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.
213
datasets available to search
ShareScore release 0.9.0
Dataset results
213 results for “Environmental gradients”
Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories
<p>The following files are contained in this repository:</p> <p><br> README.Hume_et_al_2022.zenodov4.txt - This document.</p> <p>scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.</p> <p>acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.</p> <p>TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis.</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.</p> <p>Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.</p> <p> </p> <p>mtORF Phylogeny</p> <p>TP-Johnston_mtORF-Pocillo.fa = all sequences</p> <p>TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment</p> <p>TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick</p> <p> </p> <p>Hellberg genotype network Porites</p> <p>TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,</p> <p>TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,</p> <p>TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format</p> <p><br> Gradient Forest Analysis</p> <p>Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island</p> <p>Por_abund.csv - Porites SSH Occurrences per Site er Island</p> <p>mean_depth_por.csv - per site per island mean depth among Porites colonies</p> <p>mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies</p>
Red Oak Root and Soil Environmental Gradient Study, Midwest U.S., 2022-2023.
Fine root trait and soils data for Quercus rubra L. (northern red oak) sampled along a Midwestern latitudinal gradient. Fourteen sites spanning 5-14 degrees C were sampled. Each sample represents 2 6 cm deep x 5 cm wide soil cores obtained from near the base of a Q. rubra individuals, with 6 sampled plots per site. Plots were located approximately 40 m apart along a linear transect to be at a cluster of Q. rubra individuals. All 14 sites were visited twice in the growing season of 2022: between June 1st and June 21st, and between July 5th and July 21st. Root traits sampled include average diameter, root tissue density, specific root length, branching intensity, and specific respiration rate. A 1 mm diameter limit cut-off was used. These traits were measured in the field (respiration rates) or from output from RhizoVision Explorer image analysis. Traits are associated with the smaller fine root sample used for respiration measurement in the field (~2 g dry weight). Fine root biomass was also obtained by removing all remaining fine roots in the core, drying, and weighing, and then was multiplied by weight-normalized respiration rates to obtain estimates of fine root ecosystem respiration. This data package is complete, but will be associated with data from 4 sites revisited in 2023 to obtain repeat fine root trait measurements and fungal community community metrics.
Data from "Evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient"
Synthesized fish, benthic invertebrate, and water quality dataset used for analysis in: Rogers, T., S. Bashevkin, C. Burdi, D. Colombano, P. Dudley, B. Mahardja, L. Mitchell, S. Perry, and P. Saffarinia. 2022. Evaluating top-down, bottom-up, and environmental drivers of pelagic food web dynamics along an estuarine gradient. preprint, EcoEvoRxiv. https://doi.org/10.32942/X2MK5Z
Dataset for journal article: Nava et al. (2021) "Microalgae colonization of different microplastic polymers in experimental mesocosms across an environmental gradient"
<p>Dataset and R script for the article "Microalgae colonization of different microplastic polymers in experimental mesocosms across an environmental gradient" by Nava V., Matias M., Castillo-Escrivà A., Messyasz B. and Leoni B. accepted by Global Change Biology.</p>
Environmental and physiochemical controls on coral calcification along a latitudinal temperature gradient in Western Australia
<p>Supplementary data for: Environmental and physiochemical controls on coral calcification along a latitudinal temperature gradient in Western Australia</p>
Light and confocal micrographs on the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, the accumulation of lipid droplets, and the heterologous expression and localisation of signature LD protein homologs to tobacco pollen tubes
<p>These micrographs accompany the work "Environmental gradients reveal stress hubs predating plant terrestrialization", posted as a pre-print on bioRxiv https://doi.org/10.1101/2022.10.17.512551 </p> <p>The light and confocal micrographs show the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, especially their accumulation of lipid droplets (LDs); in confocal micrographs, LDs appeared as distinct structures upon staining with BODIPY.</p> <p>Further confocal micrographs show the heterologous expression and localisation of signature LD protein homologs detected in Mesotaenium endlicherianum SAG 12.97; heterologous expression was carried out in tobacco pollen tubes were also stained with BODIPY and proteins were tagged with mCherry.</p>
