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.
1,037
datasets available to search
ShareScore release 0.9.0
Dataset results
1,037 results for “large-scale”
Data from: Spatial and temporal aridity gradients provide poor proxies for plant-plant interactions under climate change: a large-scale experiment
1. Plant-plant interactions may critically modify the impact of climate change on plant communities. However, the magnitude and even direction of potential future interactions remains highly debated, especially for water limited ecosystems. Predictions range from increasing facilitation to increasing competition with future aridification. 2. The different methodologies used for assessing plant-plant interactions under changing environmental conditions may affect the outcome but they are not equally represented in the literature. Mechanistic experimental manipulations are rare compared to correlative approaches that infer future patterns from current observations along spatial climatic gradients. 3. Here, we utilize a unique climatic gradient in combination with a large-scale, long-term experiment to test whether predictions about plant-plant interactions yield similar results when using experimental manipulations, spatial gradients or temporal variation. We assessed shrub-annual interactions in three different sites along a natural rainfall gradient (spatial) during 9 years of varying rainfall (temporal) and 8 years of dry and wet manipulations of ambient rainfall (experimental) that closely mimicked regional climate scenarios. 4. The results were fundamentally different among all three approaches. Experimental water manipulations hardly altered shrub effects on annual plant communities for the assessed fitness parameters biomass and survival. Along the spatial gradient, shrub effects shifted from clearly negative to mildly facilitative towards drier sites, whereas temporal variation showed the opposite trend: more negative shrub effects in drier years. 5. Based on our experimental approach, we conclude that shrub-annual interaction will remain similar under climate change. In contrast, the commonly applied space-for time approach based on spatial gradients would have suggested increasing facilitative effects with climate change. We discuss potential mechanisms governing the differences among the three approaches. 6. Our study highlights the critical importance of long-term experimental manipulations for evaluating climate change impacts. Correlative approaches, e.g. along spatial or temporal gradients, may be misleading and overestimate the response of plant-plant interactions to climate change.
Data from: Density dependence and population regulation in marine fish: a large-scale, long-term field manipulation
Do small-scale experiments showing spatial density dependence in marine fishes scale-up to temporal density dependence and regulation of relatively large local populations? If so, what are the causative mechanisms and their implications? We conducted an 8-year multi-generation study of population dynamics of bicolor damselfish (Stegastes partitus) inhabiting four large coral reefs in the Bahamas. After a 4-year baseline period, it was clear that two populations naturally received very few settlement-stage larvae, so recruitment of recently settled fish was artificially enhanced at one low-settlement reef and reduced at one high-settlement reef to ensure a broad range of population sizes over which to test for regulation. Over all 8 years, populations on the two naturally high-settlement reefs experienced temporal density dependence in multiple per capita demographic rates mortality, survival to adulthood, and fecundity. These local populations also displayed components of regulation persistence, boundedness, and return tendency. Reefs supporting regulated populations were structurally complex, providing sufficient prey refuges that ensured high survival at low densities. In contrast, populations at low-settlement reefs experienced either density-independent or slightly inversely density-dependent demographic rates, even though recruitment was artificially augmented to high levels at one reef. There was no evidence of regulation at these reefs, and indeed, one local population suffered temporary extirpation. Here, habitat complexity was relatively low, increasing the risk of predation, especially at low population densities when fish would have to travel longer distances when finding mates or home sites inhabited by conspecifics. Among all demographic parameters, density dependence in individual growth (an indicator of within-species competition for food) was least correlated with the presence or absence of local population regulation. We conclude that, for systems like these, the environmental context of a local population -- especially predation risk and the distribution and abundance of spatial refuges -- is more important than the magnitude of larval supply alone in determining the existence of regulating density dependence. At the broader metapopulation scale, density dependence in both survival and fecundity exogenously caused by predation may provide regulation for the entire stock, even when endogenous within-species competition (assumed to be important in most fisheries models) is weak.
Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada
Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with investigations into the nature of ecological interactions in a community-level data set. We collected 1,195 gastropods and crabs in British Columbia. First, the General mixed Yule-coalescent (GMYC) and the Poisson Tree Processes (PTP) methods for proposing primary species-hypotheses based on cox1 sequences were evaluated against an integrative taxonomic framework. We then used data on the geographic distribution of delineated species to test species co-occurrence patterns for non-randomness using community-wide and pairwise approaches. Results showed that PTP generally outperformed GMYC and thus constitutes a more effective option for producing species-hypotheses in community-level datasets. Non-random species co-occurrence patterns indicative of ecological relationships or habitat preferences were observed for grazer gastropods, whereas assemblages of opportunistic omnivorous gastropods and crabs appeared influenced by random processes. Species-pair associations were consistent with current ecological knowledge, thus suggesting that applying community assembly within a large taxonomical framework constitutes a valuable tool for assessing ecological interactions. Combining phylogenetic, morphological and co-occurrence data enabled an integrated view of communities, providing both a conceptual and pragmatic framework for biodiversity assessments and investigations into community dynamics.
