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4,207 results for “Corals”
Coral calcification mechanisms in a warming ocean and the interactive effects of temperature and light
<p>Ross et al 2022 Supplementary data for coral (<em>Acropora nasuta</em>) temperature and light experiments. </p>
Within Population Variability of Coral Heat Tolerance - Images
<p>Image dataset used for a colour analysis of coral branches throughout a long-term marine heatwave emulation experiment using machine learning. Article: "Within population variability in coral heat tolerance indicates climate adaptation potential" by Humanes and Lachs et al. Code to analyse the dataset is found at 10.5281/zenodo.6256164.</p>
Data from 'Deoxygenation lowers thermal threshold of coral bleaching.'
<p>Increasing exposure to deoxygenation as a result of climate warming and localised pollution is emerging as an important contributing factor for widespread coral bleaching and mortality. Some corals have been observed to thrive under multiple extreme conditions including very low O<sub>2</sub> levels and high temperatures yet the combined effects of heating and deoxygenation on coral bleaching susceptibility remain unknown. Here, we incorporated deoxygenated seawater into short-term heat assays (CBASS) to show that deoxygenation can lower the thermal limit of an <em>Acropora</em> coral species. </p> <p>Data files provided:</p> <p>'CBASS_deoxy_ref_transcriptome.fasta' contains the reference transcriptome assembled <em>de novo</em> using SOAPdenovo-Trans using non-bleached samples of the CBASS assay (i.e., 30°C and 33°C) and then filtered to keep only reads ≥ 500 bp in length (20,115 contigs).</p> <p>'CBASS_deoxy_BIS_photos_Initial_and_poststress.pdf' contains images of coral fragments alongside a colour reference chart for estimating bleaching index scores (BIS) before experiment starts (initial) and post 6hr stress phase. Sample IDs are denoted as: H0/HH = normoxia/deoxygenation treatment, 30/33/36/39 = temperature in °C, T1 = time point 1, R1/2/3/4 = replicate 1/2/3/4.</p> <p>'CBASS_deoxy_SymPortal_output_files.zip' contains all SymPortal (https://symportal.org) output files.</p>
Dimethylsulfoniopropionate-derived compound concentrations, volatile organic compound concentrations, and microorganism abundances around two corals and a seaweed in the reefs of Moorea (French Polynesia)
<p>These data belong in the paper: </p> <p>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. <em>Frontiers in Marine Science</em>.</p> <p>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. </p> <p>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.</p>
Supporting data of: Hydrography and food distribution during a tidal cycle above a cold-water coral mound
<p>This file contains the raw data and data analyses scripts to:</p> <p>Hydrography and food distribution during a tidal cycle above a cold-water coral mound</p> <p>Evert de Froe, Sandra R. Maier, Henriette G. Horn, George A. Wolff, Sabena Blackbird, Christian Mohn, Mads Schultz, Anna-Selma van der Kaaden, Chiu H. Cheng, Evi Wubben, Britt van Haastregt, Eva Friis Moller, Marc Lavaleye, Karline Soetaert, Gert-Jan Reichart, Dick van Oevelen.</p> <p>Deep Sea Research Part I: Oceanographic Research Papers, 2022,<br> ISSN 0967-0637,<br> https://doi.org/10.1016/j.dsr.2022.103854.