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.
5,530
datasets available to search
ShareScore release 0.9.0
Dataset results
5,530 results for “informal”
Supplementary material 3 from: Duron Q, Cornulier T, Vidal E, Bourguet E, Ruffino L (2020) Combining live and lethal trapping to inform the management of alien invasive rodent populations in a tropical montane forest. NeoBiota 63: 101-125. https://doi.org/10.3897/neobiota.63.53811
Mean distances (± se) of trapped rats from the edge of the removal area during the four trapping sessions
Supplementary material 4 from: Duron Q, Cornulier T, Vidal E, Bourguet E, Ruffino L (2020) Combining live and lethal trapping to inform the management of alien invasive rodent populations in a tropical montane forest. NeoBiota 63: 101-125. https://doi.org/10.3897/neobiota.63.53811
Distances (in meters) travelled between rats' home range centers in the CMR area and their recapture in the removal area for 27 individuals
Data from: Genetic diversity of the rain tree (Albizia saman) in Colombian seasonally dry tropical forest for informing conservation and restoration interventions
<p><i>Albizia saman</i> is a multipurpose tree species of seasonally dry tropical forests (SDTFs) of Mesoamerica and northern South America typically cultivated in silvopastoral and other agroforestry systems around the world, a trend that is bound to increase in light of multimillion hectare commitments for forest and landscape restoration. The effective conservation and sustainable use of <i>A. saman</i> requires detailed knowledge of its genetic diversity across its native distribution range of which surprisingly little is known to date. We assessed the genetic diversity and structure of <i>A.saman</i> across twelve representative locations of SDTF in Colombia, and how they may have been shaped by past climatic changes and human influence. We found four different genetic groups which may be the result of differentiation due to isolation of populations in pre-glacial times. The current distribution and mixture of genetic groups across STDF fragments we observed might be the result of range expansion of SDTFs during the last glacial period followed by range contraction during the Holocene and human-influenced movement of germplasm associated with cattle ranching. Despite the fragmented state of the presumed natural <i>A. saman</i> stands we sampled we did not find any signs of inbreeding, suggesting that gene flow is not jeopardized in humanized landscapes. However, further research is needed to assess potential deleterious effects of fragmentation on progeny. Climate change is not expected to seriously threaten the <i>in situ</i> persistence of <i>A. saman</i> populations and might present opportunities for future range expansion. However, the sourcing of germplasm for tree planting activities needs to be aligned with the genetic affinity of reference populations across the distribution of Colombian SDTFs. We identify priority source populations for i<i>n situ</i> conservation based on their high genetic diversity, lack or limited signs of admixture and/or genetic uniqueness.</p>
FIGURE 3 in Amphipoda species (Suborders: Amphilochidea and Senticaudata) from Vasiliko Bay, Cyprus: New records, information on their biogeography and an annotated checklist from the coasts of Cyprus
FIGURE 3. Number of species per family (individuals classified to higher taxa are not included in the figure).
FIGURE 2 in Amphipoda species (Suborders: Amphilochidea and Senticaudata) from Vasiliko Bay, Cyprus: New records, information on their biogeography and an annotated checklist from the coasts of Cyprus
FIGURE 2. Number of individuals per family. (80 individuals that were classified to higher taxa (Amphilochidea) are not included in the figure).
FIGURE 1 in Amphipoda species (Suborders: Amphilochidea and Senticaudata) from Vasiliko Bay, Cyprus: New records, information on their biogeography and an annotated checklist from the coasts of Cyprus
FIGURE 1. Study area, sampling stations and Posidonia oceanica distribution in Vasiliko Bay, Cyprus.
Supporting Information of the article "mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress"
<p>Supporting Information of the article "mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress". </p>
Data from: Foraging zebra finches (Taeniopygia guttata) are public information users rather than conformists
<p>Social learning enables adaptive information acquisition provided that it is not random but selective. To understand species typical decision-making and to trace the evolutionary origins of social learning, the heuristics social learners use need to be identified. Here, we experimentally tested the nature of majority influence in the zebra finch. Subjects simultaneously observed two demonstrator groups differing in relative and absolute numbers (ratios 1:2 / 2:4 / 3:3 / 1:5) foraging from two novel food sources (black and white feeders). We find that demonstrator groups influenced observers' feeder choices (social learning), but that zebra finches did not copy the majority of individuals. Instead, observers were influenced by the pecks of their demonstrators, and in an anti-conformist fashion. These results indicate that zebra finches are not conformist, but are public information users.</p>
Microbial structures in the surface sediments of Shenhu Area, South China Sea-Appendix A. Supporting information
<p>Microbial structures in the surface sediments of Shenhu Area, South China Sea-Appendix A. Supporting information</p>
Using genomic information for management planning of an endangered perennial, Viola uliginosa
Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadically flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site associated DNA sequencing (ddRAD-seq). We found monophyletic populations, high levels of inbreeding (mean population FSNP = 0.407 – 0.945), low effective population sizes (Ne = 0.8 – 50.9), indications of past demographic expansion and rare long-distance dispersal. Our results are important in implementing conservation strategies for Viola uliginosa, which should include founding of seed banks, ex situ cultivations, and re-introductions with individuals of proper origin, combined with continuous population monitoring and habitat management.
