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.
3,855
datasets available to search
ShareScore release 0.7.1
Dataset results
3,855 results for “reefs”
MCR LTER: Coral Reef: Coral mortality in the lagoon of Moorea in 2019
The data included in this data package were collected in the lagoon of Moorea, French Polynesia. Data on coral mortality were collected in July 2019. Data on nitrogen content (%N) in the long-lived brown macroalga Turbinaria ornata were collected during six sampling campaigns between January 2016 and May 2021 to characterize nitrogen availability at each site. Data on seawater temperatures at six LTER sites in the back reef were collected from 2005-2019, but temperature loggers at two sites (LTER 1 and LTER 6) only recorded partial ocean temperature records during the heatwave from 2018-2019. We used our entire time series (spanning from 2005 to 2018) of temperature across our four long-term sites for which we have data in 2019 to predict ocean temperature data for LTER 1 and LTER 6 in 2019. These data were used for analyses in the manuscript entitled "Effects of nitrogen enrichment on coral mortality depend on the intensity of heat stress".
MCR LTER: Coral Reef: Patterns and implications of spatial covariation in herbivore functions on resilience of coral reefs
These data and code were generated in support of the manuscript: Cook DT, Holbrook SJ, and Schmitt RJ, Scientific Reports. In 2017, we collected biological and physical data from 20 sites along the north shore of Moorea, French Polynesia, to investigate spatial patterns in grazing and browsing functions of herbivorous fishes, environmental correlates, and implications for coral resilience. In addition to the data collected at the 20 north shore sites, we conducted a 10-day field experiment to assess the relationship between browsing intensity and potential of reversing a coral-to-macroalgae shift. This material uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2025).
MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Corals, ongoing since 2005
This dataset contains the percentage cover of the stony corals (Scleractinia) and other major groups analyzed from 0.5 x 0.5 m photographic quadrats in several reef habitats at the Moorea Coral Reef LTER, French Polynesia. This survey has been repeated annually in April since 2005. There are two tables available, providing different views of the same data: a long table having all values in one column and a wide table having a separate column for each dependent variable. Functional groups (i.e., dependent variables) counted are: Scleractinian Corals (by genus where appropriate, see methods), Macroalgae, Crustose Coralline Algae / Bare Space, Soft Corals, Hydrocorals (Millepora), Algal Turf, and Sand. The coral community was sampled photographically in all habitats surrounding the island: Fringing Reef, Lagoon (Backreef), and Outer Reef (Forereef.) The sampling regime consists of a repeated-measures protocol in each habitat and is structured by habitat to allow a statistical contrast of sites, shores, times, and in the case of the outer reef, depths. Detailed methods are available in the protocols section.
MCR LTER: Coral Reef: Coral Community Dynamics: Coral Recruitment
These data describe the recruitment of scleractinian corals to unglazed terracotta tiles secured independently to horizontal reef surfaces. The tiles are positioned horizontally to create a cryptic habitat beneath (approximately 1 cm high) and are in place approximately 6 months at a time; they are replaced ca. January and September. The tiles are bleached and inspected for coral skeletons using a dissecting microscope. Coral recruits are resolved to three families (Poritidae, Acroporidae, Pocilloporidae, and "others") and are scored on upper, lower and side surfaces. Data are available for the back reef (2006-present) and outer reef (2007-present).
MCR LTER: Coral Reef: In Situ Light Data, ongoing since 2021
This time series describes light (PAR, 400-700 nm) recorded in the air, on the surface, and at depth (17.1 m depth) at the LTER2 fore reef site. Surface data originate from twin cosine collectors (Hobo/Onset brand, model S-LIA-M003) attached to USB micro weather stations (Hobo/Onset brand, model H21-USB). Sensors are attached to the roof of the waterfront building at the UCB Gump station (-17.490598, -149.826208) with the sensors ~ 6 m above sea level. In situ light is recorded with a single PME miniPAR logger fitted with a Li-COR LI-192 cosine correct PAR sensor attached to a PME miniWiper. The sensor is mounted underwater with the top of the sensor at 17.1 m depth. The objective is to measure K dPAR , the diffuse attenuation coefficient for PAR wavelengths, over long periods. The technique relies on the assumption that ~96% of surface PAR is transmitted through the air-sea interface when sun altitudes are > 46° and wind speeds are < 5 m s-1 (Gregg and Carder 1990). Departures from this assumption degrade the estimation of subsurface PAR from surface PAR, which is required to calculate K dPAR .
