cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5ck3n
title: Data from: Social learners require process information to outperform individual learners

description: Humans exhibit a rich and complex material culture with no equivalent in
 animals. Also, social learning, a crucial requirement for culture, is
 particularly developed in humans and provides a means to accumulate
 knowledge over time and to develop advanced technologies. However, the
 type of social learning required for the evolution of this complex
 material culture is still debated. Here, using a complex and opaque
 virtual task, the efficiency of individual learning and two types of
 social learning (product-copying and process-copying) were compared. We
 found that (1) individuals from process-copying groups outperformed
 individuals from product-copying groups or individual learners, whereas
 access to product information was not a sufficient condition for providing
 an advantage to social learners compared to individual learners; (2)
 social learning did not seem to affect the exploration of the fitness
 landscape; (3) social learning led to strong within-group convergence and
 also to between-group convergence and (4) individuals used widely variable
 social learning strategies. The implications of these results for
 cumulative culture evolution are discussed.
description: Data
DOI: 10.6084/m9.figshare.31155208
title: Multicolor interband solitons in microcombs

description: This is the data supporting the finding of the paper titled "Multicolor interband solitons in microcombs".
DOI: 10.6084/m9.figshare.31155208.v1
title: Multicolor interband solitons in microcombs

description: This is the data supporting the finding of the paper titled "Multicolor interband solitons in microcombs".
DOI: 10.15468/dl.msdfgv
title: Occurrence Download

description: A dataset containing 10046 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca"
 ]
}

 The dataset includes 10046 records from 311 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001587-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tk400
title: Data from: Coevolution and the architecture of mutualistic networks

description: Although coevolution is widely recognized as an important evolutionary
 process for pairs of reciprocally specialized species, its importance
 within species-rich communities of generalized species has been
 questioned. Here we develop and analyze mathematical models of mutualistic
 communities, such as those between plants and pollinators or plants and
 seed-dispersers to evaluate the importance of coevolutionary selection
 within complex communities. Our analyses reveal that coevolutionary
 selection can drive significant changes in trait distributions with
 important consequences for the network structure of mutualistic
 communities. One such consequence is greater connectance caused by an
 almost invariable increase in the rate of mutualistic interaction within
 the community. Another important consequence is altered patterns of
 nestedness. Specifically, interactions mediated by a mechanism of
 phenotype matching tend to be anti-nested when coevolutionary selection is
 weak and even more strongly anti-nested as increasing coevolutionary
 selection favors the emergence of reciprocal specialization. In contrast,
 interactions mediated by a mechanism of phenotype differences tend to be
 nested when coevolutionary selection is weak, but less nested as
 increasing coevolutionary selection favors greater levels of
 generalization in both plants and animals. Taken together, our results
 show that coevolutionary selection can be an important force within
 mutualistic communities, driving changes in trait distributions,
 interaction rates, and even network structure.
description: Matching Model
 Simulations Alpha = 0.02Simulation data for
 generation 2000 for the phenotype matching model where alpha has been set
 to 0.02.AnalyticalPredictions_Match_Compiled_G2000_Only.csvMatching Model Simulation Alpha = 2.0Simulation data for generation 1000 derived from the phenotype matching model with Alpha set to 2.0NetworkSummary_MatchA2_Compiled_G1000_Only_JORDI_CORRECTION.csvSimulation Data for Differences Model Alpha = 0.02Simulation data for the phenotype differences model in generation 2000 with alpha set to 0.02.AnalyticalPredictions_Esc_Compiled_G2000_Only.csvSimulation Data for Differences Model Alpha = 2.0Simulation data for generation 1000 of the phenotype differences model with Alpha set to 2.0.NetworkSummary_EscA2_Compiled_G1000_Only_JORDI_CORRECTION.csv
DOI: 10.5061/dryad.44cb5
title: Data from: TreeFix: statistically informed gene tree error correction using species trees

description: Accurate gene tree reconstruction is a fundamental problem in
 phylogenetics, with many important applications. However, sequence data
 alone often lack enough information to confidently support one gene tree
 topology over many competing alternatives. Here, we present a novel
 framework for combining sequence data and species tree information, and we
 describe an implementation of this framework in TreeFix, a new
 phylogenetic program for improving gene tree reconstructions. Given a gene
 tree (preferably computed using a maximum likelihood phylogenetic
 program), TreeFix finds a "statistically equivalent" gene tree
 that minimizes a species tree based cost function. We have applied TreeFix
 to two clades of 12 Drosophila and 16 fungal genomes, as well as to
 simulated phylogenies, and show that it dramatically improves
 reconstructions compared to current state-of-the-art programs. Given its
 accuracy, speed, and simplicity, TreeFix should be applicable to a wide
 range of analyses and have many important implications for future
 investigations of gene evolution. The source code and a sample dataset are
 available at http://compbio.mit.edu/treefix.
description: Supplementary
 Materialsupp.pdf
DOI: 10.5061/dryad.g1gd8
title: Data from: Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

