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.
1,478
datasets available to search
ShareScore release 0.7.1
Dataset results
1,478 results for “coral reefs”
Figure 4 from: McFadden CS, Benayahu Y, Samimi-Namin K (2024) A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. ZooKeys 1188: 275-304. https://doi.org/10.3897/zookeys.1188.110617
Figure 4 Ofwegenum colli sp. nov., holotype NTM C13089 A sclerites of the coenenchyme and polyp body B sclerites of the tentacles.
Figure 3 from: McFadden CS, Benayahu Y, Samimi-Namin K (2024) A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. ZooKeys 1188: 275-304. https://doi.org/10.3897/zookeys.1188.110617
Figure 3 Preserved type colonies of Ofwegenum gen. nov. AO. colli sp. nov., holotype NTM C13089 BO. colli sp. nov. several paratype colonies NTM C015578 CO. aff. coronalucis, SMNHTAU_Co_38223 DO. kloogi sp. nov. holotype SMNHTAU_Co_34426, grooves on polypary are indicated by arrows, distal ends of tentacles protrude from polyp mounds EO. kloogi sp. nov., several paratype colonies SMNHTAU_Co_38299 FO. verseveldti comb. nov., holotype SMNHTAU_Co_25554 GO. verseveldti comb. nov., paratypes, SMNHTAU_Co_25544, grooves on polypary are indicated by arrow HO. coronalucis sp. nov., holotype, UF 17263 IO. coronalucis sp. nov., paratype SMNHTAU_Co_39048).
Figure 15 from: McFadden CS, Benayahu Y, Samimi-Namin K (2024) A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. ZooKeys 1188: 275-304. https://doi.org/10.3897/zookeys.1188.110617
Figure 15 Ofwegenum verseveldti comb. nov., paratype, RMNH COEL. 13903 A sclerites of the coenenchyme and polyp body B sclerites of the tentacles.
Figure 7 from: McFadden CS, Benayahu Y, Samimi-Namin K (2024) A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. ZooKeys 1188: 275-304. https://doi.org/10.3897/zookeys.1188.110617
Figure 7 Ofwegenum coronalucis sp. nov., holotype UF 17263 A sclerites of the coenenchyme and polyp body B sclerites of the tentacles C sclerites around the polyp mouth opening. Scale at B also applies to C.
Figure 13 from: McFadden CS, Benayahu Y, Samimi-Namin K (2024) A new genus of soft coral (Octocorallia, Malacalcyonacea, Cladiellidae) and three new species from Indo-Pacific coral reefs. ZooKeys 1188: 275-304. https://doi.org/10.3897/zookeys.1188.110617
Figure 13 Ofwegenum kloogi sp. nov., paratype, SMNHTAU_Co_38229 A sclerites of the coenenchyme and polyp body B tentacle sclerites, with ellipsoidal platelets and flattened rods with lateral notches.
Coral Reef Soundscapes - French Polynesia
<p>Repository to support the publication: Unlocking the soundscapes of coral reefs with artificial intelligence. Williams et al (2024) https://doi.org/10.1101/2024.02.02.578582.</p> <p>If using this data please cite or acknowledge the paper.</p> <p>This repository contains all the raw data from the French Polynesian coral reef soundscape dataset.</p>
Hide 'n seq: direct versus indirect metabarcoding of coral reef cryptic communities
<p>Ecological patterns in biodiversity are primarily based on conspicuous organisms. Few methods are used to survey the taxonomically rich cryptobiome, which is made up of inhabitants from within microhabitats. One way that cryptic marine biodiversity can be non-invasively surveyed is by analyzing environmental DNA (eDNA) present in seawater. Using coral reefs as a model system, here we compare estimates of cryptic diversity among community biomass and eDNA metabarcoding sampling methods with a broad eukaryotic marker (COI). First, contributions to eDNA were investigated across cryptobiomes through a comparison of community metabarcoded biomass from standardized autonomous reef monitoring structures (ARMS) to eDNA acquired from seawater in which individual ARMS were soaked. Second, we compared these results to those from eDNA samples taken from within reef crevices and the ambient water column. Metabarcoding of community biomass from ARMS and eDNA from the two types of water samples revealed significantly different communities of cryptic coral reef habitat with little overlap between methods. Taxa that were unique to metabarcoding of ARMS biomass were predominantly from chitinous and calcifying groups (polychaetes, palaemonid shrimp, molluscs, brittle stars, and red algae), which suggests that these taxa are underrepresented in eDNA surveys. Other than the corals themselves, sponges and red algae were significant drivers of reef crevice community differences, while ambient seawater samples detected mostly planktonic organisms and reef fishes. Our data indicate that both eDNA and ARMS provide incomplete accounting of cryptic diversity. Direct sampling of biomass is best suited for building taxonomies and improving databases, whereas eDNA methods offer rapid insights into the composition of cryptobiomes. Because each method likely captures different taxa, multiple targeted assays can be used to provide the greatest estimates of metazoan and macroalgal richness.</p>