MCR LTER: Coral Reef: Farmerfish gardens help buffer stony corals against marine heat waves, data for Honeycutt et al., PLOS One 2023
These data were generated in support of the manuscript: Honeycutt RC, Holbrook SJ, Brooks, AJ, and RJ Schmitt, PLOS One In Moorea, French Polynesia, we evaluated the response and fate of stony coral following a major thermal stress event in 2019 that caused a substantial amount of branching coral (dominantly Pocillopora) to bleach and die. We investigated whether Pocillopora colonies that occurred within territorial gardens protected by the farmerfish Stegastes nigricans were less susceptible to or survived bleaching better than Pocillopora on adjacent, undefended substrate. Bleaching prevalence and severity, which were quantified for >1,100 colonies shortly after they bleached, did not differ between colonies within or outside of defended gardens. By contrast, 399 focal colonies followed for one year revealed that a bleached coral within a garden was a third less likely to suffer complete colony death and, for survivors, about twice as likely to recover to its pre-bleaching cover of living tissue compared to Pocillopora outside of a farmerfish garden. Our findings indicate that while residing in a farmerfish garden may not reduce the bleaching susceptibility of a coral during thermal stress, it does help buffer a bleached coral against severe outcomes. This oasis effect of farmerfish gardens, where survival and recovery of thermally-damaged corals are enhanced, is another mechanism that helps explain why large Pocillopora colonies are far more abundant in farmerfish territories than elsewhere in the lagoons of Moorea, despite gardens being much less common. As such, farmerfish may have a growing role in maintaining the resilience of branching corals as the frequency and intensity of marine heat waves continue to increase. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued
MCR LTER: Coral Reef: Asynchrony in coral community structure contributes to reef‑scale community stability, data for Srednick et al., Nature 2023
These data were generated in support of the manuscript: Srednick G, Davis K, and Edmunds P, Nature To evaluate whether spatial insurance effects are important on coral reefs, we explored variation over 2006–2019 in coral community structure and environmental conditions in Moorea, French Polynesia. We studied coral community structure at a single site with fringing, back reef, and fore reef habitats, and used this system to explore associations among community asynchrony, asynchrony of environmental conditions, and community stability. The daily range in seawater temperature among habitats suggests it could be a factor contributing to the variation in coral community structure. Wave-forced seawater flow facilitated larval exchange among connected habitats, differing in strength among years, and accentuated periodic connectivity among habitats at 1-7 year intervals. At this site, connected habitats harboring taxonomically similar coral assemblages and exhibiting asynchronous population dynamics can provide insurance against extirpation and may promote community stability. If these effects apply at larger spatial scale, then among-habitat community asynchrony is likely to play an important role in determining reef-wide coral community resilience. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
MCR LTER: Coral Reef: Quantifying 2019 coral bleaching; data for Kopecky et al., 2023 Remote Sensing
This data package contains a dataset generated using image AI-assisted image segmentation of live and dead corals within ortho-photomosaics of benthic reef habitat on the North shore fore reef of Moorea, French Polynesia. The orthophotomosaics were produced through a rigorous method of underwater photogrammetry that allowed for spatial and temporal co-registration of ortho-photomosaics of the same location over time (for full photogrammetric methods, see Nocerino et al. 2020: https://doi.org/10.3390/rs12183036). Using the image segmentation software, TagLab (see Pavoni et al. 2021: https://doi.org/10.1002/rob.22049), we quantified live and dead coral before and after a bleaching event to estimate the amount of coral loss as a result of this event. This data package also contains code necessary to conduct the analyses of the dataset described above and create data visualizations used in the manuscript “Quantifying the Loss of Coral from a Bleaching Event Using Underwater Photogrammetry and AI-Assisted Image Segmentation”, published in the journal Remote Sensing in 2023, and as part of the dissertation of K. Kopecky. Analyses of these data and full methods descriptions can be found at https://doi.org/10.3390/rs15164077. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 22-24354 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2024). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.
