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818 results for “Neutrality”
Data from: Latitudinal divergence in a wide-spread amphibian: contrasting patterns of neutral and adaptive genomic variation
Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation over large-scale geographic gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1700 km latitudinal gradient from northern Germany to northern Sweden. Using ddRAD-seq we obtained 27590 SNPs, and identified differentiation outliers and SNPs associated with growing season length. Populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post-glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate-mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes.
Neutral and adaptive drivers of genomic change in introduced brook trout (Salvelinus fontinalis) populations revealed by pooled sequencing
<p>Understanding the drivers of successful species invasions is important for conserving native biodiversity and for mitigating the economic impacts of introduced species. However, whole-genome resolution investigations of the underlying contributions of neutral and adaptive genetic variation in successful introductions are rare. Increased propagule pressure should result in greater neutral genetic variation, while environmental differences should elicit selective pressures on introduced populations, leading to adaptive differentiation. We investigated neutral and adaptive variation among nine introduced brook trout (<em>Salvelinus fontinalis</em>) populations using whole-genome pooled sequencing. The populations inhabit isolated alpine lakes in western Canada and descend from a common source, with an average of ~19 (range of 7-41) generations since introduction. We found some evidence of bottlenecks without recovery, no strong evidence of purifying selection, and little support that varying propagule pressure or differences in local environments shaped observed neutral genetic variation differences. Putative adaptive loci analysis revealed non-convergent patterns of adaptive differentiation among lakes with minimal putatively adaptive loci (0.001%-0.15%) that did not correspond with tested environmental variables. Our results suggest that (i) introduction success is not always strongly influenced by genetic load, (ii) observed differentiation among introduced populations can be idiosyncratic, population-specific, or stochastic, and (iii) conservatively, in some introduced species, colonization barriers may be overcome by support through one aspect of propagule pressure or benign environmental conditions.</p>
Data for: Alfvén Pulse-Driven Spicule-like jets in the presence of thermal conduction and ion-neutral collision in a two-fluid regime
<p>The uploaded folder consists of the numerical simulation data and analyses routines of two-fluid JOANNA code that studied the Alfvén pulse-driven spicule-like jets in the presence of thermal conduction and Ion-neutral collision. The code produced the data in .xmf and .h5 formats, which are available for the analysis in the Data folder. The slices folder within Data consists of grid information in X- and -Y, as well as time. Apart from that, these slices consist of the temporal variations of various physical variables, e.g., pressure, density, velocity for ions and neutrals, magnetic field, etc. These slices are utilized in making the distance-time maps as presented in Figs 4-5 in the paper. Each physical variable is finally converted from code units to physical units (S.I or C.G.S. as required) and presented in the paper. The data and its analysis tree are self-descriptive, and each folder contains the instruction files in this context.</p>
Resource for Hatch et al (2024), "What is the neutral wind in height-integrated electrodynamics?"