Supplementary information for integrating sequence capture and restriction-site associated DNA sequencing to resolve recent radiations of Pelagic seabirds
<p><b>The diversification of modern birds has been shaped by a number of radiations. Rapid diversification events make reconstructing the evolutionary relationships among taxa challenging due to the convoluted effects of incomplete lineage sorting (ILS) and introgression. Phylogenomic datasets have the potential to detect patterns of phylogenetic incongruence, and to address their causes. However, the footprints of ILS and introgression on sequence data can vary between different phylogenomic markers at different phylogenetic scales depending on factors such as their evolutionary rates or their selection pressures. We show that combining phylogenomic markers that evolve at different rates, such as paired-end double-digest restriction site-associated DNA (PE-ddRAD) and ultraconserved elements (UCEs), allows a comprehensive exploration of the causes of phylogenetic discordance associated with short internodes at different timescales. We used thousands of UCE and PE-ddRAD markers to produce the first well-resolved phylogeny of shearwaters, a group of medium-sized pelagic seabirds amongst the most phylogenetically controversial and endangered bird groups. We found that phylogenomic conflict was mainly derived from high levels of ILS due to rapid speciation events. We also documented a case of introgression, despite the high philopatry of shearwaters to their breeding sites, which typically limits gene flow. We integrated state-of-the-art concatenated and coalescent-based approaches to expand on previous comparisons of UCE and RAD-Seq datasets for phylogenetics, divergence time estimation and inference of introgression, and we propose a strategy to optimise RAD-Seq data for phylogenetic analyses. Our results highlight the usefulness of combining phylogenomic markers evolving at different rates to understand the causes of phylogenetic discordance at different timescales.</b></p>
Data from: Real-time assessment of hybridization between wolves and dogs: combining non-invasive samples with ancestry informative markers
Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in Northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in non-invasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization, and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.
Data from: Observed fitness may affect niche overlap in competing species via selective social information use
Social information transmission is important because it enables horizontal spread of behaviors, not only between conspecifics, but also between individuals of different species. Because interspecific social information use is expected to take place among species with similar resource needs, it may have major consequences for the emergence of local adaptations, resource sharing and community organization. Social information use is expected to be selective, but the conditions promoting it in an interspecific context are not well known. Here, we experimentally test whether pied flycatchers (Ficedula hypoleuca) use the clutch size of great tits (Parus major) in determining the quality of the observed individual and use it as a basis in decision-making. We show that pied flycatchers (Ficedula hypoleuca) copied or rejected a novel nest-site feature preference of great tits (Parus major), experimentally manipulated to exhibit high or low fitness (clutch size), respectively. Our results demonstrate that the social transmission of behaviors across species can be highly selective in response to observed fitness, plausibly making the phenomenon adaptive. In contrast with the current theory of species coexistence, overlap between realized niches of species could dynamically increase or decrease depending on the observed success of surrounding individuals.
Data from: Description of a new species of Hedruris Nitzsch, 1821 (Nematoda, Hedruridae) from freshwater turtles in Argentina, with information on its life cycle and a review of the genus's host and geographic distribution
Hedruris dratini n. sp. (Nematoda, Hedruridae) is described from freshwater turtles in Argentina and information about its life cycle provided. The new species differs from the remaining species of the genus by possessing an excretory pore, and the nerve ring and deirids being positioned at equal distance from the anterior end. Additionally, H. dratini n. sp. has mammilated eggs and males possess nine pairs of caudal papillae. The first life cycle within the genus including an amphipod as intermediate host and a reptile as a definitive host is presented. Furthermore, the host and geographic distribution of species of the genus Hedruris Nitzsch, 1821 are analyzed. Although the genus has a cosmopolitan distribution and parasitizes a great diversity of hosts, the majority of its species follow a Gondwanian distribution and its preferred hosts are amphibians.
Data from: A four-questions perspective on public information use in sticklebacks (Gasterosteidae)
Whether learning primarily reflects general processes or species-specific challenges is a longstanding matter of dispute. Here we present a comprehensive analysis of public information use (PI-use) in sticklebacks (Gasterosteidae). PI-use is a form of social learning by which animals are able to assess the relative quality of resources, here prey patches, by observing the behaviour of others. PI-use was highly species-specific with only two of the assayed species, Pungitius spp. and their closest relative Culaea inconstans showing evidence of PI-use. We saw no effects of ontogenetic experience upon PI-use in P. pungitius. Experiments with live demonstrators and animated fish revealed that heightened activity and feeding strikes by foraging conspecifics are important cues in the transmission of PI. Finally, PI-use was the only form of learning in which P. pungitius and another stickleback, Gasterosteus aculeatus differed. PI-use in sticklebacks is species-specific and may represent an 'ecological specialisation' for social foraging. Whether this reflects selection on perception, attentional or cognitive processes remains to be determined.
