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.
165
datasets available to search
ShareScore release 0.9.0
Dataset results
165 results for “specific diversity”
Energy input, habitat heterogeneity, and host specificity drive avian haemosporidian diversity at continental scales
Open the record for dataset details and reuse information.
Data from: The polygenic strategies of host-specific and general virulence of Botrytis cinerea across diverse eudicot hosts
Open the record for dataset details and reuse information.
High functional diversity in deep-sea fish communities and increasing intra-specific trait variation with increasing latitude
Open the record for dataset details and reuse information.
Fig. 2 in Silk Spinning Behavior Varies from Species-Specific to Individualistic in Embioptera: Do Environmental Correlates Account for this Diversity?
Fig. 2. Continued.
Data from: Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages
<p>Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 different sites around Bielefeld in Germany revealed little in the way of population structure over a geographic scale of several kilometers. However, on a more local scale we found evidence for elevated relatedness as well as inbreeding. We also observed a significant negative association between the genetic diversity of fruit and the age of the trees under which they were sampled. Taken together, our results suggest that as genets mature, they compete and potentially create conditions under which further spores struggle to become established. By implication, even though this species is widely picked, propagules remain common enough to create strong competition when new habitats become available.</p>
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
<p class="Corps"><span><span><span><span><span><span><span><span><span><span>Sporocarps (fruit bodies) are the sexual reproductive stage in the life cycle of many fungi. They are highly nutritious and consequently vulnerable to grazing by birds and small mammals, and invertebrates, and can be infected by microbial and fungal parasites and pathogens. The complexity of communities thriving inside sporocarps is largely unknown. In this study, we revealed the diversity, taxonomic composition and host-preference of fungicolous fungi (i.e fungi that feed on other fungi) in sporocarps. We carried out DNA metabarcoding of the ITS2 region from 176 sporocarps of 11 wood-decay fungal host species, all collected within a forest in northeast Finland. We assessed the influence of sporocarp traits, such as lifespan, morphology and size, on the fungicolous fungal community. The level of colonisation by fungicolous fungi, measured as the proportion of non-host ITS2 reads, varied between 2.8-39.8% across the 11 host species and was largely dominated by Ascomycota. Host species was the major determinant of the community composition and diversity of fungicolous fungi, suggesting that host adaptation is important for many fungicolous fungi. Furthermore, the alpha-diversity was consistently higher in short-lived and resupinate sporocarps compared to long-lived and pileate ones, perhaps due to a more hostile environment for fungal growth in the latter too. The fungicolous fungi represented numerous lineages in the fungal tree of life, among which a significant portion was poorly represented with reference sequences in databases. </span></span></span></span></span></span></span></span></span></span></p>
Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity
Fungi in the genus Geosmithia (Ascomycota: Hypocreales) are frequent associates of bark beetles and woodborers that colonize hardwood and coniferous trees. One species, Geosmithia morbida, is an economically damaging invasive species. The authors surveyed the Geosmithia species of California and Colorado, USA, to (i) provide baseline data on taxonomy of Geosmithia and beetle vector specificity across the western USA; (ii) investigate the subcortical beetle fauna for alternative vectors of the invasive G. morbida; and (iii) interpret the community composition of this region within the emerging global biogeography of Geosmithia. Geosmithia was detected in 87% of 126 beetle samples obtained from 39 plant species. Twenty-nine species of Geosmithia were distinguished, of which 13 may be new species. Bark beetles from hardwoods, Cupressus, and Sequoia appear to be regular vectors, with Geosmithia present in all beetle gallery systems examined. Other subcortical insects appear to vector Geosmithia at lower frequencies. Overall, most Geosmithia have a distinct level of vector specificity (mostly high, sometimes low) enabling their separation to generalists and specialists. Plant pathogenic Geosmithia morbida was not found in association with any other beetle besides Pityophthorus juglandis. However, four additional Geosmithia species were found in P. juglandis galleries. When integrated with recent data from other continents, a global pattern of Geosmithia distribution across continents, latitudes, and vectors is emerging: of the 29 Geosmithia species found in the western USA, 12 have not been reported outside of the USA. The most frequently encountered species with the widest global distribution also had the broadest range of beetle vectors. Several Geosmithia spp. with very narrow vector ranges in Europe exhibited the similar degree of specialization in the USA. Such strong canalization in association could reflect an ancient origin of each individual association, or a recent origin and a subsequent diversification in North America.
