Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
419
datasets available to search
ShareScore release 0.9.0
Dataset results
419 results for “Octocorals”
FIGURE 1 in The stoloniferous octocoral, Hanabira yukibana, gen. nov., sp. nov., of the southern Ryukyus has morphological and symbiont variation
FIGURE 1 Map of sampling locations in Okinawa Prefecture around Okinawa Island (11 sites) and Iriomote Island (seven sites); collection sites Hanabira yukibana, gen. nov., sp. nov., () and Clavularia spp. () specimens.
FIGURE 4 Phylogenetic relationships among 134 in The stoloniferous octocoral, Hanabira yukibana, gen. nov., sp. nov., of the southern Ryukyus has morphological and symbiont variation
FIGURE 4 Phylogenetic relationships among 134 species of octocorals, including Hanabira yukibana, gen. nov., sp. nov., using the combined 28S rDNA+COI+mtMutS dataset. The best maximum likelihood tree is shown, with values at branches representing bootstrap probabilities shown when>70%. Bayesian posterior probabilities are shown at branches when>0.80 (A = 1.00; B = 0.95–0.99; C = 0.90–0.94; D = 0.80–0.89). * represents 100/1.00 for both analyses. Stoloniferous species are highlighted in grey boxes and non-stoloniferous octocorals are shown with family classification only. Cornularia spp. were used as outgroup.
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
Open the record for dataset details and reuse information.
Data from Stranger Things: Organismal traits of two octocorals associated with singular Symbiodiniaceae in a high-latitude coral community from northern Taiwan
<p>Scrutinizing the traits of octocorals that could affect their physiological performance becomes increasingly important as several of these species are observed to become dominant on reefs pressured by the Anthropocene. In the present study, we compare the organismal traits of two branching octocorals <em>Litophyton</em><em> </em>sp. and <em>Stereonephthya</em><em> </em>sp. commonly populating in sympatry the high-latitude coral communities of northern Taiwan. Using 13 traits, we describe and compare performance traits in these two symbiotic species that we discuss in light of the association they maintain with their algal partners. <em>Litophyton</em><em> </em>sp. and <em>Stereonephthya</em><em> </em>sp. hosted <em>Durusdinium</em><em> </em>and <em>Gerakladium</em>, respectively. Both genera represent singular associations, with the latter further establishing the first solid report of <em>Gerakladium</em><em> </em>in octocorals. Traits distinguished two groups explained by the two partnerships considered. <em>Litophyton</em><em> </em>sp. associated with <em>Durusdinium</em><em> </em>had significantly higher organic matter, chlorophyll (chl) <em>a</em>, total lipid and lower chl <em>c</em>/chl <em>a</em> ratio than <em>Stereonephthya</em><em> </em>sp. associated with <em>Gerakladium</em>. The δ<sup><sup>15</sup></sup>N in the host and algae, as well as δ<sup><sup>13</sup></sup>C in the host were also higher in <em>Litophyton</em><em> </em>species. Although no significant difference was observed in the δ<sup><sup>13</sup></sup>C of the algae, <em>Litophyton</em><em> </em>sp. presented a significantly higher variance for this trait and for chl <em>a</em> content than <em>Stereonephthya</em><em> </em>species. Altogether, the traits examined suggested contrasting performances among the two octocorals. Both octocoral species clearly deviate from an autotrophic diet. <em>Litophyton</em><em> </em>sp. appears to complement its heterotrophic diet with photosynthetically acquired energy, while <em>Stereonephthya</em><em> </em>sp. tends to be more specialized and benefits relatively little from its symbiotic relationship. Our study calls for greater consideration of the individual variation in octocoral physiology and in the definition of their ecological strategies.</p> <p> </p>
OctocoralTraits: a global database of trait information for octocoral species
