cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf7g5.2/36.2
title: Breinholt_et_al_degen12_DS2

description: Dataset 2 (acrossLEP_AHE+PARTtrans). Nexus file containing codon position 1 & 2 for 557 loci and 75 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5.2/37.2
title: Breinholt_et_al_degen12_DS1

description: Dataset 1 (acrossLEP_AHE). Nexus file containing codon position 1 & 2 for 557 loci and 23 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5/10
title: taxa_list

description: List of Sample ID's used in nexus files and corresponding species names in tab-delimited text
DOI: 10.5061/dryad.rf7g5/11
title: Scripts_README

description: Description of the python scripts and direction how to run them.
DOI: 10.5061/dryad.rf7g5/12
title: Breinholt_et_al_LOG_COMMANDS

description: Set of commands used to run the bioinformatic pipeline to generate data for Breinholt et al. 2017
DOI: 10.5061/dryad.rf7g5/13
title: Breinholt_et_al_Supplementary_File_2_Lep1

description: Specification file for the Lep1 probe set used to order probes from Agilent Technologies (http://www.agilent.com/)
DOI: 10.5061/dryad.rf7g5/14
title: Lep1_ref

description: Compressed file containing the data for each reference for each loci in the Lep1 kit  as well as used in the IBA assembly.
DOI: 10.5061/dryad.rf7g5/17
title: IBA

description: python script to assemble AHE data loci by loci
DOI: 10.5061/dryad.rf7g5/18
title: extract_probe_region

description: python script to split alignment into head, probe, and tail regions based on the beginning and end of a reference sequence in the alignment
DOI: 10.5061/dryad.rf7g5/19
title: s_hit_checker

description: python script to process the output of BLAST to find sequences that fit the single hit critera
DOI: 10.5061/dryad.rf7g5/20
title: ortholog_filter

description: python script to process the output of BLAST to find if the location of the best hit on the genome is the same location as the probe target from that genome.
DOI: 10.5061/dryad.sq72d.1
title: Data from: Multiple stressors and the cause of amphibian abnormalities
DOI: 10.5061/dryad.sq72d.1/1.1
title: AnalyticAttributes

description: Descriptions and comments about samples logged by field personnel at the time of sample collection. Some location information for snow transect samples.
DOI: 10.5061/dryad.sq72d.1/2.1
title: AnalyticResults

description: File provides analytical chemistry information for metals, anions, and organic carbon concentrations in wetland water, sediment, tadpole tissue, and soil, dust, and snow collected on transects from roads adjacent to the wetlands from 2010-2012.
DOI: 10.5061/dryad.sq72d.1/3.1
title: BreedingMetamorphicDates

description: This file details the first observed date of egg mass deposition and the date of metamorphosis. Sites were monitored approximately once per two weeks to provide these dates. Additional site monitoring data is provided in other data files.
DOI: 10.5061/dryad.sq72d.1/4.1
title: Conductivity

description: File provides information from 6 wetlands instrumented with continuous specific conductance loggers. Wetland position can be obtained in the "SiteLocation" file and road traffic and distance are in the "RoadsInfo" file.
DOI: 10.5061/dryad.sq72d.1/5.1
title: FrogAbnormalities

description: Information on abnormalities, size, and developmental stage for the over 9,000 frogs examined for abnormalities on the Kenai Peninsula from 2000 through 2012.
DOI: 10.5061/dryad.sq72d.1/6.1
title: FrogDevelopment

description: This table describes each site visit during the follow up study to the published study, whether frogs were found and what developmental stage they were, and how much time was spent assessing the site and performing the frog survey.
DOI: 10.5061/dryad.sq72d.1/7.1
title: Habitat

description: This data set includes habitat data that were collected from 2010-2012.
DOI: 10.5061/dryad.sq72d.1/8.1
title: Invert

description: This file contains data on the invertebrate community composition for lentic wetlands sampled to determine the effects of roads on water quality and the invertebrate community.
DOI: 10.5061/dryad.sq72d.2/28.2
title: Temperature_Anomolies

