cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf7g5.2/6.2
title: Breinholt_et_al_Supplementary_Figure_S2

description: Supplementary Figure S2 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.2/7.2
title: Breinholt_et_al_Supplementary_Figure_S3

description: Supplementary Figure S3 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.2/8.2
title: Breinholt_et_al_Supplementary_Figure_S4

description: Supplementary Figure S4 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.2/9.2
title: Breinholt_et_al_Supplementary_Figure_S5

description: Supplementary Figure S5 from Breinholt et al. (2017)
DOI: 10.5061/dryad.s114h/1
title: DataForBehavioralEcologyReedy_etal_2017

description: Behavioral observations following staged same-sex territorial intrusions using tethered stimulus lizards.
DOI: 10.5061/dryad.sq72d.2/1.2
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.st621/6
title: Fig2A_Blot2

description: Original blot to quantify Fig2A
DOI: 10.5061/dryad.st621/7
title: Fig2A_Blot1

description: Original blot to quantify Fig2A
DOI: 10.5061/dryad.st621/8
title: Fig2_2A

description: Raw data values for Fig2A quantification
DOI: 10.5061/dryad.tc07j/1
title: S1_Botrychium_matK_368_sequences

description: non-coding chloroplast locus matK intron
DOI: 10.5061/dryad.tc07j/2
title: S2_Botrychium_rpL16_367_sequences

description: non-coding chloroplast locus rpL16 intron
DOI: 10.5061/dryad.tc07j/3
title: S3_Botrychium_trnLF_368_sequences

description: non-coding chloroplast locus trnL-trnF intergenic spacer
DOI: 10.5061/dryad.tc07j/4
title: S4_Botrychium_trnHpsbA_368_sequences

description: non-coding chloroplast locus trnH–psbA  intergenic spacer
DOI: 10.5061/dryad.vg1g6/4
title: Parsimony tree for molecular data

description: Molecular analysis using PAUP and parsimony ratchet. Consensus tree is presented with bootstrap support values.
DOI: 10.5061/dryad.vg1g6/5
title: Combined analysis tree

description: Consensus tree for PAUP and parsimony Ratchet analysis of combined dataset, with bootstrap support values above branches.
DOI: 10.6084/m9.figshare.12980861
title: UnAmbiguouslyMapped_ds.buccal_trim2-centrifuge-report.tsv

description: work documented here: https://hackmd.io/@astrobiomike/centrifuge-db-build
DOI: 10.6084/m9.figshare.12980861.v1
title: UnAmbiguouslyMapped_ds.buccal_trim2-centrifuge-report.tsv

description: work documented here: https://hackmd.io/@astrobiomike/centrifuge-db-build
DOI: 10.5061/dryad.17tf0/1
title: Datasets_Fitness_CG_RT

description: See README.txt
DOI: 10.5061/dryad.1q8h3/1
title: Adherence research in Malaysia

description: Adherence research in Malaysia
DOI: 10.5061/dryad.21m3t/10
title: far_tree

description: MCC tree for the first African radiation (FAR tree) of bufonids, recovered from time-calibrated Bayesian MCMC tree searches using BEAST under a birth-death uncorrelated lognormal relaxed clock model.
DOI: 10.5061/dryad.21m3t/11
title: global_tree_alignment

description: concatenated alignment used to generate the global tree
DOI: 10.5061/dryad.21m3t/12
title: far_clade_alignment

description: concatenated alignment used to generate the far tree
DOI: 10.5061/dryad.21m3t/8
title: SuppInf8

description: Supporting Information S8. Investigating the effects of bGMYC oversplitting.
DOI: 10.5061/dryad.21m3t/9
title: global_tree

description: MCC tree for Bufonidae (Global Tree) recovered from time-calibrated Bayesian MCMC tree searches using BEAST under a birth-death uncorrelated lognormal relaxed clock model.
DOI: 10.5061/dryad.31048/10
title: figures_rhynchComb_08-03-16

description: R script for generating all figures in manuscript from provided R workspace file
DOI: 10.5061/dryad.31048/11
title: figures_for_EvolTalk_06-20-16

description: R script for generating all figures in associated Evolution 2016 from provided R workspace file
DOI: 10.5061/dryad.31048/12
title: SuppTable1_contraTable