MCR LTER: Coral Reef: Growth-predation risk trade-offs constrain the local distribution of a thicket-forming staghorn coral to marginal reef habitats; Data for Ladd et al., 2025, Scientific Reports.
This dataset is in support of the manuscript: Growth-predation risk tradeoffs constrain the local distribution of a thicket-forming staghorn coral to marginal reef habitats. These data were collected to 1) document how Acropora pulchra is distributed around the island of Moorea, and 2) to better understand the ecological processes that shape that distribution. Data include 1) results from surveys around the island of Moorea documenting the presence and size distribution of Acropora pulchra thickets, 2) results from an experiment measuring the growth and survivorship of Acropora pulchra fragments in the presence and absence of fish predators at nearshore fringing reef sites and adjacent sites in the mid lagoon (n = 20 sites in total), and 3) ancillary data on nitrogen content and dN15 in the tissue of the macroalgae Turbinaria ornata, sediment accumulation, and corallivore biomass at the experimental sites. All data were collected in 2016 and 2017.
MCR LTER: Coral Reef: Spatial portfolios in coral metapopulations are shaped by spatiotemporal asynchrony in environmental conditions; Data for Srednick et al., 2026 Ecology Letters
Using wavelet analyses of a 19-year coral community timeseries from Moorea, French Polynesia, we quantified timescale-specific population synchrony in four common coral genera and evaluated the predictors of spatial portfolio effects. We detected synchrony within genera associated with synchrony in degree heating days, diurnal temperature range (DTR), and macroalgal cover at different timescales. Synchrony in DTR and macroalgal cover was associated with lower synchrony of Pocillopora and Porites populations, respectively. Population (for three of four genera) and environmental synchrony were stronger within than among habitats across timescales, underscoring the role of habitat-specific conditions in driving spatial synchrony and spatial portfolios. These results describe how the spatial and temporal scales of heterogeneity in environmental and ecological conditions determine synchrony in coral population dynamics and support a spatial portfolio effect, which may buffer coral metapopulations from island-scale collapse. Data in support of analyses for: Spatial portfolios in coral metapopulations are shaped by spatiotemporal asynchrony in environmental conditions. Published in Ecology Letters 2026.
MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Fishes, ongoing since 2005
These data describe the estimated species abundances and individual sizes of fishes surveyed in late July or early August of each year by researchers associated with the Moorea Coral Reef Long Term Ecological Research site. This study began in 2005, and the dataset is updated annually. Divers using SCUBA estimate the number and total length (total body length to the greatest precision possible) of all mobile and semi-cryptic fishes observed on four 50m long transects within each of the three principal habitat types, fore reef, back reef, and fringing reef, found around Moorea. These three habitats are each surveyed at six permanently marked sites, two sites on each of Moorea's three shores, yielding a total of 18 unique habitats (3) by location (6) combinations and 72 transects. Estimated total lengths are converted to estimates of species biomass using published length-weight relationships for each species. Data from the initial survey conducted in 2005 are presented in a separate data table as the protocol used in 2005 differed from the standard protocol adopted in 2006, and no estimates of fish body lengths were made in 2005. These data are a component of the MCR LTER core time series program and provide insight into the spatial and temporal patterns of reef fish abundance and biomass around the island of Moorea, French Polynesia.
MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Other Benthic Invertebrates, ongoing since 2005
The data presented here are the abundances of the major invertebrate herbivores and corallivores on Moorea coral reefs. Abundances are estimated in 4 fixed quadrats along 5 permanent transects at each of 4 habitats at 2 sites on each of the 3 shores of Moorea each year. Counts are made in one-meter-squared quadrats.
