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.
122
datasets available to search
ShareScore release 0.9.0
Dataset results
122 results for “Incongruence”
Morphometric data from: Incongruent molecular and morphological variation in the crab spider Synema globosum (Araneae: Thomisidae) in Europe
<p>Here we provide the complete set of files used by <a href="https://doi.org/10.3897/zookeys.1078.64116">Urfer et al. (2021</a>, see References section below for the complete citation of the publication) for the morphometric and the molecular analysis. In particular, we provide the following documents:</p> <p><br> PART 1: MORPHOMETRIC ANALYSIS</p> <p>- 1_Synema_data_multiple_imputation_mice.R: R-script used for replacing NAs.</p> <p>- 1_Synema_data_NA_imputed.csv: Dataset with raw values (in millimeters) of all 28 specimens used for the morphometric analysis. Each specimen was measured 4 times. NAs replaced using the R-script "Synema_multiple_imputation_mice.R" above. This is the datafile used for all morphometric analyses.</p> <p>- 1_Synema_data_with_NA.csv: Dataset with raw values (in millimeters) of all 28 specimens. Each specimen was measured 4 times. NAs not replaced.<br> <br> - 1_Synema_Reliability.R: R-script for calculating reliability.<br> <br> - 1_Synema_Reliability_supplementary_figure.pdf: Results of reliability analysis presented in a bar plot.</p> <p>- 1_Synema_Reliability_supplementary_table.txt: Results of reliability analysis presented in a table.<br> <br> - 1_Synema_Shape_PCA_and_PCA_Ratio_Spectrum.R: R-script for calculating the shape PCA and the PCA Ratio Spectrum of the first shape PC. You may get the necessary MRA source script from http://doi.org/10.5281/zenodo.4250142<br> <br> - Synema_globosum_AR9379_PV.jpg, Synema_globosum_AR9379_PV.jpg, Synema_globosum_AR9379_PV.jpg, etc.: Photographs taken with a LEICA M205 C stere-omicroscope.</p> <p> 1. Numbers after AR_ refer to the inventory number of the specimens in the Natural History Musuem Bern (NMBE). The specimen number was also used in the data file.<br> 2. The photo named "Synema_globosum_AR9163_with_measurements" shows the position of the measurements. Otherwise, the measurements are not indicated in the raw photos.</p> <p><br> Example image Character name Definition<br> Synema_globosum_AR9163_with_measurements cym.l Cymbium lenght Distance of the anterior margin to the tip of the cymbium<br> Synema_globosum_AR9163_with_measurements cym.b Cymbium breadth widest breadth of the cymbium<br> Synema_globosum_AR9163_with_measurements bul.b Bulb breadth widest breadth of the genital bulbus<br> Synema_globosum_AR9163_with_measurements tib.b Tibia breadth breadth of the tibia base at the patella joint</p>
Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)
<p>Nuclear and plastid datasets and phylogenomic workflow associated to "Genomic Incongruence Accompanies the Evolution of Flower Symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales)", published in <em>Frontiers in Plant Science </em>15:1340056.<br>This compressed file (poppy_repo.zip) contains a markdown readme file (poppy_readme.md) describing the phylogenomic workflow followed, as well as two dataset folders (poppy_nuc and poppy_pl) divided into four (aln_nuc, gtr_nuc, sptr_nuc, and chrono_nuc) and three (aln_pl, sptr_pl, and chrono_pl) subfolders, respectively.<br>The nuclear folder (poppy_nuc) comprises shrunk and trimmed alignments (aln_nuc), ML gene trees (gtr_nuc), coalescent species trees (sptr_nuc), and a time tree (chrono_nuc).<br>The plastid folder (poppy_pl) comprises shrunk and trimmed alignments (aln_pl), a concatenated ML species tree (sptr_pl), and a time tree (chrono_pl).<br>The research article is available at https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1340056 (doi: 10.3389/fpls.2024.1340056).</p>
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
<p>Phylogenetic analyses are increasingly being performed with datasets that incorporate hundreds of loci. Due to incomplete lineage sorting, hybridization, and horizontal gene transfer, the gene trees for these loci may often have topologies that differ from each other and from the species tree. The effect of these topological incongruences on divergence time estimation has not been fully investigated. Using a series of simulation experiments and empirical analyses, we demonstrate that when topological incongruence between gene trees and the species tree is not accounted for, the temporal duration of branches in regions of the species tree that are affected by incongruence is underestimated, whilst the duration of other branches is considerably overestimated. This effect becomes more pronounced with higher levels of topological incongruence. We show that this pattern results from erroneous estimation of the number of substitutions along branches in the species tree, although the effect is modulated by the assumptions inherent to divergence time estimation, such as those relating to the fossil record or among-branch-substitution-rate variation. By only analysing loci with gene trees that are topologically congruent with the species tree, or only taking into account the branches from each gene tree that are topologically congruent with species tree, we demonstrate that the effects of topological incongruence can be ameliorated. Nonetheless, even when topologically congruent gene trees or topologically congruent branches are selected, error in divergence time estimates remains. This stems from temporal incongruences between divergence times in species trees and divergence times in gene trees, and more importantly, the difficulty of incorporating necessary assumptions for divergence time estimation.</p>