description: Supplemental Table 1 as a PDF, reporting pair-wise CDs between considered summary topologies.
DOI: 10.5061/dryad.31048/13
title: SuppMat_allTreesPlotted_suppFigures

description: PDF Supplementary Material containing plots of all summary trees considered in this paper, with associated support values.
DOI: 10.5061/dryad.31048/3
title: runScripts.zip

description: Zip file containing a necessary directory for recreating analyses
DOI: 10.5061/dryad.31048/4
title: datafiles.zip

description: Zip file containing a necessary directory for recreating analyses
DOI: 10.5061/dryad.31048/5
title: make_runI_06-29-15

description: R Script for creating MrBayes script for simulation-based sensitivity analyses
DOI: 10.5061/dryad.31048/7
title: rhynchComb_07-25-16

description: Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.31048/8
title: rhynchComb_07-25-16

description: PDF generated from knitting Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.31048/9
title: rhynchComb_workspace_07-25-2016.Rdata

description: Saved R Workspace from running Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.3nf8b/1
title: Stable isotope and nitrogen concentration data

description: Single and mean δ15N, δ13C, δ2H, δ18O values, enrichment factors ε15N, ε13C, ε2H, ε18O and total nitrogen concentration data of 17 Orchidaceae species and 34 autotrophic reference species.
DOI: 10.5061/dryad.488rt/1
title: AgematsuetalSupplementdata

description: movie, wmv file
DOI: 10.5061/dryad.4q08q/1
title: FP_ABI_files

description: Raw sequence data for KIAA, SACS, COI and CytB for the genus Ommatotriton in ABI format
DOI: 10.5061/dryad.4q08q/2
title: FP_Bayesian_skyline

description: Input and output data for Bayesian Skyline analyses
DOI: 10.5061/dryad.7b8vb/1
title: Simulation results: Ne = 1.0E6

description: Results of evolutionary simulations for Ne = 1.0E6
DOI: 10.5061/dryad.7b8vb/2
title: Simulation results: Ne = 1.0E4

description: Results of evolutionary simulations for Ne = 1.0E4
DOI: 10.5061/dryad.7b8vb/4
title: Simulation results (null amino acid): Ne = 1.0E4

description: Results of evolutionary simulations for Ne = 1.0E4: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)
DOI: 10.5061/dryad.c641b/1
title: Microsatellite data of giant pandas in Arlequin format

description: This file includes the microsatellite genotypes of 153 giant panda individuals, in Arlequin format.
DOI: 10.5061/dryad.f866r/1
title: Perkins.etal.Dryad.Data_Multichannel.Feeding

description: This file contains three tabs each with a separate data set. The first contains biomass values for spider functional groups per grassland; the second contains source (prey) stable isotope values (d15N and d13C) for use in stable isotope mixing models; the third contains the d15N and d13C values for individual spiders per grassland. All other data used in this study is reported in the main paper.
DOI: 10.5061/dryad.gq8m9/1
title: MacLachlan_etal.(2017)_PhenotypicData_June9th2017

description: Phenotypic data and associated categories of metadata for each seedling studied
DOI: 10.5061/dryad.gq8m9/2
title: MacLachlan_etal.(2017)_ClimateData_June9th2017

description: Climate date for each seedling used for both the phenotype-climate and hybrid index-climate analyses
DOI: 10.5061/dryad.gq8m9/3
title: MacLachlan_etal.(2017)_AdmixtureRefernceIndivs_SNPpedfile_June9th2017

description: Genotype data in .ped file format (with two columns per SNP) for the 500 individual seedlings used as the reference population for the ADMIXTURE projection analysis.
DOI: 10.5061/dryad.gq8m9/4
title: MacLachlan_etal.(2017)_AdmixtureProjectedIndivs_SNPpedfile_June9th2017

description: Genotype data in .ped file format (with two columns per SNP) for the 1572 individuals for which hybrid ancestry was estimated using the ADMIXTURE projection analysis function
DOI: 10.5061/dryad.gq8m9/5
title: MacLachlan_etal.(2017)_README_climatemetadata_June9th2017

description: Metadata explaining the climate variables used in this study
DOI: 10.5061/dryad.gq8m9/6
title: MacLachlan_etal.(2017)_README_phenotypicmetadata_June9th2017

description: Metadata explaining the phenotypic traits analysed and how they were measured
DOI: 10.5061/dryad.gq8m9/7
title: MacLachlan_etal.(2017)_SNPmapfile_June9th2017