<p>The OctocoralTraits_v2_2 ZIP file contains structured data and code to create all figures from the manuscript: “The Octocoral Trait Database: a global database of trait information for octocoral species”. The folder also contains the code used to validate the data descriptor.</p> <p>Specifically, the folder contains the following files:</p> <p>· Code.R – This is the annotated code used to create all figures in R. (v R studio; 2023.06.0+421)</p> <p>· OctocoralTraits_v2_2.csv – This is the first data realase of the octocoral trait database, used to create all figures of the manuscript.</p> <p>· sp_id.csv – This is a file containing the list of accepted octocoral species contained in the database</p> <p>· iqtree.tre – This is a tree object used to create a family-resolved tree of octocorals. It has been downloaded from McFadden et al. 2022. Revisionary systematics of Octocorallia (Cnidaria: Anthozoa) guided by phylogenomics</p> <p>· MEOW folder – A folder containing regional information from Spalding et al. 2007. Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas</p> <p>· Provinces_coord.csv: A file containing the coordinates of marine provinces, also derived from Spalding et al. 2007</p> <p>· Table_ids folder - A folder containing tables with information of the corresponding ids that appear in the file database.</p> <p>· Validation folder: A folder containing a Technical_validation.R file that was used to flag outliers and extreme outliers, duplicated rows and potential structural errors in the data (e.g., a given observation_id linked to more than one resource, species or location). </p>
Phenology in the deep sea: Seasonal and tidal feeding rhythms in a keystone octocoral
<p>Biological rhythms are widely known in terrestrial and marine systems, where the behavior or function of organisms may be tuned to environmental variation over periods from minutes to seasons or longer. Although well characterized in coastal environments, phenology remains poorly understood in the deep sea. Here we characterized intra-annual dynamics of feeding activity for the deep-sea octocoral <em>Paragorgia</em> <em>arborea</em>. Hourly changes in polyp activity were quantified using a time-lapse camera deployed for a year on Sur Ridge (1230 m depth; Northeast Pacific). The relationship between feeding and environmental variables, including surface primary production, temperature, acoustic backscatter, current speed and direction, was evaluated. Feeding activity was highly seasonal, with a dormancy period identified between January and early April, reflecting seasonal changes in food availability as suggested by primary production and acoustic backscatter data. Moreover, feeding varied with tides, which likely affected food delivery through cyclic oscillation in current speed and direction. This study provides the first evidence of behavioral rhythms in a coral species at depth greater than 1km. Information on the feeding biology of this cosmopolitan deep-sea octocoral will contribute to a better understanding of how future environmental change may affect deep-sea coral communities and the ecosystem services they provide.</p>
Transcriptome analysis of dark-induced bleaching octocoral
<h3>Transcriptome of dark-induced bleaching soft coral, <em>Lobophytum hsiehi</em></h3> <p>The raw transcriptomic data has been archived in NCBI BioProject under accession number PRJNA1037697.</p> <p>The transcript reads (transcript_sequence.fasta) deposited here were processed using Trinity, TransDecoder, and CD-HIT.</p> <p>The dataset (transcript_and_deg_information.xlsx) provided transcript annotations and results from the differential expression analysis.</p>
FIG. 5. — Sinularia shlagmani n in Octocorals (Cnidaria, Anthozoa) from Reunion, with a description of two new species of the genus Sinularia May, 1898 and notes on the occurrence of other species
FIG. 5. — Sinularia shlagmani n. sp., holotype (ZMTAU Co 34418). Scale bar: 10 mm.
FIG. 2 in Octocorals (Cnidaria, Anthozoa) from Reunion, with a description of two new species of the genus Sinularia May, 1898 and notes on the occurrence of other species
FIG. 2. — Sarcophyton subviride Tixier-Durivault, 1958 (ZMTAU Co 34408). Scale bar: 10 mm.