description: Provides dates, issues, and resolution when temperature loggers included in the Temperature.csv file were out of water or otherwise malfunctioning. If blocks of data are missing from the Temperature.csv file, check here for dates.
DOI: 10.17632/5w24ft7wwm.1
title: Data for: The movement of cool-adapted taxa in lowland last glacial north-western Amazonia

description: Raw pollen counts from lake Pata, Six Lakes Hill, Amazonas, Brazil
DOI: 10.17632/696r3x5pbj.1
title: Data for: Synthesis of gem-difluorocyclopentane/hexane building blocks

description: Copies of spectra for the manuscript "Synthesis of gem-difluorocyclopentane/hexane building blocks"
DOI: 10.17632/wrf6t8v9jc.1
title: Complementary literature review and analysis for: The impact of Swedish SO2 policy instruments on SO2 emissions 1990-2012

description: The supplementary material contains a literature review and complementary mass balance analysis of sulphur in oil imports.
DOI: 10.17632/wrf6t8v9jc.2
title: Complementary literature review and analysis for: The impact of Swedish SO2 policy instruments on SO2 emissions 1990-2012

description: The supplementary material contains a literature review and complementary mass balance analysis of sulphur in oil imports.
DOI: 10.17632/xr77r28gch.2
title: Data for: What Exactly, Regression of Atherosclerosis or Foreign Body Reaction With Hyaline Arteriosclerosis, Drives Transient Scaffolding of Coronary Arteries? A Serial Multimodality Imaging Subanalysis of ABSORB Cohort B1 Trial

description: The dataset contains the information regarding to the permission of the sponsor and involved CRO to conduct the intravascular imaging (QCA, IVUS, OCT, MSCT) and statistical analysis at the loop between Cardialysis B.V. (Rotterdam, The Netherlands), Erasmus MC (Rotterdam, The Netherlands) and Abbott Vascular (Santa Clara, CA). Moreover, the dataset includes lists of the studied variables with the definitions.
DOI: 10.5061/dryad.25f7g/1
title: Supplementary_Files_Edwards_CNEEs_2017

description: Supplementary Files S1, S3, S4, S5, and S6.
DOI: 10.5061/dryad.25f7g/2
title: Supplementary File S2

description: Alignment summary measures for all loci.
DOI: 10.5061/dryad.25f7g/4
title: Supplementary_Figures_CNEEs_Edwards_2017

description: Supplementary Figures S1-7.
DOI: 10.5061/dryad.26bv4/10
title: Receptor protein tyrosine kinase phylogeny

description: Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, orange, blue, and brown texts indicate C. owczarzaki,
Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis (strain Colp-12) and H.
sapiens, respectively. The query sequence is indicated in red and with a grey box. An
asterisk next to the Opistho-1/-2 and Colp-12 transcript(s) indicates the presence of a
transmembrane domain plus a catalytic tyrosine kinase domain. The presence of
Fibronectin-3 (FN3) and signal peptides indicating N-terminal complete proteins (SP) or
of catalytic tyrosine kinase domains only (TyrKc only) is also indicated. Selected clades
are collapsed to increase clarity; annotated H. sapiens homologs in all clades are
indicated. Node supports are nonparametric ML bootstrap values obtained from 1000
ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes
represent bootstrap supports of greater than 50%. The scale bar represents the
estimated number of amino acid substitutions per site. TIE, tyrosine kinase with
immunoglobulin like and EGF like domains; INSR, insulin receptor; INSRR, insulin
receptor related receptor; IGF1R, insulin like growth factor 1 receptor; ERBB3, erb-b2
receptor tyrosine kinase 3; EPHB1, EPH receptor B1.
DOI: 10.5061/dryad.26bv4/11
title: Phylogenetic trees in newick format

description: All phylogenetic trees shown as Main Figure or Supplemental Figures in the manuscript are collected in this file as unrooted trees in newick format. Descriptions for the single trees can be found within the file.
DOI: 10.5061/dryad.26bv4/6
title: Phylogenomic reconstruction without novel taxa