description: The details of each SNP analysed in the .ped files for reference and projected ADMIXTURE populations. SNPs (rows) in the .map file match the order of SNPs (columns) in the .ped file. Each locus in the .ped file has two columns per SNP
DOI: 10.5061/dryad.kt8k2/1
title: Data Lenaerts et al. Functional Ecology
DOI: 10.5061/dryad.n410t/1
title: THC_Data
DOI: 10.5061/dryad.np4hs/1
title: Exp1_S1a

description: This data file contains functional MRI data of subject 1 in Experiment 1. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) for test runs 1-2 and for training runs 1-2. For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment1”
DOI: 10.5061/dryad.np4hs/2
title: Exp1_S1b

description: This data file contains functional MRI data of subject 1 in Experiment 1. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) for training runs 3-6 and the structural MRI data (T1w and PD contrast, nifti format, de-faced).
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment1”
DOI: 10.5061/dryad.np4hs/3
title: Exp1_S2a

description: This data file contains functional MRI data of subject 2 in Experiment 1. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) for test runs 1-2 and training runs 1-2.
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment1”
DOI: 10.5061/dryad.np4hs/4
title: Exp1_S2b

description: This data file contains functional MRI data of subject 2 in Experiment 1. Specifically, the data file contains the functional MRI time series (EPI T2*w, nifti format) for training runs 3-6 and the structural MRI data (T1w and PD contrast, nifti format, de-faced).
For details on stimuli and experimental design please see the data file: “DesignProtocolsStimuli_Experiment1”
DOI: 10.5061/dryad.qp4kb/1
title: Individual fastq files for Anopheles funestus from Cameroon
DOI: 10.5061/dryad.rf7g5.2/11.2
title: Scripts_README

description: Description of the python scripts and direction how to run them.
DOI: 10.5061/dryad.rf7g5.2/12.2
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.rf7g5.2/13.2
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.rf7g5.2/14.2
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.rf7g5.2/15.2
title: JAVA_SourceCode

description: Compressed directory holding A.R.L (alemmon@evotutor.org) java source code
	This directory contains readme and instructions for use and to compile the java code for IdentifySpacedKmers7, QuickScan5, and ShallowMapper4. It also contain the Lep1_ProbeDesign directory used with the java programs to design the Lep1 probe set
	(IdentifySpacedKmers7, IdentifySpacedKmers7_readme.txt, Lep1_ProbeDesign, LepRefFiles.txt, QuickScan5_readme.txt, QuickScan5.java, ShallowMapper4_readme.txt, ShallowMapper4.java)
	ShallowMapper4: java script by A.R.L used to identify intron boundaries in genes for five reference taxa by mapping raw genomic reads to the corresponding transcriptomic sequences 
	QuickScan5: java script by A.R.L used to scan the additional 23 transcriptomes and ESTs by generating reference kmers using the 5-species alignments and using those kmers to map contig sequences from the transcriptomes to the candidate locus set
DOI: 10.5061/dryad.rf7g5.2/17.2
title: IBA

description: python script to assemble AHE data loci by loci
DOI: 10.5061/dryad.rf7g5.2/4.2
title: Breinholt_et_al_Supplementary_File_1__S1-S11

description: Supplementary File 1: Microsoft excel document including Supplementary Table S1-S11 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.2/40.2
title: IBA_trans

description: python script to assemble AHE data loci by loci for using a fastq file from transcriptome data
DOI: 10.5061/dryad.rf7g5.2/42.2
title: Breinholt_et_al_Supplementary_File_3

description: Word document that expands discussion of  Breinholt et al. (2017) and discusses Lepidopteran relationships in more details
DOI: 10.5061/dryad.sj416/1
title: R-script_Oecologia_Wilkins_et_al_2017

description: R script that was used for all analyses and figures.
DOI: 10.5061/dryad.sj416/2
title: Parents_sheet_230616

description: Input data for statistical analyses with all parental characteristics (e.g., skin colouration, carotenoid measures in unfertilized eggs, egg sizes).
DOI: 10.5061/dryad.sj416/3
title: data24_carotenoids_230616

description: Embryo characteristics for statistical analysis before individual embryos were transferred from 24-well to 12-well plates (e.g., survival, origin, plate position and ID).
DOI: 10.5061/dryad.sj416/4
title: data12_carotenoids_230616