Data for: Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals
<p><span>Constant nitrogen limitation is the foundation of a stable coral-algal symbiosis. Diazotrophs, i.e., prokaryotes capable of fixing N<sub>2</sub> into ammonia, are key players in coral holobionts. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress stimulated the growth and activity of diazotrophs, resulting in excess nitrogen availability. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (assessed via relative quantification of <em>nifH</em> gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral <em>Xenia</em> <em>umbellata</em> and the more autotrophic gorgonian <em>Pinnigorgia</em> <em>flava</em>, under a) labile DOC enrichment for 21 days, followed by b) combined labile DOC enrichment and heat stress for 24 days. In the absence of heat stress, relative diazotroph abundances in X<em>.</em> <em>umbellata</em> and <em>P</em>. <em>flava</em> were unaffected by DOC enrichment. During heat stress, DOC enrichment (higher than 20 mg glucose L<sub>-1</sub>) increased the relative abundances of diazotrophs by 6-fold in <em>X</em>. <em>umbellata</em> and 4-fold in <em>P</em>. <em>flava</em>, compared to their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals through stimulating diazotroph proliferations. Reducing labile DOC loading may effectively help octocorals cope with future ocean warming scenarios.</span></p>
Data and code from: Active restoration of a long-lived octocoral drives rapid functional recovery in a temperate reef
Open the record for dataset details and reuse information.
Data for: Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals
Open the record for dataset details and reuse information.
Phenology in the deep sea: Seasonal and tidal feeding rhythms in a keystone octocoral
Open the record for dataset details and reuse information.
Data from Stranger Things: Organismal traits of two octocorals associated with singular Symbiodiniaceae in a high-latitude coral community from northern Taiwan
Open the record for dataset details and reuse information.
Ecological factors mediate immunity and parasitic co-infection in sea fan octocorals
<p>The interplay among environment, demography, and host-parasite interactions is a challenging frontier. In the ocean, fundamental changes are occurring due to anthropogenic pressures, including increased disease outbreaks on coral reefs. These outbreaks often include multiple parasites, calling into question how coral immunity functions in this complex milieu. Corals provide an interesting model to study ecological immunity during co-infection, being highly sensitive to environmental change, susceptible to many diseases, and defended by the innate immune system. Our work investigates the interplay of factors influencing coral co-infection using metrics of the innate immune response: levels of cellular immunity and the expression of candidate immune genes. We used existing copepod infections and live pathogen inoculation with <i>Aspergillus</i> fungus to test the effect of sequential co-infections in a laboratory experiment. We profile significant increases in the expression of the immune recognition gene Tachylectin 5A in response to both of these naturally occurring parasites of the Caribbean sea fan octocoral, <i>Gorgonia ventalina</i>. Cellular immunity increased significantly by 8.16% in copepod infections compared to controls and single <i>Aspergillus</i> infections. We evaluated immunity in reef populations and again detected activation of cellular immunity, with a 13.6% increase in copepod infections and no detectable increase in fungal infections. Thus, cellular immunity measured in the field and lab were similar, increasing with copepod infections and not <i>Aspergillus</i>. We found random co-occurrence of copepods and fungus across 15 reefs in Puerto Rico, suggesting other factors prevail in structuring parasite infection. Sea fan colony size strongly predicted infection by the copepod parasite. Moreover, the effect of parasitic infection on immunity was small relative to the explanatory power of site differences and coral cover, and roughly equivalent to the effect of reproductive status. We suggest that host size, reproductive status, live coral cover, and site-specific factors have large effects on parasitic infections and host immunity that overwhelm effects of the parasites on each other. Thus, host size and site-specific features emerge as critical drivers in this multi-parasite system. Parsing the effects of immunity and ecological factors in coral co-infection shows how disease depends on more than one host and one parasite.</p>
Data from: Molecular operational taxonomic units reveal restricted geographic ranges and regional endemism in the Indo‐Pacific octocoral family Xeniidae
