cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sp800/1
title: allQPCRdata

description: Includes all relevant relative expression data from the paper.  In particular, F3'h, F3'5'h, Dfr, and Fls expression data.  All data is relative to a single Penstemon neomexicanus floral cDNA sample and has been relativized to expression of elongation factor alpha.
DOI: 10.5061/dryad.sp800/2
title: DFRenzymeData

description: Data from DFR in vitro enzyme assays - includes relative amounts of DHK, DHQ, and DHM converted by each species.
DOI: 10.5061/dryad.sp800/3
title: F2sAlleleSpecificExpr

description: Allele specific expression at F3'5'h in selected F2 individuals.  The gene was amplified and cloned from cDNA.  Then individual colonies were subjected to PCR and CAPS marker genotyping to determine the relative abundance of the two alleles in the cDNA sample.
DOI: 10.5061/dryad.sp800/4
title: F3'5'hInVitroAssayData

description: F3'5'h in vitro enzyme assay data for Penstemon neomexicanus, P. barbatus, and our experimental constructs.  DHQ production is considered an intermediate reaction product and was included in our measurement of "amount of DHK converted".
DOI: 10.5061/dryad.sp800/5
title: PyroseqData

description: Allele-specific expression data obtained through pyrosequencing.  We compared differences in F3'5'h allelic expression in cDNA to gDNA for three F1 individuals
DOI: 10.5061/dryad.vh151q1c/10
title: FinalNuclearLoci_ECM7210_ECM7278
DOI: 10.5061/dryad.vh151q1c/11
title: FinalNuclearLoci_ECM7144_ECM7210_ECM7278
DOI: 10.5061/dryad.vh151q1c/12
title: ReadMe
DOI: 10.5061/dryad.vh151q1c/7
title: FinalNuclearLoci_ECM7278
DOI: 10.5061/dryad.vh151q1c/8
title: FinalNuclearLoci_ECM7144_ECM7210
DOI: 10.5061/dryad.vh151q1c/9
title: FinalNuclearLoci_ECM7144_ECM7278
DOI: 10.5061/dryad.03g17/1
title: simulator_v1_5

description: Wright-Fisher implementing population simulation (in python)
DOI: 10.5061/dryad.03g17/2
title: sim

description: Example parameter file
DOI: 10.5061/dryad.03g17/3
title: Experimental Results

description: Mutator frequencies in experimental yeast populations
DOI: 10.5061/dryad.1s834/1
title: Microsatellite genotypes and locations of New England cottontails in Maine and New Hampshire

description: Microsatellite genotypes for 11 loci, including a Y chromosome marker, are provided in Excel spreadsheet format. These genotypes are from individual New England cottontails identified from fecal pellet samples collected during field surveys. Location data, in the form of lat/long geographic coordinates, are provided for each sample collected. Column headings and other metadata are found in the spreadsheet.
DOI: 10.5061/dryad.231g746f/1
title: New World Arenavirus Z protein alignment

description: Alignment of the Z protein of 51 NWA sequences, labelled with Genbank accessions numbers.
DOI: 10.5061/dryad.231g746f/2
title: New World Arenavirus -L protein alignment

description: Alignment of the L protein of 37 NWA sequences, labelled with Genbank accessions numbers.
DOI: 10.5061/dryad.231g746f/3
title: New World Arenavirus -Nucleoprotien alignment

description: Alignment of the nucleoprotien  of 64 NWA sequences, labelled with Genbank accessions numbers.
DOI: 10.5061/dryad.231g746f/4
title: New World Arenavirus -Glycoprotein alignment

description: Alignment of the glycoprotein of 62 NWA sequences, labelled with Genbank accessions numbers.
DOI: 10.5061/dryad.256qh/2
title: isophya_dochia_song_characters
DOI: 10.5061/dryad.3hc8s/1
title: datafiles
DOI: 10.5061/dryad.3hc8s/2
title: SupplementaryFigs&Table

description: Table describing characteristics of loci used to simulate DNA data and figures for results that complement those in the printed text.
DOI: 10.5061/dryad.41dq8/2
title: Deletion_Calls

description: Spreadsheet containing genomic deletion calls for all deletion alleles.  Columns include: include accession and chromosomal location information, estimated deletion size (size), count of supporting illumina reads (num_reads), deletion allele includes ref. genome (contains_IM62), sequence read coverage in deleted interval (cov), "N" bases in deleted interval in ref. genome (prop_Ns).  Annotation of gene and Transposable element hits (gene_hits and TE_hits; includes annoation and proportion deleted in parenthesis).
DOI: 10.5061/dryad.41dq8/3
title: SNP.data.Supp.Table.txt