description: Embryo characteristics for statistical analysis after individual embryos were transferred from 24-well to 12-well plates (e.g., this includes only survivors and their size and growth measures).
DOI: 10.5061/dryad.sq72d.2
title: Data from: Multiple stressors and the cause of amphibian abnormalities
DOI: 10.5061/dryad.sq72d.2/2.2
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.2/3.2
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.2/4.2
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.2/5.2
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.2/6.2
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.2/7.2
title: Habitat

description: This data set includes habitat data that were collected from 2010-2012.
DOI: 10.5061/dryad.sq72d.2/8.2
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.2/9.2
title: RoadsInfo

description: This file contains the measured distance from each wetland to the nearest road and whether the road was paved or gravel.
DOI: 10.5061/dryad.st621/10
title: Fig2_2C

description: Raw data values for Fig2C quantification
DOI: 10.5061/dryad.st621/11
title: Fig3_Fig 3 A,B

description: Raw counts and percentages for lifespan of both control and experimental adult flies.  Figure 3.
DOI: 10.5061/dryad.st621/12
title: Fig4_4B Control

description: Raw response amplitudes per fiber for control evoked responses. Figure 4B.
DOI: 10.5061/dryad.st621/13
title: Fig4_4B P-L

description: Raw response amplitudes per fiber for experimental genotype evoked responses. Figure 4B.
DOI: 10.5061/dryad.st621/14
title: Fig4_4B STATS

description: Statistical analysis for Fig4B
DOI: 10.5061/dryad.st621/15
title: Fig4_4D

description: Raw data values and statistical analysis for Fig 4D
DOI: 10.5061/dryad.st621/16
title: Fig4_4E

description: Raw data values and statistical analysis for Fig4E.
DOI: 10.5061/dryad.st621/17
title: Fig5_5A

description: Raw data values and statistical analysis for Fig5A.
DOI: 10.5061/dryad.st621/9
title: Fig2_2B

description: Raw data values for quantification of Fig2B
DOI: 10.5061/dryad.t5pr5/1
title: Womens' daily reports of emotional and sexual attraction towards partners and extra-pair men.

description: Data used for mixed models.
DOI: 10.5061/dryad.t5pr5/2
title: Womens' reports of emotional and sexual attraction towards partners and extra-pair men in two phases.

description: Data used for repeated measure ANCOVA.
DOI: 10.5061/dryad.t5pr5/3
title: Womens' reports of emotional and sexual attraction towards partners and extra-pair men in five phases.

description: Data used for repeated measure ANCOVA.
DOI: 10.5061/dryad.v25vk/1
title: ResultsSection2.1

description: This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral host (Hanc) and plasmid (Panc), evolved host (Hev) and plasmid (Pev), permutations HancPev and HevPanc, as well as control evolved hosts containing the ancestral plasmid (Hev*Panc).
DOI: 10.5061/dryad.v25vk/2
title: ResultsSection2.2

description: This competition assay dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 48 generation period for mixed populations consisting of plasmid-containing (ancestral host and plasmid or evolved host and plasmid) and their respective plasmid-free segregants (ancestral host or evolved host only, respectively).
DOI: 10.5061/dryad.v25vk/3
title: ResultsSection2.3

description: This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral or evolved hosts containing one of three alternative plasmids, pB10, Rsa and IncQ.
DOI: 10.5061/dryad.v25vk/4
title: ResultsSection2.4

description: This plasmid persistence dataset contains the number of plasmid-containing and plasmid-free cells sampled every 10 generations (24 h) over a 100 generation period for populations consisting of ancestral or evolved hosts with reconstructed mutant or ancestral helicase alleles.
DOI: 10.5061/dryad.0qk1h/1
title: Data used to compare ELISA techniques

description: This file includes all the data used to produce Figure 1. Species are included both as full names and a shorthand used in the provided code. ELISA results are reported as PI (competition ELISA) and as SP (indirect ELISA).
DOI: 10.5061/dryad.0qk1h/2
title: Data used to statistically estimate a cut-off in vaccinated birds

description: This file includes the data used to produce figure 2A. The vaccination status is provided as an indication (but not used for the statistical approach), and the ELISA result is provided in the PI column.
DOI: 10.5061/dryad.0qk1h/3
title: Data use to statistically estimate a cut-off in serological analyses of wild birds exposed to Borrelia

