Find research datasets worth reusing

MCR LTER: Coral Reef Resilience: Short-term Accumulation of Algal Biomass on Unglazed Ceramic Tiles from July 2010-August 2011

Caged tiles were placed at various sites to measure short-term algal accumulation in the absence of grazing by fishes or large invertebrates. These data document biomass of algae that accumulated on unglazed ceramic tiles (2.5 cm X 2.5 cm) placed inside cages (mesh size = 2.5 cm x 2.5 cm) at various sites around the island of Moorea for a period of 3 to 4 weeks. Three separate experiments were conducted (one during July-August 2010 and two in July-August 2011). In the first experiment (2010_Production), we measured the accumulation of algae after 24 days at two different depths on the forereef (10 and 17 m), and within the lagoon at four different distances from the reef crest (approximately 25, 100, 400, and 700 m). In the second experiment (2011_Production_Summary), we measured the accumulation of algae after 24 or 25 days at six forereef sites (LTER 1, Resilience 2, LTER 3, LTER 4, LTER 5, LTER 6). In this experiment, tiles were placed adjacent to the fish transects (see knb-lter-mcr.6) at a depth of 12 m. In the final experiment (Production_Time_Series), we measured the accumulation of algae on tiles at three day intervals over a period of 31 days. This experiment was conducted at Resilience 2. 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 by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.

MCR LTER: Coral Reef Resilience: Algae, Coral, and Sediment data from Grazing Intensity Experiment, 2010 - 2012

These data describe the percent cover of benthic space holders (primarily algae), the biomass of algae and sediment, and the number of corals recruiting on 15 cm X 15 cm terra cota tiles experimentally manipulated on the forereef on the north shore of Moorea. The experiment was established to test whether and how different levels of grazing influence benthic community development. Five treatments were initially established to create a gradient in grazing pressure with a sixth treatment established shortly thereafter. Each treatment was replicated ten times using a randomized block design. Each cage initially contained four tiles, and one tile from each cage has been photographed and destructively sampled for biomass at regular intervals. In addition to the original tiles deployed in July 2010, tiles were subsequently deployed in March 2011, August 2011, and March 2012 to test whether community development varies among seasons. 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 by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.

MCR LTER: Coral Reef Resilience: Benthic Dynamics on 5m by 5m Plots on the Forereef, 2009 - 2011

These data describe the dynamics of corals, invertebrates, and fishes on 5 m X 5 m plots on the forereef following an outbreak of corallivorous crown-of-thorns seastars (Acanthaster planci) that caused mass coral mortality (see Adam et al. 2011). Twenty plots were first established at Resilience 2 during July 2009. Half of these plots were randomly assigned to a structure removal treatment and all dead coral structure was removed by divers, while the other half remained unmanipulated. Following the establishment of these plots, in February 2010 this site was impacted strongly by tropical cyclone Oli with the result that most of the structure was removed from all plots. Consequently, during July 2010, a structure/no structure experiment was initiated on ten plots (5 removals and 5 controls) at a site not impacted by Cyclone Oli (Resilience 3). Finally, during July 2011, five unmanipulated plots were established at each of four additional sites (Resilience 1, 4, 5, 6) so that community trajectories could be compared among sites. Counts of fishes, invertebrates, and corals are made regularily (at least annually). Coral and invertebrate counts are each separated into two data tables to reflect slightly different methodology. Initial coral counts included counts (and size estimates) of all stony corals, while later counts focused on corals from three genera, Pocillopora, Acropora, and Porites. Initial counts of invertebrates did not include information on size; all invertebrates were measured in later counts. In addition to in situ counts, all plots are photographed annually in 0.5 m by 0.5 m segments (e.g., 100 photos per plot). 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 by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la Rép

MCR LTER: Coral Reef Resilience: Live and Dead Pocillopora and Acropora Coral Colony Time Series from 2006 to 2011

These data describe the abundance, size structure, and morphologies of living and dead corals belonging to the genera Pocillopora and Acropora on the forereef (depth = 10 meters) in 2006, 2009, 2010, and 2011. Data were derived from a randomly chosen subset of photo quadrats associated with knb-lter-mcr.4. For each quadrat, individual coral colonies were identified to genus, scored as living or dead, and the total area of their footprint calculated. In addition, branch morphology was scored on a scale from 1 to 3, with 1 representing very tight spacing, and 3 representing open spacing among adjacent branches. 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 by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2018). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site.

openCC (other)Oct 2025View details →

MCR LTER: Coral Reef: Gump Station Meteorological Data, ongoing since 2006

These data provide meteorological information measured at the GUMP research station on the north shore of Moorea island, French Polynesia. Data collection began in August 2006 and include air temperature, relative humidity, wind speed and direction, solar radiation, atmospheric pressure, and integrated rainfall. All sensors are sampled every 5 minutes. Post-processing of these data is limited to some unit conversion and exclusion of corrupted data records. Aggregate data are provided in daily, weekly, monthly, and yearly time bins. ClimDB data for station GUMPM were derived from the same data source.

