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1,636 results for “marine species”
2-Dimensional habitat files for 47 representative marine species
<p><strong>2D marine species habitats in NetCDF format on 0.5*0.5 degree global regular grid.</strong></p> <p>Based on Close et al. (2006) and converted from .CSV format. </p> <p>Filename is in format 'presence_speciesnumber.nc' where species numbers are listed in the README.txt file (identifier for each species). The README.txt file further contains each species' species_group which is the assigned depth group for each species (1=0-200m epipelagic, 2=200-1000m mesopelagic, 3=sea floor demersal) and species_name which is the Latin name of each species with underscore in between.</p> <p>The species occurs where the variable 'presence' equals 1 (in the accompanying paper we assume this to be the 1995-2014 climatological mean distribution).</p> <p>In the NetCDF files, the variable 'presence' has as an attribute 'species' which contains the Latin species name without underscore.</p>
Smartbay Marine Species Object Detection Training dataset
<h1>Training dataset</h1> <p>The SmartBay Observatory in Galway Bay is an important contribution by Ireland to the growing global network of real-time data capture systems deployed within the ocean – technology giving us new insights into the ocean which we have not had before.</p> <p>The observatory was installed on the seafloor 1.5km off the coast of Spiddal, County Galway, Ireland . The observatory uses cameras, probes and sensors to permit continuous and remote live underwater monitoring. This observatory equipment allows ocean researchers unique real-time access to monitor ongoing changes in the marine environment. Data relating to the marine environment at the site is transferred in real-time from the SmartBay Observatory through a fibre optic telecommunications cable to the Marine Institute headquarters and onwards onto the internet. The data includes a live video stream, the depth of the observatory node, the sea temperature and salinity, and estimates of the chlorophyll and turbidity levels in the water which give an indication of the volume of phytoplankton and other particles, such as sediment, in the water.</p> <p>The Smartbay Marine Species Object Detection training Dataset is an initial Bounding Box Annotated image dataset used in attempting to Train a YOLOv8 Object Detection Model to classify the Marine Fauna observed in the Smartbay Observatory Video footage using species names.</p> <p>The imagery used in this training dataset consists of image frame captures from the <a href="https://smartbay.marine.ie">Smartbay</a> video Archive files, CC-BY imagery from the <a href="https://www.minka-sdg.org">www.minka-sdg.org</a> website and images taken by Eva Cullen in the "<a href="https://nationalaquarium.ie/">Galway Atlantaquaria</a>" Aquarium in Galway, Ireland.</p> <p>The imagery were annotated using CVAT, collated on <a href="https://www.roboflow.com/">Roboflow</a> and exported in YOLOv8 training dataset format. </p>
ZooBase: A global synthesis of marine zooplankton species occurrences.
<p><em><strong>Description of the methods used to implement the present ZooBase dataset (extarct from Section A.2 from the Methods of Benedetti et al., 2021).</strong></em></p> <p>A new dataset of global zooplankton species occurrences was compiled in a comparable fashion to that put together for phytoplankton (Righetti et al., 2020). Prior to retrieving the occurrence data online, we first identified the phyla (Order/Class/Family) that comprise the bulk of extant oceanic zooplankton communities: Copelata (i.e. appendicularians), Ctenophora, Cubozoa (i.e. box jellyfish), Euphausiidae (i.e. krill), Foraminifera, Gymnosomata (i.e. sea angels, pteropods), Hydrozoa (i.e. jellyfish), Hyperiidea (i.e. amphipods), Myodocopina (i.e. ostracods), Mysidae (i.e. small pelagic shrimps resembling krill), Neocopepoda, Podonidae and <em>Penilia</em> <em>avirostris</em> (i.e. cladocerans), Sagittoidea (i.e. chaetognaths), Scyphozoa (i.e. jellyfish), Thaliacea (i.e. salps, doliolids and pyrosomes), Thecosomata (i.e. pteropods), and four families of pelagic Polychaeta (i.e. worms) that are often found in the zooplankton and whose species are known to display holoplanktonic lifecycles (Tomopteridae, Alciopidae, Lopadorrhynchidae, Typhloscolecidae). The presence data associated with species belonging to these groups were retrieved from OBIS and GBIF between the 12/04/2018 and the 18/04/2018 using online queries via the R packages RPostgreSQL, robis and rgbif. Since the Neocopepoda infra-class comprise several thousands of benthic and parasitic taxa (https://copepodes.obs-banyuls.fr/en/), a preliminary selection of the non-parasitic planktonic species had to be carried out prior to the online downloading using the species list of Razouls et al. (https://copepodes.obs-banyuls.fr/en/) as a reference. The spatial distributions of the groups cited above were first inspected using GBIF’s and OBIS’s online mapping tools to evaluate the potential number of overlapping observations between the two databases. As a result of their relatively low contributions to total observations/diversity, and very high overlap between databases, the occurrences of Cladocera and Polychaeta were retrieved from OBIS only (which usually harbours more occurrences). On top of the data collected from OBIS and GBIF, the copepod occurrences from Cornils et al. (2018) and the pteropod occurrences from the MAREDAT initiative (Buitenhuis et al., 2013) were added to the dataset. We discarded records that: (i) presented at