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187 results for “genetic correlations”
Data from: Baseline and stress-induced corticosterone levels are heritable and genetically correlated in a barn owl population
The hypothalamic-pituitary-adrenal (HPA) axis is responsible for the regulation of corticosterone, a hormone that is essential in the mediation of energy allocation and physiological stress. As a continuous source of challenge and stress for organisms, the environment has promoted the evolution of physiological adaptations and led to a great variation in corticosterone profiles within or among individuals, populations and species. In order to evolve via natural selection, corticosterone levels do not only depend on the strength of selection exerted on them but also on the extent to which the regulation of corticosterone is heritable. Nevertheless, heritability of corticosterone profiles in wild populations is still poorly understood. In this study, we estimated the heritability of baseline and stress-induced corticosterone levels in barn owl (Tyto alba) nestlings from 8 years of data, using a multivariate animal model based on a behavioural pedigree. We found that baseline and stress-induced corticosterone levels are strongly genetically correlated (r = 0.68 – 0.80) and that the heritability of stress-induced corticosterone levels (h2 = 0.24 – 0.33) was moderate and similar to the heritability of baseline corticosterone levels (h2 = 0.19 – 0.30). These findings suggest that the regulation of stress-induced corticosterone and baseline levels evolve at a similar pace when selection acts with the same intensity on both traits, and that contrary to previous studies, the evolution of baseline and stress-induced level is interdependent in barn owls, as they may be strongly genetically correlated.
Data from: Evolution of resistance to a multiple-herbavore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection
Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities—particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance.
Data from: Testing the species–genetic diversity correlation in the Aegean archipelago: towards a haplotype-based macroecology?
A positive correlation between species and genetic diversity (SGDC) has been proposed, consistent with neutral predictions in macroecology. We assessed the SGDC in tenebrionid beetle communities of the Aegean archipelago on fifteen islands of different sizes, distances to mainland, and ages of isolation. Alpha- and beta-diversity of species and haplotypes were assessed using sequences of >1000 individuals (mitochondrial Cytochrome Oxidase I and nuclear Muscular Protein 20) to test the SGDC. We show that: (i) there is a strong species-area and haplotype-area relationship; (ii) species richness in island communities is correlated with intraspecific genetic diversity in the constituent species except when island size or distance to mainland are factored out in partial correlations; (iii) community similarity declines exponentially at an increasing rate when calculated based on species, nuclear and mtDNA haplotypes; and (iv) distance decay of community similarity is slower in dispersive sand-dwelling lineages compared to less dispersive lineages that are not sand-obligate. Taken together, these correlated patterns at the species and haplotype level are consistent with individual-based stochastic dispersal proposed by neutral theories of biodiversity. The results also demonstrate the utility of haplotype data for exploring macroecological patterns in poorly known biota and predicting large-scale biodiversity patterns based on genetic inventories of local samples.
Data from: Genetic parameters in subtropical pine F1 hybrids: heritabilities, between-trait correlations and genotype-by-environment interactions
Growth and stem straightness traits of 29 Pinus caribaea var. hondurensis × Pinus tecunumanii (PCH × PTEC) and 26 P. caribaea var. hondurensis × Pinus oocarpa (PCH × POOC) hybrid pair-crosses plus a total of 16 intraspecific families were assessed at ages 5, 8 and 15 years from planting at two sites. The PCH × PTEC hybrid was the most productive, yielding 37 % more than a Pinus elliottii local control and was 21 % superior to either parental species in DBH growth. PCH × POOC hybrid was, on average, 16 % superior to either parental species for DBH. Narrow-sense heritability estimates were low to moderate for growth traits (average of 0.27) and stem straightness (0.16). The estimated additive genetic correlations between growth traits and ages within traits were high (>0.8) and positive, providing confidence in early selection based on diameter at breast height. The high proportion of estimated additive genetic variance compared to dominance variance in the F1 pine hybrids suggests that breeding strategies that maximize the use of additive genetic variance may be effective. The ranking of the 11 PCH parents based on general hybridizing ability predictions (estimated breeding values as hybrids) was somewhat inconsistent between PTEC and POOC hybrid crosses for all traits (r 9 d.f. = 0.38–0.45; p ∼0.15–0.25). There was no evidence of practically important G × E interaction for the hybrids except for PCH × PTEC height growth. This study suggests that a single, multi-hybrid breeding population seems appropriate in Zimbabwe if the trial sites are representative of the planting target zone.