opencc-by-4.0Feb 2024View details →

Data for Paper "Scalable Semantic 3D Mapping of Coral Reefs with Deep Learning"

Example Data for DeepReefMap This dataset contains input videos in MP4 format taken with GoPro Hero 10 Cameras in Reefs in the Red Sea to demonstrate the DeepReefMap tool, which is described in the paper "Scalable Semantic 3D Mapping of Coral Reefs with Deep Learning" by Sauder et al. It contains a directory for model checkpoints for semantic segmentation, and for the 3D SLAM component: ``` checkpoints/         segmentation_net.pth         sfm_net.pth ``` It also contains videos to run the reconstruction with. See the detailed instructions for running reconstructions in https://github.com/josauder/mee-deepreefmap ``` input_videos/         GX_SINGLE_VIDEO.MP4         GX_VIDEO_1_OF_2.MP4         GX_VIDEO_2_OF_2.MP4 ```

opencc-by-4.0Sep 2022View details →

Dimethylsulfoniopropionate-derived compound concentrations, volatile organic compound concentrations, and microorganism abundances around two corals and a seaweed in the reefs of Moorea (French Polynesia)

These data belong in the paper:  M. Masdeu-Navarro, J-F. Mangot, L. Xue, M. Cabrera-Brufau, S.G. Gardner, D.J. Kieber, J.M. González, R. Simó (2022). Spatial and diel patterns of volatile organic compounds, DMSP-derived compopunds and planktonic microorganisms around a tropical scleractinian coral colony. Frontiers in Marine Science. Concentrations of DMSP, acrylate, DMSO, DMS, DMDS, COS, CS2, isoprene, CH3I, CH2ClI, CH2Br2 and CHBr3 in seawater samples around colonies of the corals Acropora pulchra and Pocillopora sp., and the brown seaweed Turbinaria ornata. Abundances of high-DNA and low-DNA bacteria, Prochlorococcus, Synechococcus, picoeukaryotes and nanoeukaryotes in the same samples, as determined by flow cytometry. All samples were collected in April 2018 in the coral reefs of Mo'orea, French Polynesia.  The upper set of data contains concentrations at the distance of 0.5 cm from the coral polyps on the branch tips or verrucae, as well as from the seaweed thalli (samples IN), and 2 m away, downcurrent (samples OUT). The second set of data corresponds to A. pulchra only, and contains seawater samples IN, OUT and AL, the latter being sampled at 0.5 cm from the base of the dead branches colonized by a turf alga. IN, OUT and AL samples were collected over an entire diel cycle, every 6 hours for a period of 30 hours.

opencc-by-4.0Jun 2024View details →

DATASET Invertebrate sounds from photic to mesophotic coral reefs reveal vertical stratification and diel diversity

This dataset contains 17 wave folders. The original files were used for the study published by Raick et al. (2024) in Oecologia (10.1007/s00442-024-05572-5), while subsampled versions of these files were used for the studies published by Raick et al. (2023) in Coral Reefs (10.1007/s00338-022-02343-7) and Raick et al. (2023) in Scientia Marina (10.3989/scimar.05395.078).

opencc-by-4.0Aug 2024View details →

Coping with Collapse: Functional Robustness of Coral-Reef Fish Network to Simulated Cascade Extinction

Data set, codes and results related to the article "Coping with Collapse: Functional Robustness of Coral-Reef Fish Network to Simulated Cascade Extinction", accepted in the periodic Global Change Biology. Stored are the full results of site occupancy models fitted to fish data, with coral and turf algae cover as predictor variables (results published in Luza et al. 2022, Scientific Reports), and the results of the present article. The RData also contains site coordinates, and the fish traits used in trait-based analyzes.

opencc-by-4.0Jul 2021View details →

Short-term Monitoring of Coral Reef Marine Protected Areas (MPAs) in the Municipality of Liloan, Central Visayas, Philippines