MCR LTER: Coral Reef: Long-term Population and Community Dynamics: Benthic Algae and Other Community Components, ongoing since 2005
Coral reefs are comprised of scleractinian corals and many other benthic organims. The sampling described here quantifies the relative abundances of corals (aggregate abundance) and the other major benthic components including algal turfs, macroalgae, crustose corallines, and other sessile invertebrates. Abundance is estimated yearly at each of 6 sites (2 per shore) around the island. At each site, and in each of 4 habitats (fringing reef, backreef, forereef 10-m depth, forereef 17-m depth), 5 permanent 10-m long transects have been established and abundance estimates are made at fixed positions along each transect (n=10, 0.25 m2 quadrats per transect) allowing a repeated measures statistical analysis for the detection of temporal trends.
SBC LTER: REEF: Net primary production, growth and standing crop of Macrocystis pyrifera in Southern California
The giant kelp Macrocystis pyrifera forms subtidal forests on shallow reefs in temperate regions of the world. It is one of the fastest-growing multicellular autotrophs on Earth and its high productivity supports diverse marine food webs. In 2008, we published a method for estimating biomass and net primary production (NPP) of giant kelp along with five years of data, to provide a more integrated measure of NPP than those yielded by previous methods. Our method combines monthly field measurements of standing crop and loss rates with a model of kelp biomass dynamics to estimate instantaneous mass-specific growth rates and NPP for each season of each year. We have since improved our approach to account for several previously unresolved sources of biomass loss. These improvements have led to a near doubling of our prior estimates of growth and NPP. At our site with the most persistent stand of giant kelp, NPP averages ~5.2 kg dry mass m-2 y-1 and results from the rapid growth (~3.5% per day) of a relatively small standing biomass (~ 0.4 kg dry mass m-2 on average) that turns over ~ 12 times annually. Here we provide revised estimates of seasonal biomass, growth and NPP for the five years covered by our previous publication (2002-2006), along with an additional data collect since then (2007-present). We also present updated relationships for predicting giant kelp biomass and NPP from much more easily obtained measurements of frond density. These data can be used to understand the mechanisms that drive variation in giant kelp NPP at a wide range of temporal scales.
SBC LTER: Reef: Bottom Temperature: Continuous water temperature, ongoing since 2000
Giant kelp forests and the organisms living within them are exposed to a variable environment where biotic and abiotic drivers may affect populations and biological processes on the scale of hours to decades. To examine temporal and spatial patterns of temperature in giant kelp forests, SBC has measured ambient water temperature at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side Santa Cruz Island beginning in 2000. Two submersible temperature loggers, sampling every 30 minutes and offset from each other by 15 minutes, are deployed so that data is recorded every 15 minutes at each site. Temperature loggers were retrieved and replaced bi-annually with a new logger, typically in the early summer (June-July) and in early winter (January-March). These temperature loggers measure temperature in water within a range of -20°C to 30°C, and accuracy of ± 0.20°C at 25°C.
SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of bottom substrate and sand depth
These data describe the percent cover of eight bottom substrate types as determined by a uniform point contact method. The type of bottom substrate is recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Percent cover of each substrate type on a transect is estimated as the proportion of the 80 points contacted by that substrate type x 100. In cases where the substrate type is sand, the depth of the sand is measured. These data are part of the SBC LTER’s time series observations of kelp forest dynamics, which began in 2000 and was designed to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset include nine reef sites along the mainland coast of the Santa Barbara Channel and two on the north side of Santa Cruz Island. These 11 sites were chosen to reflect the wide range of oceanographic conditions present in the Channel and proximity to sources of terrestrial runoff. Data are collected at each site once per year in summer and this dataset is updated annually. The time period of data collection varied among the 11 reef sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The two tables in this data package include: 1) The percent cover of eight bottom substrate types; and 2) the sand depth of each sampling point (sand depth = 0 if substrate type ≠sand).
