cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8j60q
title: Data from: Synthesis of phylogeny and taxonomy into a comprehensive tree of life

description: Reconstructing the phylogenetic relationships that unite all lineages (the
 tree of life) is a grand challenge. The paucity of homologous character
 data across disparately related lineages currently renders direct
 phylogenetic inference untenable. To reconstruct a comprehensive tree of
 life, we therefore synthesized published phylogenies, together with
 taxonomic classifications for taxa never incorporated into a phylogeny. We
 present a draft tree containing 2.3 million tips—the Open Tree of Life.
 Realization of this tree required the assembly of two additional community
 resources: (i) a comprehensive global reference taxonomy and (ii) a
 database of published phylogenetic trees mapped to this taxonomy. Our open
 source framework facilitates community comment and contribution, enabling
 the tree to be continuously updated when new phylogenetic and taxonomic
 data become digitally available. Although data coverage and phylogenetic
 conflict across the Open Tree of Life illuminate gaps in both the
 underlying data available for phylogenetic reconstruction and the
 publication of trees as digital objects, the tree provides a compelling
 starting point for community contribution. This comprehensive tree will
 fuel fundamental research on the nature of biological diversity,
 ultimately providing up-to-date phylogenies for downstream applications in
 comparative biology, ecology, conservation biology, climate change,
 agriculture, and genomics.
description: Open Tree Taxonomy v
 2.8When unpacked, contains
 files for the Open Tree Taxonomy. Also contains a separate README with
 more information.ott2.8.tgzList of input phylogenies for synthetic treeRanked list of input phylogenies, including publication metadata, tree metadata, study ID, tree IDlist_of_input_trees.csvProcessed source treesInput trees, post-processing, in newick format. Tip labels are Open Tree Taxonomy IDs.Processed_sourcetree_newicks_v3.0.tgzInput trees, decomposed into subproblemsInput trees, decomposed into subproblems, where the root of each subproblem is a taxon that is uncontested by the set of tree + taxonomy inputs.subproblems-v3.tar.gzOpen Tree of Life draft tree v. 3.0The Open Tree of Life synthetic tree in newick format, with tip labels as Open Tree Taxonomy IDs.draftversion3.tre.gz
DOI: 10.5061/dryad.n1mn9
title: Data from: RAD-sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American eel (Anguilla rostrata)

description: The two primary ways that species respond to heterogeneous environments is
 through local adaptation and phenotypic plasticity. The American eel
 (Anguilla rostrata) presents a paradox; despite inhabiting drastically
 different environments, the species is panmictic. Spawning takes place
 only in the southern Sargasso Sea in the Atlantic Ocean. Then, the
 planktonic larvae (leptocephali) disperse to rearing locations from Cuba
 to Greenland, and juveniles colonize either freshwater or
 brackish/saltwater habitats, where they spend 3–25 years before returning
 to the Sargasso Sea to spawn as a panmictic species. Depending on rearing
 habitat, individuals exhibit drastically different ecotypes. In
 particular, individuals rearing in freshwater tend to grow slowly and
 mature older and are more likely to be female in comparison to individuals
 that rear in brackish/saltwater. The hypothesis that phenotypic plasticity
 alone can account for all of the differences was not supported by three
 independent controlled experiments. Here, we present a genome-wide
 association study that demonstrates a polygenic basis that discriminates
 these habitat-specific ecotypes belonging to the same panmictic
 population. We found that 331 co-varying loci out of 42,424 initially
 considered were associated with the divergent ecotypes, allowing a
 reclassification of 89.6%. These 331 SNPs are associated with 101 genes
 that represent vascular and morphological development, calcium ion
 regulation, growth and transcription factors, and olfactory receptors. Our
 results are consistent with divergent natural selection of phenotypes
 and/or genotype-dependent habitat choice by individuals that results in
 these genetic differences between habitats, occurring every generation
 anew in this panmictic species.
description: 325 contigs that contain
 the 331 important SNPs325 contigs that contain
 the 331 important SNPs most important for distinguishing freshwater and
 brackish/saltwater ecotypes of American eel325_rf_contigs.fastaPavey_2015_eel_genotypesGenepop file containing all raw genotypes for 16 sampling sites (8 freshwater 8 saltwater) for 42,424 SNPs
DOI: 10.5061/dryad.h7h32
title: Data from: Improvement of the threespine stickleback genome using a Hi-C-based Proximity-Guided Assembly

