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1,157 results for “Limited data”
Data for: Limited host availability disrupts the genetic correlation between virulence and transmission
<p>Virulence is expected to be linked to parasite fitness via transmission. However, it is not clear whether this relationship is genetically determined, nor if it differs when transmission occurs continuously during, or only at the end of, the infection period. Here, we used inbred lines of the macro-parasitic spider mite <em>Tetranychus urticae</em> to disentangle genetic vs non-genetic correlations among traits, while varying parasite density and opportunities for transmission. A positive genetic correlation between virulence and the number of transmitting stages produced was found under continuous transmission. However, if transmission occurred only at the end of the infection period, this genetic correlation disappeared. Instead, we observed a negative relationship between virulence and the number of transmitting stages, driven by density dependence. Thus, within-host density dependence caused by reduced opportunities for transmission may hamper selection for higher virulence, providing a novel explanation as to why limited host availability leads to lower virulence.</p>
Data for: Hedgerows have contrasting effects on pollinators and natural enemies and limited spillover effects on apple production
<p>Agricultural intensification has resulted in a decline in insect biodiversity and threatens the provision of valuable ecosystem services. Agri-environment schemes (AESs) have been implemented in an effort to conserve biodiversity on farmland and increase agricultural sustainability, but their effectiveness can vary widely. To better determine which factors influence AES effectiveness, the relative roles of local habitat features, habitat quality, and landscape context need to be further explored. The aim of this study was to determine the most important factors influencing field margin AES effectiveness in commercial apple orchards, in terms of arthropod biodiversity conservation and ecosystem service provision. We surveyed wild bees and aphid natural enemies in field margins and apple trees in 20 orchards, ten bordered by hedgerow field margins (an AES) and ten with herbaceous field margins (no hedgerows present, not an AES). We considered field margin floral resources and the cover of semi-natural habitat in the surrounding landscape as indicators of local habitat quality and landscape context, respectively. We furthermore quantified pollination and pest control as measures of ecosystem service delivery and the relationship between arthropod communities and apple yield (initial and final fruit set) and quality. We found that hedgerow presence strongly predicted both pollinator and natural enemy communities and that these relationships were more pronounced than those with local habitat quality and landscape context. Hedgerows were negatively related to wild bee richness and abundance within the orchard, and positively related to natural enemy richness and abundance at the field margin but not within the orchard. We found no relationships between local and landscape factors and ecosystem service delivery, and no relationship between wild bee communities and apple yield, suggesting that apple is not pollen limited in our study system. There was, however, a negative relationship between natural enemy richness and initial fruit set. We conclude that annually cut hedgerows can benefit the conservation of natural enemies, but have limited arthropod-mediated private benefits for apple production, and likely need to be supplemented with additional local habitat resources for the conservation of wild bees. Our findings indicate that local habitat factors can strongly influence biodiversity regardless of landscape context, but that AESs likely need to be designed with separate biodiversity and ecosystem service targets, and specific taxonomic groups, in mind.</p>
Consilience across multiple, independent genomic data sets reveals species in a complex with limited phenotypic variation
<p>Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus <em>Ehrharta, </em>whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of <em>Ehrharta </em>and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualises multiple values of K. Given that the two genomic data sets are fully independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the <em>E. setacea</em> and <em>E. rehmannii </em>complexes, with the <em>E. ramosa</em> complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach.</p>
Generated data for "Limited ventilation of the central Baltic Sea due to elevated oxygen consumption" paper
<p>This data are essential for reproducing the figures from Naumov et al. "Limited ventilation of the central Baltic Sea due to elevated oxygen consumption" paper. Each archive is named after one of the ten figures and includes the data necessary for that specific figure. Some data are used in more than one figure. In some cases, performing a particular type of analysis with the given data (linear regression, for instance) is necessary to fully reproduce the figure.</p>
Data from: Phosphorus limitation determines the quality of dissolved organic matter released by marine heterotrophic prokaryotes