Data from: Bat communities respond positively to large-scale thinning of forest regrowth
Over half of the world's forests are secondary regrowth and support considerable biodiversity. Thinning of these forests is a widespread management practice that can affect forest species, including echolocating bats and their prey. We compared total activity of 11 bat taxa, foraging activity of six bat guilds and biomass of 11 insect orders across four forest thinning categories in managed remnant eucalypt forests in south-eastern Australia: unthinned regrowth, forest thinned recently (0–4 years) and in the medium term (5–10 years) and reference (mature open forest). Thinning had been carried out at large (˜350 ha) spatial scales. Total bat activity was 60% less and foraging activity was 80% less in unthinned regrowth, compared to reference sites, but activity levels were similar among thinned and reference sites. Insect biomass was greatest in unthinned sites, and while bat activity was related to prey biomass, this relationship was weak in unthinned sites. Together, this suggests that forest structure was more important than prey availability or time since thinning in influencing bat activity patterns. Synthesizing our findings with the broader literature on bats and thinning, we found support for a clutter threshold of 1100 stems ha−1, above which bat activity was markedly lower, across two continents (the USA and Australia) and four broad vegetation types (eucalypt, conifer, deciduous and mixed forests). While elsewhere bats with adaptive traits for open habitats generally respond positively to thinning, in our study, species with traits consistent with clutter tolerance (high call frequency and low wing aspect ratio) had lowest activity levels (up to 22 times) in unthinned regrowth compared to all other forest types. Synthesis and applications. Widespread dense regrowth forest can restrict movement and foraging of bats, even those adapted to clutter. We recommend thinning dense regrowth or plantations to below 1100 stems ha−1 when targeting bat foraging habitat, but effects of thinning on roost habitat and other forest biota require further investigation.
Data from: Restriction to large-scale gene flow versus regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)
The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for many other taxa. Three species of Escarpia, Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have been described based on morphology, but are not discriminated through the use of mitochondrial markers (cytochrome oxidase subunit 1; large ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28 microsatellites to (i) determine the level of genetic differentiation, if any, among the three geographically separated entities and (ii) identify possible population structure at the regional scale within the GoM and West Africa. Results at the global scale support the occurrence of three genetically distinct groups. At the regional scale among eight sampling sites of E. laminata (n = 129) and among three sampling sites of E. southwardae (n = 80), no population structure was detected. These findings suggest that despite the patchiness and isolation of seep habitats, connectivity is high on regional scales.
Data from: Automated DNA-based plant identification for large-scale biodiversity assessment
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA-barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic reconstruction. We describe the strategies used to establish these steps and the optimisation of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.
Data from: Large-scale phylogeny of chameleons suggests African origins and Eocene diversification
Oceanic dispersal has emerged as an important factor contributing to biogeographic patterns in numerous taxa. Chameleons are a clear example of this, as they are primarily found in Africa and Madagascar, but the age of the family is post-Gondwanan break-up. A Malagasy origin for the family has been suggested, yet this hypothesis has not been tested using modern biogeographic methods with a dated phylogeny. To examine competing hypotheses of African and Malagasy origins, we generated a dated phylogeny using between six and 13 genetic markers, for up to 174 taxa representing greater than 90 per cent of all named species. Using three different ancestral-state reconstruction methods (Bayesian and likelihood approaches), we show that the family most probably originated in Africa, with two separate oceanic dispersals to Madagascar during the Palaeocene and the Oligocene, when prevailing oceanic currents would have favoured eastward dispersal. Diversification of genus-level clades took place in the Eocene, and species-level diversification occurred primarily in the Oligocene. Plio-Pleistocene speciation is rare, resulting in a phylogeny dominated by palaeo-endemic species. We suggest that contraction and fragmentation of the Pan-African forest coupled to an increase in open habitats (savannah, grassland, heathland), since the Oligocene played a key role in diversification of this group through vicariance.
Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada
Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774–individual, 267–population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
Data from: Kicking Triturus arntzeni when it's down: large-scale nuclear genetic data confirm that newts from the type locality are genetically admixed
We collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality at Vrtovać in eastern Serbia. We compare these data to a reference set composed of the four crested newt species distributed in eastern Serbia namely T. cristatus, T. dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of these species the newts from the type locality of T. arntzeni should be attributed. The majority of alleles in individuals from Vrtovać is derived from T. macedonicus, but a considerable number of T. ivanbureschi alleles is also present; alleles typical for T. cristatus and T. dobrogicus are found at low frequency. Accordingly, we interpret Vrtovać as a T. macedonicus – T. ivanbureschi hybrid population, albeit not composed of F1 hybrids but of genetically admixed individuals derived through multiple generations of backcrossing. The data support the notion that the name T. arntzeni should not be applied to a species newly distinguished in T. karelinii sensu lato (to which the name T. ivanbureschi has been given). We conclude that because of the hybrid nature of the individuals from Vrtovać, the name T. arntzeni should be placed not only in the synonymy of T. macedonicus but also in the synonymy of T. ivanbureschi. In this study we demonstrate that next-generation sequencing can provide high quality data for type material with degraded DNA and therefore can play an important role in taxonomy.
FIGURE 11 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 11. Distribution of Pseudotomias species in Tanzania. Square: P. kisarawe n. sp. Circle: P. usambaricus n. sp.