<p>Data and python scripts for creating figures in Hatch et al (2024), "What is the neutral wind in height-integrated ionospheric electrodynamics?"</p> <p>The 'data' folder contains PFISR measurements and neutral wind profiles needed for calculating the Hall- and Pedersen-weighted neutral winds. The 'scripts' folder contains python scripts.</p> <p>Figure 1: journal__20231228__plot_wind_profiles_grouped_by_day.py</p> <p>Figure 2: journal__20231209__look_at_swipe_for_rocket_times.py</p> <p>Figure 3: journal__20231220__is_it_any_better_to_use_neutralwind_at_160km_than_to_assume_uEq0QQ.py</p> <p>Figure 4: journal__20231209__look_at_swipe_for_rocket_times.py</p>
Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish
<p>This dataset is associated to the following publication:</p> <p>Vilcot M, Faure N, Andrews KR, Bowen BW, Leprieur F, Manel S. (2024) <strong>Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish</strong>. <em>Molecular Ecology</em> <strong>33</strong>, e17423. (doi:<a href="https://doi.org/10.1111/mec.17423">10.1111/mec.17423</a>)</p> <p> </p> <h2><strong>Data: </strong></h2> <ul> <li> <p>"Report_DEtel22-6705_SNP_2_ordered_Bowen.csv": SNP data from Dart Sequencing on <em>Etelis coruscans</em>, from Andrews et al. (2020) samples</p> </li> <li>"PA_Mat_GaspObis.RDS": fish species presence data, gathered from an updated version of Albouy et al. (2019)</li> <li> <p>"metadata_samples_full.csv": all <em>Etelis coruscans</em> sample information, from Andrews et al. (2020) and the SEAMOUNTS project</p> </li> <li> <p>"metadata_samples.csv": <em>Etelis coruscans</em> sample information, only for samples that have passed the genetic filtering and were used for subsequent analyses </p> </li> <li> <p>"metadata_stations.csv": sampling station information</p> </li> <li> <p>"Taxonomy_Fishbase.csv": species taxonomic information, downloaded with rfishbase::load_taxa() </p> </li> <li> <p>"traits_Luiz_et_al_2013.csv": species trait information from Luiz et al. (2013) </p> </li> </ul> <h2><strong>Related dataset</strong><strong>: </strong></h2> <p><em>Etelis coruscans </em>SNP data on samples from the SEAMOUNTS project are available at <a href="https://doi.org/10.5281/zenodo.11201065">https://doi.org/10.5281/zenodo.11201065</a></p> <h2><strong>Scripts: </strong></h2> <p>Scripts used to reproduce the analyses and figures of the final article are available at <a href="https://github.com/mvilcot/etelis_SGDCs">https://github.com/mvilcot/etelis_SGDCs</a> </p> <p> </p> <h2><strong>References: </strong></h2> <p>Albouy, C., Archambault, P., Appeltans, W., Araújo, M. B., Beauchesne, D., Cazelles, K., Cirtwill, A. R., Fortin, M.-J., Galiana, N., Leroux, S. J., Pellissier, L., Poisot, T., Stouffer, D. B., Wood, S. A., & Gravel, D. (2019). The marine fish food web is globally connected. Nature Ecology & Evolution, 3(8), Article 8. <a href="https://doi.org/10.1038/s41559-019-0950-y" target="_blank" rel="noopener">https://doi.org/10.1038/s41559-019-0950-y</a> </p> <p>Andrews, K. R., Copus, J. M., Wilcox, C., Williams, A. J., Newman, S. J., Wakefield, C. B., & Bowen, B. W. (2020). Range-Wide population structure of 3 deepwater Eteline snappers across the Indo-Pacific Basin. Journal of Heredity, 111(5), 471‑485. <a href="https://doi.org/10.1093/jhered/esaa029" target="_blank" rel="noopener">https://doi.org/10.1093/jhered/esaa029</a> </p> <p>Luiz, O. J., Allen, A. P., Robertson, D. R., Floeter, S. R., Kulbicki, M., Vigliola, L., Becheler, R., & Madin, J. S. (2013). Adult and larval traits as determinants of geographic range size among tropical reef fishes. Proceedings of the National Academy of Sciences, 110(41), 16498‑16502. <a href="https://doi.org/10.1073/pnas.1304074110" target="_blank" rel="noopener">https://doi.org/10.1073/pnas.1304074110</a> </p> <p>Boettiger, C., Lang, D. T., & Wainwright, P. C. (2012). rfishbase: Exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology, 81(6), 2030‑2039. <a href="https://doi.org/10.1111/j.1095-8649.2012.03464.x" target="_blank" rel="noopener">https://doi.org/10.1111/j.1095-8649.2012.03464.x</a></p> <p> </p>
Temperature Map of the Magnetotail Using Energetic Neutral Atoms.