Data from: Predictors of alcohol consumption among in-school adolescents in the Central Region of Ghana: a baseline information for developing cognitive-behavioural interventions
Background and purpose: Despite a recent shift in school going adolescents' engagement in health compromising behaviours has serious socio-economic implications on developing societies, it is surprising that baseline information through research that would influence planned interventions is sparse. The purpose of this study was to investigate the prevalence of alcohol drinking behaviours among in-school adolescents in the Junior High Schools (JHS) in the Central Region of Ghana. Methods and results: Using a descriptive cross-sectional design, multistage sampling procedures were used to sample 1400 school going adolescents in JHS in the Central Region. Preliminary results using simple frequencies and percentages revealed 42% alcohol drinking prevalence in the region. High prevalence of drunkenness (73%, n = 405) and early exposure to alcohol drinking when students were in primary school (52%, n = 286) were noted. Community festivals and use of alcohol as a form of medicine were enabling factors of alcohol consumption in the region. Binary logistic regression analysis also showed that geographical location was a significant predictor of alcohol drinking among school going adolescents, with students in the southern and central part of the region at greater risks of drinking alcohol than those from the northern part (OR = .696, 95% CI = 0.52-926, p = .013). However, no statistical significant variations were found in the odds of drinking alcohol within age (OR = 1.13, 95% CI = 0.86-1.48, p = .370), gender (OR = .81, 95% CI = 0.65-1.01, p = .06), religious affiliation (OR = 1.33, 95% CI = 0.94-1.89, p = .10), parental communication (OR = .86, 95% CI = 0.66-1.06, p = .13), academic performance (OR = 1.07, 95% CI = 0.79-1.45, p = .05) and socioeconomic status (OR = 1.20, 95% CI = 0.95-1.53, p = .12). Conclusions: With this baseline data, it was recommended that schools' curricula should include preventive cognitive-behavioural interventions that teach drug resistance skills and anti-drug norms. These interventions would foster the development of requisite knowledge and social skills (e.g., developing competence) for resisting social and peer influences that may trigger alcohol use and perhaps other drugs. Potentially, the motivation for alcohol use among school going adolescents in the region would be minimized, if not prevented.
Data from: Bacterial biophotons as non-local information carriers: species-specific spectral characteristics of a stress response
Studies by Alexander Gurwitsch in the 1920's with onion root cells revealed the phenomenon of mitogenetic radiation. Subsequent works by Popp, Van Wijk, Quickenden, Tillbury and Trushin have demonstrated a link between Gurwitsch's mitogenetic radiation and the biophoton, emissions of light correlated with biological processes. The present study seeks to expand upon these works and explore whether biophoton emissions of bacterial cultures is used as an information carrier of environmental stress. Bacterial cultures (Escherichia coli and Serratia marcescens) were incubated for 24 h in 5 mL of Nutrient Broth to stationary phase and cell densities of ~107 cells/mL. Cultures of E. coli were placed upon a photomultiplier tube housed within a dark box. A second bacterial culture, either E. coli or S. marcescens, was placed in an identical dark box at a distance of 5 m and received injections of hydrogen peroxide. Spectral analyses revealed significant differences in peak frequencies of 7.2, 10.1, and 24.9 Hz in the amplitude modulation of the emitted biophoton signal with respect to whether a peroxide injection occurred or not, and whether the species receiving the injection was E. coli or S. marcescens. These and the subsequent results of discriminant functions suggest that bacteria may release biophotons as a non-local communication system in response to stress, and that these biophotons are species specific.
Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein–DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each siteʼs locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal–Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
Data from: Constructing more informative plant-pollinator networks: visitation and pollen deposition networks in a heathland plant community
Interaction networks are widely used as tools to understand plant–pollinator communities, and to examine potential threats to plant diversity and food security if the ecosystem service provided by pollinating animals declines. However, most networks to date are based on recording visits to flowers, rather than recording clearly defined effective pollination events. Here we provide the first networks that explicitly incorporate measures of pollinator effectiveness (PE) from pollen deposition on stigmas per visit, and pollinator importance (PI) as the product of PE and visit frequency. These more informative networks, here produced for a low diversity heathland habitat, reveal that plant–pollinator interactions are more specialized than shown in most previous studies. At the studied site, the specialization index Embedded Image was lower for the visitation network than the PE network, which was in turn lower than Embedded Image for the PI network. Our study shows that collecting PE data is feasible for community-level studies in low diversity communities and that including information about PE can change the structure of interaction networks. This could have important consequences for our understanding of threats to pollination systems.
Data from: Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray–Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity—a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
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.