description: Squamate reptiles (lizards and snakes) are one of the most diverse groups
 of terrestrial vertebrates. Recent molecular analyses have suggested a
 very different squamate phylogeny relative to morphological hypotheses,
 but many aspects remain uncertain from molecular data. Here, we analyse
 higher-level squamate phylogeny with a molecular dataset of unprecedented
 size, including 161 squamate species for up to 44 nuclear genes each
 (33,717 base pairs), using both concatenated and species-tree methods for
 the first time. Our results strongly resolve most squamate relationships
 and reveal some surprising results. In contrast to most other recent
 studies, we find that dibamids and gekkotans are together the sister group
 to all other squamates. Remarkably, we find that the distinctive
 scolecophidians (blind snakes) are paraphyletic with respect to other
 snakes, suggesting that snakes were primitively burrowers and subsequently
 re-invaded surface habitats. Finally, we find that some clades remain
 poorly supported, despite our extensive data. Our analyses show that
 weakly supported clades are associated with relatively short branches for
 which individual genes often show conflicting relationships. These latter
 results have important implications for all studies that attempt to
 resolve phylogenies with large-scale phylogenomic data sets.
description: Data matrix for
 likelihood analysisData matrix of 44 genes
 for 161 squamate reptile species and 10 outgroup species. The matrix is
 used for maximum likelihood analysis with RAxML. A separate file specifies
 the models and data partitions.sq44locus_RAXMLModels and partitions for likelihood analysisThis file specifies the models and partitions used in the likelihood analysis (with RAxML).sq_models_RAXMLData matrix for concatenated Bayesian analysisData matrix used for concatenated Bayesian analysis of 44 genes and 161 squamate species (and 10 outgroup species), utilizing MrBayes.squam44locus_MrB.nexusData matrix for Bayesian species-tree analysisData matrix of 44 genes and 29 squamate species (and 2 outgroup species) for Bayesian species-tree analysis utilizing *BEAST.squamate44locus_*BEAST.xml
DOI: 10.5061/dryad.5pr86
title: Data from: A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction

description: Size is among the most important traits of any organism, yet the factors
 that control its evolution remain poorly understood. In this study, we
 investigate controls on the evolution of organismal size using a newly
 compiled database of nearly 25,000 foraminiferan species and subspecies
 spanning the past 400 million years. We find a transition in the pattern
 of foraminiferan size evolution from correlation with atmospheric pO2
 during the Paleozoic (400-250 Mya) to long-term stasis during the
 post-Paleozoic (250 Mya to present). Thus, a dramatic shift in the
 evolutionary mode coincides with the most severe biotic catastrophe of the
 Phanerozoic (543 Mya to present). Paleozoic tracking of pO2 was confined
 to Order Fusulinida, whereas Paleozoic lagenides, miliolids, and
 textulariids were best described by the stasis model. Stasis continued to
 best describe miliolids and textulariids during post-Paleozoic time, while
 random walk was the best supported mode for the other diverse orders. The
 shift in evolutionary dynamics thus appears to have resulted primarily
 from the selective elimination of fusulinids at the end of the Permian
 Period. These findings illustrate the potential for mass extinction to
 alter macroevolutionary dynamics for hundreds of millions of years.
description: dryad_ellis_datadryad_stage_summary
DOI: 10.5061/dryad.jn16g
title: Data from: A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis

description: Lignin engineering is an attractive strategy to improve lignocellulosic
 biomass quality for processing to biofuels and other bio-based products.
 However, lignin engineering also results in profound metabolic
 consequences in the plant. We used a systems biology approach to study the
 plant’s response to lignin perturbations. To this end, inflorescence stems
 of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the
 lignin biosynthetic pathway (PAL1 , PAL2, C4H, 4CL1, 4CL2, CCoAOMT1, CCR1,
 F5H1, COMT and CAD6, two mutant alleles each), were analyzed by
 transcriptomics and metabolomics. 566 compounds were detected, of which
 187 could be tentatively identified based on MS fragmentation and many
 were new for Arabidopsis. Up to 675 genes were differentially expressed in
 mutants that did not have any obvious visible phenotypes. Comparing the
 responses of all mutants indicated that c4h, 4cl1, ccoaomt1 and ccr1,
 mutants that produced less lignin, upregulated the shikimate, methyl-donor
 and phenylpropanoid pathways, i.e. the pathways supplying the monolignols.
 In By contrast, f5h1 and comt, mutants that provoked lignin compositional
 shifts, downregulated the very same pathways. Reductions in the flux to
 lignin were associated with the accumulation of various classes of 4-O and
 9-O hexosylated phenylpropanoids. By combining metabolomic and
 transcriptomic data in a correlation network, system-wide consequences of
 the perturbations were revealed and genes with a putative role in phenolic
 metabolism were identified. Together, our data provide novel insight into
 lignin biosynthesis and the metabolic network it is embedded in and
 provide a systems view of the plant’s response to pathway perturbations.
description: microarraydata_vanholme_etal_2012_tpc102574Microarray data of infloresence stems of twenty arabidopsis mutants in the lignin pathway and four wild type developmental stages.
DOI: 10.5061/dryad.p8b82
title: Data from: Evolution of conjugation and type IV secretion systems