<p>This repository contains Energetic Neutral Atoms Temperature Maps used to analyze the geomagnetic substorm event that occurred on Oct. 10, 2014. Files of the temperature maps plotted in the paper (Merging Mesoscale Magnetotail Features and Ground B-Field Perturbation Network Connectivity During Substorm Activity (Currently Under Review)) are contained in the 20141010 zip file, while the Cannonical-Correlation file contains the codes used for the network analysis. The temperature files are .sav files, and contains the image along with its metadata. To plot the temperature maps, the gen_function python file contains a temp_map function that takes in the files and plots the corresponding temperature map. </p>
MD simulations of bilayers containing PC/PS mixtures and CaCl_2: 250POPC_50POPS_neutral
<p>NMRLipids IV project (nmrlipids.blogspot.fi)</p> <p>Gromacs, CHARMM36 FF, 1 atm, 298K, 200ns (no pre-equilibration)</p> <p>250 POPC lipids, 50 POPS lipids, 73521 Atoms</p>
MD simulations of bilayers containing PC/PS mixtures and CaCl_2: 150POPC_150POPS_neutral
<p>NMRLipids IV project (nmrlipids.blogspot.fi)</p> <p>Gromacs, CHARMM36 FF, 1 atm, 298K, 200ns (no pre-equilibration)</p> <p>150 POPC lipids, 150 POPS lipids, 71655 Atoms</p>
Separating the roles of magnetic topology and neutral trapping in modifying the detachment threshold for TCV
<p>Dataset for the plasma physics paper "Separating the roles of magnetic topology and neutral<br> trapping in modifying the detachment threshold for TCV". </p>
MD simulations of bilayers containing PC/PG mixtures and CaCl_2: 250POPC_250POPG_neutral
<p>NMRLipids IVb project (nmrlipids.blogspot.fi)</p> <p>Gromacs, CHARMM36 FF, 1 atm, 298K, 200ns (no pre-equilibration)</p> <p>250 POPC lipids, 250 POPG lipids, 119974 Atoms</p>
MD simulations of bilayers containing PC/PG mixtures and CaCl_2: 400POPC_100POPG_neutral
<p>NMRLipids IVb project (nmrlipids.blogspot.fi)</p> <p>Gromacs, CHARMM36 FF, 1 atm, 298K, 200ns (no pre-equilibration)</p> <p>400 POPC lipids, 100 POPG lipids, 122392 Atoms</p>
Quality Assessment of YUNYAO GNSS-RO Refractivity Data in the Neutral Atmosphere
Open the record for dataset details and reuse information.
MOC composites with filler from MOC recyclate: towards waste-free and CO2-neutral technology
Open the record for dataset details and reuse information.
Dataset for "Dynamical Study of the Reaction of N+ Ions with O2 Neutrals"
<p>Dataset for "Dynamical Study of the Reaction of N+ Ions with O2 Neutrals"</p>
Neutral-current DIS event samples generated with MadGraph5 at leading order with $E_e = 27.5$ GeV, $E_p = 820$ GeV, and $\mu^2_\mathrm{F} = \mu^2_\mathrm{R} = Q^2$
<p>Neutral-current deep inelastic scattering event samples at leading order, generated with MadGraph5 version 3.5.5 and saved in the Les Houches Event File format as a tarball. Beam energies of 27.5 GeV for the electron, 820 GeV for the proton. Renormalization and factorization scales (squared) set to photon virtuality $Q^2$. All cuts and parameter values are specified in the header of the event files. </p>
Predicting the solubility of amino acids and peptides with the SAFT-γ Mie approach: Neutral and charged models
<p>Calculated data accompanying the IECR 2024 publication "Predicting the Solubility of Amino Acids and Peptides with the SAFT‑γ Mie Approach: Neutral and Charged Models", by Ahmed Alyazidi, Shubhani Paliwal, Felipe A. Perdomo, Amy Mead, Mingxia Guo, Jerry Y. Y. Heng, Thomas Bernet, Andrew Haslam, Claire S. Adjiman, George Jackson, and Amparo Galindo. </p>
Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.
Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively adaptive SNPs were similar, but provided greater resolution of stocks compared with a putatively neutral panel of 3911 SNPs or previous estimates with 14 microsatellites. A cline of increasing measures of genetic diversity from south to north was found in the adaptive panel, but not in the neutral markers (SNPs or microsatellites). This may indicate divergent selective pressures in differing freshwater and marine environments between regional eulachon populations and that these adaptive diversity patterns not seen with neutral markers could be a consideration when determining genetic boundaries for conservation purposes. Estimates of effective population size (Ne) were similar with the neutral SNP panel and microsatellites and may be utilized to monitor population status for eulachon where census sizes are difficult to obtain. Greater differentiation with the panel of putatively adaptive SNPs provided higher individual assignment accuracy compared to the neutral panel or microsatellites for stock identification purposes. This study presents the first SNPs that have been developed for eulachon, and analyses with these markers highlighted the importance of integrating genome-wide neutral and adaptive genetic variation for the applications of conservation and management.