description: Scaffolding genomes into complete chromosome assemblies remains
 challenging even with the rapidly increasing sequence coverage generated
 by current next-generation sequence technologies. Even with scaffolding
 information, many genome assemblies remain incomplete. The genome of the
 threespine stickleback (Gasterosteus aculeatus), a fish model system in
 evolutionary genetics and genomics, is not completely assembled despite
 scaffolding with high-density linkage maps. Here, we first test the
 ability of a Hi-C based Proximity-Guided Assembly to perform a de novo
 genome assembly from relatively short contigs. Using Hi-C based
 Proximity-Guided Assembly, we generated complete chromosome assemblies
 from a distribution of short contigs (20–100 kb). We found that 96.40% of
 contigs were correctly assigned to linkage groups, with ordering nearly
 identical to the previous genome assembly. Using available bacterial
 artificial chromosome (BAC) end sequences, we provide evidence that some
 of the few discrepancies between the Hi-C assembly and the existing
 assembly are due to structural variation between the populations used for
 the two assemblies or errors in the existing assembly. This Hi-C assembly
 also allowed us to improve the existing assembly, assigning over 60%
 (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to linkage
 groups. Together, our results highlight the potential of the Hi-C based
 Proximity-Guided Assembly method to be used in combination with short read
 data to perform relatively inexpensive de novo genome assemblies. This
 approach will be particularly useful in organisms in which it is difficult
 to perform linkage mapping or to obtain high molecular weight DNA required
 for other scaffolding methods.
description: Gac-HiC revised genome
 assemblyG. aculeatus Hi-C
 revised genome assembly with 125 previously unassigned contigs assigned to
 gaps.Gac-HiC_revised_genome_assembly.fa.gzUnassigned contigs narrowed to linkage groups1,263 previously unassigned contigs narrowed to linkage groupsunassignedContigs_narrowed_to_linkage_groups.fa.gzG. aculeatus BioNano Irys optical genome mapG_aculeatus_bionano_genome_map.cmap.gz
DOI: 10.5061/dryad.21jj2
title: Data from: Constructing phylogenies in the presence of Intra-Individual Site Polymorphisms (2ISPs) with a focus on the nuclear ribosomal cistron

description: Nuclear DNA is widely used to estimate phylogenetic and phylogeographic
 relationships. Nuclear gene variants may be present in an
 individual's genome, and these result in Intra-Individual Site
 Polymorphisms (2ISP; pronounced 'twisp') in direct-PCR or
 individual-consensus sequences based on a clone sample. 2ISPs can occur
 fairly often, especially within, but not restricted to, high-copy-number
 regions such as the widely used internal transcribed spacers of the
 nuclear ribosomal cistron. Dealing with 2ISPs has been problematic as
 phylogeny reconstruction optimality criteria generally do not take account
 of this variation. Here we test whether an approach that treats 2ISPs as
 additional (termed ‘informative’), rather than ambiguous, characters
 offers improved support in three common criteria used for phylogenetic
 inference: Minimum Evolution (via Neighbour Joining), Maximum Parsimony
 and Maximum Likelihood. We demonstrate significant improvements using the
 2ISP-informative treatment with simulated, real-world and case study
 datasets. We envisage that this 2ISP-informative approach will greatly aid
 phylogenetic inference using any nuclear DNA regions that contain
 polymorphisms within individuals (including consensus sequences generated
 from next generation sequencing), especially at the intrageneric or
 intraspecific level.
description: Online Appendix
 S1Supplementary
 TableOnline Appendix
 S2Detailed methods
 description for simulation and real-world dataset
 analyses.Online Appendix
 S3Neighbour-Net networks
 with bootstrap bipartition support for a range of published
 datasetsSimulation.datasetsDatasets simulated to include polymorphism inheritance (using two independent copies or variants) and determine the effects of these polymorphisms on a range of phylogenetic inference methods.Real.world.datasetsThe real-world datasets plus outputted bootstrap trees used to test the effects of intra-individual site polymorphisms (2ISPs) on a range of phylogenetic methodsNymania.capensis.ITS.alignmentsThe raw and edited alignments for the Nymania capensis alignment of DNA sequences from the internal transcribed spacers and 5.8S regions.
DOI: 10.5061/dryad.sm1vt
title: Data from: Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

