Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
88
datasets available to search
ShareScore release 0.9.0
Dataset results
88 results for “marine environment”
Fig. 4 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 4 | Associations between fishmass and collection location as measuredby and d distance from shore with gill microbial biomass. e Comparison of fish mass distancefrom shorewith fishgill microbialbiomassand alphadiversity. Subset and f distancefromshorewithalpha diversitymetrics (Chao1).g Comparison of fish of fish from EPO and Atlantic (n = 54) collected from ocean (excludes bay and mass and h distance from shore with alpha diversity metric: Faith's PD. estuary samples) and from the neritic zone (<200 m depth). a Correlation matrix c–h (Confidenceintervalsof 95% aredisplayedasdotted lines). habita- between sample metadata where values are rho and significance indicated by t_act_collection refers to the metadata column name from where this habitat clas- *p <0.05, **p <0.01, ***p <0.001, ****p <0.0001 (Spearmancorrelation). sification can be found…, SZsurf zone, RIT rocky intertidal, RST rocky subtidal, IS b Comparison of gill microbial biomass (log cells per gram) across habitat types inner shelf, KBRF kelp bed rocky reef, MDRF mid depth rocky reef, CP coastal from which the fish were collected. Distribution is in median and interquartile pelagic, P pelagic. Mass_g_log = log 10 (mass of the fish in grams), dis- range. Statistical differences determined using non-parametric testing tance_from_shore_m_log = log 10 (distance from nearest point on shore in meters Kruskal–Wallistest with 0.05 FDRBenjamini–Hochberg. c Comparison of fish mass from where the fish was caught).
Fig. 2 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 2 | Limit of detection, sample exclusion, and microbial biomassestimation for FMP101 dataset. a Application of KatharoSeq formula to calculate limit of detection of microbiota platesusing the Bacillus/Paracoccus mock community (1150 reads at 90%). b Limit of detection based on cell counts of Bacillus/ Paracoccus mock community (~16 cells into extraction at 90%). c Model fit of the log(sequencing read counts) of positive extraction controls vs. the log cell counts of those positive extraction controls (empirically determined using plate counts. The linear regression of the line is indicative of the quality of method to estimate microbial biomass from sequencing read counts. Con- fidenceintervalsof 95% aredisplayedas dottedlines. Thismethodissimilar to a qPCR curvewherethe log (Ct) would beequivalent to the log(read counts).This equation is then used to estimate the number of "microbial density" of the existing samples which is then further normalized by the volume of the DNA extraction,biomass of materialgoinginto theextraction and finallynormalized to at estimated microbial cells per gram of tissue. d Community analysis comparison and validation of compositionality of controls of twosets of mock community controls (section 1 = Bacillus/Paracoccus mock community; section 2 = zymo mock community). Putative contaminant g__Geobacillus identified (presentin 93% of negatives and higherrelative abundance ascompared to positives and samples). e Number of samples successful across the four body sites collected from the broad fish microbiota dataset. QC quality control, g__ refers to a genus of bacteria, HM mock homemade mock or human made mixture of bacteria to use as a control whereas zymo mock = mock microbial community created by a company "Zymo".
Fig. 1 in Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species
Fig. 1 | Samplingdesignof 116 speciesof marine fish. a Using ArcGIS todepictthe general area from which fish were sampled: black dots indicate the locations of the 101 unique species of marine fish sampled from the California Current Ecosystem in the Eastern Pacific Ocean primarily in the waters of San Diego CA. Red circles depict the locations of an additional 17 species of fish (15 unique species with 2 species duplicates) collected from the Western Atlantic primarily in the waters of New York. When multiple species of fish were caught in the same location, a single circle is used to indicate the location. b Fish were sampled across a gradient of depth and distances from shore. c Biometric measurements taken for nearly all fish include total length, fork length, mass, gape, and GI length. Various ratios from these lengths were also calculated. Microbiota samples from the gill were primarily whole tissue specimens from the entire left second gill arch or a section of the top middle and bottom of the entire filament. Skin mucus samples were taken by scraping using a razor blade. Midgut digesta material was collected from directly posterior of the stomach or if stomach was absent, the beginning of the GI tract. Hindgut digesta samples were taken from near the anus. Image from phylopic. MG midgut, HG hindgut, GI gastrointestinal tract, m meters.