least one missing spatial coordinate, (ii) were associated with an incomplete sampling date (d/m/y), (iii) were associated with a year of collection older than 1800, (iv) were not associated with any sampling depth, (v) were not identified down to the species level. Occurrences associated with grid cells shallower than 10m were removed (bathymetry data from ETOPOv1 at a 15min resolution, downloaded using the 'marmap' R package). Finally, every species name was then carefully examined and compared to the taxonomic reference list of the World Register of Marine Species (WoRMS; <a href="http://www.marinespecies.org">http://www.marinespecies.org</a>) for all taxa. The AphiaID and the Status were retreived from WoRMS based on the ScientificName. To remove the duplicate occurrences due to the highly overlapping source archives (GBIF and OBIS), a unique occurrenceID was given to each record based on rounded spatial coordinates (closest 0.1°x0.1°), rounded depth layer (10m depth layers), month and year of the occurrence and the acccpted species name (e.g., AphiaID).</p> <p><strong>This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 862923. This output reflects only the author’s view, and the European Union cannot be held responsible for any use that may be made of the information contained therein.</strong></p>
Data for Marine Ecological Niche Models, for 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100: Global-scale Environmental parameters at 0.1° and 0.5° resolutions, Presence and Absence Records of 1508 European-seas Species
<p>Data for Ecological Niche Models: Global-scale Environmental parameters at 0.1° and 0.5° resolutions, Presence and Absence Records of 1508 European-seas Species.</p>
Ecological Niche Models, in 2019 and across RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, of 1508 European Marine Species, developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Native ecological niche models of 1508 European species (894 fish and 614 non fish) developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines, for 2019 and under RCP 2.6, 4.5, and 8.5 scenarios in 2050 and 2100, at 0.5° spatial resolution.</p>
Biodiversity Index, in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European Marine Species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution
<p>Biodiversity Index in 2019 and across RCP 4.5, and 8.5 scenarios in 2050 and 2100 of 1508 European marine species based on ensemble Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, Support Vector Machines, and AquaMaps at 0.5° Resolution. The Index counts the number of species (among the 1508) potentially present in each 0.5° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
Ecological Niche Models of 96 European Marine Species, for 2019, developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines at 0.1° Resolution
<p>Native ecological niche models of 96 European marine species of particular commercial and conservation interest developed with AquaMaps, Artificial Neural Networks, Maximum Entropy, and Support Vector Machines, for 2019 at 0.1° spatial resolution.</p>
Ensemble Ecological Niche Models and Biodiversity Index for 2019 of 96 European Marine Species based on Ecological Niche Models developed with Artificial Neural Networks, Maximum Entropy, AquaMaps, and Support Vector Machines at 0.1° Resolution
<p>Ensemble Ecological Niche Models for 2019 of 96 European marine species of particular commercial and conservation interest, based on Ecological Niche Models developed with (i) Artificial Neural Networks, (ii) Maximum Entropy, (iii) Support Vector Machines, and (iv) AquaMaps at 0.1° Resolution. The data report, for each 0.1° cell, how many models (from 0 to 4) overcome a model-specific decision threshold to assess species presence in the cell. A Biodiversity Index is also provided as the count of the number of species (among the 96) potentially present in each 0.1° cell according to the ensemble models. For each ensemble model, a threshold of at least 3 models agreeing on species presence in the cell was used to indicate species presence.</p>
Height and density data for marine animal forest forming species
<p>Data file (.csv) of values of height and density for marine animal forest (MAF) forming species collected from the literature. Fields are for discrete observations:</p> <table> <tbody> <tr> <td>Species</td> <td>Species name</td> </tr> <tr> <td>Santavy</td> <td> <p>Morphology class using categories in </p> <p><span>Santavy DL, Lee A. Courtney, William S. Fisher, Robert L. Quarles, Stephen J. Jordan (2013) Estimating surface area of sponges and gorgonians as indicators of habitat availability on Caribbean coral reefs. Hydrobiologia 707:1-16. <span>https://doi.org/10.1007/s10750-012-1359-7</span><br></span></p> </td> </tr> <tr> <td>Height</td> <td>Mean colony height (cm)</td> </tr> <tr> <td>Density</td> <td>Mean colony density m-2</td> </tr> <tr> <td>Btemp</td> <td>Average bottom temperature for species based on OBIS records (K)</td> </tr> <tr> <td>Depth</td> <td>Average depth for species based on OBIS records (m)</td> </tr> <tr> <td>Phylum</td> <td>Taxonomy</td> </tr> <tr> <td>Class</td> <td>Taxonomy</td> </tr> <tr> <td>Order</td> <td>Taxonomy</td> </tr> <tr> <td>Family</td> <td>Taxonomy</td> </tr> <tr> <td>Genus</td> <td>Taxonomy</td> </tr> <tr> <td>Source</td> <td>Publication source for data</td> </tr> <tr> <td>Title</td> <td>Publication title</td> </tr> <tr> <td>DOI/link</td> <td>DOI for source data</td> </tr> </tbody> </table>
Supplemental material for the manuscript "Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species".
