov., P. subtilissp. nov., and P. stokvisisp. nov., which are all sclerite-free. Additionally, we report a possibly undescribed species, closely related to the clavulariid genera Azoriella Lopez-Gonzalez & Gili, 2001 and Cervera Lopez-Gonzalez et al., 1995. As this and other recent studies have shown, discoveries of small stoloniferous octocorals are helping to fill gaps in our knowledge of the overall systematics of Octocorallia.