Data from: Manipulation of habitat isolation and area implicates deterministic factors and limited neutrality in community assembly
Theory predicts deterministic and stochastic factors will contribute to community assembly in different ways: environmental filters should regulate those species that establish in a particular area resulting in the ecological requirements of species being the primary driver of species distributions, while chance and dispersal limitation should dictate the likelihood of species reaching certain areas with the ecology of species being largely neutral. These factors are specifically relevant for understanding how the area and isolation of different habitats or islands interact to affect community composition. Our review of the literature found few experimental studies have examined the interactive effect of habitat area and isolation on community assembly, and the results of those experiments have been mixed. We manipulated the area and isolation of rock 'islands' created de novo in a grassland matrix to experimentally test how deterministic and stochastic factors shape colonizing animal communities. Over 64 weeks, the experiment revealed the primacy of deterministic factors in community assembly, with habitat islands of the same size exhibiting remarkable consistency in community composition and diversity, irrespective of isolation. Nevertheless, tangible differences still existed in abundance inequality among taxa: large, near islands had consistently higher numbers of common taxa compared to all other island types. Dispersal limitation is often assumed to be negligible at small spatial scales, but our data shows this not to be the case. Furthermore, the dispersal limitation of a subset of species has potentially complex flow-on effects for dictating the type of deterministic factors affecting other colonising species.
Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype
Given the possibility of yellow fever virus reintroduction in epidemiologically receptive geographic areas, the risk of vaccine supply disruption is a serious issue. New strategies to reduce the doses of injected vaccines should be evaluated very carefully in terms of immunogenicity. The plaque reduction test for the determination of neutralizing antibodies (PRNT) is particularly time-consuming and requires the use of a confinement laboratory. We have developed a new test based on the use of a non-infectious pseudovirus (WN/YF17D). The presence of a reporter gene allows sensitive determination of neutralizing antibodies by flow cytometry. This WN/YF17D test was as sensitive as PRNT for the follow-up of yellow fever vaccinees. Both tests lacked specificity with sera from patients hospitalized for acute Dengue virus infection. Conversely, both assays were strictly negative in adults never exposed to flavivirus infection or vaccination, and in patients sampled some time after acute Dengue infection. This WN/YF17D test will be particularly useful for large epidemiological studies and for screening for neutralizing antibodies against yellow fever virus.
Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species-pair
<p><b>Aim:</b> Estimating genetic diversity is key for understanging biogeographic and evolutionary processes. However, gathering genetic information is not feasible for all taxa or populations, particularly in the tropical regions. Identifying proxies for inferring such values has thus become essential. Here, we built on the niche centrality hypothesis (NCH; or central-abundance hypothesis) and the nearly neutral theory of evolution (NNT) to identify some of such proxies using a montane tropical conifer species-pair as model. The NCH predicts more genetic diversity under optimal ecological conditions, which should also allow for more efficient purifying selection, according to the NNT.</p> <p><b>Location:</b> The Transmexican Volcanic Belt, central Mexico.</p> <p><b>Taxa:</b> A fir species-pair endemic to central Mexico,<b> </b><i>Abies flinckii </i>and<i> A. religiosa.</i></p> <p><b>Methods:</b> We estimated patterns of genetic diversity from nuclear SSRs (<i>A</i>, <i>H</i><sub>E</sub>), and gene-coding sequences (<i>π</i><sub>S</sub>, <i>π</i><sub>N</sub>), together with the efficacy of purifying selection, measured as <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub>. After testing for niche overlap, we used several geographic and ecological proxies (i.e. longitude, latitude, elevation, estimated area, and distance to the niche centroid in the present and in the LGM) to predict genetic diversity and <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub> using general linear models.</p> <p><b>Results:</b> Populations at the west of the Trans Mexican Volcanic Belt (TVB) had lower genetic diversity than populations in the east of this mountain chain. Both species had significant niche overlap. The principal predictors for neutral genetic diversity (<i>H</i><sub>E</sub>, <i>A</i> and <i>π</i><sub>S</sub>) were longitude and latitude, followed by the current distance to the niche centroid; the efficiency of purifying selection was mostly accounted for by the current distance to the niche centroid (which was also correlated to elevation). No correlation was observed between genetic diversity or <i>π</i><sub>N</sub>/<i>π</i><sub>S</sub> and current population area.</p> <p><b>Main conclusions:</b> Historical and ecological factors have to be taken into account for explaining the amounts of genetic diversity in mountain tropical species. Following the NTT, populations closer to the niche centroid are more efficient at eliminating slightly deleterious mutations than marginal stands, independently of their size or geographical location (longitude). Expanding the central-abundance theory within the scope of the NTT might help reconciling conflicting views concerning the extent of its empirical support.</p>
ScienceDex guides
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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.