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194 results for “marine habitat”
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>
Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats - Datasets and supporting files
<p>The supporting datasets, scripts, and supplementary information for the manuscript, "Habitat Protection Indexes - new monitoring measures for the conservation of threatened marine habitats," are available within this repository.</p> <p>We conduct an analysis on the coverage of protected areas that cover six threatened marine and coastal and developed two indexes, the Local Proportion of Habitat Protected Index and the Global Proportion of Habitat Protected Index, describing the protection of these habitats locally and globally. The habitats considered are the following: cold corals, warm water corals, knolls and seamounts, mangroves, saltmarshes, and seagrasses.</p> <p>The index scores of each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes_average.csv</em></p> <p>The habitat specific index scores for each jurisdiction are made available for download in the dataset: <em>habitat_protection_indexes.csv. </em></p> <p>Column name descriptions are available in the text file: <em>Column_name_descriptions_20220301</em></p> <p>The scripts used to run the workflow to calculate the indexes, create figures, and calculate statistics for the manuscript are also included. The script <em>01_Workflow sources</em> the first 9 scripts in the <em>scripts</em> folder to calculate the indexes which relies on the functions script within the functions folder. The rest of the scripts in the folder create the figures and calculate the statistics for the manuscript.</p> <p>A readme pdf file is included here to ease with reproducing the workflow, but we strongly suggest to please visit our github (<a href="https://github.com/jkumagai96/Marine_Habitat_protection">https://github.com/jkumagai96/Marine_Habitat_protection</a>) to reproduce the entire calculation where we provide detailed information on how to run the workflow and package management.</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>
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>
Code and data for "Global warming generates predictable extinctions of warm- and cold-water marine benthic invertebrates via thermal habitat loss"
<pre>This repository contains the following information: Datasets S1 to S4 can all be loaded, manipulated, and analysed in R using script provided in Data S5 to obtain the results of the paper, Reddin et al. 2022, "Global warming generates predictable extinctions of warm and cold-water marine benthic invertebrates via thermal habitat loss". Data S1. (separate file) The original downloaded PaleoDB dataset. Data S2. (separate file) The pre-prepared dataset of occurrences. Data S3. (separate file) The finished environmental dataset. Data S4. (separate file) Additional environmental dataset. Data S5. (separate file) The R-code for the main analysis. Data S6. (compressed directory) Output data and code from the simulations. Table S7 (separate file). List of data source publications for PaleoDB data used in our study. Listed are the data source author list (ref_author), year (ref_pubyr), and reference number as appears in the PaleoDB (reference_no). </pre>
Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
<p>Accurate knowledge on spatiotemporal distributions of marine species and their association with surrounding habitats is crucial to inform adaptive management actions responding to coastal degradation across the globe. Here, we investigate the potential use of environmental DNA (eDNA) to detect species-habitat associations in a patchy coastal area of the Baltic Sea. We directly compare species-specific qPCR analysis of eDNA with baited remote underwater video systems (BRUVS), two non-invasive methods widely used to monitor marine habitats. Four focal species (cod Gadus morhua, flounder Platichthys flesus, plaice Pleuronectes platessa and goldsinny wrasse Ctenolabrus rupestris) were selected based on contrasting habitat associations (reef- vs. sand-associated species), as well as differential levels of mobility and residency, to investigate whether these factors affected the detection of species-habitat associations from eDNA. To this end, a species-specific qPCR assay for goldsinny wrasse is developed and made available herein. In addition, potential correlations between eDNA signals and abundance counts (MaxN) from videos were assessed. Results from Bayesian multi-level models revealed strong evidence for a sand association for sedentary flounder (98% posterior probability) and a reef association for highly resident wrasse (99% posterior probability) using eDNA, in agreement with BRUVS. However, contrary to BRUVS, eDNA sampling did not detect habitat associations for cod or plaice. We found a positive correlation between eDNA detection and MaxN for wrasse (posterior probability 95%), but not for the remaining species and explanatory power of all relationships was generally limited. Our results indicate that eDNA sampling can detect species-habitat associations on a fine spatial scale, yet this ability likely depends on the mobility and residency of the target organism, with associations for sedentary or resident species most likely to be detected. Combined sampling with conventional non-invasive methods is advised to improve detection of habitat associations for mobile and transient species, or for species with low eDNA concentrations. </p>