Data from: The quantitative genetics of incipient speciation: heritability and genetic correlations of skeletal traits in populations of diverging Favia fragum ecomorphs.
Recent speciation events provide potential opportunities to understand the microevolution of reproductive isolation. We used a marker-based approach and a common garden to estimate the additive genetic variation in skeletal traits in a system of two ecomorphs within the coral species Favia fragum: a Tall ecomorph that is a seagrass specialist, and a Short ecomorph that is most abundant on coral reefs. Considering both ecomorphs, we found significant narrow-sense heritability (h²) in a suite of measurements that define corallite architecture, and could partition additive and non-additive variation for some traits. We found positive genetic correlations for homologous height and length measurements among different types of vertical plates (costosepta) within corallites, but negative correlations between height and length within, as well as between costosepta. Within ecomorphs, h² estimates were generally lower, compared to the combined ecomorph analysis. Marker-based estimates of h² were comparable to broad-sense heritability (H) obtained from parent-offspring regressions in a common garden for most traits, and similar genetic co-variance matrices for common garden and wild populations may indicate relatively small G × E interactions. The patterns of additive genetic variation in this system invite hypotheses of divergent selection or genetic drift as potential evolutionary drivers of reproductive isolation.
Data from: Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account
The hindcast of shifts in the geographical ranges of species as estimated by ecological niche modelling (ENM) has been coupled with phylogeographical patterns, allowing the inference of past processes that drove population differentiation and genetic variability. However, more recently, some studies have suggested that maps of environmental suitability estimated by ENM may be correlated to species' abundance, raising the possibility of using environmental suitability to infer processes related to population demographic dynamics and genetic variability. In both cases, one of the main problems is that there is a wide variation in ENM development methods and climatic models. In this study, we analyse the relationship between heterozygosity (He) and environmental suitability from multiple ENMs for 25 population estimates for Dipteryx alata, a widely distributed, endemic tree species of the Cerrado region of central Brazil. We propose a new approach for generating a statistical distribution of correlations under randomly generated ENM. The confidence intervals from these distributions indicate how model selection with different properties affects the ability to detect a correlation of interest (e.g. the correlation between He and suitability). Additionally, our approach allows us to explore which particular ensemble of ENMs produces the better result for finding an association between environmental suitability and He. Caution is necessary when choosing a method or a climatic data set for modelling geographical distributions, but the new approach proposed here provides a conservative way to evaluate the ability of ensembles to detect patterns of interest.
Data from: Heritability and genetic correlations of personality, life history, and morphology in the grey mouse lemur (M. murinus)
<p class="Style1">The recent interest in animal personality has sparked a number of studies on the heritability of personality traits. Yet, how the sources variance these traits can be decomposed remains unclear. Moreover, whether genetic correlations with life-history traits, personality traits and other phenotypic traits exist as predicted by the pace-of-life syndrome hypothesis remains poorly understood. Our aim was to compare the heritability of personality, life-history, and morphological traits and their potential genetic correlations in a small primate (<i>Microcebus murinus</i>). We performed an animal model analysis on six traits measured in a large sample of captive mouse lemurs (<i>N</i>=486). We chose two personality traits, two life history traits, and two morphological traits to 1) estimate the genetic and/or environmental contribution to their variance, and 2) test for genetic correlations between these traits. We found modest narrow-sense heritability for personality traits, morphological traits, and life history traits. Other factors including maternal effects also influence the sources of variation in life history and morphological traits. We found genetic correlations between emergence latency on the one hand and radius length and growth rate on the other hand. Emergence latency was also genetically correlated with birth weight and was influenced by maternal identity. These results provide insights into the influence of genes and maternal effects on the partitioning of sources of variation in personality, life-history, and morphological traits in a captive primate model and suggest that the pace-of-life syndrome may be partly explained by genetic trait covariances.</p>
Data from: Multilocus approaches for the measurement of selection on correlated genetic loci
The study of ecological speciation is inherently linked to the study of selection. Methods for estimating phenotypic selection within a generation based on associations between trait values and fitness (e.g. survival) of individuals are established. These methods attempt to disentangle selection acting directly on a trait from indirect selection caused by correlations with other traits via multivariate statistical approaches (i.e. inference of selection gradients). The estimation of selection on genotypic or genomic variation could also benefit from disentangling direct and indirect selection on genetic loci. However, achieving this goal is difficult with genomic data because the number of potentially correlated genetic loci (p) is very large relative to the number of individuals sampled (n). In other words, the number of model parameters exceeds the number of observations (p ≫ n). We present simulations examining the utility of whole-genome regression approaches (i.e. Bayesian sparse linear mixed models) for quantifying direct selection in cases where p ≫ n. Such models have been used for genome-wide association mapping and are common in artificial breeding. Our results show they hold promise for studies of natural selection in the wild and thus of ecological speciation. But we also demonstrate important limitations to the approach and discuss study designs required for more robust inferences.