description: All SNPs collected from 12 Mimulus accessions.  Columns listed include SNP position (scaffold and base position (pos)), SNP type (if coding, synonymous or nonsynonymous), and allele state for all 12 accessions.  Missing data represented by a hyphen.
DOI: 10.5061/dryad.41dq8/4
title: SV.read.data.Supp.Table.txt

description: Read meta-data for all illumina reads implicated in a structural variant.  Including read name, accession (line), structural variant category (kind), re-alignment status with Novoalign (reject_by_Novoalign), cluster formation status (failed_to_form_cluster), cluster ID (cluster), status of ref. genome line in cluster (cluster_includes_ref_line), status of cluster cov or alignment quality QC (failed_cov_or_abnormally_mapped_QC).
DOI: 10.5061/dryad.5j7m6/1
title: Lea_et_al_2014_data

description: Data used for analyses described in 'Complex sources of variance in female dominance rank in a nepotistic society'. See the README file for explanations of column headings.
DOI: 10.5061/dryad.61649/2
title: TRAGUST_In-vitroConidiosporeGermination_data
DOI: 10.5061/dryad.62380/1
title: Genotype input file for GridQTL

description: Genotypes of 226 microsatellite markers used in GridQTL analyses. Line 1: Number of markers Line 2: List of names of the markers Line 3: Names given to each of the generations. Line 4: Names given to males and females. Line 5: Symbol or symbols for missing genotype data. Line 6 on Data for each individual in turn. Contains in order: Individual ID Sire ID Dam ID Sex Line or generation Marker genotypes
DOI: 10.5061/dryad.6q44t/11
title: Figure S4. Morphometric plots

description: Boxplots of morphometric size variation among subspecies of the varied tit (Sittiparus varius) complex: (a) bill length, (b) bill depth, (c) bill width, (d) tarsus length, (e) wing chord, and (f) tail length. The taxon castaneoventris showed non-overlapping size variation in bill depth, wing chord, and tail length. Heavy lines inside boxes represent the mediums (second quartiles). Each box is bounded by the first and third quartiles, and plot whiskers extend to 1.5 times the interquartile range or to the maximum and minimum value, as appropriate. Data points outside the whisker range are represented by open circles.
DOI: 10.5061/dryad.6q44t/12
title: Figure S5. Luminance plots

description: Boxplots of luminance measurements obtained from plumage patches with &lt;0.05 luminance reflectance: (a) mantle, (b) throat, and (c) black of head. Hue measurements were excluded from these patches because very dark colors yield random hues when converted into opponent colorspace. Each box is bounded by the first and third quartiles, and plot whiskers extend to 1.5 times the interquartile range or to the maximum and minimum value, as appropriate. Data points outside the whisker range are represented by open circles.
DOI: 10.5061/dryad.6q44t/13
title: Table S6. Loci table

description: Descriptive statistics for the seven molecular loci used to construct phylogenetic relationships among S. varius, S. castaneoventris, S. owstoni, and S. olivaceus. The summary includes the length of the sequences (in base pairs), the number of alleles, the number of segregating sites (s), the number of parsimony-informative sites (PI sites), nucleotide diversity (π), and the nucleotide substitution model. Statistics are drawn from ingroup sequences only. Note that ND2 statistics are drawn from a reduced ND2 alignment, which comprised the 16 samples sequenced for nuclear loci.
DOI: 10.5061/dryad.6q44t/14
title: Figure S7. Nuclear intron networks

description: Statistical parsimony networks of nuclear intron sequences: (a) 08352, (b) 09385, (c) 10179, (d) 11887, (e) 12884, and (f) 15349. Each circle represents a haplotype; the size of the circle is proportional to a haplotype’s frequency. Small black circles represent inferred haplotypes. Colors distinguish the four species recognized in this study.
DOI: 10.5061/dryad.7k14q/7
title: Fig. S6

description: Juxtaposed mitochondrial trees calibrated using different placement of the Macaca libyca fossil: as stem macaque on the right and as crown macaque on the left.
DOI: 10.5061/dryad.88233/1
title: Color spectra for all individuals (raw data)