[Stimulus Set] Evoking the N400 event-related potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
<p>During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.</p>
Evoking the N400 Event-Related Potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
<p class="MsoNoSpacing"><span>During speech comprehension, the ongoing context of a sentence is used to predict sentence outcome by limiting subsequent word likelihood. Neurophysiologically, violations of context-dependent predictions result in amplitude modulations of the N400 event-related potential (ERP) component. While N400 is widely used to measure semantic processing and integration, </span><span>no publicly-available auditory stimulus set is available to standardize approaches across the field. Here, we developed an auditory stimulus set of 442 sentences that utilized the semantic anomaly paradigm, provided cloze probability for all stimuli, and was developed for both children and adults. With 20 neurotypical adults, we validated that this set elicits robust N400's, as well as two additional semantically-related ERP components: the recognition potential (~250 ms) and the late positivity component (~600 ms). This stimulus set (<a href="https://doi.org/10.5061/dryad.9ghx3ffkg">https://doi.org/10.5061/dryad.9ghx3ffkg</a>) and the 20 high-density (128-channel) electrophysiological datasets (<a href="https://doi.org/10.5061/dryad.6wwpzgmx4">https://doi.org/10.5061/dryad.6wwpzgmx4</a>) </span><span>are made publicly available to promote data sharing and reuse. Future studies that use this stimulus set to investigate sentential semantic comprehension in both control and clinical populations may benefit from the increased comparability and reproducibility within this field of research.</span></p>
Visual Abstract for "Incongruent Humour, Advertising Effectiveness and Women: An Experiment On Facebook"
<p>Visual Abstract for "Incongruent Humour, Advertising Effectiveness and Women: An Experiment On Facebook".</p> <p>Ribeiro, L., Petroll, M., Scussel, F., & Damacena, C. (2018). Incongruent Humour, Advertising Effectiveness and Women: An Experiment On Facebook. <em>Revista de Administração Contemporânea, 23</em>(1), 1-22. doi:<a href="https://doi.org/10.1590/1982-7849rac2019180034">https://doi.org/10.1590/1982-7849rac2019180034</a></p>
Evoking the N400 Event-Related Potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
Open the record for dataset details and reuse information.
[Stimulus Set] Evoking the N400 event-related potential (ERP) component using a publicly available novel set of sentences with semantically incongruent or congruent eggplants (endings)
Open the record for dataset details and reuse information.
The implications of incongruence between gene tree and species tree topologies for divergence time estimation
Open the record for dataset details and reuse information.
Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
<p>Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (<i>Desmognathus</i>), a common model-system for ecology, evolution, and behavior. Only 22 species are described; 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods fail to provide satisfactory resolution for relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in <i>Desmognathus</i> may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.</p>
Perceiving tempo in incongruent audiovisual presentation of human motion: Evidence for a visual driving effect
<p>The video set includes 81 audiovisual stimuli which served in the bisection experiment of the study "Perceiving tempo in incongruent audiovisual presentation of human motion: Evidence for a visual driving effect". The auditory sound tracks (bass drum) and visual stimuli (point-light displays of biological motions) each cover the tempo range from 60 to 180BPM, 15BPM per step. Coupling of the stimuli from both modalities results in 81 stimuli in total. </p>
Data from: Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence
Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode Certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complement regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inference. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, IC score calculation typically requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing taxa is high, the scores yielded by current approaches that adjust bipartition frequencies in partial gene trees differ substantially from each other and tend to be overestimates. To overcome these issues, we developed three new IC measures based on the frequencies of quartets, which naturally apply to both complete and partial trees. Comparison of our new quartet-based measures to previous bipartition-based measures on simulated data shows that: 1) on complete data sets, both quartet-based and bipartition-based measures yield very similar IC scores; 2) IC scores of quartet-based measures on a given data set with and without missing taxa are more similar than the scores of bipartition-based measures; and 3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in phylogenetic inference than bipartition-based measures. Additionally, the analysis of an empirical mammalian phylogenomic data set using our quartet-based measures reveals the presence of substantial levels of incongruence for numerous internal branches. An efficient open-source implementation of these quartet-based measures is freely available in the program QuartetScores (https://github.com/lutteropp/QuartetScores).
Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification
<p class="MsoNormal"><strong><span>Premise</span></strong></p> <p class="MsoNormal"><span>Bryophytes, land plants defined by a free-living gametophyte and an unbranched sporophyte, form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. </span><span>Our understanding of the evolutionary history of hornworts, liverworts and mosses has been significantly reshaped by inferences from molecular data, highlighting extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, and the degree to which the observed homoplasy represents error or biological processes, remain poorly resolved.</span></p> <p class="MsoNormal"><strong><span>Methods</span></strong></p> <p class="MsoNormal"><span>Using the GoFlag probe set, we sampled 405 exons representing 228 nuclear genes for 531 species from 51 of the 53 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.</span></p> <p class="MsoNormal"><strong><span>Results</span></strong></p> <p class="MsoNormal"><span>The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more, and propose ten new orders of mosses. Most orders originated in the Jurassic or earlier and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene tree topology. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong></p> <p class="MsoNormal"><span>We sampled hundreds of homologous loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution, and these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of bryophytes and for investigating the transformations of traits in this important group of plants.</span></p>
Data from: Low-copy nuclear genes reveal new evidence of incongruence in relationships within Malvaceae s.l.
<p>The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s.l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plant Project (1KP) and publicly available genome information from cotton, cacao, and <i>Arabidopsis, </i>we designed a set of molecular markers of potentially single-or low-copy nuclear genes for Malvaceae s.l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e., plastid <i>trnK</i>-<i>matK</i> region and <i>rbcL</i> gene and the <a>nrDNA </a>ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.</p>
Perceiving Tempo in Incongruent Audiovisual Presentations of Human Motion: Evidence for a Visual Driving Effect
<p>Data set from the study published in Timing & Time Perception.</p>
Data set for "Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas"
<p>Data set for: Esmaeili V, Oryshchuk A, Asri R, Tamura K, Foustoukos G, Liu Y, Guiet R, Crochet S, Petersen CCH (2022) Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas. PLoS Biol 20: e3001667. doi: 10.1371/journal.pbio.3001667</p> <p>There are 2 files in this upload:</p> <p>1. The file named "2022_Esmaeili_PLOSBiol.pdf" is the Open Access pdf of the online publication in PLoS Biology.</p> <p>2. The file named "Esmaeili_data_code.zip" (~3 GB) is a zipped version of a folder "Esmaeili_data_code" (~3 GB), which contains four subfolders named as “data”, “codes”, “figures” and “excel files” and a README.txt file with the descriptions of files and required toolboxes to run the codes. To access the data and codes, first unzip the file. The “code” subfolder contains all the Matlab codes and their dependencies for generating all the main and supplementary figures. The “data” subfolder contains the data analysed in the study used to generate different figures. When running the code, you will have to select the path of the unzipped data containing the subfolders data, code, figures and excel files (\Esmaeili_data_code\). Some parts of the code rely upon previous results, and need to be executed sequentially in the order of the figure panels in the journal publication. Running the codes will save the figure panels and the related excel files in the “figures” and “excel files” subfolders respectively.</p> <p> </p>
Raw data corresponding to Huestegge, S. M., Raettig, T., & Huestegge, L. (2019). "Are face-incongruent voices harder to process? Effects of face-voice gender incongruency on basic cognitive information processing." Journal: Experimental Psychology.
<p>Raw data file prior to subject-based aggregation. Variables and values are decribed within the file. For further reference and specifications please also refer to the original publication in the journal Experimental Psychology.</p>
Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)
<p>Coloration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Mullerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes <em>Eulaema</em> <em>meriana</em> and <em>Eulaema</em> <em>bombiformis</em> (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that <em>E. atleticana </em>and <em>E. niveofasciata</em> are subspecies of <em>E. meriana</em> and <em>E. bombiformis</em>, respectively, and not different species as previously suggested. Therefore, we recognize <em>Eulaema meriana atleticana</em> comb. n. and <em>Eulaema bombiformis niveofasciata</em> comb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts.</p>
Data from: Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus)
Open the record for dataset details and reuse information.
Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification
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.