This is a sampling-event dataset of the short-term monitoring of Poblacion and Kadurong Reefs, two of the marine protected areas Municipality of Liloan, Cebu, Philippines. Water quality and ecological assessments were carried out to monitor the status and trends of biological and physical parameters associated with coral reefs using the standard protocols for surveying tropical marine resources. Specifically, the following measurements were conducted: (1) physico-chemical parameters, (2) phytoplankton and zooplankton occurrence and abundance, (3) fish occurrence and density, and (4) percent cover of benthic components of coral reef. The data can serve as the basis for the formulation and implementation of relevant measures for conservation and protection management of the Poblacion and Kadurong Reefs in Liloan, Cebu, Philippines. In this version, occurrence.csv was revised as described below: <ul> <li>taxonID for Abudefduf vaigiensis (Quoy & Gaimard, 1825) and  Hemiaulus P.A.C. Heiberg, 1863  were corrected.</li> <li>Author names with corrupted characters/symbols were corrected. </li> </ul>

opencc-by-4.0Jul 2021View details →

Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean

Data associated with the study "Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean". ITS.fasta, ITS_bmge.fasta, LSU.fasta, LSU_bmge.fasta, SSU.fasta, SSU_bmge.fasta: SSU rDNA, LSU rDNA and rDNA ITS sequences used in phylogenetic analyses. Sequences of Brilliantia kiribatiensis were added to updated phylogenetic datasets used previously (Leliaert et al. 2007a, Leliaert et al. 2009b), aligned in MAFFT v7.215 (Katoh and Standley 2013), and stripped of hypervariable sites in BMGE v1.1 (Criscuolo and Gribaldo 2010) by using the -h 0.4 -g 0.35 parameters. Alignments were visually checked and concatenated in Seaview v4.4.2. concatenated_SSU_ITS_LSU.fasta: concatenated alignment with following partitions: SSU: 1-1797, ITS1+5.8S+ITS2: 1798-3335, LSU: 3336-3926. Table_S1_sequence_sources.xls: GenBank accessions, sample isolate codes and sites of collection for sequences included in the concatenated phylogenetic data set. Table S2. Percent cover of different algal groups in 1 m2 photoquadrats. Algal groups are identified to genus level for fleshy macroalgae or functional group for turf algae, branched red algae, crustose coralline algae, and cyanobacteria. Table SX. Morphological measurements of Brilliantia kiribatiensis.

opencc-by-4.0Jun 2022View details →

Raw data: Local-scale feedbacks influencing cold-water coral growth and subsequent reef formation

Spreadsheets with the raw data of ADV-measured current velocity, coral growth derived from buoyant weight measurements and stress-related protein activities and concentrations.

opencc-by-4.0Jan 2023View details →

DATASET From the Reef to the Ocean: Revealing the Acoustic Range of the Biophony of a Coral Reef (Moorea Island, French Polynesia)

Dataset corresponding to the article "From the Reef to the Ocean: Revealing the Acoustic Range of the Biophony of a Coral Reef (Moorea Island, French Polynesia)". 90 sites were recorded from the reef crest to 10 km in the open ocean off Moorea Island (French Polynesia) in 2016. Recordings were realized with drifting antennas made of a floater and an autonomous recorder EA-SDA14 (RTSys®, Caudan, France) connected to a wideband low-noise hydrophone HTI-92 (High Tech Inc., Long Beach, MS, USA) with a sensitivity of −155 ± 3 dB re 1 V µPa−1 and a flat frequency response from 2 Hz to 50 kHz.

opencc-by-4.0Jan 2023View details →

Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs (Raw data)

Datasets for the analysis developed in the Article "Geographic range size and species morphology determines the organization of sponge host-guest interaction networks across tropical coral reefs". For more information, please refer to the original publication. Network_Structural_Index_&_SpogeTraits.csv <- Structural Index for the sponge-dwelling fauna network, sponge accumulated area and sponges’ morphology. NWTA_CoralReefs_Sponges_ interactions.csv <- Relationship between host sponges and guest fauna in the Northwester Atlantic coral reefs NWTA_CoralReefs_Sponge_reacords.csv <- Sponge species incidence records in the Northwester Atlantic coral reefs sponges_morphological_description.csv <- Sponge morphological standardization Network.html <- Interactive sponge-dwelling fauna network Enjoy!

Virgin Islands National Park: Coral Reef: Population Dynamics: Landscape-scale Variation in Scleractinian Corals

This study provides a landscape-scale context to a decadal-scale analysis of community structure on shallow reefs along 4 km of the south shore of St. John, US Virgin Islands. By focusing on 12-14 sites along ~100 km of the shores of St. John and St. Thomas, surveys conducted in 2011 were used to contrast: (1) a local-scale with a landscape-scale analysis on two islands, (2) reefs around St. John and St. Thomas, and (3) reefs on north and south shores. Reefs were censused using photoquadrats that were analyzed for percentage cover first by functional groups (coral, macraolagae and CTB), and then by coral genus. In general, among-site variation for the coarse-resolution analysis eclipsed shore and island effects, but the fine-resolution analysis revealed strong site-specific differences for multiple coral genera that could be the product of priority effects in community succession. Over the next decade these differences probably will create unique community trajectories at each site.

openCC (other)Jul 2022View details →

Bioerosion on Fungia pieces and coral recruits, calcification and settlement data on Palmyra Atoll reef.