<p>We determined phosphorus (P) limitation effect on the quantity and quality of dissolved organic matter (DOM) released by heterotrophic prokaryotes (HP). We grew 2 single bacterial strains, Photobacterium angustum and Sphingopyxis alaskensis, and natural HP communities collected in fall and spring from the Mediterranean Sea, on glucose under 2 treatments: P-replete vs. P-limiting. DOM release by HP comprised up to 30 % of the initial carbon provided for growth. P availability influenced carbon allocation to different cellular processes (respiration vs. growth), but did not significantly affect the quantity of DOM released by HP. However, using fluorescence spectroscopy, we demonstrated an effect of P-limitation on DOM quality, with a predominance of humic-like compounds under P-limitation but protein-like compounds under P-repletion. Our results suggest that P-limitation could determine the fate of HP-derived DOM in the ocean, thus affecting the microbial carbon pump.</p>
Data from: Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild
<p>The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection, or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.</p>
Code and data for: Setting sustainable limits on anchoring to improve the resilience of coral reefs
<p>This dataset relates to the journal article: Mason, R. A. B., Bozec, Y.-M., Mumby, P. J. (2023) "Setting sustainable limits on anchoring to improve the resilience of coral reefs" <em>Marine Pollution Bulletin</em> 189: 114721 and is comprised of the following components:</p> <p>- The code and data used to perform the modelling that is described in the journal article. </p> <p>- The data outputs that resulted from running the code.</p> <p>- The code used to make figures using these data outputs, which are illustrated in the journal article</p>
Data from: Replicate contact zones suggest a limited role of plumage in reproductive isolation among subspecies of the Variable Seedeater (Sporophila corvina)
<p>After establishing secondary contact, recently diverged populations may remain reproductively isolated or may hybridize to a varying extent depending on factors such as hybrid fitness and the strength of assortative mating. Here, we used genomic and phenotypic data from three independent contact zones between subspecies of the Variable Seedeater (<em>Sporophila corvina</em>) to examine how coloration and genetic divergence shape patterns of hybridization. We found that differences in plumage coloration are likely maintained by divergent selection across contact zones; however, the degree of plumage differentiation does not match overall patterns of hybridization. Across two parallel contact zones between populations with divergent phenotypes (entirely black vs. pied plumage), populations hybridized extensively across one contact zone but not the other, suggesting that plumage divergence is not sufficient to maintain reproductive isolation. Where subspecies hybridized, hybrid zones were wide and formed by later-generation hybrids, suggesting frequent reproduction and high survivorship for hybrid individuals. Moreover, contemporary gene flow has played an important role in shaping patterns of genetic structure between populations. Replicated contact zones between hybridizing taxa offer a unique opportunity to explore how different factors interact to shape patterns of hybridization. Overall, our results demonstrate that divergence in plumage coloration is important in reducing gene flow but insufficient in maintaining reproductive isolation in this clade, and that other factors such as divergence in song and time since secondary contact may also play an important role in driving patterns of reduced hybridization and gene flow.</p>
Data for: Dispersal-limited symbionts exhibit unexpectedly wide variation in host specificity
<p>A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macroevolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode versus multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. Comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts.</p>
Data from: Increased male-induced harm in response to female-limited selection: interactive effects between intra- and interlocus sexual conflict?
<p><span>Interlocus sexual conflict (IRSC) occurs because of shared interactions that have opposite effects on male and female fitness. Typically, it is assumed that loci involved in IRSC have sex-limited expression and are thus not directly affected by selective pressures acting on the other sex. However, if loci involved in IRSC have pleiotropic effects in the other sex, intersexual selection can shape the evolutionary dynamics of conflict escalation and resolution, as well as the evolution of reproductive traits linked to IRSC loci, and vice versa. Here we used an artificial selection approach in</span><span> Japanese quail (<em>Coturnix</em> <em>japonica</em>) to test if female-limited selection on reproductive investment affects the amount of harm caused by males during mating. We found that males originating from lines selected for high female reproductive investment caused more oxidative damage in the female reproductive tract than males originating from lines selected for low female reproductive investment. This male-induced damage was specific to the oviduct and not found in other female tissues, suggesting that it was ejaculate-mediated. Our results suggest that intersexual selection shapes the evolution of IRSC and that male-induced harm may contribute to the maintenance of variation in female reproductive investment.</span></p>
Dataset for "Generalizing property prediction of ionic liquids from limited labeled data: a one-stop framework empowered by transfer learning"
<p>Dataset for "Generalizing property prediction of ionic liquids from limited labeled data: a one-stop framework empowered by transfer learning", codes can be found <a href="https://github.com/GuzhongChen/ILTransR">here</a>.</p>
Epistemic Insight Initiative Data set: Findings from a hands-on science intervention to build school students' agency and epistemic insight into the power and limitations of science.