<p><strong>Supplementary material for the manuscript “Extreme genome scrambling in marine planktonic <em>Oikopleura dioica</em> cryptic species”.<br></strong></p> <p><strong><em>BreakpointsData.tar.xz contains:</em></strong></p> <ul> <li>Pairwise genome alignment files for <em>Oikopleura</em>, <em>Ciona</em>, <em>Caenorhabditis</em>, insects and muntjaks in GFF format in `inst/extdata/`.</li> <li>dN / dS computation results in `inst/extdata/dNdS/`.</li> <li>Annotations of gene models and repeat elements in GFF format in `inst/extdata/Annotations/`.</li> <li>OrthoGroups in `inst/extdata/OrthoFinder/`, where N19 represents the _O. dioica_ clade,</li> <li>N3 the tunicates and N20 the _Ciona_ clade.</li> <li>`BreakpointsData_3.11.0.tar.gz`, a R package installing the above files in the R environments where we ran our computations.</li> <li>The files needed to build the `BreakpointsData` package.</li> </ul> <p><em><strong>Oidioi_pairwise_v3.tar.gz contains:</strong></em></p> <ul> <li>The pairwise alignment files between genomes, in MAF format.</li> <li>A copy of the Nextflow pipeline used to generate them.</li> </ul> <p><em><strong>oist-assembler.tar.gz contains:</strong></em></p> <ul> <li>A Singularity image and its definition file for flye version 2.8.3-b1763` Flye-flye.2.8.3-b1763.sif` and `Flye-flye.def`.</li> <li>A copy of the Nextflow pipeline used to assemble the Bar2_p4 genome in `oist-assembler-Bar2_p4`.</li> <li>A copy of the Nextflow pipeline used to assemble the other genome in `oist-assembler-other_genomes`.</li> </ul> <p><em>Please note that these files are provided for reproducibility only and probably can not be used easily for other purposes.</em></p> <p><em><strong>Oidioi_genomes.tar.gz contains:</strong></em></p> <ul> <li>For each genome, one file (`<genome>.fa`) containing the whole genome sequence and one directory (`<genome>`) containing each chromosome, scaffold or contig of the genome as a separate file.</li> <li>For each genome, one R package, its source directory, and the vignette to create it, providing the genome information as a `BSgenome` object.</li> </ul> <p><em><strong>OrthoFinderRun.tar.xz contains:</strong></em></p> <ul> <li>A full copy of the OrthoFinder2 run that we used to compute hierarchical orthogroups.</li> </ul> <p><em><strong>Supplemental_Code.tar.gz contains:</strong></em></p> <ul> <li>A copy of <https://github.com/oist/LuscombeU_OikScrambling>, where the `.git` and `doc` directories were removed to save space.</li> </ul> <p><em><strong>AugustusAnnotation.tar.gz (added July 26th 2024) contains:</strong></em></p> <ul> <li>AUGUSTUS runs to produce the annotations that were input to OrthoFinder2. We provide them for reproducibility, with no guarantee that they are suitable for other purposes. The annotations used in the manuscript are AOM-5-5f.sm.OSKA-CDS, Bar2_p4_Flye.sm, Bsty_SCLE01.1.sm.abi.cionamodel, Fbor_SDII01.1.sm.abi, KUM-M3-7f.sm.OKI-CDS, Mery_SCLF01.1.sm.abi.cionamodel, Oalb_SCLG01.1.sm.abi.cionamodel, OKI2018_I69_annotv2.sm, Olon_SCLD01.1.sm.abi, OSKA2016v1.9.sm and Ovan_SCLH01.1.sm.abi.cionamodel.</li> </ul>
Distribution of functionally distinct native and non-indigenous species within marine urban habitats
<p>This data file (.xls) is composed of 5 sheets:</p> <ol> <li>The “Taxon labels”: Taxon code, full name, authority and status/type (Abiotic, Unassigned, Native, Cryptogenic, Non-Indigenous Species)</li> <li>The “Trait labels”: Trait modality and labels and correspondences.</li> <li>The “Taxon-by-Trait matrix”: Fuzzy coded scores for each trait modality and taxon</li> <li>The “Taxon-by-sample matrix”: Abundance data of retained taxa in samples</li> <li>The “Sample labels and description”: Site and experimental factors (Habitat, Age, Experimental Unit, Replicate, nested within site) corresponding to each sample.</li> </ol> <p>Sheets 4 and 5 are extracted from a published dataset, which cannot be shared at this stage of revision without revealing the name of several of the manuscript authors. This is done in respect with the journal guidelines about data storage.</p>