<br> <strong>Abstract: </strong>Cold-water corals (CWCs) are important ecosystem engineers in the deep sea that provide habitat for numerous species and can form large coral mounds. These mounds influence surrounding currents and induce distinct hydrodynamic features, such as internal waves and episodic downwelling events that accelerate transport of organic matter towards the mounds, supplying the corals with food. To date, research on organic matter distribution at coral mounds has focussed either on seasonal timescales or has provided single point snapshots. Data on food distribution at the timescale of a diurnal tidal cycle is currently limited. Here, we integrate physical, biogeochemical, and biological data throughout the water column and along a transect on the south-eastern slope of Rockall Bank, Northeast Atlantic Ocean. This transect consisted of 24-hour sampling stations at four locations: Bank, Upper slope, Lower slope, and the Oreo coral mound. We investigated how the organic matter distribution in the water column along the transect is affected by tidal activity. Repeated CTD casts indicated that the water column above Oreo mound was more dynamic than above other stations in multiple ways. First, the bottom water showed high variability in physical parameters and nutrient concentrations, possibly due to the interaction of the tide with the mound topography. Second, in the surface water a diurnal tidal wave replenished nutrients in the photic zone, supporting new primary production. Third, above the coral mound an internal wave (200 m amplitude) was recorded at 400 m depth after the turning of the barotropic tide. After this wave passed, high quality organic matter was recorded in bottom waters on the mound coinciding with shallow water physical characteristics such as high oxygen concentration and high temperature. Trophic markers in the benthic community suggest feeding on a variety of food sources, including phytodetritus and zooplankton. We suggest that there are three transport mechanisms that supply food to the CWC ecosystem. First, small phytodetritus particles are transported downwards to the seafloor by advection from internal waves, supplying high quality organic matter to the CWC reef community. Second, the shoaling of deeper nutrient-rich water into the surface water layer above the coral mound could stimulate diatom growth, which form fast-sinking aggregates. Third, evidence from lipid analysis indicates that zooplankton faecal pellets also enhance supply of organic matter to the reef communities. This study is the first to report organic matter quality and composition over a tidal cycle at a coral mound and provides evidence that fresh high-quality organic matter is transported towards a coral reef during a tidal cycle.</p> <p> </p>
DATASET Invertebrate sounds from photic to mesophotic coral reefs reveal vertical stratification and diel diversity
<p>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).</p>
Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition
<p>This repository contains code to accompany the manuscript titled</p> <p><strong>Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition</strong></p> <p>by <strong>Carly D. Kenkel and Line K. Bay</strong><br> </p> <p>In this study, we used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism predicted to enhance cooperation and holobiont fitness of reef-building corals. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, were fragmented and subjected to a two-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological metrics of fitness and cooperation. Amplicon sequencing of the <em>Symbiodinium</em> ITS-2 locus was used to investigate differences in symbiont community composition among focal species. We did not observe universally higher levels of cooperation in vertically transmitting species. However, the reduction in cooperation at the onset of bleaching was marginally associated with symbiont community diversity. Analysis of ITS2 amplicon sequence data suggest that it may not be vertical transmission <em>per se</em> that influences host-symbiont cooperation, but genetic uniformity of the symbiont community.