description: Phylogenomic tree based on 255 concatenated proteins inferred by IQ-TREE under the LG+C40+F+G4
model. Novel species have been removed from the 255-gene data set. Node supports are ultrafast bootstrap
(UF) values obtained from IQ-TREE. Black dots on branches correspond to &gt;95% UF.
DOI: 10.5061/dryad.26bv4/7
title: Src protein tyrosine kinase phylogeny

description: Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis
(strain Colp-12), C. limacisporum and H. sapiens, respectively. The query sequence is indicated in red. A shaded rectangle indicates the protein in question in filastereans and Pluriformea. An asterisk indicates annotated human proteins belonging to the Src family. Other protein tyrosine kinases (Tec, Abl2 and Csk) are indicated and were identified by the annotated C. owczarzaki homolog present in the respective clade. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site.
DOI: 10.5061/dryad.26bv4/8
title: Csk and FAK protein tyrosine kinase phylogenies

description: (A) and (B) Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis (strain Colp-12), C. limacisporum and H. sapiens, respectively. The query sequence is indicated in red. A shaded rectangle indicates the protein in question in filastereans and Pluriformea, if present. An asterisk indicates human proteins annotated as Csk (A) and FAK (B), respectively. Other protein tyrosine kinases are indicated and were identified by the annotated C. owczarzaki homolog(s) present in the respective clade if not otherwise indicated. Clades in (B) are collapsed to increase clarity. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number
of amino acid substitutions per site.
DOI: 10.5061/dryad.26bv4/9
title: Receptor protein tyrosine phosphatase phylogeny

description: Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor, S. multiformis, C. limacisporum and H. sapiens,
respectively. The query sequence is indicated in red. The Pigoraptor (strains Opistho-1 and Opistho-2) and S. multiformis (strain Colp-12) sequences cluster with an annotated C. owczarzaki receptor protein tyrosine phosphatase also containing Fibronectin-3
domains (XP_004365141); note the Opistho-1 and the Colp-12 homolog are truncated.
Other protein tyrosine kinases (receptor and non-receptor) are indicated and were identified by the annotated H. sapiens homologs present in the respective clade. Selected clades are collapsed to increase clarity. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site.
DOI: 10.5061/dryad.6m20j/6
title: Quartet Sampling Branch Replicate Simulations

description: A gzipped tar archive containing the results of the effect of number of replicates on QC values.
DOI: 10.5061/dryad.6m20j/7
title: Quartet Sampling ILS/Introgression Simulations

description: A gzipped tar archive containing the results of the effect of ILS and introgression on QC/QC values.
DOI: 10.5061/dryad.6m20j/8
title: Quartet Sampling Results/Data: Zanne, et al. 2014

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Zanne, et al. 2014 study.
DOI: 10.5061/dryad.6m20j/9
title: Quartet Sampling Results/Data: Pease, et al. 2016

description: A gzipped tar archive containing the input alignment and tree, and results of various Quartet Sampling analyses for the Pease, et al. 2016 study.
DOI: 10.5061/dryad.7fq07/1
title: Species occurence and trait data

description: Long form community data showing each potential species X site combination, with species-level trait data and site-level environmental variables for each.
DOI: 10.5061/dryad.7k23g/1
title: datafile_Filippi_et_al_2017

description: Data was collected in a laboratory setting. The
experimental interface was created in PsychoPy (standalone version). Abbreviations used in column headings: HNR = Harmonic-to-noise-ratio, F0 = mean fundamental frequency, SCG = spectral center of gravity. For each acoustic parameter, ratios between low and high arousal vocalizations within each pair were included in the analysis.
DOI: 10.5061/dryad.9pq6k/19
title: NIP51mRNA670_PP2AmRNA570_(9)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/20
title: NIP51mRNA670_PP2AmRNA570_(10)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/21
title: NIP51mRNA670_PP2AmRNA570_(11)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/22
title: NIP51mRNA670_PP2AmRNA570_(12)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.9pq6k/23
title: NIP51mRNA670_PP2AmRNA570_(13)

description: NIP5;1 mRNA (exon) probes (Quasar 670, channel 1), PP2A mRNA (exon) probes (Quasar 570, channel 2) and DAPI, channel 3.
DOI: 10.5061/dryad.bp81r/1
title: Mancozeb tolerance at three concentrations in the 215 isolates of Alternaria alternata collected from seven potato fields across China.

