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1,478 results for “coral reefs”
Data from: Warming has a greater effect than elevated CO2 on predator–prey interactions in coral reef fish
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Environmental DNA in a global biodiversity hotspot: Lessons from coral reef fish diversity across the Indonesian archipelago
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Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon)
GEO Series GSE124093. Haemulon flavolineatum; Haemulon macrostomum; Haemulon carbonarium. 36 samples. Type: Expression profiling by high throughput sequencing.
Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals (smRNA)
GEO Series GSE47373. Symbiodinium sp. A1. 9 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis
GEO Series GSE7499. Pomacentrus moluccensis; Danio rerio. 59 samples. Type: Expression profiling by array.
Integrating microRNA and mRNA expression profiling in Symbiodinium, the dinoflagellate symbiont of reef-building corals
GEO Series GSE47374. Symbiodinium sp. A1. 18 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Surviving climate change – the role of acclimatization in reef-building corals [16S]
GEO Series GSE124256. Acropora palmata. 36 samples. Type: Other.
Responses of urban reef corals during the 2016 mass bleaching event
<p>Datasets and R scripts</p> <p>60Taxa.csv : 60 species with 5 or more colonies over study duration, and documented in all monitoring periods<br> SGBleachAllSites.csv : Survey data of all coral species for all time points and locations, showing respective colour scores, live area and GMD of each colony<br> SGBleachChronogram.tre : Phylogenetic tree for 60 species extracted from Kitahara et al. (2016)<br> SGBleachCode.R : R script for analysing bleaching prevalence, susceptibility and resilience<br> SGBleachJun2016.csv : Bleaching prevalence of all sites in June 2016<br> SGBleachModel.csv : Bleaching Index and traits of the 60 species; analysed for susceptibility and resilience</p>
Data from: Strong effects of coral species on the diversity and structure of reef fish communities: a multi-scale analysis
While there is increasing evidence for habitat specialization in coral reef fishes, the extent to which different corals support different fish communities is not well understood. Here we quantitatively assess the relative importance of different coral species in structuring fish communities and evaluate whether sampling scale and coral colony size affect the perceived strength of fish-habitat relationships. Fish communities present on colonies of 8 coral species (Porites cylindrica, Echinopora horrida, Hydnophora rigida, Stylophora pistillata, Seriatopora hystrix, Acropora formosa, A. tenuis and A. millepora) were examined in the Lizard Island lagoon. Additionally, the differences in fish communities supported by 3 coral species (P. cylindrica, E. horrida, H. rigida) were investigated at 3 spatial scales of sampling (2x2 m, 1x1 m, 0.5x0.5 m). Substantial differences in fish communities were observed across the different coral species, with E. horrida and H. rigida supporting the most fish species and individuals. Coral species explained more of the variability in fish species richness (20.9-53.6%), than in fish abundance (0-15%). Most coral species supported distinctive fish communities, with dissimilarities ranging from 50 to 90%. For 3 focal coral species, a greater amount of total variation in fish species richness and fish abundance was evident at a larger scale of sampling. Together, these results indicate that the structure of reef fish communities is finely tuned to coral species. Loss of preferred coral species could have profound effects on reef fish biodiversity, more so than would be predicted on the basis of declining coral cover alone.
Data from: High-frequency sampling and piecewise models reshape dispersal kernels of a common reef coral
Models of dispersal potential are required to predict connectivity between populations of sessile organisms. However, to date, such models do not allow for time‐varying rates of acquisition and loss of competence to settle and metamorphose, and permit only a limited range of possible survivorship curves. We collect high‐resolution observations of coral larval survival and metamorphosis, and apply a piecewise modeling approach that incorporates a broad range of temporally‐varying rates of mortality and loss of competence. Our analysis identified marked changes in competence loss and mortality rates, whose timing implicates developmental failure and depletion of energy reserves. Asymmetric demographic rates suggest more intermediate‐range dispersal, less local retention, and less long‐distance dispersal than predicted by previously‐employed non‐piecewise models. Because vital rates are likely temporally asymmetric, at least for non‐feeding broadcast‐spawned larvae, piecewise analysis of demographic rates will likely yield more reliable predictions of dispersal potential.