description: Understanding the genetic basis of traits involved in adaptation is a
 major challenge in evolutionary biology but remains poorly understood.
 Here, we use genome-wide association mapping using a custom 50 k single
 nucleotide polymorphism (SNP) array in a natural population of collared
 flycatchers to examine the genetic basis of clutch size, an important
 life-history trait in many animal species. We found evidence for an
 association on chromosome 18 where one SNP significant at the genome-wide
 level explained 3.9% of the phenotypic variance. We also detected two
 suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness
 differences among genotypes were generally weak and not significant,
 although there was some indication of a sex-by-genotype interaction for
 lifetime reproductive success at the suggestive QTL on chromosome 26. This
 implies that sexual antagonism may play a role in maintaining genetic
 variation at this QTL. Our findings provide candidate regions for a
 classic avian life-history trait that will be useful for future studies
 examining the molecular and cellular function of, as well as evolutionary
 mechanisms operating at, these loci.
description: .map
 filePLINK format .map file
 with marker information and positionNewcfdata.map.PED filePLINK format .ped file with individual genotype dataNewcfdata.pedMorphology females.txt file with ringnumber and clutch size and recruitment information for females genotyped.female_morph_ProcBpaper.txtmale reproductive success.txt file with ring number of male and number of recruits for genotyped individuals.male_morph_ProcBpaper.txt
DOI: 10.5061/dryad.sj5t2
title: Data from: Morphological convergence between an allopolyploid and one of its parental species correlates with biased gene expression and DNA loss

description: The contribution of gene expression modulation to phenotypic evolution is
 of major importance to an understanding of the origin of divergent or
 convergent phenotypes during and following polyploid speciation. Here we
 analysed genome-wide gene expression in two subspecies of the
 allotetraploid species, Senecio mohavensis A. Gray, and its diploid
 parents S. flavus (Decne.) Sch. Bip. and S. glaucus L.. The tetraploid is
 morphologically much more similar to S. flavus, leading to earlier
 confusion over its taxonomic status. By means of an analysis of
 transcriptomes of all three species, we show that gene expression
 divergence between the parent species is relatively low (ca. 14% of loci),
 whereas there is significant unequal expression between ca. 20-25% of the
 parental homoeologues (gene copies) in the tetraploid. The majority of the
 expression bias in the tetraploid is in favour of S. flavus homoeologues
 (ca. 65% of the differentially expressed loci), and overall expression of
 this parental species sub-genome is higher than that of the S. glaucus
 sub-genome. To determine whether absence of expression of a particular S.
 glaucus homoeologue in the allotetraploid could be due to loss of DNA, we
 carried out a PCR-based assay and confirmed that in three out of 10 loci
 the S. glaucus homoeologue appeared absent. Our results suggest that
 biased gene expression is one cause of the allotetraploid S. mohavensis
 being more similar in morphology to one of its parent, S. flavus, and that
 such bias could result, in part, from loss of S. glaucus homoeologues at
 some loci in the allotetraploid.
description: Senecio flavus
 transcriptome assemblyTranscriptome assembled
 from 4 individuals of Senecio flavus leaf tissue using
 TrinityFassembly.fasSenecio glaucus transcriptome assemblyTranscriptome assembled from 3 individuals of Senecio glaucus leaf tissue using TrinityGassembly.fas
DOI: 10.5061/dryad.5b85783
title: Data from: Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data