description: This file includes the data used to produce figure 2B. The species name is included in both scientific and regular formats. All birds are adult, as shown in the age column. The ELISA result is provided as an optical density in the OD column.
DOI: 10.5061/dryad.2r05d/1
title: Tolleter et al_highly enriched

description: COPASI file of numerical modelling used for the the generation of time courses for changes in dually labelled CO2 (highly enriched 18O bicarbonate)
DOI: 10.5061/dryad.2r05d/2
title: Tolleter et al_lowly enriched

description: COPASI file of numerical modelling used for the generation of times courses for changes in singly labelled CO2 species (lowly enriched 18O bicarbonate)
DOI: 10.5061/dryad.31048/15
title: test_which_parsimony_informative_01-16-17

description: Revised script for testing whether characters are parsimony informative.
DOI: 10.5061/dryad.31048/17
title: write_simple_sumt_01-16-17

description: Revised script for obtaining the simple summary tree files from MrBayes
DOI: 10.5061/dryad.31048/18
title: runFiles.zip

description: Zipped directory containing output from phylogenetic analyses, necessary for use with analyses in Rmd file. All tree files are contained in this zipped directory.
DOI: 10.5061/dryad.31048/19
title: run_coding_12-15-16a.pdf

description: PDF table explaining how the identifiers, labels and conditions of the different phylogenetic analyses as given in the main text and in the supplemental data materials relate.
DOI: 10.5061/dryad.31048/20
title: README

description: README file describes the file type and contents of all files in this data repository.
DOI: 10.5061/dryad.31048/21
title: raw_morphMat_MrBayes_04-21-17.nex

description: The raw morphological matrix, as used in the Bayesian analyses, as a Nexus-formatted text file.
DOI: 10.5061/dryad.4q08q/3
title: FP_ENM

description: Ecological Niche Modeling in- and output data
DOI: 10.5061/dryad.4q08q/4
title: FP_jModelTest

description: jModelTest in- and output data
DOI: 10.5061/dryad.4q08q/5
title: FP_Mismatch_analysis

description: In- and output data for mismatch analyses
DOI: 10.5061/dryad.4q08q/6
title: FP_Phylogenetics

description: In- and output data for phylogenetic analyses (RAxML, MrBayes,  BEAST)
DOI: 10.5061/dryad.4q08q/7
title: FP_SPF_files

description: Contig files of sequence data for KIAA, SACS, COI and CytB for genus Ommatotriton.
DOI: 10.5061/dryad.7b8vb/3
title: Simulation results: Ne = 1.0E8

description: Results of evolutionary simulations for Ne = 1.0E8
DOI: 10.5061/dryad.7b8vb/5
title: ReadMe file

description: Description of data files
DOI: 10.5061/dryad.7b8vb/6
title: Simulation results (null amino acid): Ne = 1.0E6

description: Results of evolutionary simulations for Ne = 1.0E6: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)
DOI: 10.5061/dryad.7b8vb/7
title: Simulation results (null amino acid): Ne = 1.0E8

description: Results of evolutionary simulations for Ne = 1.0E8: One residue is fixed to be a non-interacting 'null' residue 'X'. Identity of fixed residue indicated by number at end of file name. (zero based numbering)
DOI: 10.5061/dryad.9tg56/1
title: Dryad Salep PGM data

description: Salep samples 1-55 (chip 1 and chip 2). Per chip raw demultiplexed data. Per chip demultiplexed and split on primer data processed. Primer sequences. The number of reads per MOTU as well as the top BLAST hits per MOTU were compiled using custom scripts available online as part of the HTS-barcode-checker pipeline http://145.136.240.164:8080/ [56].
DOI: 10.5061/dryad.bs06h/1
title: Sudanese and South Sudanese genomic variation

description: Uncleaned plink (bed bim fam) files from 18 Sudanese and South Sudanese populations. Created using Illumina Human Omni 5M Exo SNP array.
DOI: 10.5061/dryad.gq8m9/8
title: MacLachlan_etal.(2017)_README_SNPpedfile_mapfile_metadata_June9th2017

description: Metadata describing the contents of the .map and .ped files
DOI: 10.5061/dryad.jb268/1
title: Submit MS

description: MS data
DOI: 10.5061/dryad.jb268/2
title: Submit Data

description: sequential data
DOI: 10.5061/dryad.jb268/3
title: Pathogenic data