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
<p>Climate change is impacting ecosystems worldwide, and the Mediterranean Sea is no exception. Extreme climatic events, such as marine heat waves (MHWs), are increasing in frequency, extent, and intensity during the last decades, which has been associated with an increase in mass mortality events for multiple species. Coralligenous assemblages, where the octocoral <em>Paramuricea clavata</em> lives, are strongly affected by MHWs. The Medes Islands Marine Reserve (NW Mediterranean) was considered a climate refugia for <em>P. clavata</em>, as their populations were showing some resilience to these changing conditions. In this study, we assessed the impacts of the MHWs that occurred between 2016 and 2022 in seven shallow populations of the octocoral <em>P. clavata</em> from a Mediterranean Marine Protected Area. The years that the mortality rates increased significantly were associated with the ones with strong MHWs, 2022 being the one with higher mortalities. In 2022, with 50 MHW days, the proportion of total affected colonies was almost 70%, with a proportion of the injured surface of almost 40%, reaching levels never attained in our study site since the monitoring was started. We also found spatial variability between the monitored populations. Whereas few of them showed low levels of mortality, others lost around 75% of their biomass. The significant impacts documented here raise concerns about the future of shallow <em>P. clavata</em> populations across the Mediterranean, suggesting that the resilience of this species may not be maintained to sustain these populations face the ongoing warming trends.</p>
FIGURE 8 in The Sea Slug Phanerophthalmus luteus (Gastropoda: Opisthobranchia) and its Habitat and Ecology at the Marine Jellyfish Lake (Ongeim'l Tketau), Palau, Western Pacific Ocean
FIGURE 8. Central and Western Pacific showing the distribution of Phanerophthalmus luteus (black stars) and the location of Jellyfish Lake, Palau (large gray star). Modified from distribution map for P. luteus in Austin, Gosliner, and Malaquias (2018, fig. 23).
FIGURE 5 in The Sea Slug Phanerophthalmus luteus (Gastropoda: Opisthobranchia) and its Habitat and Ecology at the Marine Jellyfish Lake (Ongeim'l Tketau), Palau, Western Pacific Ocean
FIGURE 5. Hydrography of Jellyfish Lake. The water column is divided into an oxic and an anoxic zone by a bacterial plate that creates a chemo- and thermocline. The bacteria absorb all the light and digest most of the vegetation (except larger branches). No foraminifera or animals are known to live below the bacterial plate due to the absence of oxygen in the water column. Phanerophthalmus luteus is restricted to the upper 3 to 10 m in the oxygenated part of the water column; they are most abundant between 4.5 and 7.6 m. Figure modified from Venkateswaran et al. (1993) by adding the depth distribution of P. luteus.
FIGURE 4 in The Sea Slug Phanerophthalmus luteus (Gastropoda: Opisthobranchia) and its Habitat and Ecology at the Marine Jellyfish Lake (Ongeim'l Tketau), Palau, Western Pacific Ocean
FIGURE 4. Bathymetry of Jellyfish Lake, Mecherchar Island. The gray line with arrows indicates the area in the lake of our marine survey to 10 m deep for sea slugs along the north and east sides of the lake. Black circles indicate the transect and collecting stations for foraminifera used to estimate the depth distribution of Phanerophthalmus luteus. Map and transect from Lipps and Langer 1999.
FIGURE 3 in The Sea Slug Phanerophthalmus luteus (Gastropoda: Opisthobranchia) and its Habitat and Ecology at the Marine Jellyfish Lake (Ongeim'l Tketau), Palau, Western Pacific Ocean
FIGURE 3. Vegetation of Jellyfish Lake, Mecherchar Island. A. The lake, slightly less than 400 m long, is in a hole at least 230 m deep (150 to 200 m from the top of the hole to the Lake's surface and 30 m to the bottom of the lake) in the Miocene limestone. North is at the top of the image. B. Dense terrestrial vegetation, including mangroves at the lake edges, hangs over the lake. The surrounding vegetation contributes organic debris to the lake. C. Bottom of the lake from 0 to 13 m is covered with plant debris and algal growth. Photograph is at 2 m deep looking down slope. D. One of many logs that have fallen into the lake and are now inhabited by a wide variety of algae and animals including P. luteus. View is down the log from a depth of about 0.5 m. Credits: A. Aerial photograph courtesy of Dr. Pat Colin. B.-D. Photographs by Jere H. Lipps, 2013.