Aim: To quantify taxon diversity, biogeographic distributions and patterns of community assembly in xeniid octocorals using molecular operational taxonomic units (MOTUs). Location Red Sea, Indian and western Pacific Oceans. Taxon Xeniidae, a family of reef-dwelling octocorals (Anthozoa, Octocorallia). Methods Xeniids collected at 13 locations were sequenced at three barcode loci, and assigned to molecular operational taxonomic units (MOTUs) defined by minimum genetic distance thresholds. Taxon richness (no. of MOTUs) and endemicity (percent of MOTUs found at a single location) were quantified. Patterns of β-diversity (species turnover) and phylogenetic β-diversity (lineage turnover) among geographical regions were visualized using hierarchical clustering, NMDS plots, and distance-decay relationships. Community assembly was investigated by comparing the mean pairwise distance (MPD) and mean nearest taxon distance (MNTD) separating species in each assemblage to values generated for null communities. Results A genetic distance threshold of 0.3% discriminated 67 MOTUs, with taxon richness ranging from 2-18 MOTUs per site. Out of the 67 MOTUs, 48 (72%) were found at only a single location, and only two spanned both the western Indian and Pacific Oceans. Species turnover among sites was high, but phylogenetic β-diversity was lower than β-diversity and differed significantly from null models of community assembly at only two sites. β-diversity and phylogenetic β-diversity both increased significantly with geographic distance, and sites clustered into three distinct biogeographic regions (Red Sea and western Indian Ocean; Western Australia; western Pacific and Great Barrier Reef, Australia). All five major clades of xeniids were represented in each region. Main Conclusions A genetic approach to biodiversity estimation suggests that most xeniid taxa are regional endemics whose geographic distribution is likely governed by dispersal limitation. This conclusion contrasts with published records of certain morphospecies occurrences, which imply that they have broad geographic ranges. So far, the distribution of xeniid biodiversity mirrors that of scleractinian corals, with species richness highest in the Coral Triangle, but endemicity peaking in peripheral areas.
Data from: Niche divergence by deep-sea octocorals in the genus Callogorgia across the continental slope of the Gulf of Mexico
Environmental variables that are correlated with depth have been suggested to be among the major forces underlying speciation in the deep sea. This study incorporated phylogenetics and ecological niche models (ENM) to examine whether congeneric species of Callogorgia (Octocorallia: Primnoidae) occupy different ecological niches across the continental slope of the Gulf of Mexico (GoM), and whether this niche divergence could be important in the evolution of these closely related species. Callogorgia americana americana, C. americana delta, and C. gracilis were documented at 13 sites in the GoM (250-1000 m) from specimen collections and extensive video observations. On a first order, these species were separated by depth, with C. gracilis occurring at the shallowest sites, C. a. americana at mid-depths, and C. a. delta at the deepest sites. Callogorgia a. delta was associated with areas of increased seep activity whereas C. gracilis and C. a. americana were associated with narrow, yet warmer, temperature ranges and did not occur near cold seeps. ENM background and identity tests revealed little to no overlap in ecological niches between species. Temporal calibration of the phylogeny revealed the formation of the Isthmus of Panama was a vicariance event that may explain some of the patterns of speciation within this genus. These results elucidate the potential mechanisms for speciation in the deep sea, emphasizing both bathymetric speciation and vicariance events in the evolution of a genus across multiple regions.
FIGURE 13 in Octocorals from Costa Rica: The genus Pacifigorgia (Coelenterata: Octocorallia: Gorgoniidae)
FIGURE 13. Pacifigorgia tupperi new species, holotype (UCR 920), SEMmicrographs of the sclerites: A, spindles; B, fourradiate; C–D, capstans; E, immature sclerites; F, anthocodial rods.
FIGURE 12 in Octocorals from Costa Rica: The genus Pacifigorgia (Coelenterata: Octocorallia: Gorgoniidae)
FIGURE 12. Pacifigorgia stenobrochis Valenciennes (UCR 831), SEMmicrographs of the sclerites: A–B, spindles; C, capstans; D, sixradiates, E, immature sclerites; F, anthocodial rods.
FIGURE 8 in Octocorals from Costa Rica: The genus Pacifigorgia (Coelenterata: Octocorallia: Gorgoniidae)
FIGURE 8. Pacifigorgia lacerata new species, holotype (UCR 921), SEMmicrographs of the sclerites: A–B, spindles; C, capstans; D, immature sclerites; E, anthocodial rods.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.