Data from: Population genetics of a broadcast-spawning coral across a tropical-temperate transition zone reveals regional differentiation and isolation of high-latitude reefs
<p>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.</p> <p>Location: Western Australia (WA).</p> <p>Taxon: <i>Turbinaria </i>species complex. <i>Turbinaria reniformis </i>Oken, 1815 (Dendrophylliidae).</p> <p>Methods: Samples from 930 target corals were collected from ten locations between 13 - 32<sup> o</sup> latitude spanning a 9° C mean temperature range. <i>In-situ</i> species identification of <i>T. reniformis </i>is hindered by morphological plasticity and homoplasy with sister species. We<i> </i>combined Sanger sequencing of two mitochondrial DNA markers and high-throughput genotyping by sequencing (GBS) to isolate a single genetic <i>Turbinaria</i> lineage from our dataset through which patterns of genetic flow and diversity along the WA coastline could be explored using population- and individual-based analyses.</p> <p>Results: Mitochondrial DNA sequence variation was low among <i>Turbinaria</i> 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.</p> <p>Main Conclusions: Temperate coral populations in Western Australia are genetically isolated from their tropical counterparts. Tropical populations of <i>T. 'reniformis' </i>exhibit adequate connectivity.<i> </i>Shark Bay represents the current southern limit of the tropical population of <i>T. 'reniformis'</i>. Interestingly, temperate <i>T. 'reniformis'</i> in this study exhibit some genetic resilience due to their relatively high genetic diversity, yet the strong patterns of genetic subdivision for this widely dispersing coral species potentially limit their resilience to future climate scenarios.</p>
Maldives Coral Reef Crest Accretion Data 2018-2020
<p>Annual monitoring data of coral reef accretion between 2018 and 2020 on the Keleihutta reef flat, Huvadhoo atoll, southern Maldives.</p> <p>Data generated using a coral reef accretion frame at four sites on the outer reef flat.</p>
Data from: The sound of recovery: coral reef restoration success is detectable in the soundscape
<p><span>1. Pantropical degradation of coral reefs is prompting considerable investment in their active restoration. However, current measures of restoration success are based largely on coral cover, which does not fully reflect ecosystem function or reef health. </span></p> <p><span>2. Soundscapes are an important aspect of reef health; loud and diverse soundscapes guide the recruitment of reef organisms, but this process is compromised when degradation denudes soundscapes. As such, acoustic recovery is a functionally important component of ecosystem recovery. </span></p> <p><span>3. Here, we use acoustic recordings taken at one of the world's largest coral reef restoration projects to test whether successful restoration of benthic and fish communities is accompanied by a restored soundscape. We analyse recordings taken simultaneously on healthy, degraded (extensive historic blast fishing) and restored reefs (restoration carried out for 1–3 years on previously-degraded reefs). We compare soundscapes using manual counts of biotic sounds (phonic richness), and two commonly used computational analyses (acoustic complexity index [ACI] and sound-pressure level [SPL]).</span></p> <p><span>4. Healthy and restored reef soundscapes exhibited a similar diversity of biotic sounds (phonic richness), which was significantly higher than degraded reef soundscapes. This pattern was replicated in some automated analyses but not others; the ACI exhibited the same qualitative result as phonic richness in a low-frequency, but not a high-frequency bandwidth, and there was no significant difference between SPL values in either frequency bandwidth. Further, the low-frequency ACI and phonic richness scores were only weakly correlated despite showing a qualitatively equivalent overall result, suggesting that these metrics are likely to be driven by different aspects of the reef soundscape. </span></p> <p><span>5<i>. Synthesis and applications: </i>These data show that coral restoration can lead to soundscape recovery, demonstrating the return of an important ecosystem function. They also suggest that passive acoustic monitoring (PAM) might provide functionally important measures of ecosystem-level recovery – but only some PAM metrics reflect ecological status, and those that did are likely to be driven by different communities of soniferous animals. Recording soundscapes represents a potentially valuable tool for evaluating restoration success across ecosystems, but caution must be exercised when choosing metrics and interpreting results. </span></p>
