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”
Data from 'Planktivores as trophic drivers of global coral reef fish diversity patterns'
<p>Datasets and scripts generated in the paper 'Planktivores as trophic drivers of global coral reef fish diversity patterns', published in PNAS. More details can be found in the README file.</p>
Data from: Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes
<p>Coral reefs host hundreds of thousands of animal species that are increasingly threatened by anthropogenic disturbances. These animals host microbial communities at their surface, playing crucial roles for their fitness. However the diversity of such microbiomes is mostly described in a few coral species, and still poorly defined in other invertebrates and vertebrates. Given the diversity of animal microbiomes, and the diversity of host species inhabiting coral reefs, the contribution of such microbiomes to the total microbial diversity of coral reefs could be important, yet potentially vulnerable to the loss of animal species.</p> <p>Analysis of the surface microbiome from 74 taxa, including teleost fishes, hard and soft corals, crustaceans, echinoderms, bivalves and sponges, revealed that more than 90% of their prokaryotic phylogenetic diversity was specific and not recovered in surrounding plankton.</p> <p>Estimate of the total diversity associated to coral reef animal surface microbiomes reached up to 2.5% of current estimates of Earth prokaryotic diversity. Therefore, coral reef animal surfaces should be recognized as a hotspot of marine microbial diversity. Loss of the most vulnerable reef animals expected under present-day scenarios of reef degradation would induce an erosion of 28% of the prokaryotic richness, with unknown consequences on coral reef ecosystem functioning.</p>
Bermuda Reef Ecosystem Assessment and Mapping Programme: Baseline Coral Reef and Fish data
<p>BREAM: Bermuda Reef Ecosystem Analysis and Mapping Programme, mapped all coral reefs across the Bermuda platform in 2003. We then surveyed over 200 sites for benthic and fish assemblages using the AGRRA.org v4 methods, with local modifications. See www.bermudaBREAM.org for more information about the baseline monitoring work, or to contact us for additional data and information.</p> <p>Contributors:</p> <p>Research Associates:</p> <p>Jessie Murdoch MSc; Robert Fisher, BFA; Gretchen Goodbody-Gringley, PhD, Matthew Strong BSc; Struan R. Smith PhD</p> <p>Undergraduate Interns</p> <p>Taylor Gorham, Anke Moesinger, Molly Sinnott, D’mitri Williams</p> <p>Graduate Interns</p> <p>Gerardo Toro-Farmer, Mike Colella, Brittany Huntington, Katherine Yates</p> <p>Volunteers</p> <p>Ian Murdoch; Judie Clee; Teddy Gosling; Gil Nolan; Lynn Wolfe</p> <p>RV Endurance Captain: Tim Hasselbring</p> <p> </p>
Genome-resolved diversity and biosynthetic potential of the coral reef microbiome
<p>This repository hosts the supplementary data associated with the manuscript entitled "Genome-resolved diversity and biosynthetic potential of the coral reef microbiome".</p>
Coral connections within an atoll reef system underlie reef resilience and persistence
<p><span>This study investigates the coral reef connectivity a coral reef atoll using fine-scale bio-physical model along with network analysis. </span></p>
List of references used in the bibliometric analysis of Chapter 2 - History of Research About the Tropical Brazilian Coral Reef Systems - Book: Brazilian Coral Reefs
<p>This list contains 755 references related to coral reefs research. This list was obtained through a search for articles and book chapters in the databases Web of Science and Scopus, using the terms "reef" and "Brazil" in Title, Abstract and Keywords, added to references included from the authors own databases. The search was made in February, 12th 2021.</p>
Coral Reef Soundscapes - Lizard Island, Australia
<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 Australian coral reef soundscape dataset. Note, some site names were switched for the publication, so differ to the raw files in this repository. For conversions use:</p> <p>This repo -> The publication</p> <p>SiteA -> Site A<br>SiteB -> Site G<br>SiteC -> Site D<br>SiteD -> Site E<br>SiteE -> Site B<br>SiteF -> Site I<br>SiteG -> Site H<br>SiteH -> Site L<br>SiteI -> Site C<br>SiteJ -> Site F<br>SiteK -> Site J<br>SiteL -> Site K</p>
Data from 'The rise of dietary diversity in coral reef fishes'
Open the record for dataset details and reuse information.
