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.
23
datasets available to search
ShareScore release 0.9.0
Dataset results
23 results for “Red Queen”
The Red Queen in the Repository: metadata quality in an ever-changing environment (preprint of paper, presentation slides and dataset collection with validation schemas to IDCC2019 conference paper)
<p>This fileset contains a preprint version of the conference paper (.pdf), presentation slides (as .pptx) and the dataset(s) and validation schema(s) for the IDCC 2019 (Melbourne) conference paper: <em>The Red Queen in the Repository: metadata quality in an ever-changing environment. </em>Datasets and schemas are in .xml, .xsd , Excel (.xlsx) and .csv (two files representing two different sheets in the .xslx -file). The <em>validationSchemas.zip</em> holds the additional validation schemas (.xsd), that were not found in the schemaLocations of the metadata xml-files to be validated. The schemas must all be placed in the same folder, and are to be used for validating the Dataverse <em>dcterms</em> records (with <em>metadataDCT.xsd</em>) and the Zenodo <em>oai_datacite</em> feeds respectively (<em>schema.datacite.org_oai_oai-1.0_oai.xsd</em>). In the latter case, a simpler way of doing it might be to replace the incorrect URL "<em>http://schema.datacite.org/oai/oai-1.0/ oai_datacite.xsd</em>" in the <em>schemaLocation </em>of these xml-files by the CORRECT: <em>schemaLocation="http://schema.datacite.org/oai/oai-1.0/ http://schema.datacite.org/oai/oai-1.0/oai.xsd"</em> as has been done already in the sample files here. The sample file folders <em>testDVNcoll.zip </em>(Dataverse), <em>testFigColl.zip </em>(Figshare)<em> </em>and <em>testZenColl.zip </em>(Zenodo)<em> </em>contain all the metadata files tested and validated that are registered in the spreadsheet with objectIDs.<br> In the case of Zenodo, one original file feed,<br> <em>zen2018oai_datacite3orig-https%20_zenodo.org_oai2d%20verb=ListRecords%26metadata<br> Prefix=oai_datacite%26from=2018-11-29%26until=2018-11-30.xml</em> ,<br> is also supplied to show what was necessary to change in order to perform validation as indicated in the paper.</p> <p>For Dataverse, a corrected version of a file,<br> <em>dvn2014ddi-27595<strong>Corr</strong>_https%20_dataverse.harvard.edu_api_datasets_export%20<br> exporter=ddi%26persistentId=doi%253A10.7910_DVN_27595<strong>Corr</strong>.xml</em> ,<br> is also supplied in order to show the changes it would take to make the file validate without error.</p>
Dataset for Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods
<p>This dataset contains the Matlab codes used in "Evolution of Cooperation in Costly Institutions: Red Queen and Black Queen Dynamics in Heterogenous Public Goods".</p> <p>The zip file contains Matlab codes used in simulation and numerical solutions of the replicator dynamics. The zip file "Figures" contains the Matlab code and data used to produce figures in this study.</p>
Data from: Infection dynamics in coexisting sexual and asexual host populations: support for the Red Queen hypothesis
The persistence of sexual reproduction is a classic problem in evolutionary biology. The problem stems from the fact that, all else equal, asexual lineages should rapidly replace coexisting sexual individuals due to the cost of producing males in sexual populations. One possible countervailing advantage to sexual reproduction is that, on average, outcrossed offspring are more resistant than common clones to coevolving parasites, as predicted under the Red Queen hypothesis. In the present study, we evaluated the prevalence of infection by a sterilizing trematode (Microphallus sp.) in a natural population of freshwater snails that was composed of both sexual and asexual individuals (Potamopyrgus antipodarum). More specifically, we compared the frequency of infection in sexual and asexual individuals over a five-year period at four sites at a natural glacial lake (Lake Alexandrina, South Island, New Zealand). We found that at most sites and over most years, the sexual population was less infected than the coexisting asexual population. Moreover, the frequency of uninfected sexual females was periodically greater than two times the frequency of uninfected asexual females. These results give clear support for a fluctuating parasite-mediated advantage to sexual reproduction in a natural population.
Data from: The escalatory Red Queen: population extinction and replacement following arms-race dynamics in poplar rust
Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory – that arms-race dynamics can result in extinction – has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study we used a 25-years temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations, and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) – above all – the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics.