Accompanying Data - Nitrogenous Compound Utilization and Production of Volatile Organic Compounds among Commercial Wine Yeasts Highlight Strain-Specific Metabolic Diversity
<p>This repository contains all the data and some of the performed statistical analysis from all the measurements in the following paper: Scott Jr WT, Van Mastrigt O, Block DE, Notebaart RA, Smid EJ. Nitrogenous compound utilization and production of volatile organic compounds among commercial wine yeasts highlight strain-specific metabolic diversity. Microbiology spectrum. 2021 Aug 31;9(1):10-128.</p><p>Please cite: Scott Jr WT, Van Mastrigt O, Block DE, Notebaart RA, Smid EJ. Nitrogenous compound utilization and production of volatile organic compounds among commercial wine yeasts highlight strain-specific metabolic diversity. Microbiology spectrum. 2021 Aug 31;9(1):10-128.</p><p>Contact: Dr. William T. Scott (william.scott@wur.nl) or Dr. Eddy J. Smid (eddy.smid@wur.nl) for more information</p>
Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs
<p class="MsoNormal"><span>Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pre-treatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three <em>Viola</em> species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through </span><span>double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pre-treatments.</span></p>
Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections
<p>Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. <em>Borrelia burgdorferi</em>, a bacterium that causes Lyme disease, is typically transmitted among wildlife by <em>Ixodes</em> ticks. Despite the existence of many alleles of <em>B. burgdorferi</em>'s <em>sensu stricto</em> outer surface protein C (<em>ospC</em>) gene, most human infections are caused by a small number of <em>ospC</em> alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with <em>ospC</em>. To characterize the wildlife host association of <em>B. burgdorferi</em>'s <em>ospC</em> alleles, we used metagenomics to sequence <em>ospC</em> alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (<em>Peromyscus</em> spp.) and only one HIA was detected at a site where mice were rarely captured. <em>OspC </em>allele U was exclusively found in chipmunks (<em>Tamias striatus</em>), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.</p>
First insights into population structure and genetic diversity versus host specificity in trypanorhynch tapeworms using multiplexed shotgun genotyping
<p>Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) datasets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted <em>Rhinoptericola megacantha</em> (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of <em>R. megacantha</em> are more host-specific and less broadly distributed than adults of <em>C. gracilis</em>, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For <em>R. megacantha</em>, population structure coincided with geography rather than host species. For <em>C. gracilis</em>, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.</p>
Lineage-Specific Class-A GPCR Dynamics Reflect Diverse Chemosensory Adaptations in Lophotrochozoa
Open the record for dataset details and reuse information.
Data for: Cavity-breeding birds create specific microhabitats for diverse arthropod communities in boreal forests
<p class="MsoNormal">The nests of secondary cavity-nesters located in tree cavities may form specific microhabitats of conservation importance due to their limited accessibility and availability. Species-specific nesting materials in nests of different secondary cavity-nesters may furthermore provide very different microhabitats for arthropods. The potential differences in arthropod communities inhabiting nests of different bird species in excavated cavities or nest boxes have, however, rarely been studied despite their relevance for conservation. Here we investigated the diversity and composition of arthropod communities in these different cavity types and bird species' nests in managed boreal forests. We identified morphologically and by DNA-metabarcoding arthropods in nest materials that were collected in and compared between i) woodpecker-size cavities from seven different combinations of cavity type (nest box or excavated cavity), tree species (aspen or pine) and accumulation history of nest materials (single-season cleaned or uncleaned nest boxes that accumulated nests of passerines or an owl species); and ii) nests of two different passerine species in small nest boxes. We identified 64 arthropod taxa in ten orders, from which Diptera, Coleoptera, Siphonaptera, and Lepidoptera were the most abundant. Shannon diversity index was similar among the cavity-nest-type combinations, but taxa richness was the highest in the owl nests. The arthropod communities (especially Histeridae beetles) deviated most from the other types of nests in owl and aspen cavity nests with more advanced decomposition of nest material (soil or wet environment-related taxa). The differences in arthropod communities between the different nest types point out the importance of the ecological chain "tree cavities – bird nests – arthropod communities".</p>
Data for "Analysis of Wilms' tumor protein 1 specific TCR repertoire in AML patients uncovers higher diversity in patients in remission than in relapsed"
<p>This folder holds the data for the paper "Analysis of Wilms' tumor protein 1 specific TCR repertoire in AML patients uncovers higher diversity in patients in remission than in relapsed" (in submission) More information regarding this paper and the data is given in the GitHub repository (https://github.com/sgielis/WT1_TCR)</p> <p>The raw folder contains all MiXCR files for the two studied WT1 epitopes and two VZV epitopes. The VZV epitopes were not taken into account in this paper, but were used to build VZV-specific TCRex models for another paper [in submission]. Since all TCRs for the 4 epitopes were sequences together, this data was used for quality control purposes as explained in the paper. Following 4 folders are present:</p> <ul> <li>run1: TCR data from the first run for WT1-126, WT1-37 and IE62</li> <li>run1_orf18: TCR data from the first run for ORF18</li> <li>run2: WT1-37 data filtered on high and low threshold gating.</li> <li>run 3: extra TCR data for WT1-126, WT1-37 aligned with MiXCR</li> </ul> <p> </p>
Data from: Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages
Open the record for dataset details and reuse information.
Data from: Geosmithia associated with bark beetles and woodborers in the western USA: taxonomic diversity and vector specificity
Open the record for dataset details and reuse information.
Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Open the record for dataset details and reuse information.
Data from: Specific island biogeographic and landscape features shape plant diversity and habitat specialism on edaphic quartz islands in an arid ocean
Open the record for dataset details and reuse information.
Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections
Open the record for dataset details and reuse information.
Species-specific root-shoot ratios in a diverse grassland community
Open the record for dataset details and reuse information.
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.