FIGURE 7 in The Sea Slug Phanerophthalmus luteus (Gastropoda: Opisthobranchia) and its Habitat and Ecology at the Marine Jellyfish Lake (Ongeim'l Tketau), Palau, Western Pacific Ocean
FIGURE 7. Egg masses (more or less spherical to oblong white objects) of Phanerophthalmus luteus attached to filamentous and other algae on a slope in Jellyfish Lake. Photograph taken November 16, 2009, courtesy of Lori J. Bell.
Fig. 1 in Morphological reports of four ciliates (Ciliophora) from coastal marine and brackish water habitats in Korea
Fig. 1. Photomicrographs of four ciliates on the basis of live observation (A, C, E, H) and after protargol impregnation (B, D, F, G, I). A, B, Gruberia calkinsi, left side view of a living specimen (A) and right side view of a protargolimpregnated specimen (B); C, D, Dysteria crassipes, left side views of living (C) and protargolimpregnated (D) specimens; EG, Zosterodasys agamaliev, ventral view of a living specimen (E), and ventral (F) and dorsal (G) views of potargolimpregnated specimens; H, I, Pleuronema salmastra, ventral views of living (H) and protargolimpregnated (I) specimens. Scale bars: A = 500 μm, B = 300 μm, C, D = 30 μm, E, H = 50 μm.
Fig. 7. Laophontella horrida dentata Mielke, 1992 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 7. Laophontella horrida dentata Mielke, 1992, SEM photographs, adult male, lateral view; A, anterior part of cephalothorax and first segment of antennula; B, apical setae on first leg endopod; C, sixth leg and last two exopodal segments of fourth swimming leg; D, caudal ramus; E, detail of armature and ornamentation of proximal part of caudal ramus; F, detail of principal caudal seta.
Fig. 4. Laophontodes norvegicus George, 2018, male 1 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 4. Laophontodes norvegicus George, 2018, male 1, ventral view; A, CLM photograph; B-H, SEM photographs; A, habitus; B, habitus; C, antennula; D, detail of armature and ornamentation of proximal part of antennula; E, detail of armature and ornamentation of central part of antennula; F, detail of armature and ornamentation of distal part of antennula; G, labrum and mouth appendages; H, first swimming leg.
Fig. 5. Laophontodes norvegicus George, 2018, male 1 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 5. Laophontodes norvegicus George, 2018, male 1, ventral view, SEM photographs; A, distal part of maxilliped and basis of first swimming leg; B, third exopodal segment of second swimming leg; C, tubular pore on second exopodal segment of second swimming leg; D, distal frill of fourth urosomite; E, caudal ramus; F, detail of ornamentation of proximal part of caudal ramus; G, lateral setae on caudal ramus; H, distal part of caudal ramus.
Fig. 3. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 3. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989; A-D, SEM photographs; E-H, CLM photographs; A, B, male 1, lateral view; C, D, male 2, ventral view; E-H, female 4, dissected and mounted on microscope slides, anterior view: A, habitus; B, anal somite and caudal rami; C, habitus; D, distal part of antennula; E, first swimming leg; F, second swimming leg; G, third swimming leg; H, fourth swimming leg.
Fig. 2. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 2. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989, SEM photographs; A-C, female 2, dorsal view; D-G, female 3, ventral view; H, male 1, lateral view: A, habitus; B, anterior part of cephalothorax with rostrum and first segment of antennula; C, anal somite and caudal rami; D, habitus; E, anal somite and caudal rami; F, endopod and first two exopodal segment of second swimming leg; G, distal part of third exopodal segment of fourth swimming leg; H, distal part of antennula.
Fig. 1. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989 in Three new harpacticoid copepods for Korea from marine interstitial habitats
Fig. 1. Phyllopodopsyllus thiebaudi santacruzensis Mielke, 1989, SEM photographs, female 1, lateral view: A, habitus; B, cephalothoracic shield; C, tergites of free prosomites; D, genital somite with proximal part of fifth leg; E, distal part of fifth leg; F, anal somite and caudal ramus; G, second endopodal segment of first swimming leg; H, exopod of antenna.
Fig. 2 in Use Of Intertidal Mangrove And Sea Wall Habitats By Coral Reef Fishes In The Wakatobi Marine Park, Indonesia
Fig. 2. Number of species seen at the two intertidal sites, and the number showing low (<33%), medium (33-67%) and high (>67%) site-fidelity
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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.