<p>Data set that reports on the Findings from a hands-on science intervention to build school students’ agency and epistemic insight into the power and limitations of science.</p> <p>We report on an empirical study that sought to address three questions:</p> <ul> <li>A study to extend the cognitive science of insight into the field of children’s developing understanding of the power and limitations of science</li> <li>A study to examine the effectiveness of the Epistemic Insight (EI) strategy which is designed to give each child hands-on, minds-on science</li> <li>A study to examine the effectiveness of the EI strategy to sustain science activity in schools during the challenging conditions of the pandemic</li> </ul> <p>1919 children and 63 teachers from 24 schools in England took part in the project. This includes both primary and secondary schools. The data reported here are taken from ten primary schools representing 1045 children aged 8-12 in years 4 to 7.</p> <p> </p>
Reproducibility Package (Raw Data) for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding
<p>Raw data results from the simulations using PINN methods and PetIBM for the paper at: https://github.com/barbagroup/jcs_paper_pinn</p>
Data from: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river
<p>Hybridization between coastal cutthroat trout (<em>Oncorhynchus clarkii clarkii</em>) and steelhead (<em>O. mykiss</em>) was assessed in the Smith River, California. Individuals were categorized as pure or as one of 10 hybrid classes using 30 'diagnostic' single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e., jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.</p>
Data from: Parasites, depredators, and limited resources as potential drivers of winter mortality of feral honeybee colonies in German forests
<p>Wild honeybees (<em>Apis mellifera</em>) are considered extinct in most parts of Europe. The likely causes of their decline include increased parasite burden, lack of high-quality nesting sites and associated depredation pressure, and food scarcity. In Germany, feral honeybees still colonize managed forests, but their survival rate is too low to maintain viable populations. Based on colony observations collected during a monitoring study, data on parasite prevalence, experiments on nest depredation, and analyses of land cover maps, we explored whether parasite pressure, depredation or expected landscape-level food availability explain feral colony winter mortality. Considering the colony-level occurrence of 18 microparasites in the previous summer, colonies that died did not have a higher parasite burden than colonies that survived. Camera traps installed at cavity trees revealed that four woodpecker species, great tits, and pine martens act as nest depredators. In a depredator exclusion experiment, the winter survival rate of colonies in cavities with protected entrances was 50% higher than that of colonies with unmanipulated entrances. Landscapes surrounding surviving colonies contained on average 6.4 percentage points more cropland than landscapes surrounding dying colonies, with cropland being known to disproportionately provide forage for bees in our study system. We conclude that the lack of spacious but well-protected nesting cavities and the shortage of food are currently more important than parasites in limiting populations of wild-living honeybees in German forests. Increasing the density and diversity of large tree cavities and promoting bee forage plants in forests will probably promote wild-living honeybees despite parasite pressure.</p>
Data from: Limited evidence for extensive genetic differentiation between X and Y chromosomes in Hybognathus amarus (Cypriniformes:Leuciscidae)
<p>We used Nextera-tagmented reductively amplified DNA (nextRAD) sequencing data to discover SNPs in Rio Grande silvery minnow samples of known and unknown sex; and we produced two contig level genomes from<span> Nanopore long-read sequencing. </span><span>Raw NextRAD was aligned to each of the genomes. </span><span>Subsequent SNP calling and filtering were repeated independently to obtain two datasets, one using the female genome as reference (female-referenced dataset) and another using the male genome (male-referenced dataset). The SNP calling identified 4.46 M raw variants in female-referenced dataset and of these 16,714 biallelic SNPs were retained after all filtering steps. For this set of SNPs, the average depth of coverage for the retained 64 females was 35.81 (ranging from 8.94 to 86.88) and 33.14 for the retained 53 males (ranging from 18.93 to 65.56). When using the male genome as reference we obtained 3.77 M raw variants and 17,920 biallelic SNPs. In this case the average depth of coverage for the same 64 females was 36.01 (ranging from 8.99 to 87.34) and for the same 53 males was 33.36 (ranging from 19.23 to 66.27).</span></p>