description: Genetic exchange by conjugation is responsible for the spread of
 resistance, virulence and social traits among prokaryotes. Recent works
 unraveled the functioning of the underlying type IV secretion systems
 (T4SS), its distribution and its recruitment for other biological
 processes (exaptation), notably pathogenesis. We analyzed the phylogeny of
 key conjugation proteins to infer the evolutionary history of conjugation
 and T4SS. We show that ssDNA and dsDNA conjugation, while both based on a
 key AAA+ ATPase, diverged before the last common ancestor of bacteria. The
 two key ATPases of ssDNA conjugation are monophyletic, having diverged at
 an early stage from dsDNA translocases. Our data suggests that ssDNA
 conjugation arose first in diderm bacteria, possibly Proteobacteria, and
 then spread to other bacterial phyla, including bacterial monoderms and
 Archaea. Identifiable T4SS fall within 8 monophyletic groups, determined
 by both taxonomy and the structure of the cell envelope. Transfer to
 monoderms might have occurred only once, but followed diverse adaptive
 paths. Remarkably, some Firmicutes developed a new conjugation system
 based on an atypical relaxase and an ATPase derived from a dsDNA
 translocase. The observed evolutionary rates and patterns of
 presence/absence of specific T4SS proteins show that conjugation systems
 are often and independently exapted for other functions. This work brings
 a natural basis for the classification of all kinds of conjugative
 systems, thus tackling a problem that is growing as fast as genomic
 databases. Our analysis provides the first global picture of the evolution
 of conjugation and shows how a self-transferrable complex multi-protein
 system has adapted to different taxa and often been recruited by the host.
 As conjugation systems became specific to certain clades and cell
 envelopes, they may have biased the rate and direction of gene transfer by
 conjugation within prokaryotes.
description: trees_and_alignmentsThis file contains all the alignments and trees that were used for this work.
DOI: 10.5061/dryad.kv3k3
title: Data from: Refining the conditions for sympatric ecological speciation

description: Can speciation occur in a single population when different types of
 resources are available, in the absence of any geographical isolation, or
 any spatial or temporal variation in selection? The controversial topics
 of sympatric speciation and ecological speciation have already stimulated
 many theoretical studies, most of them agreeing on the fact that
 mechanisms generating disruptive selection, some level of assortment, and
 enough heterogeneity in the available resources, are critical for
 sympatric speciation to occur. Few studies, however, have combined the
 three factors and investigated their interactions. In this article, I
 analytically derive conditions for sympatric speciation in a general model
 where the distribution of resources can be uni- or bimodal, and where a
 parameter controls the range of resources that an individual can exploit.
 This approach bridges the gap between models of a unimodal continuum of
 resources and Levene-type models with discrete resources. I then test
 these conditions against simulation results from a recently published
 article (Thibert-Plante and Hendry 2011) and confirm that sympatric
 ecological speciation is favoured when (i) selection is disruptive (ie,
 individuals with an intermediate trait are at a local fitness minimum),
 (ii) resources are differentiated enough, and (iii) mating is assortative.
 I also discuss the role of mating preference functions, and the need (or
 lack thereof) for bimodality in resource distributions for
 diversification.
description: FDebarre_JEB-2621_SuppInfo-MathematicaMathematica notebook with the analytical derivations of the results.FDebarre_JEB-2621_R-scriptsZipped folder with all the R scripts used in the study. To evaluate them, unzip the folder, launch R, go to the folder where the scripts are, and type source('MASTERFILE.R') . All the figures will be created and saved as pdfs in the figures folder.FDebarre_JEB_2621_Appendixpdf printout of the Mathematica and R files.FDebarre-JEB_2621_Appendix.pdfFDebarre_JEB-2621_FigsS1-4Supplementary figures.
DOI: 10.5281/zenodo.12822543
title: Input data for Coalispr

description: Datasets to illustrate the use of Coalispr, a Python tool to clean up (small) RNA sequencing results. Coalispr can visualize over 100 bedgraphs in one panel and helps to retrieve read counts from associated alignment files without reliance on reference features like GTF annotations. The archives contain bedgraphs (also in processed form), reference data, bam-alignment files for counting, and descriptions for experiments, ncRNAs and genes.
description: Datasets of STAR-mapped RNA-seq reads for analysis with Coalispr as described in the essay "Bio informatics: Integrate negative controls to get the good data." Preparation and analysis are detailed in the tutorials "Cryptococcus siRNAs", and "Mouse miRNAs".