SBC LTER: Reef: Long-term experiment: Kelp removal: Cover of bottom substrate and sand depth
These data describe the percent cover of eight bottom substrate types within permanent plots of a long-term experiment designed to examine trajectories of change in the structure and productivity of kelp forest communities in response to changes in the frequency and severity of disturbance to giant kelp. The type of bottom substrate was recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Percent cover of each substrate type on transect was estimated as the proportion of the 80 points contacted by the substrate type x 100. In cases where the substrate type was sand the depth of the sand was measured. The experiment was initiated in 2008 at five reef sites along the mainland coast of the Santa Barbara Channel and included an annual kelp removal treatment designed to simulate increases in the frequency and severity of winter wave disturbance and a continual kelp removal treatment that allowed the effects of giant kelp on the community to be evaluated. The last experimental removals of giant kelp occurred in winter 2016 or winter 2017, depending on the site. Data collection continued in all plots until spring 2023 to document the recovery trajectory of the reef fish community following the cessation of experimental kelp removal. The two tables in this data package include: 1) The percent cover of eight bottom substrate types; and 2) the sand depth of each sampling point (sand depth = 0 if substrate type is not sand)
SBC LTER: Reef: Historical Kelp Database for giant kelp (Macrocystis pyrifera) biomass in California and Mexico
ISP Alginates (formerly Kelco Co.) has collected information on the abundance of giant kelp (Macrocystis pyrifera) in California and Mexico from routine aerial surveys since 1957. The standard protocol consists of an observer visually estimating the amount of harvestable giant kelp biomass within designated kelp beds from a small fixed-wing aircraft. Observations were recorded on paper data sheets in the field and archived in notebooks housed at ISP Alginates. With cooperation from ISP Alginates, the SBCLTER converted ISP Alginates long-term records of giant kelp biomass into a digital format. The database consists of a data table containing kelp biomass, a catalog of maps. The format ISP Alginates used to report kelp abundance data changed periodically over the course of the collecting period. These details, pus descriptions of designated kelp beds are described in the protocol document.
SBC LTER: Reef: Benthic community structure along a gradient of historic kelp variability
These data are estimates of biomass of approximately 225 taxa of reef algae, invertebrates, and fish in transects at 11 non-core sites in the Santa Barbara Channel in summer 2018 (3 transects per site). Sites were selected along a gradient of historic kelp (Macrocystis pyrifera) variability, from sites with highly persistent kelp to sites exhibiting extensive variation in kelp biomass since 2008. See the site characteristics data table for site locations and depths. The purpose of the sampling was to explore to what extent the findings from the long-term experiment (e.g. Castorani et al. 2018) apply to natural gradients in kelp persistence. Surveys were conducted following the same methodology used in the annual surveys of kelp forest community structure, such that data from the non-core sites may be paired with annual survey data collected in summer 2018.
SBC LTER: Reef: Kelp Forest Community Dynamics: Cover of sessile organisms, Uniform Point Contact
These data describe the cover of sessile invertebrates, understory macroalgae, and bottom substrate types as determined by a uniform point contact method. The presence of over 150 taxa of sessile invertebrates and macroalgae are recorded at 80 uniformly spaced points along permanent 40m x 2m transects. Multiple species can be recorded at any given point. Percent cover of a given species on a transect can be estimated from UPC observations as the fraction of total points at which that species was present x 100. The total percent cover of all species combined using this method can exceed 100%; however, the percent cover of any single species cannot exceed 100%. These data are part of SBC LTERs kelp forest monitoring program, which began in 2000 and was designed to track long-term patterns in species abundance and diversity of reef-associated organisms in the Santa Barbara Channel, California, USA. The sampling locations in this dataset include nine reef sites along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. Data collection began in 2000 and this dataset is updated annually. The time period of data collection varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. See Methods for more information. The two tables in this data package include: 1) The percent cover of sessile invertebrate and understory macroalage; and 2) the percent cover of bottom substrate.
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.