GDPR and the principle of purpose limitation in connecting Data Spaces demonstrators
<p>The presentation focuses on legal challenges arising from the GDPR when connecting Data Spaces using the Demonstrators. Special attention is given to the principle of purpose limitation of the GDPR. The Demonstrators serve a crucial role in connecting the data spaces of the NFDI and GAIA-X. The data in the two data spaces is gathered and used for usually completely different purposes. Thus, when connecting the spaces, the data may be processed for completely different purposes. The GDPR – when applicable – limits legitimate purposes of such further processing. Even if a purpose is legitimate, the GDPR imposes different obligations on controllers and processors. The presentation will dive into the applicability of the GDPR to the demonstrators, the roles of controller and processor regarding the demonstrators and will discuss the principle of purpose limitation and the obligations connected to it.</p>
Data repository of the paper "Quantum-noise-limited optical neural networks operating at a few quanta per activation"
<p>This data repository includes the requisite data and code for deriving the primary results from the paper, "Quantum-noise-limited optical neural networks operating at a few quanta per activation". The repository is structured to provide everything needed to reproduce the figures included in the main manuscript, along with the source code for training the neural network models and the collected experimental data mentioned in the paper.</p> <p>The code in this repository is primarily intended for reproducing the results discussed in the paper. Those interested in developing their own applications may refer to our Github repository: https://github.com/mcmahon-lab/Single-Photon-Detection-Neural-Networks.</p> <p><strong>Where to Start</strong></p> <p>The directory 'main_figures' includes Jupyter notebooks to generate each panel in Figure 3 and Figure 4 in the main text, using the data from the directory 'results', which can be generated by notebooks in the directory 'test'. </p> <p>The simulations, experiments, and figure generation were all conducted in Python. As certain parts of the code require specific versions of Python packages, the necessary packages are listed in the 'requirements.txt' file.</p> <p>For more information, please refer to 'README.txt'.</p>
Data from: Scoring thermal limits in small insects using open-source, computer assisted motion detection
<p>Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.</p>
Data from: Herbivory limits success of vegetation restoration globally
<p>Herbivory limits success of vegetation restoration globally. Restoring vegetation in degraded ecosystems is an increasingly common practice for promoting biodiversity and ecological function, but successful implementation is hampered by an incomplete understanding of the processes limiting restoration success. By assembling terrestrial and aquatic studies globally (2594 experimental tests from 610 articles), we reveal substantial herbivore control of vegetation under restoration. Herbivores at restoration sites reduced vegetation abundance more strongly (by 89%, on average) than at relatively undegraded sites, and suppressed, rather than fostered, plant diversity. These effects were particularly pronounced in regions with higher temperatures and lower precipitation. Temporally excluding targeted herbivores or introducing their predators improved restoration by magnitudes similar to or greater than managing plant competition or facilitation. Thus, managing herbivory is a promising strategy for enhancing vegetation restoration efforts.</p> <p>This ZIP file contains the following datasets and code for the above paper:</p> <p>1) Xu_ConsumerEffects.xlsx This file contains the Global Consumer Effects dataset (and several subsets)<br> 2) Xu_PlantInteractions.xlsx This file contains the Global Plant Interactions and Restoration dataset<br> 3) Code_Xu_Restoration_Ms.R This file contains examples of main R code used. </p> <p>See the Supplementary Materials of the paper for methods used to collect and analyze these data.</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.