Phylogenetic analyses of hub genes accompanying the study "Environmental gradients reveal stress hubs predating plant terrestrialization"
<p>135 ML phylogenies of hub genes identified in the study "Environmental gradients reveal stress hubs predating plant terrestrialization"</p>
Universal microbial reworking of dissolved organic matter along environmental gradients
<p>Soils are losing increasing amounts of carbon annually to freshwaters as dissolved organic matter (DOM), which, if degraded, can increasingly offset their carbon sink capacity. DOM is more susceptible to degradation closer to its source and becomes increasingly dominated by the same (i.e., universal), difficult-to-degrade compounds as degradation proceeds. However, the processes underlying DOM degradation across environments are poorly understood. Here we found DOM changed similarly along soil-aquatic gradients irrespective of differences in environmental conditions. Using ultrahigh-resolution mass spectrometry, we tracked DOM along soil depths and hillslope positions in forest headwater catchments and related its composition to soil microbiomes and physico-chemical conditions. Along depths and hillslopes, carbohydrate-like and unsaturated hydrocarbon-like compounds increased in abundance-weighted mass, suggestive of microbial reworking of plant material. More than half of the variation in the abundance of these compounds was related to the expression of genes essential for degrading plant-derived carbohydrates. Our results implicate continuous microbial reworking in shifting DOM towards universal compounds in soils. By synthesising data from the land-to-ocean continuum, we suggest these processes can be generalised across ecosystems and spatiotemporal scales. Such general degradation patterns can be leveraged to predict DOM composition and its downstream reactivity along environmental gradients to inform management of soil-to-stream carbon losses.</p>
Relyea, R. A., and E. E. Werner. 2000. Morphological plasticity of four larval anurans distributed along an environmental gradient. Copeia 2000:178-190.
We investigated morphological plasticity to the presence of predators in the tadpoles of four ranid frog species distributed along a pond hydroperiod gradient in southeast Michigan. We first reared all four species (Wood Frog, Rana sylvatica; Leopard Frog R. pipiens; Green Frog, R. clamitans; and Bullfrog, R. catesbeiana) under identical laboratory conditions in the presence and absence of caged larval dragonflies (Anax spp.). We then reared wood frog and leopard frog in outdoor mesocosms to examine the predator-induced responses during ontogeny. Finally, we reared leopard frog with predators fed either leopard frog or wood frog larvae to determine whether prey responses depended upon predators consuming conspecific prey. All four ranids exhibited some degree of morphological change in the presence of Anax; these differences were species specific and fairly robust to different experimental conditions. The responses over ontogeny indicated that the changes were direct responses to the predator’s presence and not an indirect result of the predator slowing anuran growth or development. Finally, larval leopard frog responded similarly to predators feeding on conspecifics and congenerics. Taken together, these results suggest that morphological responses to predators may be relatively common in larval anurans. Further, because many of the responses are known to be adaptive antipredator strategies, predator-induced morphological plasticity has important evolutionary and ecological implications.
Fig. 2 in Fish assemblage of the Mamanguape Environmental Protection Area, NE Brazil: abundance, composition and microhabitat availability along the mangrove-reef gradient
Fig. 2. Ontogenetic patterns of habitat use in Abudefduf saxatilis, Anisotremus surinamensis, Lutjanus alexandrei, and L. jocu along the sub-areas of Mamanguape Mangrove-Reef system, NE Brazil, showing an increase in individual size classes from the Estuarine to the Reef zone. Mann Whitney U Test showed significant size differences between all sub-areas (for A. saxatilis, Transition vs. Reefs: U = 491, Z = -6.02, p = 0.00; for A. surinamensis, Transition vs. Reefs: U = 1338, Z = -6.83, p = 0.00; for L. alexandrei, Peixe-Boi vs. Transition: U = 0.00, Z = -3.39, p = 0.00; and Tanques vs. Transition: U = 0.00, Z = -2.92, p = 0.00; for L. jocu, Peixe-Boi vs. Transition: U = 7.5, Z = -3.38, p = 0.00), except between Tanques and Peixe-Boi for L. alexandrei (U = 65, Z = 0.76, p = 0.46).