Coral recruitment and calcium carbonate (CaCO₃) accretion are fundamental processes that help maintain coral reefs. Many reefs worldwide have experienced degradation, including a decrease in coral cover and biodiversity. Successful coral recruitment helps degraded reefs to recover, while CaCO₃ accretion by early successional benthic organisms maintains the topographic complexity of a coral reef system. It is therefore important to understand the processes that affect coral recruitment and CaCO₃ accretion rates in order to understand how coral reefs recover from disturbances. The aim of this thesis was to determine how biophysical forcing factors affect coral recruitment, calcification and bioerosion on a pristine coral reef.

Virgin Islands National Park: Coral Reef: Decadal-scale changes in community structure from 1987 to 2011

These time series data sample percent cover of Scleractinian corals by genus measured from photo quadrats. Percent cover is given for each quadrat, each site, each year from 1987 to 2011. Counts of juvenile corals conducted in situ and small colonies less than 4 cm diameter are pooled from all sites. Supplementary data include in situ seawater temperature daily mean from 1989 to 2011. These data were used to create the figures in Edmunds, P.J., 2013, Decadal-scale changes in the community structure of coral reefs in St. John, US Virgin Islands, Marine ecology Progress Series. doi:10.3354/meps10424

Virgin Islands National Park: Coral Reef: Populations Dynamics: Population Projections

In this study, size-based matrix models for the reef-building coral Orbicella annularis at 14-m depth on the Tektite reef in St. John, U.S. Virgin Islands, were used to: (1) explore the demography of changing coral cover over 25 yr, (2) test for spatial homogeneity in demographic properties through a contrast with a previous study (at Yawzi Point, Edmunds and Elahi 2007), and (3) evaluate the potential for future population stability. During three, five year intervals from 1988 to 2002, St. John was affected by hurricanes and bleaching, yet coral cover at Tektite increased from 33% to 49%; from 2002 to 2007, it declined to 27%; and from 2010 to 2013, it stabilized at ∼ 28%. Over a quarter-century, colonies > 50 cm2 became rare, the abundance of colonies ≤ 50 cm2 increased from 58% (1988) to 92% (2013), and population density doubled to 67 colonies m-2 by 2013. Population growth (λ) was greater at Tektite (1.152 ≥ λ ≥ 1.018) than Yawzi Point (0.679 ≥ λ ≥ 0.586), and while population size at Tektite declined due to bleaching and disease in 2005 (λ = 0.753 over 2003–2008), it recovered between 2008 and 2013 (λ = 0.966); the population at Yawzi Point declined from 1988 to 2003 without signs of recovery. Projections suggest a continuation of recent conditions could allow O. annularis at Tektite to retain ∼ 9% cover after 100 yr, but with a return to the rates of growth and survival of 1993–1998, it could attain coverage similar to that of 1988 (33%) in ∼ 15 yr.

Virgin Islands National Park: Coral Reef: Population Dynamics: Octocorals

These data are evidence of the the long-term dynamics of shallow coral reefs along the south coast of St. John from as early as 1987. These data describe coral reef community structure by density based on the analysis of color photographs. All of these data originate from color images of photoquadrats recorded annually (usually in the summer) from as early as 1987. The data falls into three groups. The two groups that are contained in this data package are (1) Tektite & Yawzi and (2) Random sites. Tektite – this is at 14 m depth on the eastern side of Great Lameshur Bay and is the original site of the Tektite man-in-the sea project in 1969; this project marked the birth of the Virgin Islands Ecological Research Station (later the Virgin Islands Environmental Resource Station) that hosts the field component of the project. The reef in this location consists of a single buttress that has remained dominated by Montastraea anularis since the start of the research (1987). These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Yawzi – this is at 9 m depth and is on the western side of Great Lameshur Bay and has been recorded photographically since 1987. This reef also started the study period dominated by Montastraea annularis, but has degraded much more rapidly that the Tektite site. These surveys consist of 30 photoquadrats (1 x 1 m) distributed along three, 10 m transects. Random sites – were added in 1992 to address the concern that the original sites (Yawzi and Tektite) were selected on “good” areas of reef and, therefore, could only decline in condition. The Random sites were selected using random coordinates in 1992, and consist of 6 sites (at 7-9 m depth) scattered between Cabritte Point and White Point. All lie a little shoreward of Yawzi and Tektite, and have always been characterized by low coral cover (< 10% cover). The surveys consist of 18-40 photoquadrats (0.5 x 0.5 m; with sample size determined by the exposures on a 3

Virgin Islands National Park: Coral Reef: Reference: Taxonomy

In early years photos were analyzed with less refined taxonomic classsification. This reference table may be used to aggregate taxa to align with coarse analysis. Use this table to define sub-categories and super-categories such as the M. annularis complex. This is a reference dataset containing the taxonomic classifications, groupings of taxonomic classifications, and functional groups. It has been updated in accordance with Budd, et al., 2012.