</p> <p>Repository contents:</p> <ul> <li> <p><strong>TraitDataAnalysis.R:</strong> Annotated R script for generating figures and re-creating statistical analyses</p> <ul> <li> <p><strong>RsquaredGLMM.R:</strong> Accessory R script for running RsquaredGLMM analyses, called by <strong>TraitDataAnalysis.R</strong></p> </li> <li> <p><strong>NSF_RunningPam.csv</strong>: Input file for statistical analysis. Contains photophysiological data. Column headers are as follows:</p> <ul> <li> <p>Tank: Number of experimental tank in which experimental coral fragment was held</p> </li> <li> <p>Treatment: short-hand notation for sample treatments (e.g. ctrl1-5 = control temperature, genotypes 1-5)</p> </li> <li> <p>Water: source sump for temperature controlled water jackets for each set of treatment tanks</p> </li> <li> <p>Position: numerical rack position of coral fragment within experimental treatment tank</p> </li> <li> <p>Species: Coral species (Amil=<em>A. millepora</em>, Maqe=<em>M. aequituberculata</em>, Gast=<em>G. astreata</em>, Gach=<em>G. acrhelia</em>, Plob=<em>P. lobata</em>, Gcol=<em>G. columna</em>)</p> </li> <li> <p>Genotype: source colony origin of individual coral fragments within species</p> </li> <li> <p>Temp: experimental temperature treatment (ctrl: 27°C ; heat: 31°C)</p> </li> <li> <p>Treat: whether experimental corals received C14-labeled bicarbonate (bicarb), artemia or were sampled separately for Gene Expression Analysis (not presented in this manuscript)</p> </li> <li> <p>EQY: Effective quantum yield of <em>Symbiodinium</em> photosystem II as measured using PAM fluorometry</p> </li> <li> <p>Date: Actual calendar date of measure</p> </li> <li> <p>Transmission: coral symbiont transmission mode</p> </li> <li> <p>Reef: reef site of original coral collection</p> </li> <li> <p>Date: experimental date of measure</p> </li> </ul> </li> <li> <p><strong>TraitData.csv:</strong> Input file for statistical analysis. Contains all physiological trait data.</p> <ul> <li> <p>Includes columns as described above for the Running_Pam file in addition to columns containing raw trait data as described in the manuscript.</p> </li> </ul> </li> <li> <p><strong>TraitData_DaysAsCols.csv:</strong> Reformatted input file with trait data split by sampling day across columns</p> </li> </ul> </li> <li> <p><strong>DADA2Analysis.R:</strong> Annotated R script for generating figures and running ITS2 amplicon analyses</p> <ul> <li> <p>GeoSymbio_ITS2_LocalDatabase_verForPhyloseq.fasta: FASTA file of the GeoSymbio ITS2 reference database <a href="https://sites.google.com/site/geosymbio/">https://sites.google.com/site/geosymbio/</a>, formatted for use with the R prograom Phyloseq</p> </li> <li> <p>SeqVars_6Feb.fasta: FASTA file of identified sequence variants resulting from DADA2 analysis</p> </li> <li> <p>OutputDADA_6Feb.csv: Counts of sequence variants by sample</p> </li> <li> <p>Raw FASTQ paired end read files can be downloaded from NCBI's SRA: PRJNA338365</p> </li> </ul> </li> </ul>
Connectivity networks for Acropora corals on the GBR to investigate split spawning
<p>Connectivity networks for Acropora corals on the GBR to investigate split spawning.</p> <p>If using these outputs please cite the article:</p> <p>Hock K, Doropoulos C, Gorton R, Condie SA, Mumby PJ. (2019). <strong>Split spawning increases robustness of coral larval supply and inter-reef connectivity</strong>. Nature Communications <strong>10</strong>, 3463.</p> <p>Link to the paper:</p> <p>https://rdcu.be/bOW1x</p> <p> </p> <p> </p> <p> </p>
Water Body Checklists 2019: Coral Sea Species List
Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.<p></p>List of species collected from the Coral Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
Water Body Checklists: Coral Sea Species List
Species checklists created using effechecka and modified polygons from IHO. The polygons were reduced in resolution.<p></p>List of species collected from the Coral Sea using effechecka and a modified polygon from the International Hydrographic Association. A filter was applied (based on data from WoRMS) to remove all non-marine taxa.