description: Here are the spectra for each measures: on each individual and on each color patch.
DOI: 10.5061/dryad.9898r/3
title: MinSen
DOI: 10.5061/dryad.9898r/4
title: MinSenData
DOI: 10.5061/dryad.9898r/5
title: MinSenG
DOI: 10.5061/dryad.9898r/6
title: MinSenGraphics
DOI: 10.5061/dryad.bf6m4/1
title: Code R for stochastic simulations
DOI: 10.5061/dryad.bf6m4/2
title: Outcome_Stochastic_unstable_Nplant_5000_N_par_5000
DOI: 10.5061/dryad.bf6m4/3
title: Outcome_Stochastic_stable_Nplant_5000_N_par_5000
DOI: 10.5061/dryad.bn249/2
title: MEC-12-0879_DRYAD_phenotype_data

description: Phenotypic data and non-genetic data used for parentage analysis.
DOI: 10.5061/dryad.d2441/1
title: VisualEnv-Attn-Learning-Data

description: The data file includes the pre-test scores, post-test scores, total time-off-task, and time-off-task by distracter type in the Decorated and Sparse experimental condition. Additional tabs include a  detailed summary about these outcome variables for each science lesson in each experimental condition.
DOI: 10.5061/dryad.d3m85/1
title: Season 1 Flocks

description: Individuals in flocks during Season 1
DOI: 10.5061/dryad.d3m85/2
title: Season 2 Flocks

description: Individuals in flocks during Season 2
DOI: 10.5061/dryad.d3m85/3
title: Season 3 Flocks

description: Individuals in flocks during Season 3
DOI: 10.5061/dryad.f260s/1
title: Movement and Growth

description: Individual movement and growth data in each tributary given together with the associated mean family egg mass and metabolic rate.
DOI: 10.5061/dryad.f260s/2
title: Apparent survival

description: Proportional recapture (apparent survival) of each each Atlantic salmon family in each of the tributaries. Associated family egg metabolism and mass is given.
DOI: 10.5061/dryad.f81sf/5
title: Larval_dispersal_modeling_raw results
DOI: 10.5061/dryad.fr27m/3
title: Candidate gene expression using qRT-PCR on A_alluaudi LPJs

description: This file contains the relative expression values of candidate genes, amplifying cDNA from lower pharyngeal jaws (LPJ) of the A. alluaudi specimens. The reported values have been scaled against normalisation factors (NF) that were calculated from 2 housekeeeping genes. These expression values were subjected to statistical analyses that are reported in Figure 4 a-c and Table S4. Specimen names correspond those assigned in Table S1.
DOI: 10.5061/dryad.fr27m/4
title: Fasta files of RNA-seq contigs generated from A_alluaudi LPJs

description: This file contains .fasta files, generated through assembly of RNA-seq transcripts, derived from A. alluaudi specimens used in our study. These .fasta files were used for differential expression (DE) analyses and BLAST queries, the results of which are depicted in Figure 5 and Tables S5. In tables S6 and S7, these .fasta sequences were used as queries against the human genome, and significant hits were then used for relative enrichment analyses in DAVID.
DOI: 10.5061/dryad.ft12r/1
title: data-JEB
DOI: 10.5061/dryad.g0g1h/1
title: Sep_dryad

description: Data from breeding protocol experiment
DOI: 10.5061/dryad.g0g1h/2
title: Inf_exp_dryad

description: Data from infection experiment.
DOI: 10.5061/dryad.g645d/1
title: Aligned, phased elongation factor 1-alpha DNA sequences

description: Aligned, phased elongation factor 1-alpha (ef1a) DNA sequences in NEXUS format.
DOI: 10.5061/dryad.g645d/2
title: Aligned, phased glyceraldehyde 3-phosphate dehydrogenase DNA sequences

description: Aligned, phased glyceraldehyde 3-phosphate dehydrogenase (g3pdh) DNA sequences in NEXUS format
DOI: 10.5061/dryad.g645d/3
title: Microsatellite (SSR) data

description: Sheet 1 contains genotypes for 6 chloroplast microsatellite (cpSSR) loci and Sheet 2 contains genotypes for 6 nuclear microsatellite (nSSR) loci for each valley oak (Quercus lobata) sample.  GPS coordinates, sample code and population codes are also given. Sheet 3 is a readme file indicating which additional articles to cite when using the data.
DOI: 10.5061/dryad.g645d/4
title: Occurrence points for ecological niche models

description: Occurrence points used to construct ecological niche models for Quercus lobata (Sheet 1) and Quercus alba (Sheet 2).
DOI: 10.5061/dryad.jk42p/1
title: Salmo_salar_for_DRYAD

description: Microsatellite genotype data for 312 specimens of Atlantic salmon at eight microsatellite loci
DOI: 10.5061/dryad.jn14d/4
title: Griffiths2013LengthMass2010ChignikLake