Fig. 3 in Fish assemblage of the Mamanguape Environmental Protection Area, NE Brazil: abundance, composition and microhabitat availability along the mangrove-reef gradient
Fig. 3. Canonical Correspondence Analysis of fishes and environmental parameters from Mamanguape Mangrove-Reef system, NE Brazil: (a) fish species (symbols) in relation to microhabitat categories (vectors) - Eigenvalues: axis 1, 0.56; axis 2, 0,20; r species-environment: axis 1, 0.87; axis 2, 0.56; First two axes accounted for 64.9 % of the variance; (b) fish trophic groups and subareas (symbols) in relation to environmental categories (vectors) - Eigenvalues: axis 1, 0.49; axis 2, 0.39; r species-environment: axis 1, 0.79; axis 2, 0.76; First two axes accounted for 51.6 % of the variance. Monte-Carlo test of all canonical axes were significant (p <0.01), 999 permutations. Abbreviations as follows - fish species: Abusax: Abudefduf saxatilis; Acabah: Acanthurus bahianus; Acacoe: A. coeruleus; Achlin: Achirus lineatus; Anisur: Anisotremus surinamensis; Anivir: A. virginicus; Batsop: Bathygobius soporator; Centrop: Centropomus sp.; Cithspil - Citharichthys spilopterus; Corglau - Coryphopterus glaucofraenum; Dactvol - Dactylopterus volitans; Echnau: Echeneis naucrates; Epiadc: Epinephelus adscensionis; Eucmel: Eucinostomus melanopterus; Haepar: Haemulon parra; Hipprei: Hippocampus reidi; Lutana: Lutjanus analis; Lutale: L. alexandrei; Lutjoc: L. jocu; Micrbra: Microphis brachyurus; Myroce: Myrichthys ocellatus; Rypran: Rypticus randalli; Scarus: Scarus sp.; Sparis: Sparisoma sp.; Sphtes: Sphoeroides testudineus; Stefus: Stegastes fuscus; Stevar: S. variabilis; trophic groups: RH - Roving herbivore; TH - Territorial herbivore; OM - Omnivore; CA - Carnivore; IM - Invertivore of mobile prey.
Fig. 1 in Fish assemblage of the Mamanguape Environmental Protection Area, NE Brazil: abundance, composition and microhabitat availability along the mangrove-reef gradient
Fig. 1. Mamanguape estuary, State of Paraíba, NE Brazil, showing surveyed sub-areas: 1) Tanques; 2) Peixe-Boi; 3) Cação; 4) Transition; and 5) Reefs. Dashed areas represent sandbanks.
Data from: Environmental variation associated with topography explains butterfly diversity along a tropical elevation gradient
<p>Few studies have evaluated the role of topography on the diversity patterns of biological communities along elevation gradients. We evaluated the influence of microclimate and vegetation structure associated with topographic variation on the richness and composition of species of different families of butterflies on a mountain located in a dry enclave (Chicamocha River Canyon) in the northern Andes, Colombia. We captured butterflies over four months at 18 elevations (300 to 1500 m a.s.l.) in two topographic positions (riverbed and hillslope) using an entomological net and traps baited with fermented fruit. In general, butterfly richness increased with elevation in both topographic positions. However, the richness-elevation relationship changed with butterfly family. The riverbed and hillslope sites host different assemblages of butterflies, and this pattern that was consistent for most families. In the riverbed, two sets of species are recognized along the elevation gradient (one below 700 m a.s.l. and the other above 1000 m a.s.l.), mainly owing to species replacement. On the hillslopes there was no clear pattern of grouping associated with elevation. Microclimate differences between the riverbed and hillslope sites along the elevation gradient were related to the vegetation structure and explained the variation in butterfly species composition. Our results highlight the role of topography not only by explaining the response of species richness and composition to environmental variation determined by elevation, but also as a factor that must be considered in the planning and management of biodiversity conservation in the mountains.</p>
The impact of species phylogenetic relatedness on invasion varies distinctly along resource versus nonresource environmental gradients