description: Our understanding of phylogenetic relationships among bony fishes has been
 transformed by analysis of a small number of genes, but uncertainty
 remains around critical nodes. Genome-scale inferences so far have sampled
 a limited number of taxa and genes. Here we leveraged 144 genomes and 159
 transcriptomes to investigate fish evolution with an unparalleled scale of
 data: &gt;0.5 Mb from 1,105 orthologous exon sequences from 303
 species, representing 66 out of 72 ray-finned fish orders. We apply
 phylogenetic tests designed to trace the effect of whole-genome
 duplication events on gene trees and find paralogy-free loci using a
 bioinformatics approach. Genome-wide data support the structure of the
 fish phylogeny, and hypothesis-testing procedures appropriate for
 phylogenomic datasets using explicit gene genealogy interrogation settle
 some long-standing uncertainties, such as the branching order at the base
 of the teleosts and among early euteleosts, and the sister lineage to the
 acanthomorph and percomorph radiations. Comprehensive fossil calibrations
 date the origin of all major fish lineages before the end of the
 Cretaceous.
description: Alignments- Concatenated nucleotide alignment - Concatenated protein alignment - 1,105 exon alignments (protein and nucleotide) - 1,721 exon alignments, with all nHmmer hits aligned - 616 exon alignments of discarded loci, with only the best hit per locus -8-model-species-alignmentsTreeFilesSee Appendix 1 in the Supplementary Appendix for the correspondence between these tree files and the figures in the paper.GGI-Constraint-TreesMaster constraint trees for all hypotheses tested. See Arcila et al. 2017 for a full tutorial of the GGI method.ScriptsScripts used to extract markers from genomes/transcriptomes. There is a short tutorial included in the zip archive that explains the pipeline. Scripts are provided without warranty.MCMCTreeFilesFiles for running divergence time estimation in MCMCTree. See Supplementary Appendix for list of fossil calibrations and details on our three calibration schemes.BGI-Sequencing-ResultsAssembly metrics from BGI-sequenced transcriptomes for Fish T1K
DOI: 10.5061/dryad.mh8c1
title: Data from: A method for time-resolved measurements of the mechanics of phagocytic cups

description: The internalization of matter by phagocytosis is of key importance in the
 defense against bacterial pathogens and in the control of cancerous tumor
 growth. Despite the fact that phagocytosis is an inherently mechanical
 process, little is known about the forces and energies that a cell
 requires for internalization. Here we use functionalized magnetic
 particles as phagocytic targets and track their motion while actuating
 them in an oscillating magnetic field, in order to measure the
 translational and rotational stiffnesses of the phagocytic cup as a
 function of time. The measured evolution of stiffness reveals a
 characteristic pattern with a pronounced peak preceding the finalization
 of uptake. The measured stiffness values and their time-dependence can be
 interpreted with a model that describes the phagocytic cup as a
 prestressed membrane connected to an elastically deformable actin cortex.
 In the context of this model, the stiffness peak is a direct manifestation
 of a previously described mechanical bottleneck and a comparison of model
 and data suggests that the membrane advances around the particle at a
 speed of about 20 nm/s. This approach is a novel way of measuring the
 progression of emerging phagocytic cups and their mechanical properties in
 situ and in real-time.
description: s642c2The supplied video file
 s661c1.avi shows the successful particle internalization event from Fig. 2
 and Fig. 4 of the manuscript. The movie was recorded at 63x magnification
 on an Andor Neo sCMOS camera with an effective pixel size of 90 nm and at
 a frame rate of 7.5 Hz. The particle was actuated by a continuously
 rotating magnetic field at a frequency of 0.5 Hz. Camera acquisition was
 phase-locked to the actuation to record 15 frames per cycle. The movie
 file has been compressed using the Cinepak codec. Please contact the
 authors to obtain more information.s661c1The supplied video file
 s661c1.avi shows the successful particle internalization event from Fig. 2
 and Fig. 4 of the manuscript. The supplied video file s661c1.avi shows the
 successful particle internalization event from Fig. 2 and Fig. 4 of the
 manuscript. The movie was recorded at 63x magnification on an Andor Neo
 sCMOS camera with an effective pixel size of 90 nm and at a frame rate of
 7.5 Hz. The particle was actuated by a continuously rotating magnetic
 field at a frequency of 0.5 Hz. Camera acquisition was phase-locked to the
 actuation to record 15 frames per cycle. The movie file has been
 compressed using the Cinepak codec. Please contact the authors to obtain
 more information.
DOI: 10.5061/dryad.g0141g7
title: Data from: Genomic signatures of adaptation to a precipitation gradient in Nigerian sorghum