description: Mancozeb tolerance at three concentrations in the 215 isolates of Alternaria alternata collected from seven potato fields across China. Mancozeb tolerance of isolates was measured with relative growth rate (RGR) of the isolates in the presence of mancozeb to the absence of mancozeb.
DOI: 10.5061/dryad.c8k7q/1
title: Genome-wide association analysis identifies potential regulatory genes for eumelanin pigmentation in chicken plumage

description: The Roshal ARchive (RAR) contains the genotype and the phenotype of this study. Association analysis was conducted by the PLINK software using the “Basic case/control association” test after affinity adjustment. Pearson Chi-square test was used for significance testing, and then Bonferroni correction was used to adjust for multiple comparisons. The R programming codes were used to generate the Manhattan plot of genome wide P values.
DOI: 10.5061/dryad.cb0b8/1
title: Database of unique Macrorhynchia phoenicea unique MLGs per population

description: Tab delimited text. On each line is represented a unique MLG, with haplotypes for 15 loci used in all analyses of the publication
DOI: 10.5061/dryad.ch8d7/1
title: Common Garden Performance Data

description: Includes data related to the performance of Verbascum thapsus rosettes grown in a common garden.  Columns include: 'Plant' (unique ID associated with each rosette; numbers are not consecutive due to attrition before planting and plants that were excluded due to faulty irrigation), 'Population' (unique ID associated with each population; numbers are also not consecutive due to attrition before planting and plants that were excluded due to faulty irrigation), 'Origin' (continental range of seed collection; North American or European), 'Block' (1 or 2; a spatial block that coincides with maternal line), 'Treatment' (Ambient or Reduced Herbivory), 'PC1' (Principle Component associated mainly with temperature), 'PC2' (Principle Component associated mainly with precipitation during warm or wet periods), 'PC3' (Principle Component associated mainly with precipitation during warm and dry periods), 'Rosette.Area' (cm^2), 'Alive' (indicates where the rosette survived [1] or died [0] before September of the first growing season), 'Survival.to.Beginning.of.the.Second.Growing.Season' (0=no, 1=yes), 'Young.Leaf.Chewing.Damage' (estimate of average percent leaf tissue removed on young leaves by insect herbivores), 'Binomial.Young.Leaf.Chewing.Damage' (0=no visible damage, 1=visible damage on young leaves), 'Old.Leaf.Average.Chewing.Damage' (estimate of average percent leaf tissue removed on old leaves by insect herbivores), Binomial.Old.Leaf.Chewing.Damage (0=no visible damage, 1=visible damage on young leaves), 'Garden' (Garden Location; either U.S. or Czech Republic).
DOI: 10.5061/dryad.ch8d7/2
title: Resistance to Herbivory Data

description: Includes data related to resistance against herbivory of native and introduced populations of Verbascum thapsus. Columns include: 'Garden' (Garden Location; either U.S. or Czech Republic), 'Block' (1 or 2; a spatial block that also coincides with maternal line), 'Population' (unique ID associated with each population; numbers are also not consecutive due to attrition before planting and plants that were excluded due to faulty irrigation), 'Origin' (continental range of seed collection; North American or European),  'Latitude' (of seed source), 'Longitude' (of seed source), 'PC1' (Principle Component associated mainly with temperature), 'PC2' (Principle Component associated mainly with precipitation during warm or wet periods), 'PC3' (Principle Component associated mainly with precipitation during warm and dry periods), 'Average.Rosette.Area.under.Reduced.Herbivory' (cm^2; rosette area for plants sprayed with systemic insecticide), 'Average.Ambient.Old.Leaf.Damage' (estimate of average percent leaf tissue removed on old leaves by insect herbivores when plants were sprayed with a water control).
DOI: 10.5061/dryad.ch8d7/3
title: Tolerance to Herbivory Data