Data from: How long does a brachiopod shell last on a seafloor? Modern mid-bathyal environments as taphonomic analogues of continental shelves prior to the Mesozoic Marine Revolution
<p class="MsoNormal">Carbonate skeletal remains are altered and disintegrate at yearly to decadal scales in present-day shallow-marine environments with intense bioerosion and dissolution. Present-day brachiopod death assemblages are invariably characterized by poor preservation on continental shelves, and abundant articulated shells of brachiopods with well-preserved brachidia are thus not expected to be preserved if not rapidly buried. However, such preservation is paradoxically observed in shallow-water Paleozoic and Mesozoic brachiopod assemblages. Here, we show that a bathyal death assemblage time-averaged to several millennia (Adriatic Sea) consists of sediment-filled articulated shells of <em>Gryphus</em> <em>vitreus</em> with complete brachidia. Postmortem age distributions indicate that disintegration half-lives exceed several centuries (~500-1,700 years). The high frequency of articulated but centuries-old shells (>50%) and the fitting of taphonomic models to postmortem ages indicate that disarticulation half-life is unusually long (~200 years). Rapid sediment filling of shells (1) inhibited disarticulation, loop fragmentation and colonization by coelobites and (2) induced precipitation of ferromanganese oxides at redox fronts within shells. Sediment-filled articulated shells, however, still resided at the sediment-water interface as indicated by encrusters and sponges that infested them after death. Sediment-filled shells disintegrated through bioerosion and wear when residence time in the taphonomically active zone exceeded ~2,000 years. We suggest that the articulation paradox is driven by the Mesozoic Marine Revolution (MMR) that escalated predation, bioturbation and organic matter recycling, all intensifying shell disintegration. A scenario with slow disarticulation in bathyal environments can be an analogue of conditions leading to preservation of articulated shells in shallow-water assemblages prior to the MMR.</p>
Supplementary Material - Marine animal forests in turbid environments are overlooked seascapes in urban areas
<p>Figures S1, S2, and S3 of the manuscript "Marine animal forests in turbid environments are overlooked seascapes in urban areas" accepted in the open-access journal Ocean and Coastal Research (Soares et al. 2023)</p>
Dataset from: Ultraviolet refractive index values of organic aerosol extracted from deciduous forestry, urban and marine environments
<p>The refractive index values of atmospheric aerosols are required to address the large uncertainties in the magnitude of atmospheric radiative forcing and measurements of the refractive index dispersion with wavelength of particulate matter sampled from the atmosphere are rare over ultraviolet wavelengths. An ultraviolet-optimized spectroscopic system illuminates optically-trapped single particles from a range of tropospheric environments to determine the particle’s optical properties. Aerosol from remote marine, polluted urban, and forestry environments is collected on quartz filters, and the organic fraction is extracted and nebulized to form micron-sized spherical particles. The radius and the real component of refractive index dispersion with wavelength of the optically trapped particles are determined to a precision of 0.001 µm and 0.002 respectively over a near-ultraviolet-visible wavelength range of 0.320–0.480 µm. Remote marine aerosol is observed to have the lowest refractive index (n=1.442 (λ=0.350 µm)), with above-canopy rural forestry aerosol (n=1.462–1.481 (λ=0.350 µm)) and polluted urban aerosol (n=1.444–1.485 (λ=0.350 µm)) showing similar refractive index dispersions with wavelength. In-canopy rural forestry aerosol is observed to have the highest refractive index value (n=1.508 (λ=0.350 µm)). The study presents the first single particle measurements of the dispersion of refractive index with wavelength of atmospheric aerosol samples below wavelengths of 0.350 µm. The Cauchy dispersion equation, commonly used to describe the visible refractive index variation of aerosol particles, is demonstrated to extend to ultraviolet wavelengths below 0.350 µm for the urban, forestry, and atmospheric aerosol water-insoluble extracts from these environments. A 1D radiative-transfer calculation of the difference in top-of-the-atmosphere albedo between atmospheric core-shell mineral aerosol with and without films of this material demonstrates the importance of organic films forming on mineral aerosol.</p> <p>The raw experimental spectra collected and analysed in this study are provided, as well as files for the calibrated wavelengths.</p>
Data from: How long does a brachiopod shell last on a seafloor? Modern mid-bathyal environments as taphonomic analogues of continental shelves prior to the Mesozoic Marine Revolution
Open the record for dataset details and reuse information.