Supplementary material for: Coral reef potential connectivity in the southwest Indian Ocean
<p>Supplementary datasets and scripts for <em>Coral reef potential connectivity in the southwest Indian Ocean</em>. Please see the readme!</p>
Strength of sexual selection and sex roles vary between social groups in a coral reef cardinalfish
<p>The strength and direction of sexual selection can vary among populations. However, spatial variability is rarely explored at the level of the social group. Here we investigate sexual selection and sex roles in the paternally mouthbrooding, socially monogamous, and site-attached pajama cardinalfish, <em>Sphaeramia nematoptera</em>. Females were larger, more aggressive, and had a longer dorsal fin filament, indicating reversed sex roles. At the scale of social groups, we show the Bateman gradient and reproductive variance depending on the sex ratio and size of the groups. In small and medium-sized groups with balanced or male-biased sex ratios, Bateman gradients were steeper for females, whereas gradients were equally steep for both sexes in large groups or when the sex ratio was female-biased. For both sexes, reproductive variance increased with group size and with a higher male-to-female sex ratio. In <em>S. nematoptera</em>, mating opportunities outside the socially monogamous pair appear to impact sexual selection. We conclude that the strength and direction of sexual selection can be masked by social dynamics in group-living species when considering only population and large-scale demographic processes.</p>
Figure 1 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India
Figure 1. Map of the Mandapam group of Islands in GoM showing the collection sites.
Figure 3. Silhouettea indica Visweswara Rao, 1971 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India
Figure 3. Silhouettea indica Visweswara Rao, 1971.
Figure 2 in First report of two gobiid fishes from the coral reefs of Gulf of Mannar, Tamil Nadu, India
Figure 2. Istigobius ornatus (Rüppell, 1830).
Data From: Shortened food chain length in a fished versus unfished coral reef
<p>Direct exploitation through fishing is driving dramatic declines in wildlife populations in ocean environments, particularly for predatory and large-bodied taxa. Despite wide recognition of this pattern and well-established consequences of such trophic downgrading on ecosystem function, there have been few empirical studies examining the effects of fishing on whole system trophic architecture. Understanding these kinds of structural impacts is especially important in coral reef ecosystems - often heavily fished and facing multiple stressors. Given often high dietary flexibility and numerous functional redundancies, especially in diverse ecosystems such as coral reefs, it is important to establish if web architecture is strongly impacted by fishing pressure, or if it might be resilient, at least to moderate intensity pressure. To examine this question, we used a combination of bulk and compound-specific stable isotope analyses measured across a range of predatory and low trophic level consumers between two coral reef ecosystems that differed with respect to fishing pressure but otherwise remained largely similar. We find that even in a high diversity system with relatively modest fishing pressure, there are strong reductions in the trophic position of the three highest trophic position consumers examined in the fished system but no effects on the trophic position of lower-level consumers. We see no evidence that this shortening of these affected food webs is being driven by changes in basal resource consumption, e.g., through changes in spatial location of foraging by consumers. Instead, this likely reflects internal changes in food web architecture suggesting that even in diverse systems, and with relatively modest pressure, human harvest causes significant compressions in food chain length. This observed shortening of these food webs may have many important emergent ecological consequences for the functioning of ecosystems impacted by fishing or hunting. Such important structural shifts may be widespread but unnoticed by traditional surveys. This insight may also be useful for applied ecosystems managers grappling with choices about the relative importance of protection for remote and pristine areas and the value of strict no-take areas to protect not just the raw constituents of systems affected by fishing and hunting but also the health and functionality of whole systems.</p>
Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands
<p>Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from 9 species were marked and sampled in 2017, and following hurricanes in September 2017, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes and the onset of stony coral tissue loss disease. While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.</p>
The processing results, dataset and original codes of Coral reef PtCloud segmentation model (based on proposed underwater camera systems)
<p><strong># Data Introduction</strong><br>The proposed camera system includes three operation modes: Surface Mode, Horizontal Mode, and Curved Mode.</p> <ul> <li><strong>Surface Mode</strong>: Provides 3D reconstructions (point cloud), DEM, and orthophoto maps of the seabed (covering a line of 70m in length).</li> <li><strong>Horizontal Mode</strong>: Provides 3D reconstructions (point cloud and mesh) and orthophoto maps of a single transect line.</li> <li><strong>Curved Mode</strong>: Offers 3D reconstructions (mesh) of various targets, including artificial coral reefs, coral reefs with snails, and coral reefs with starfish.</li> </ul> <p>All mesh results are saved in <code>.FBX</code> format, and point cloud results are saved in <code>.TXT</code> format.</p> <p><strong># Code Introduction</strong><br>The backbone of our point cloud segmentation model is the KPConv model.<br>If you encounter any issues during code deployment, please refer to the original KPConv repository (<a href="https://github.com/HuguesTHOMAS/KPConv" target="_new" rel="noopener">Original Code: https://github.com/HuguesTHOMAS/KPConv</a>).<br>We provide our modified code (customized for our task) along with the complete point cloud dataset.</p>