description: Includes data related to tolerance to herbivory of native and introduced populations of Verbascum thapsus. Columns include: 'Garden' (Garden Location; either U.S. or Czech Republic), 'Block' (1 or 2; a spatial block that also coincides with maternal line), 'Population' (unique ID associated with each population; numbers are also not consecutive due to attrition before planting and plants that were excluded due to faulty irrigation), 'Origin' (continental range of seed collection; North American or European), 'Latitude' (of seed source), 'Longitude' (of seed source), 'PC1' (Principle Component associated mainly with temperature), 'PC2' (Principle Component associated mainly with precipitation during warm or wet periods), 'PC3' (Principle Component associated mainly with precipitation during warm and dry periods), 'Coefficient.of.Tolerance.Slope' (the slope of the line of log-transformed rosette area plotted against percent herbivore damage experienced by each plant), 'Variance.of.Tolerance.Slope'.
DOI: 10.5061/dryad.dm82j/1
title: B. cereus sensu lato HaMStR databases

description: Contains the four B. cereus s. l. HaMStR databases used in this study. Each HaMStR database contains BLAST databases, FASTA files, protein and CDS alignments, and HMMs.
DOI: 10.5061/dryad.dm82j/2
title: B. cereus sensu lato data matrices

description: Contains the Bacillus Mash distance matrix, the B. cereus s. l. pan-genome binary data matrix, and the six B. cereus s. l. concatenated data matrices used in the study along with associated RAxML partition specifications.
DOI: 10.5061/dryad.dm82j/3
title: B. cereus sensu lato phylogenetic trees

description: Contains the Bacillus FastME tree, the B. cereus s. l. accessory binary tree produced by Roary, the RAxML maximum likelihood trees (ML_1–ML_8), and the PAUP maximum parsimony tree (MP_1).
DOI: 10.5061/dryad.dm82j/4
title: create_data_matrix Perl script

description: The create_data_matrix Perl script aligns orthologous protein groups produced by HaMStR, converts alignments to CDS equivalents, applies the consensus method, and concatenates individual gene alignments to produce the final data matrix.
DOI: 10.5061/dryad.jg470/1
title: Opertative and environmental temperatures

description: This Excel-file contains operative and environmental data for the two skink species, M. boulengeri and C. regius, in Kinchega National Park, Australia, which were used for the analyses.
DOI: 10.5061/dryad.m53r1/1
title: Turner_et_al_data_all_populations

description: This data file includes biomass, stoichiometry, and nucleic acid measurements of the twelve long-term populations at 0 and 50,000 generations.
DOI: 10.5061/dryad.m53r1/2
title: Turner_et_al_data_Population_A-1

description: This file contains measurements of biomass and stoichiometry for population A-1 at 14 time points ranging from 0 to 60,000 generations.
DOI: 10.5061/dryad.np4hs/30
title: Exp2_S5_Session2a

description: This data file contains functional MRI data of subject 5 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 1-3.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/31
title: Exp2_S5_Session2b

description: This data file contains functional MRI data of subject 5 in Experiment 2. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) of Session 2, runs 4-6, the structural MRI data (T1w and PD contrast, nifti format, de-faced), and reversed phase encoded (AP-PA) images for distortion correction.  For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment2”
DOI: 10.5061/dryad.np4hs/32
title: DesignProtocolsStimuli_Experiment2

description: This data set includes the stimuli and files describing the stimulation protocols used during the functional runs of all subjects in Experiment 2.
DOI: 10.5061/dryad.pr318/1
title: MetaData_Quality_VCF

description: This file contains 1) metadata that describes each sample used, 2) quality scores from sequencing on Illumina platform, and 3) an initial VCF file with individual genotypes compiled from the raw sequencing data (refer to methods in publication for a description of genotypes used to generate the PCA in the manuscript).
DOI: 10.5061/dryad.pr318/2
title: Eastern Wolf Raw Data

description: This file contains raw Illumina sequence data for the Eastern Wolves (Canis lycaon). Please check the metadata to confirm and cross-reference sample IDs.