The next frontier: Human settlements in the marine environment
Open the record for dataset details and reuse information.
Data from: Phylogenetic relatedness drives protists assembly in marine and terrestrial environments
Open the record for dataset details and reuse information.
Data from: Adaptive genetic variation distinguishes Chilean blue mussels (Mytilus chilensis) from different marine environments
Open the record for dataset details and reuse information.
Data from: Feeding environment and other traits shape species' roles in marine food webs
Food webs and meso-scale motifs allow us to understand the structure of ecological communities and define species' roles within them. This species-level perspective on networks permits tests for relationships between species' traits and their patterns of direct and indirect interactions. Such relationships could allow us to predict food-web structure based on more easily-obtained trait information. Here we calculated the roles of species (as vectors of motif position frequencies) in six well-resolved marine food webs and identified the motif positions associated with the greatest variation in species' roles. We then tested whether the frequencies of these positions varied with species' traits. Despite the coarse-grained traits we used, our approach identified several strong associations between traits and motifs. Feeding environment was a key trait in our models and may shape species' roles by affecting encounter probabilities. Incorporating environment into future food web models may improve predictions of an unknown network structure.
Southern Ocean Cloud and Aerosol data set: a compilation of measurements from the 2018 Southern Ocean Ross Sea Marine Ecosystems and Environment voyage
<p>Due to its remote location and extreme weather conditions, atmospheric in situ measurements are rare in the Southern Ocean. As a result, aerosol-cloud interactions in this region are poorly understood and remain a major source of uncertainty in climate models. This, in turn, contributes substantially to persistent biases in climate model simulations, numerical weather prediction models and reanalyses. It has been shown in previous studies that in situ and ground-based remote sensing measurements across the Southern Ocean are critical for complementing satellite data sets due to the importance of boundary layer and low-level cloud processes. These processes are poorly sampled by satellite-based measurements which are typically obscured by near-continuous overlying cloud cover observed in this region. Here we provide a comprehensive set of ship-based aerosol and meteorological observations collected on the TAN1802 voyage of R/V Tangaroa across the Southern Ocean, from Wellington, New Zealand, to the Ross Sea, Antarctica. The voyage was carried out from 8 February to 21 March, 2018. The compiled data set provides here includes measurements from a range of instruments, such as (i) meteorological conditions at the sea surface and profile measurements; (ii) the size and concentration of particles; (iii) trace gases dissolved in the ocean surface such as dimethyl sulfide and carbonyl sulfide; (iv) and remotely sensed observations of low clouds. We encourage the scientific community to use these measurements for further analysis and model evaluation studies, in particular, for studies of Southern Ocean clouds, aerosol and their interaction.</p>
Galaxias maculatus occurrence data in marine and freshwater environments in rivers of southern Chile
<p>In the present study, we assessed ecological and historical factors (Gondwanan vicariance, marine dispersion) and potential dispersion (niche-tracking) that explain distribution of <em>Galaxias maculatus</em> in the Southern Hemisphere based on occurrences available in the Global Biodiversity Information Facility (GBIF; period 1980 to 2022) and ichthyological sampling in five river systems in southern Chile between March and November 2019. Ocurrence data extracted from GBIF are available at <a href="http://www.gbif.org">http://www.gbif.org</a> and additional ichthyological sampling data that were used are provided here. Data provided here are based on sampling of <em>Galaxias maculatus</em> at 12 sites in five river systems in southern Chile during March, May, August, and November 2019. Sampling sites were selected to cover a continuous river gradient, including (whenever possible) the lower, middle, and upper sections of each river system. Fish were captured using beach seines (5 m long, 1.5 m high, and 10 mm stretched mesh) in shoreline habitats of each evaluated river system.</p>
Data from: Rapid radiation in a highly diverse marine environment
<p>Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is approximately 26 million years old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in <em>Heliconius</em> butterflies, capuchino finches and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.</p>