Data from: Evolution of elaborate parental care: phenotypic and genetic correlations between parent and offspring traits
The evolution of elaborate forms of parental care is an important topic in behavioral ecology, yet the factors shaping the evolution of complex suites of parental and offspring traits are poorly understood. Here, we use a multivariate quantitative genetic approach to study phenotypic and genetic correlations between parental and offspring traits in the burying beetle Nicrophorus vespilloides. To this end, we recorded 2 prenatal traits (clutch size and egg size), 2 postnatal parental behaviors (direct care directed toward larvae and indirect care directed toward resource maintenance), 1 offspring behavior (begging), and 2 measures of breeding success (larval dispersal mass and number of dispersing larvae). Females breeding on larger carcasses provided less direct care but produced larger larvae than females breeding on smaller carcasses. Furthermore, there were positive phenotypic correlations between clutch size, direct, and indirect care. Both egg size and direct care were positively correlated with dispersal mass, whereas clutch size was negatively correlated with dispersal mass. Clutch size and number of dispersed larvae showed genetic variance both in terms of differences between populations of origin and significant heritabilities. However, we found no evidence of genetic variance underlying other parental or offspring traits. Our results suggest that correlations between suites of parental traits are driven by variation in individual quality rather than trade-offs, that some parental traits promote offspring growth while others increase the number of offspring produced, and that parental and offspring traits might respond slowly to selection due to low levels of additive genetic variance.
Phylogenetically under‐dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community
<p>We are providing semi-processed datasets relevant to the paper "Phylogenetically under-dispersed gut microbiomes across a range of host genetic diversity in a reptile community point to structuring by conserved host genes." Specifically, we include VCF files of RADseq data from host individuals, which are processed versions of the raw reads available at NCBI's Short Read Archive under PRJA744273. These data were processed for heterozygosity calculation using an adapted of the pipeline presented in Singhal et al. 2017, "Genetic diversity is largely unpredictable but scales with museum occurrences in a species-rich clade of Australian lizards."</p> <p>In addition, we include a database of 16S sequences from gut microbiome amplicon sequencing from the same host animals. The raw reads are available at NCBI's Short Read Archive under PRJNA746253. The sequences accessioned here are a curated, cleaned set of reference reads to which we realigned reads from each individual host.</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>
Genetic diversity of Avena ventricosa populations along an ecogeographical transect in Cyprus is correlated to environmental variables
<p>genetic data</p>
Data from: Northern range expansion of European populations of the wasp spider Argiope bruennichi is associated with global warming correlated genetic admixture and specific temperature adaptations
Poleward range expansions are observed for an increasing number of species, which may be an effect of global warming during the past decades. However, it is still not clear in how far these expansions reflect simple geographical shifts of species ranges, or whether new genetic adaptations play a role as well. Here, we analyse the expansion of the wasp spider Argiope bruennichi into Northern Europe during the last century. We have used a range-wide sampling of contemporary populations and historical specimens from museums to trace the phylogeography and genetic changes associated with the range shift. Based on the analysis of mitochondrial, microsatellite and SNP markers, we observe a higher level of genetic diversity in the expanding populations, apparently due to admixture of formerly isolated lineages. Using reciprocal transplant experiments for testing overwintering tolerance, as well as temperature preference and tolerance tests in the laboratory, we find that the invading spiders have possibly shifted their temperature niche. This may be a key adaptation for survival in Northern latitudes. The museum samples allow a reconstruction of the invasion's genetic history. A first, small-scale range shift started around 1930, in parallel with the onset of global warming. A more massive invasion of Northern Europe associated with genetic admixture and morphological changes occurred in later decades. We suggest that the latter range expansion into far Northern latitudes may be a consequence of the admixture that provided the genetic material for adaptations to new environmental regimes. Hence, global warming could have facilitated the initial admixture of populations and this resulted in genetic lineages with new habitat preferences.