Coping with Collapse: Functional Robustness of Coral-Reef Fish Network to Simulated Cascade Extinction
<p>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.</p>
Data from: Habitat suitability models reveal extensive distribution of deep warm water coral frameworks in the Red Sea
<p>Deep-sea coral frameworks are understudied in the Red Sea, where conditions in the deep are conspicuously warm and saline compared to other basins. Habitat suitability models can be used to predict the distribution pattern of species or assemblages where direct observation is difficult. Here we show how coral frameworks, built by species within the families Caryophylliidae and Dendrophylliidae, are distributed between water depths of 150 m and 700 m in the northern Red Sea and Gulf of Aqaba. To extrapolate the known (ground-truthed) positions of these deep frameworks, we use environmental and geomorphometric variables to inform well-performing maximum entropy models. Over 250 km2 of seafloor in our study area are identified as suitable for such frameworks, equivalent to at least 35% of the area of photic-zone coral reefs in the same region. We hence contend that deep-water coral frameworks are an important and underappreciated repository of Red Sea biodiversity.</p>
Coral growth data for the research article "Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hotspot" in Journal of Animal Ecology
<p>This repository contains the coral growth data files used to generate the results for the following article:</p> <p> </p> <p>MJ. Vergotti, JP. D’Olivo, T. Brachert, P. Capdevila, J. Garrabou, C. Linares, P. Spreter, DK. Kersting (2024) Reconstruction of long-term sub-lethal effects of warming on a temperate coral in a climate change hot-spot. <em>Journal of Animal Ecology</em>. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/1365-2656.14225</p> <p> </p> <p><strong>Abstract: </strong>The impact of warming on zooxanthellate corals is widespread, from tropical to temperate seas, with their associated mortalities causing global concern. The temperate coral <em>Cladocora caespitosa</em> is the only zooxanthellate coral with reef-building capacity in the Mediterranean Sea, a climate change hotspot with warming rates triple the global average. Over the past two decades, <em>C. caespitosa</em> populations have suffered severe mortality events associated with marine heatwaves (MHWs). However, with monitoring efforts beginning, at best, in the 2000s, the occurrence of MHWs before to that period, as well as the sub-lethal effects of these events remain poorly understood. Here we use sclerochronology to reconstruct the histories of past stress events and long-term sub-lethal effects on <em>C. caespitosa</em> in three locations within the NW Mediterranean Sea, each with different environmental conditions. Skeletal extension, density and calcification rates were compared to the <em>in situ</em> seawater temperature of each site to assess their relationship. Additionally, we assessed the occurrence of skeletal growth anomalies to reconstruct stress events between 1991 and 2021, a period that encompasses the onset and evolution of warming-related mass mortality events in the NW Mediterranean Sea. Our results reveal a positive association between calcification and temperature, following a latitudinal temperature gradient. However, the evolution of the likelihood distribution of growth rates in the warmest site (Columbretes Islands) since the 1990s indicates a decrease in linear extension and calcification rates during the most recent years. With the increase in the frequency of MHWs and growth anomalies during the last decade, this decline suggests a recurrence in physiological stress events. These results unravel information on the long-term impacts of warming on coral growth and highlight the potential of applying sclerochronology to reconstruct sub-lethal effects of warming using <em>C. caespitosa</em>. </p> <p> </p> <p> </p> <p><strong>Funding</strong>: This research is supported by the Horizon 2020 program of research and innovation of the European Union under the MaCoBioS grant agreement, by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project no. 401447620) and by the Spanish Ministry of Science, Innovation and Universities under the project UndResCoral (project no. PID2022-137539OA-C22). D.K.K. was supported by a Ramon y Cajal postdoctoral grant funded by the Ministry of Science and Innovation (PEICTI 2021–2023; grant no. RYC2021-033576-I). C.L. acknowledges the support by ICREA Academia. J.G. acknowledges the grant “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S) funded by AEI 10.13039/501100011033.</p>
Suppl. Information to "The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching"