Prioritizing phylogenetic diversity to protect functional diversity of reef corals
<p>Datasets and R scripts</p>
Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding
<p><span><span><span><span><span><span><span><span><span><span><span>As elasmobranchs are becoming increasingly threatened, efficient methods for monitoring the distribution and diversity of elasmobranch populations are required. Environmental DNA (eDNA) metabarcoding is an increasingly applied technique that enables mass identification of entire communities and is an effective method for the detection of rare and elusive species. We performed an eDNA metabarcoding survey for fish communities around a coral reef atoll in the Chagos Archipelago and assessed the diversity and distribution of elasmobranch species detected within these communities. Our eDNA survey detected 353 amplicon sequence variants (ASVs) attributed to fishes, 12 of which were elasmobranchs. There were no differences in fish communities based on the presence and absence of ASVs between sample depth (surface and 40m) or sampling habitat, but communities based on read abundance were significantly different between habitats. The dominant elasmobranch species were grey reef (<i>Carcharhinus amblyrhynchos</i>) and silvertip (<i>C. albimarginatus</i>) sharks, and elasmobranch communities were significantly different between sampling depth and habitat. Overall, we find that eDNA metabarcoding can be used to reveal the diversity of elasmobranchs within broader taxonomic assays, but further research and development of targeted metabarcoding primers may be required before it can be integrated into a toolkit for monitoring these species.</span></span></span></span></span></span></span></span></span></span></span></p>
Light limitation and coral mortality in urbanised reef communities due to sea-level rise
<p>Dataset with coral mortality projections under sea-level rise</p>
Figure 2. A in Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding
Figure 2. A, taxonomic breakdown of eDNA reads by class in water samples collected around Diego Garcia atoll in September 2019. In each case, the fraction of the water column sampled is denoted by the colour key displayed below each bar. B, principal coordinate analysis (PCoA) of read abundance of all fish and elasmobranch ASVs per sample based on Bray–Curtis similarity. C, PCoA of read abundance of elasmobranch ASVs per sample based on Bray–Curtis similarity. Site numbers refer to the sites described in Figure 1.
Figure 1 in Elasmobranch diversity across a remote coral reef atoll revealed through environmental DNA metabarcoding
Figure 1. Location of water sampling sites around Diego Garcia. Triangles represent sampling sites on the outside of the atoll (N = 27), sites where samples were taken at 40 m and the surface (paired) are shown with a dark triangle inside. Circles represent lagoon samples (N = 5). Contour lines show the bottom depth in meters and colours represent the designated habitats around the atoll. Inset shows the location of Diego Garcia with respect to the other atolls in the Chagos Archipelago. Map was made using QGIS v.3.
Figure 5 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 5 - Holotype of Tosanoides obama shortly after collection, alive in a holding tank aboard the NOAA Ship Hi'ialakai. Photo by R. L. Pyle.
Figure 2 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 2 - Paratype of Tosanoides obama (USNM 440451), collected at a depth of 92 m off Pearl and Hermes Atoll, Northwestern Hawaiian Islands. Photo by R. L. Pyle.
Figure 1 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 1 - Holotype of Tosanoides obama (BPBM 41315), collected at a depth of 90 m off Kure Atoll, Northwestern Hawaiian Islands. Photo by R. L. Pyle.
Figure 4 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 4 - Holotype of Tosanoides obama (upper left) alongside presumed female (lower right, not collected) immediately prior to collection of the holotype, at a depth of 90 m off Kure Atoll, Northwestern Hawaiian Islands. Both fish retreated into the same hole moments after this image was captured. Cropped frame from video by R. L. Pyle.
Figure 6 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 6 - Paratype of Tosanoides obama shortly after collection, alive in a holding tank aboard the NOAA Ship Hi'ialakai. Photo by R. L. Pyle
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.