Data from: Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude
Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure.
Data from: Heritability, environmental effects, and genetic and phenotypic correlations of oxidative stress resistance-related enzyme activities during early life stages in Atlantic salmon
Oxidative stress (OS) may pose important physiological constraints on individuals, affecting trade-offs between growth and reproduction or ageing and survival. Despite such evolutionary and ecological importance, the results from studies on the magnitude of individual variation in OS resistance and the underlying causes of this variation such as genetic, environmental, and maternal origins, remain inconclusive. Using a high throughput methodology, we investigated the activity levels in three OS resistance-related enzymes (superoxide dismutase, SOD; glutathione reductase, GR; glutathione S-transferase, GST) during the early life stages of 1000 individuals from 50 paternal half-sib families in two populations of Atlantic salmon. Using animal mixed models, we detected the presence of narrow-sense heritability for SOD and GST; that for GST differed between populations due to differences in environmental variance. We found support for the presence of common environmental variation, including maternal effects, for only GR. Using a bivariate animal model, we detected a positive environmental correlation between activity levels of SOD and GST but were unable to detect an additive genetic correlation. Our results complement previous heritability findings for levels of reactive oxygen species or OS resistance by demonstrating the presence of heritability for OS-related enzyme activities. Our findings provide a foundation for future work, such as investigations on the evolutionary importance of variation in enzyme activities. In addition, our findings emphasise the importance of accounting for developmental stage, environmental variance, and kin relationships when investigating the OS-response at the enzyme activity level.
Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence
<p><span><span><span><span><span><span><span><span><span><span><span>Three subspecies of Northern Bahamian Rock Iguanas, <i>Cyclura cychlura</i>, are currently recognized: <i>C. c. cychlura,</i>restricted to Andros Island, and <i>C. c. figginsi</i> and <i>C. c. inornata,</i> native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of <i>C. cychlura</i> are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: <i>C. cychlura</i> iguanas, their ticks (genus <i>Amblyomma</i>, preferentially parasitizing these reptiles), and <i>Rickettsia </i>spp. endosymbionts (within tick ectoparasites). Our results indicate that while <i>C. c. cychlura</i> on Andros is consistently supported as a separate clade, patterns of relatedness among populations of <i>C. c. figginsi</i> and <i>C. c. inornata</i> within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and <i>Rickettsia</i> spp., supports the evolutionary independence of <i>C. c. inornata</i>. Further, these patterns are also consistent with two independent evolutionarily significant units within <i>C. c. figginsi</i>. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 3. Correlation between the genetic p in Complete Mitochondrial genome of Eisenia nordenskioldi pallida Malevich, 1956 from Korea, with remarks on the phylogeny of the E. nordenskiodi complex (Megadrili; Lumbricidae)
FIGURE 3. Correlation between the genetic p-distances of the barcoding region (cox1) and the 13PCGs of the E. nordenskioldi s.l. taxa.
Natural History, Genetic Bases and Phenotype-genotype Correlations in Autosomal Dominant Spinocerebellar Degenerations
ClinicalTrials.gov study NCT00136630. IPD Sharing: Not stated. Countries: 1. Publications: 13.
1st-line Activity of Dovitinib and Correlation With Genetic Changes in RCC
ClinicalTrials.gov study NCT01791387. IPD Sharing: Not stated. Countries: 1. Publications: 36.
Correlation Between Genetic Variants and Long-term Cardiac Effects Induced by Doxorubicin in Breast Cancer Patients
ClinicalTrials.gov study NCT02078388. IPD Sharing: Not stated. Countries: 1. Publications: 2.
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.