<p><strong>Supplementary File 1:</strong> Multiple alignment for protein sequences of core histones with Pocillopora acuta, Pocillopora damicornis, Acropora digitifera, Nematostella vectensis, Hydra vulgaris, Schistosoma mansoni and Mus musculus. A. Histone H2A; B. Histone H2B; C. Histone H3; D. Histone H4. An asterisk (*) means that the amino acid is conserved between all species.</p> <p><strong>Supplementary File 2</strong>: Original (uncropped and unedited) images used for Figures 1 to 4.</p> <p><strong>Supplementary File 3:</strong> <em>P. acuta</em> nuclei and <em>Symbiodinium</em> count on a Thoma cell counting chamber done over three different nuclei extractions. For each extraction, two counts were performed. P. acuta nuclei were stained with Hoechst 33342 and display a blue fluorescence at 350 nm. Symbiodinium are not damaged by our extraction method and are not permeable to Hoechst. They display a red fluorescence because of their chlorophyl content. Observations were done on a Leica DMLB with objective PL Fluotar 40x and 100x. A text version of the data in the Excel file below.</p> <p>Extraction #1 replicate 1: 102 <em>P. acuta</em> nuclei (Blue) ; 2 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 112 <em>P. acuta</em> nuclei (Blue) ; 2 <em>Symbiodinium</em> (Red)</p> <p>Extraction #1 replicate 1: 42 <em>P. acuta </em>nuclei (Blue) ; 0 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 55 <em>P. acuta </em>nuclei (Blue) ; 1 <em>Symbiodinium</em> (Red)</p> <p>Extraction #1 replicate 1: 215 <em>P. acuta </em>nuclei (Blue) ; 3 <em>Symbiodinium</em> (Red)<br> Extraction #1 replicate 2: 257 <em>P. acuta</em> nuclei (Blue) ; 5 <em>Symbiodinium</em> (Red)</p> <p>Made at IHPE.</p>
Short-term Monitoring of Coral Reef Marine Protected Areas (MPAs) in the Municipality of Liloan, Central Visayas, Philippines
<p>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.</p> <p>In this version, occurrence.csv was revised as described below:</p> <ul> <li>taxonID for <em>Abudefduf vaigiensis</em> (Quoy & Gaimard, 1825) and <em>Hemiaulus</em> P.A.C. Heiberg, 1863 were corrected.</li> <li>Author names with corrupted characters/symbols were corrected. </li> </ul>
Brilliantia kiribatiensis, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean
<p>Data associated with the study "<em>Brilliantia kiribatiensis</em>, a new genus and species of Cladophorales (Chlorophyta) from the remote coral reefs of the Southern Line Islands, Pacific Ocean".</p> <p><strong>ITS.fasta, ITS_bmge.fasta, LSU.fasta, LSU_bmge.fasta, SSU.fasta, SSU_bmge.fasta: </strong>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.</p> <p><strong>concatenated_SSU_ITS_LSU.fasta</strong>: concatenated alignment with following partitions: SSU: 1-1797, ITS1+5.8S+ITS2: 1798-3335, LSU: 3336-3926.</p> <p><strong>Table_S1_sequence_sources.xls: </strong>GenBank accessions, sample isolate codes and sites of collection for sequences included in the concatenated phylogenetic data set.</p> <p><strong>Table S2. </strong>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.</p> <p><strong>Table SX.</strong> Morphological measurements of <em>Brilliantia kiribatiensis</em>.</p>
Raw data: Local-scale feedbacks influencing cold-water coral growth and subsequent reef formation
<p>Spreadsheets with the raw data of ADV-measured current velocity, coral growth derived from buoyant weight measurements and stress-related protein activities and concentrations.</p>
DATASET From the Reef to the Ocean: Revealing the Acoustic Range of the Biophony of a Coral Reef (Moorea Island, French Polynesia)
<p>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.</p>
Master Coral database used in USVI SCTLD Transmission Experiment Gene Expression Analysis
<p>The Master Coral Database fasta file is comprised of previously published genome-derived predicted gene models and transcriptomes spanning a wide diversity of coral families. Transcriptomes are from Davies et al., 2016 (doi: 10.3389/fmars.2016.00112), Kirk et al., 2018 (DOI: 10.1111/mec.14934); Moya et al., 2012 (doi: 10.1111/j.1365-294X.2012.05554.x); van de Water et al., 2018 (DOI: 10.1111/mec.14489).</p>
From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals
<p>With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus <em>Pocillopora</em>, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve <em>Pocillopora</em> phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine <em>Pocillopora</em> species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus <em>Pocillopora</em>. These results give new insights into the usefulness of multiple criteria for resolving <em>Pocillopora</em>, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.</p> <p> </p> <p>This deposit contains the data related to Oury N, Noël C, Mona S, Aurelle D, Magalon H (2023) From genomics to integrative species delimitation? The case study of the Indo-Pacific <em>Pocillopora </em>corals. Mol Phylogenet Evol 107803. doi:10.1016/j.ympev.2023.107803</p> <p>See 0_README.txt for more content details.</p>
ScienceDex guides
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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.