description: Evolution of plants under climatic gradients may lead to clinal
 adaptation. Understanding the genomic basis of clinal adaptation in crops
 species could facilitate breeding for climate resilience. We investigated
 signatures of clinal adaptation in the cereal crop sorghum (Sorghum
 bicolor L. [Moench]) to the precipitation gradient in West Africa using a
 panel (n = 607) of sorghum accessions from diverse agroclimatic zones of
 Nigeria. Significant correlations were observed between common-garden
 phenotypes of three putative climate-adaptive traits (flowering time,
 plant height, and panicle length) and climatic variables. The panel was
 characterized at &gt;400,000 single nucleotide polymorphisms (SNPs)
 using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a
 small proportion of SNP variation can be explained by climate (1%), space
 (1%), and climate collinear with space (3%). Discriminant analysis of
 principal components identified three genetic groups that are distributed
 differently along the precipitation gradient. Genome-wide association
 studies were conducted with phenotypes and three climatic variables
 (annual mean precipitation, precipitation in the driest quarter, and
 annual mean temperature). There was no overall enrichment of associations
 near a priori candidate genes implicated in flowering time, height, and
 inflorescence architecture in cereals, but several significant
 associations were found near a priori candidates including photoperiodic
 flowering regulators SbCN12 and Ma6. Together, the findings suggest that a
 small (3%) but significant proportion of nucleotide variation in Nigerian
 sorghum landraces reflects clinal adaptation along the West African
 precipitation gradient.
description: Phenotype and geographic
 datasupplementary file
 1.xlsGlobal SNP
 dataIn vcf format,
 gzippedGlobal_1785.vcf.gzWest African SNP dataIn vcf format, gzippedWestAfrican_325.vcf.gzNigerian SNP data (unfiltered)In vcf format, gzipped. Not filtered for minor allele frequency.NGR_607_431689snps.vcf.gzNigerian SNP data (filtered)In vcf format, gzipped. Filter for minor allele frequency &gt; 0.03NGR_607_nsc_maf_003_GWAS.vcf.gz
DOI: 10.15468/dl.trmqma
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Thevetia peruviana",
 "Country is Tanzania, United Republic of",
 "HasCoordinate is true"
 ]
}

 The dataset includes 13 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025049-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/wihhun
title: Wright Files I-Z Edited; Docketed Case: 82-1707
DOI: 10.7910/dvn/y3ko7q
title: Presentación indicadores de desempeño

description: Presentación de indicadores de desempeño a empresa beneficiaria de proyecto COFFEECHAIN
DOI: 10.7910/dvn/ybeiys
title: Replication Data for: Right-wing authoritarian attitudes, fast-paced decision-making, and the spread of misinformation about COVID-19 vaccines

description: This repository contains the replication material for the article "Schulte-Cloos and Anghel (2023) 'Right-wing authoritarian attitudes, fast-paced decision-making, and the spread of misinformation about COVID-19 vaccines' in: Political Communication, DOI: 10.1080/10584609.2023.2291538".

⭐ The Quarto file 'Schulte-Cloos_Fast-Paced_Fake-News_Replication.qmd' contains all code to reproduce the results.

⭐The HTML file 'Schulte-Cloos_Fast-Paced_Fake-News_Replication.html' is the rendered output of the Quarto file. It contains all figures and tables reported in the main article and the supplemental material accompanying the published manuscript.

⭐ Reproducible environment: The Dockerfile allows you to build the Docker image used to run all analyses. Please ensure you have Docker installed.