FIGURE 10 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 10. Morphological details of female Pseudotomias kisarawe n. sp. A. Lateral view on ovipositor B. Subgenital plate.
FIGURE 9 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 9. Morphological details of male Pseudotomias kisarawe n. sp. A. Pronotum and head B. Semilateral view on abdominal apex C. Subgenital plate.
FIGURE 5 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 5. Lateral view on ovipositor of Pseudotomias usambaricus n. sp. (A) and subgenital plate (B).
FIGURE 3 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 3. Morphological details of male Pseudotomias usambaricus n. sp. A. Upper part of face showing expanded area formed by face closing gap between scapi of antennae; the fastigium verticis just protrudes above. B. Dorsal view on abdominal apex with undifferentiated 9th and 10th abdominal tergites and stout incurved cerci. C. Lateral view on abdominal apex. D. Subgenital plate.
FIGURE 4. Pseudotomias usambaricus n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 4. Pseudotomias usambaricus n. sp. female. A. Resting posture with tegmina widely spread. B. Lateral view on head and pronotum.
FIGURE 1. Male Pseudotomias usambaricus n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 1. Male Pseudotomias usambaricus n. sp. caught in the Nilo forest reserve, East Usambara Mountains.
Large-scale semantic indexing of Spanish biomedical literature using contrastive transfer learning
Open the record for dataset details and reuse information.
cigChannel: A large-scale 3D seismic dataset with labeled paleochannels for advancing deep learning in seismic interpretation
<h2>Assorted channel subset of the cigChannel dataset (V1.0)</h2> <h2>Expansion package of folded and faulted structures</h2> <div> <p>This version includes the last 100 samples (400 samples in total) of the assorted channel subset. Each sample features folded and faulted structures. Explanations of the uploaded zip files are listed below: </p> </div> <ul> <li>Assorted_Channel_Ip_xx-xx.zip: Seismic impedance volumes of sample No.xx to No.xx.</li> <li>Assorted_Channel_Label_xx-xx.zip: Binary-class label volumes of sample No.xx to No.xx, where the value 0 represents the background (non-channel areas) and 1 represents the channel.</li> <li>Assorted_Channel_Seismic_xx-xx.zip: Seismic (amplitude) volumes of sample No.xx to No.xx.</li> </ul> <h3>Portal to the assorted channel subset (main package, the first 300 samples):</h3> <ul> <li>Assorted channel subset: <a href="https://doi.org/10.5281/zenodo.11044512" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11044512</a></li> </ul> <h3>Portals to the other subsets:</h3> <ul> <li>Submarine canyon subset: <a href="https://doi.org/10.5281/zenodo.11079950" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11079950</a></li> <li>Meandering channel subset: <a href="https://doi.org/10.5281/zenodo.11078794" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11078794</a></li> <li>Tributary channel network subset: <a href="https://doi.org/10.5281/zenodo.11073030" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.11073030</a></li> </ul>
Output files for Degassing of CO2 triggers large-scale loss of helium from magma oceans
<p>This upload includes output files for the paper Degassing of CO2 triggers large-scale loss of helium from magma oceans.</p>
Data set for analyzing scaling and criticality in large-scale social systems regulated by global factors
<ul><li><strong>Research information</strong>:<ul><li>Title: Scaling and criticality in large-scale social systems regulated by global factors</li><li>Abstract: How do individuals in large-scale social systems behave in response to global factors and what kinds of macroscopic dynamics will emerge as consequences? Here we conduct a naturalistic observation of the daily consumer behaviours of 190,000 individuals from January 2018 to December 2022, extracting the long-term consumption dynamics of about 6000 types of commodities from approximately 2.2 million purchase orders. The consumption dynamics is subdivided into trend, seasonal, and random components, whose dynamic processes across scales are analyzed by a renormalization group. we discover that the coronavirus pandemic, an exogenetic factor acting on the social system, regulates the scaling and criticality of consumption dynamics. On a large time scale, the long-term dynamics of the system, regardless of arising from trend, seasonal, or random individual behaviours, is pushed towards a boundary between independent and correlated phases as the pandemic erupts. On a smaller time scale, short-term consumption dynamics exhibits more diversities in response to the pandemic. While the trend and random behaviours of individuals are driven to quasi-criticality and exhibit scale-invariance as the pandemic breaks out, seasonal behaviours are more robust against regulations. Overall, our study provides insights into the regulation mechanisms of global factors on the dynamics of large-scale and heterogeneous social systems.</li></ul></li><li><strong>Data set description</strong>:<ul><li>RawData: A csv file for approximately 2.2 million times purchase orders made by around 190,000 individuals before, during, and after the outbreak of coronavirus disease 2019 (COVID-19). </li><li>ConsumptionDynamics: A csv file that describes the daily evolution of the consumption frequencies for approximately 6,000 types of commodities. Each row denotes an extracted time series that measures the number of times a commodity is purchased each day. Each column denotes a single day.</li><li>Note that the names of commodities in current data set are writen in Chinese. </li></ul></li></ul><p> </p><p> </p>
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.