<p><span>Understanding why certain plant communities are vulnerable to alien invasive species is essential to predicting and controlling invasion in a changing environment. Darwin's naturalization hypothesis suggests that non-native species should be more successful in communities where their close relatives are absent. Empirical tests of this hypothesis, however, have produced mixed results. Using plot-level data from natural forests along elevational transects covering strong environmental gradients, we examined whether the invasion of the globally invasive species <em>Ageratina adenophora</em> can be explained by environmental filtering and/or competition from closely related species linked to environmental gradients. Abundant precipitation, warm temperatures, open canopies, and postfire environments facilitated <em>A. adenophora</em> invasion, whereas resident taxonomic richness suppressed its invasion. Importantly, we found that invader-resident relatedness had a strong negative effect on invader cover under resource scarcity conditions (e.g., low water availability), but not under nonresource environmental stress conditions (e.g., low temperature). Our findings help reconcile the varied applicability of Darwin's naturalization hypothesis to biological invasions in a changing world.</span></p>
FIGURE 1 in Trophic strategies of the invasive Twospot livebearer (Pseudoxiphophorus bimaculatus, Teleostei: Poeciliidae) in a gradient of environmental quality in central Mexico
FIGURE 1 | Geographic location of study area and sampling sites located in the Lerma-Chapala River basin and Pánuco River basin in central Mexico. XOT = El Xote; CHI = El Charco del Ingenio; GAL = Los Galvanes; PRC = Presa del Carmen; PVA = Paso de Vaqueros; OAS = Oasis; EXT = Extoraz; BUC = Bucareli.
FIGURE 2 in Trophic strategies of the invasive Twospot livebearer (Pseudoxiphophorus bimaculatus, Teleostei: Poeciliidae) in a gradient of environmental quality in central Mexico
FIGURE 2 | Physicochemical parameters of water in each study site in central Mexico: temperature (°C), TDS= Total dissolved solids (g/L) and DO= Dissolved oxygen (mg/L). XOT = El Xote; CHI = El Charco del Ingenio; GAL = Los Galvanes; PRC = Presa del Carmen; PVA = Paso de Vaqueros; OAS = Oasis; EXT = Extoraz; BUC = Bucareli.
Figure 1 in Environmental predictors for the distribution of the Caspian green lizard, Lacerta strigata Eichwald, 1831, along elevational gradients of the Elburz Mountains in northern Iran
Figure 1. Map of Iran. Colors indicate elevation and dots indicate occurrence of the Caspian green lizard (Lacerta strigata). Dots show presence of records for the species. The square shows the locality of the occurrence near Shiraz.
Figure 4 in Environmental predictors for the distribution of the Caspian green lizard, Lacerta strigata Eichwald, 1831, along elevational gradients of the Elburz Mountains in northern Iran
Figure 4. Response curves showing how the distribution of Lacerta strigata is affected by the environmental variables. Response curves were created using the GLM model. Dots are presences (at habitat suitability = 1) and absences (at habitat suitability = 0). Lacerta strigata was photographed in its natural habitat in the Elburz Mountains by Anooshe Kafash.
Fig. 1. A in Integrity of fluvial fish communities is subject to environmental gradients in mountain streams, Sierra de Aroa, north Caribbean coast, Venezuela
Fig. 1. A: The Aroa River basin. The Yurubí National Park (YNP) is indicated by the shaded polygon. B: each circle indicates one or more sample localities. The white circles denoted tributaries in group 1 (G1) and black circles are tributaries in group 2 (G2).
Fig. 5. Relationships between the PCA 1 and CCA 1 in Integrity of fluvial fish communities is subject to environmental gradients in mountain streams, Sierra de Aroa, north Caribbean coast, Venezuela
Fig. 5. Relationships between the PCA 1 and CCA 1 axes with the species richness and rivers stations. The richness (A) was moderately explained, but the multivariate (B) and canonical (C) analyses showed functional relationships with the geographical location of the rivers.
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.