Distribution of functionally distinct native and non-indigenous species within marine urban habitats
<p>This data file (.xls) is composed of 5 sheets:</p> <ol> <li>The “Taxon labels”: Taxon code, full name, authority and status/type (Abiotic, Unassigned, Native, Cryptogenic, Non-Indigenous Species)</li> <li>The “Trait labels”: Trait modality and labels and correspondences.</li> <li>The “Taxon-by-Trait matrix”: Fuzzy coded scores for each trait modality and taxon</li> <li>The “Taxon-by-sample matrix”: Abundance data of retained taxa in samples</li> <li>The “Sample labels and description”: Site and experimental factors (Habitat, Age, Experimental Unit, Replicate, nested within site) corresponding to each sample.</li> </ol> <p>Sheets 4 and 5 are extracted from a published dataset, which cannot be shared at this stage of revision without revealing the name of several of the manuscript authors. This is done in respect with the journal guidelines about data storage.</p>
Figs 40-42. Macvicaria kingscotensis n in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 40-42. Macvicaria kingscotensis n. sp. ex Haletta semifasciata. 40. Whole-mount ventral view. 41. Terminal genitalia. 42. Dorsal distribution of vitelline follicles. Scale bars: 40, 42, 250 µm; 41, 100 µm.
Figs 1-3. Macvicaria shotteri n in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 1-3. Macvicaria shotteri n. sp. ex Apogon fasciatus. 1. Whole-mount ventral view. 2. Terminal genitalia. 3. Dorsal distribution of vitelline follicles. Scale bars: 1, 3, 250 µm; 2, 100 µm.
Figs 30-32 in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 30-32. Macvicaria heronensis Bray & Cribb, 1989 ex Trachinotus coppingeri. 30. Whole-mount ventral view. 31. Terminal genitalia. 32. Dorsal distribution of vitelline follicles. Scale bars: 30, 32, 250 µm; 31, 100 µm.
Figs 7-9. Macvicaria mekistomorphe n in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 7-9. Macvicaria mekistomorphe n. sp. ex Sillago maculata. 7. Whole-mount ventral view. 8. Terminal genitalia. 9. Dorsal distribution of vitelline follicles. Scale bars: 7, 9, 250 µm; 8, 100 µm.
Figs 19-20. Macvicaria flexuomeatus n in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 19-20. Macvicaria flexuomeatus n. sp. ex Cheilodactylus rubrolabiatus. 19. Whole-mount ventral view. 20. Dorsal distribution of vitelline follicles. Scale bars: 19, 20, 250 µm.
Figs 4-6. Macvicaria shotteri n in Eight new species of Macvicaria Gibson and Bray, 1982 (Digenea: Opecoelidae) from temperate marine fishes of Australia
Figs 4-6. Macvicaria shotteri n. sp. ex Sillaginodes punctatus. 4. Whole-mount ventral view. 5. Terminal genitalia. 6. Dorsal distribution of vitelline follicles. Scale bars: 4, 6, 250 µm; 5, 100 µm.
Figure 25 in New genera and species of the marine isopod family Serolidae (Crustacea, Sphaeromatidea) from the southwestern Pacific
Figure 25. Thysanoserolis orbicula sp. n. Holotype. A dorsal view B lateral view C head, frons and antennae, ventral view D head, anterior margin E pleon and pleotelson, ventral view F coxae 2–5, ventral G right mandible H left mandible I maxilliped Į maxilliped palp.
Figure 22 in New genera and species of the marine isopod family Serolidae (Crustacea, Sphaeromatidea) from the southwestern Pacific
Figure 22. Myopiarolis systir sp. n. Paratype 3 11.4 mm, Is.6013, except H, holotype. A–D pereopods 1 2, 6 and 7 respectively a detail of pereopod 1 propodal palm setae E pereopod 2 carpus and propodus F pereopod 6 carpus and propodus.
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