Energetic constraints on body-size niches in a resource-limited marine environment
<p><span>Body size of life on Earth spans many orders of magnitude, and with it scales the energetic requirements of organisms. Thus, changes in environmental energy should impact community body-size distributions in predictable ways by reshaping ecological and niche dynamics. We examine how carbon, oxygen, and temperature, three energetic drivers, impact community size-based assembly in deep-sea bivalves. We demonstrate that body-size distributions are influenced by multiple energetic constraints. Relaxation in these constraints leads to an expansion of body-size niche space through the addition of novel large size classes, increasing the standard deviation and mean of the body-size distribution. With continued Anthropogenic increases in temperature and reductions in carbon availability and oxygen in most ocean basins, our results point to possible radical shifts in invertebrate body size with the potential to impact ecosystem function.</span></p>
Results of Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund
<p>These files contain the figures and modelled dataset used in the article "Secondary aerosol formation in marine Arctic environments: a model measurement comparison at Ny-Ålesund".</p>
Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway
<p>Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; i.e. Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F<sub>ST</sub> between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbour-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F<sub>ST</sub>) between marine and brackish sprat is larger in the comparison Norway- Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, i.e., 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.</p>
Supplementary data for the paper: "Self-healing concrete with a bacteria-based or crystalline admixture as healing agent to prevent chloride ingress and corrosion in a marine environment'"
<div> <p>Supplementary data for the paper: "Self-healing concrete with a bacteria-based or crystalline admixture as healing agent to prevent chloride ingress and corrosion in a marine environment"<br><br>Open data concerning experimental work. Bacteria-based agents (BAS) and crystalline admixtures (CA) are explored as healing agents to enhance chloride resistance and prevent corrosion. Healing of 100 µm and 300 µm wide cracks was investigated, in combination with two conditioning methods. Either the samples were subjected to wet/dry cycles for 3 months before exposure (“healed”), or they were directly exposed to artificial seawater after crack creation (“unhealed”). </p> </div> <h2>Files</h2>
Dataset for Paul et al., "Trace metals in coastal marine sediments: Natural and anthropogenic sources, correlation matrices, and proxy potentials", Science of The Total Environment (STOTEN-175789, 2024)
<p>The datafile (.xlsx format) contains the solid phase data for all study sites presented in the associated STOTEN publication <a href="https://doi.org/10.1016/j.scitotenv.2024.175789" target="_blank" rel="noopener">(10.1016/j.scitotenv.2024.175789)</a></p> <ol> <li>specifics on the ICP-MS and ICP-OES analysis</li> <li>solid-phase data (Pb, Cd, Cu, Zn, Sb, Sn, Ni, As, Tl, V, Mo, U, Re, TOC, S, Fe, Mn, and Al)</li> <li>coefficient of variation test results (as a basis for evaluating the applicability of data normalizations to the data; i.e. calculation of Enrichment Factors, cf. method section of the original publication)</li> </ol> <p>Please note that the title of the paper and the publication number has changed upon final publication. The Excel file description still refers to the original manuscript number and title "Trace metals in coastal marine sediments: anthropogenic sources, correlation patterns, and proxy potentials".</p>
Global Marine Environment Dataset (GMED)
<p>The Global Marine Environment Datasets (GMED) is a compilation of publicly available climatic, biological and geophysical environmental layers featuring present, past and future environmental conditions. GMED covers the widest available range of environmental layers from a variety of sources and depths from the surface to the deepest part of the ocean. It has a uniform spatial extent, high-resolution land mask (to eliminate land areas in the marine regions), and high spatial resolution (5 arc-minute, c. 9.2 km near equator). The free online availability of GMED enables rapid map overlay of species of interest (e.g. endangered or invasive) against different environmental conditions of the past, present and the future, and expedites mapping distribution ranges of species using popular SDM algorithms. This archive features a snapshot of GMED dataset in 2018 as a single archive which is associated with the Earth Systems Data Science Manuscript.</p>
ScienceDex guides
Understand access before you commit
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.