Red Queen processes drive positive selection on Major Histocompatibility Complex (MHC) genes
<p>The dataset for the manuscript "Red Queen processes drive positive selection on Major Histocompatibility Complex (MHC) genes" submitted to PLOS Computational Biology. The dataset is packed in ZIP archive 'MHC_PosSel_dataset.zip' and contain the results of the simulation model.</p>
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. FISH karyotype pattern diagram of 8 diploid hyacinth cultivars a.'Gypsy Queen'; b.'Purple sensation' c.'Pink pearl' d.'Gypsy princess' e.'Blue pearl' f.'Odysseus' g.'Yellowstone' h.'Red pearl' Red point: 45S rDNA loci; Green point: 45S rDNA loci; Yellow point: ITR sites
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl' in Physical mapping of 45S and 5S rDNA and telomeric repeat loci in eight diploid hyacinth cultivars
FIGURE. Results of FISH physical mapping on metaphase chromosomes of hyacinth 1. The distribution of 45S rDNA (red arrow) and 5S rDNA (green arrow) signals on the chromosomes; 2. The distribution of telomeric repeats signals on the chromosomes; 3. Chromosome karyotype with 45S rDNA and 5S rDNA; 4. Chromosome karyotype with telomeric repeats. A. 'Gypsy Queen' B.'Purple sensation' C.'Pink pearl' D.'Gypsy princess' E.'Blue pearl' F.'Odysseus' G.'Yellow stone' H.'Red pearl'
Data from: The potential for arms race and Red Queen coevolution in a protist host-parasite system
Open the record for dataset details and reuse information.
Data from: Infection dynamics in coexisting sexual and asexual host populations: support for the Red Queen hypothesis
Open the record for dataset details and reuse information.
Data from: Testing the role of the Red Queen and Court Jester as drivers of the macroevolution of Apollo butterflies
Open the record for dataset details and reuse information.
Data from: The escalatory Red Queen: population extinction and replacement following arms-race dynamics in poplar rust
Open the record for dataset details and reuse information.
Data from: Running with the Red Queen: host-parasite coevolution selects for biparental sex
Most organisms reproduce through outcrossing, even though it comes with significant costs. The Red Queen hypothesis proposes that selection from coevolving pathogens facilitates the persistence of outcrossing in spite of these costs. We utilized experimental coevolution to test the Red Queen hypothesis, and found that coevolution with a bacterial pathogen (Serratia marcescens) resulted in significantly more outcrossing in mixed mating experimental populations of the nematode Caenorhabditis elegans. Furthermore, we found that coevolution with the pathogen rapidly drove obligately selfing populations to extinction, while outcrossing populations persisted through reciprocal coevolution. Thus, consistent with the Red Queen hypothesis, coevolving pathogens can select for biparental sex.
Data from: Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations
Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated.
Data from: Hill-Robertson interference maintained by red queen dynamics favours the evolution of sex
Although it is well established theoretically that selective interference among mutations (Hill-Robertson interference) favours meiotic recombination, genome-wide mean rates of mutation and strengths of selection appear too low to support this as the mechanism favouring recombination in nature. A possible solution to this discrepancy between theory and observation is that selection is at least intermittently very strong due to the antagonistic coevolution between a host and its parasites. The Red Queen theory posits that such coevolution generates fitness epistasis among loci, which generates negative linkage disequilibrium among beneficial mutations, which in turn favours recombination. This theory has received only limited support. However, Red Queen dynamics without epistasis may provide the ecological conditions that maintain strong and frequent selective interference in finite populations that indirectly selects for recombination. This hypothesis is developed here through the simulation of Red Queen dynamics. This approach required the development of a method to calculate the exact frequencies of multi-locus haplotypes after recombination. Simulations show that recombination is favoured by the moderately weak selection of many loci involved in the interaction between a host and its parasites, which results in substitution rates that are compatible with empirical estimates. The model also reproduces the previously reported rapid increase in the rate of outcrossing in Caenorhabditis elegans coevolving with a bacterial pathogen.
Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations. Reanalyzing previously published data on Daphnia magna susceptibility to infection by Pastueria ramosa, we identify genomic regions consistent with GxG interactions. We conclude by outlining possible avenues for designing more powerful and more repeatable association studies.
Data from: Antibiotic-driven escape of host in a parasite-induced Red Queen dynamics
Open the record for dataset details and reuse information.
Data from: Hill-Robertson interference maintained by red queen dynamics favours the evolution of sex
Open the record for dataset details and reuse information.
Data from: Running with the Red Queen: host-parasite coevolution selects for biparental sex
Open the record for dataset details and reuse information.
Data from: The Red Queen lives: epistasis between linked resistance loci
Open the record for dataset details and reuse information.
Data from: Parasite transmission among relatives halts Red Queen dynamics
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.