Unusual enzymology and peptide natural products from novel Acidobacteriota spp. associated with reef-building corals
<h1>Unusual enzymology and peptide natural products from novel Acidobacteriota spp. associated with reef-building corals</h1> <p>Raw Data for characterisation of RiPP BGCs from Acidobacteriota:</p> <h2>Plasmids</h2> <p>Plasmid maps of constructs used for heterologous production of precursors and maturases in<em> E. coli</em> in .gb format.</p> <h2>Aci</h2> <p>.raw LC-MS files of proteolytic digests (GluC) of AciA1 and AciA2 produced with or without AciKC.</p> <h2>Tha</h2> <p>.raw LC-MS files of proteolytic digests (Try or AspN) of ThaA produced with or without ThaM and/or ThaO.<br>Subfolders include LC-MS files of 13C and 15N labelling data, derivatisation with IAA, RaneyNi, and Marfey's reagent, and point mutants.</p> <h2>The</h2> <p>.raw LC-MS files of proteolytic digests (AspN) of native TheA produced with or without TheO/ TheB/ TheM/ TheN, as well as LC-MS files of proteolytic digests (AspN or Try) of point mutants, truncations and cargo-fusions produced in the presence of TheO or without.<br>Additional subfolders include MS/MS data and plasmids as .gb files.</p> <h2>NMR</h2> <p>Raw data files for 1H (1), 1H-1H COSY (2), NOESY (3), HSQC (4), and HMBC (5) spectra of purified and modified tryptic fragment of ThaA.</p> <h2>MolecularNetworking</h2> <p>Output files generated from GNPS (one folder for the pellet network and one for the supernatant network).</p> <h2>CrudeExtracts</h2> <p>.raw LC-MS files of crude extracts from <em>S. corallicola</em> supernatant (SN) or pellet (P) cultured with and without coral-derived dissolved organic matter. Extracts from medium with or without DOM (but no <em>S. corallicola</em>) are labelled with "_neg".</p> <h2>RNAseq</h2> <p>R script and input files--including raw feature counts, plasmidsaurus feature annotations, antiSMASH feature annotations and DESeq2 results--used to analyse BGC transciption data from cultivating <em>S. corallicola</em> with and without coral-dervied dissolved organic matter.</p> <h2>CellCounts</h2> <p>Raw data files, metadata, and modified cell count data from cultivating <em>S. corallicola</em> with and without coral-dervied dissolved organic matter.</p>
Data for Cortese et al. (2024). Environmental change mediates plasticity in offspring traits through maternal effects in a coral reef fish. STOTEN
<p>Data used for producing figures and result of the publication <em><span>Cortese et al. (2024). </span><span>Environmental change mediates plasticity in offspring traits through maternal effects in a coral reef fish.</span></em><span> <em>STOTEN.</em></span></p> <p> </p>
Figure 7 from: Pyle RL, Greene BD, Kosaki RK (2016) Tosanoides obama, a new basslet (Perciformes, Percoidei, Serranidae) from deep coral reefs in the Northwestern Hawaiian Islands. ZooKeys 641: 165-181. https://doi.org/10.3897/zookeys.641.11500
Figure 7 - Tosanoides flavofasciatus, BPBM 40858, Palau Islands. Photo by R. L. Pyle
Data from 'The rise of dietary diversity in coral reef fishes'
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Abundance of benthic sessile fauna associated with ARMS from the research" Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México " using the point intersection method (400 points per plate on each side) with the CPCe v4.1 soft-ware (Coral Point Count with Excel extension v4.1)
<p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>This database contains information on the abundance of benthic sessile fauna associated with ARMS from the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México” using the point intersection method (400 points per plate on each side) with the CPCe v4.1 soft-ware (Coral Point Count with Excel extension v4.1) to analyze </p> <p>Krebs, C.J. Estimating Density: Quadrats Counts. In <em>Ecological Methodology</em>; Addison-Wesley Educational Publishers, Inc., 1999; p. 69 ISBN 0321021738</p> <p>Kohler, K.; Gill, S. Coral Point Count with Excel extensions (CPCe): A Visual Basic program for the determination of coral and substrate coverage using random point count methodology. <em>Comput. Geosci.</em> <strong>2006</strong>, <em>32</em>, 1259–1269</p> <div> <p><span lang="EN-US">was produced in collaboration with the Biodiversidad Marina de Yucatán project. </span><a href="https://www.bdmy.org.mx/carteles-publicaciones/" target="_blank" rel="noopener">https://www.bdmy.org.mx/,</a> Universidad Nacional Autonoma de México, Harte Research Institute for Gulf of Mexico Studies and Escuela Nacional de Estudios Superiores</p> </div>
Figure 1 from: Krapp T (2011) A new species of Leucothoid Amphipod, Anamixis bananarama, sp. n., from Shallow Coral Reefs in French Polynesia (Crustacea, Amphipoda, Leucothoidae). ZooKeys 92: 1-8. https://doi.org/10.3897/zookeys.92.1036
Figure 1 - Anamixis bananarama sp. n., holotype, anamorph male male "A", 2.34 mm.
Figure 2 from: Krapp T (2011) A new species of Leucothoid Amphipod, Anamixis bananarama, sp. n., from Shallow Coral Reefs in French Polynesia (Crustacea, Amphipoda, Leucothoidae). ZooKeys 92: 1-8. https://doi.org/10.3897/zookeys.92.1036
Figure 2 - Anamixis bananarama sp. n., paratype, leucomorph female "B", 2.10mm.
Figure 1 from: González-Muñoz R, Simões N, Tello-Musi J, Rodríguez E (2013) Sea anemones (Cnidaria, Anthozoa, Actiniaria) from coral reefs in the southern Gulf of Mexico. ZooKeys 341: 77-106. https://doi.org/10.3897/zookeys.341.5816
Figure 1 - Map of the Southern Gulf of Mexico, indicating the localities sampled in this study.
Figure 6 from: Thomas JD (2015) Leucothoe eltoni sp. n., a new species of commensal leucothoid amphipod from coral reefs in Raja Ampat, Indonesia (Crustacea, Amphipoda). ZooKeys 518: 51-66. https://doi.org/10.3897/zookeys.518.9340
Figure 6 - Leucothoe eltoni sp. n., male, whole body showing inflated gnathopod1. Photo J. Thomas.
Figure 5 from: Thomas JD (2015) Leucothoe eltoni sp. n., a new species of commensal leucothoid amphipod from coral reefs in Raja Ampat, Indonesia (Crustacea, Amphipoda). ZooKeys 518: 51-66. https://doi.org/10.3897/zookeys.518.9340
Figure 5 - Leucothoe eltoni sp. n., holotype ♂A, 8.10 mm; uropods 1-3; epimera, telson.
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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.