Invasive macroalgae shape chemical and microbial waterscapes on coral reefs
<p><span>Over the past decades, human impacts have changed the structure of tropical benthic reef communities <a name="_Hlk166256162"></a>towards coral depletion and macroalgal proliferation. However, how these changes have modified chemical and microbial waterscapes is poorly known. Here, we assessed how the experimental removal of macroalgal assemblages influences the chemical and microbial composition of two reef boundary layers, the benthic and the momentum<em>. </em>Chemical and microbial waterscapes were spatially structured, both horizontally and vertically, according to macroalgal dominance and boundary layers. Microbes associated with reef degradation were enriched in the boundary layers surrounding macroalgal-dominated substrata. Dominant macroalgae were surrounded by a distinct chemical pool of diverse lipid classes (e.g., diterpenoids and glycerolipids) and labile organic matter (e.g., organooxygen compounds), which diffused from algal tissues to boundary layers according to their polarity. Finally, our results highlighted strong co-variations between specific algal-derived metabolites and planktonic microbes, giving insight into their roles in coral reef functioning and resilience. </span></p>
Traits, landmarks and outlines: Three congruent sides of a tale on coral reef fish morphology
<p>Quantifying the morphology of organisms remains fundamental in ecology given the form-function relationship. Morphology is quantifiable in traits, landmarks, and outlines, and the choice of approach may influence ecological conclusions to an unknown extent. Here, we apply these three approaches to 111 individual coral reef fish of 40 species common in Micronesia. We investigate the major dimensions of morphological variability among individuals, families, and predefined feeding functional groups. We find that although the approaches are complementary, they coincide in capturing elongation as the main dimension of variability. Further, the choice of approach led to different interpretations regarding the degree of morphological differentiation among taxonomic and feeding functional groups. We also use each morphology dataset to compute community-scale morphological diversity on Palauan reefs and investigate how the choice of dataset affects the detection of differences among sites and wave exposure levels. The exact ranking of sites from highest to lowest morphological diversity was sensitive to the approach used, but not the broad spatial pattern of morphological diversity. Conclusions regarding the effect of wave exposure on morphological diversity were robust to the approach used. Biodiversity hotspots (e.g. areas of exceptionally high diversity and/or endemism) are considered important conservation targets but their location may depend on the biodiversity metric used. In the same vein, our results caution against labelling particular sites as morphological diversity hotspots when metrics consider only a single aspect of morphology.</p>
The effects of light intensity and flow speed on biogeochemical variability within a fringing coral reef in Onna-son, Okinawa, Japan
<p>Global warming and ocean acidification are driving gradual declines in seawater dissolved oxygen concentrations and pH. Predicting how these changes will affect shallow, near-shore environments including coral reefs is challenging due to high natural variability on both spatial (10 m to km) and temporal (diel to seasonal) scales. To make predictions, it is first necessary to identify and quantify the drivers of this natural variability. While significant efforts have been devoted to characterising the influence from metabolic processes on coral reef seawater chemistry, less attention has been devoted to physical processes such as flow speed and light intensity. Here, we measured seawater flow, photosynthetically active radiation (PAR), pH, and dissolved oxygen (DO) at three reef habitats (reef flat, lagoon, and outflow channel) in a fringing coral reef system in Okinawa, Japan for a duration of 3 weeks in October of 2019. During the study, circulation was primarily wave-driven with mean flow speeds ranging from 14-26 cm/s. Flow direction became increasingly consistent at higher flow speeds, which traced visual patterns in the benthos observed from satellite imagery. Multiple linear regression models of daytime changes in pH and DO versus daily mean flow speed and PAR described 25-74% of the observed variability across all sites while at night, flow speed alone accounted for 35-69% of the observed variability. The results demonstrate that flow speed, trajectory, and PAR play important and variable roles in controlling biogeochemical variability within coral reefs and need to be considered in assessing their vulnerability to global climate change.</p>
Fine intervals are required when using point intercept transects to assess coral reef status
The Point Intercept Transect (PIT) method has commonly been used in recent decades for estimating the status of coral reef benthic communities. It is a simple method that is efficiently performed underwater, as benthic components are recorded only as presence or absence at specific interval points along transects. Therefore, PIT is also popular in citizen science activities such as Reef Check programs. Longer intervals are commonly associated with longer transects, yet sampling interval length can significantly influence benthic coverage calculations. Despite this, the relative accuracy of longer or shorter intervals related to transect length has not been tested for PIT. In this study, we tested the optimum intervals of PIT for several commonly used transect lengths using the bootstrap method on empirical data collected on tropical coral reefs and non-reefal coral communities. Our results recommend fine intervals of 10 cm or shorter, depending on the length of the transect, to increase the accuracy of estimating benthic community status on coral reefs. Permanent transects should also be considered in long-term monitoring programs to improve data quality.
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.