Unprocessed fungal datasets were retrieved from GEO GSE128009 and GSE43363 and have been published by Dumesic et al. 2013 (DOI 10.1016/j.cell.2013.01.046) and Burke et al. 2019 (DOI 10.1534/g3.119.400330). Additional resources were gene-annotations from Wallace et.al 2020 (DOI 10.1093/nar/gkaa060) and data at GEO GSE133125.

Mouse data have been described in Sarshad et al. 2018 (DOI 10.1016/j.molcel.2018.07.020) and raw miRNA sequencing reads were kindly provided by the corresponding author, Markus Hafner.
description: The version of Coalispr released in January 2026 (v0.9.6) requires newer versions of the  configurartion files. These are in the archive 'Replacement_files'; see the NOTE for more information.
DOI: 10.5061/dryad.p63d6
title: Data from: Experiences with Global Trigger Tool reviews in five Danish hospitals – an implementation study

description: Objectives: To describe experiences with the implementation of global
 trigger tool (GTT) reviews in five Danish hospitals and to suggest ways to
 improve the performance of GTT review teams. Design: Retrospective
 observational study. Setting: The measurement and monitoring of harms are
 crucial to campaigns to improve the safety of patients. Increasingly,
 teams use the GTT to review patient records and measure harms in English
 and non-English-speaking countries. Meanwhile, it is not clear as to how
 the method performs in such diverse settings. Participants: Review teams
 from five Danish pilot hospitals of the national Danish Safer Hospital
 Programme. Primary and secondary outcome measures: We collected harm
 rates, background and anecdotal information and reported patient safety
 incidents (PSIs) from five pilot hospitals currently participating in the
 Danish Safer Hospital Programme. Experienced reviewers categorised harms
 by type. We plotted harm rates as run-charts and applied rules for the
 detection of patterns of non-random variation. Results: The hospitals
 differed in size but had similar patient populations and activity. PSIs
 varied between 3 and 12 per 1000 patient-days. The average harm rate for
 all hospitals was 60 per 1000 patient-days ranging from 34 to 84. The
 percentage of harmed patients was 25 and ranged from 18 to 33. Overall,
 96% of harms were temporary. Infections, pressure ulcers procedure-related
 and gastrointestinal problems were common. Teams reported differences in
 training and review procedures such as the role of the secondary reviewer.
 Conclusions: We found substantial variation in harm rates. Differences in
 training, review procedures and documentation in patient records probably
 contributed to these variations. Training reviewers as teams, specifying
 the roles of the different reviewers, training records and a database for
 findings of reviews may improve the application of the GTT.
description: Experiences with Global
 Trigger Tool reviews in Danish hospitalsMSExcel spreadsheet with
 data from participating hospitals. File names are in
 Danish.2012
 08 28 gtt-artikel JA.xls
DOI: 10.5061/dryad.ng93k
title: Data from: Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

description: Identifying the spatial distribution of genetic variation across the
 landscape is an essential step in informing species conservation.
 Comparison of closely related and geographically overlapping species can
 be particularly useful in cases where landscape may similarly influence
 genetic structure. Congruent patterns among species highlight the
 importance that landscape heterogeneity plays in determining genetic
 structure whereas contrasting patterns emphasize differences in
 species-specific ecology and life-history or the importance of
 species-specific adaptation to local environments. We examined the
 interacting roles of demography and adaptation in determining spatial
 genetic structure in two closely related and geographically overlapping
 species in a pristine environment. Using single nucleotide polymorphism
 (SNP) loci exhibiting both neutral and putative adaptive variation, we
 evaluated the genetic structure of sockeye salmon in the Copper River,
 Alaska; these data were compared to existing data for Chinook salmon from
 the same region. Overall, both species exhibited patterns of isolation by
 distance; the spatial distribution of populations largely determined the
 distribution of genetic variation across the landscape. Further, both
 species exhibited largely congruent patterns of within- and
 among-population genetic diversity, highlighting the role that landscape
 heterogeneity and historical processes play in determining spatial genetic
 structure. Potential adaptive differences among geographically proximate
 sockeye salmon populations were observed when high FST outlier SNPs were
 evaluated in a landscape genetics context. Results were evaluated in the
 context of conservation efforts with an emphasis on reproductive
 isolation, historical processes, and local adaptation.
description: Ackerman2012_dryad_submission(sockeye)