description: Length and mass for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2010 in Chignik Lake, AK.
DOI: 10.5061/dryad.mn6np/1
title: Raw data from experiments performed to investigate the disassortative-pollination hypothesis and sexual-interference hypothesis in distylous primroses

description: The excel file contains raw data of number of pollen grains, number of developing seeds, and anther-stigma distances from flight-cage and hand-pollination experiments performed to investigate the disassortative-pollination hypothesis and sexual-interference hypothesis in distylous primroses. Data for each experiment are presented in an individual worksheet. Names of column headings correspond with terms used in the original paper.
DOI: 10.5061/dryad.ms172/1
title: analysis by site with season included

description: Data describe abundances of V. bombylans morphs (vbp = plumata; vbb = bombylans; vbh = haemorrhoidalis) and Bombus spp (grouped as described in the paper; groups were given these names: bt = terrestris; bpr = pratorum; bl = lapidarius; bpa = pascuorum; bm = montana; bother = other Bombus species). Total numbers of V. bombylans and bees are labelled vtotal and btotal respectively. Proportion of V. bombylans in each morph, and Bombus spp. in each group, are given in columns headed propXXX. Data come from 52 sites, for which the names and latitudes and logitudes are given in columns labelled site, lat and long. Observations are pooled across 12 years (2000 to 2011) but are given for each of three seasons (early = 4th to 22nd of June; mid = 23rd June to 6th July; late = 7th July to 8th August).
DOI: 10.5061/dryad.ms172/2
title: Bispham by season

description: Data for the three best sampled sites (at Bispham) pooled, but separated by year and season. Abbreviations and definitions of seasons are as for main file.
DOI: 10.5061/dryad.p3f13/1
title: Mating_System

description: Offspring genotypes for 4 populations.
DOI: 10.5061/dryad.p3f13/2
title: SGS_dryad

description: Genotypes and locations of adults in 6 populations.
DOI: 10.5061/dryad.qp747/1
title: SupplementEpochModel

description: Supplementary Infromation
DOI: 10.5061/dryad.qp747/2
title: XML

description: BEAST XML files used for the data analysis.
DOI: 10.5061/dryad.r4026/2
title: Colletotrichum_orbiculare_104T_MAFF_240422_1_assembly

description: Genome assembly of Colletotrichum orbiculare 104T (MAFF 240422). Files include GS De Novo Assembler assembled Colletotrichum orbiculare  scaffolds, all predicted proteins and all predicted  transcripts in fasta format.
DOI: 10.5061/dryad.rd70f/3
title: mySQL Database including data

description: This file contains a mySQL database including all the data used in Evans et al. It is in the same format as the database which can be created using the files available in the Scripts package associated with this datadryad package.
DOI: 10.5061/dryad.rt61j/1
title: data_description
DOI: 10.5061/dryad.v811c/1
title: Constitutive Immunity During Breeding

description: Data for Experiment 1
DOI: 10.5061/dryad.v811c/2
title: LRS

description: Data for Experiment 2b
DOI: 10.5061/dryad.v811c/3
title: Stimulating the Immune System AMP

description: Data for Experiment 2a
DOI: 10.5061/dryad.vh151q1c/13
title: VerifiedNuclearLoci
DOI: 10.5061/dryad.vh151q1c/14
title: RRL_AnalysisScripts

description: Python scripts used to produce alleles from raw Illumina data.
DOI: 10.5061/dryad.vh151q1c/15
title: InSilicoPrediction

description: Programs used to predict the number loci given a particular restriction site. The first program (GetCutterFragLens.java) is first used to generate an expected fragment length distribution (from an uninterleaved fasta file). The second program PredictNLoci.r is used to determine the number of loci contained within a specified size range.
DOI: 10.5061/dryad.vh151q1c/16
title: All_Primers_And_PCR_Results_LocusBySpecies

description: This file contains the primer sequences for all loci tested, as well as the results we obtained for each locus x species combination tested.
DOI: 10.5061/dryad.0453k/1
title: Cetartiodactyla_life-historyTraits

description: Life-history traits values (body mass, longevity and age of sexual maturity) used in the analysis for the 201 Cetartiodactyla species (values were extracted from both AnAge and PanTHERIA databases and the mean was calculated).
DOI: 10.5061/dryad.0453k/2
title: Higher-order_taxa

description: List of Cetartiodactyla species within each of the 24 clusters (higher-order taxa) in the main analysis.
DOI: 10.5061/dryad.0453k/3
title: SuperGeneMito_Cetartio_alignment

description: Nucleotide alignment of the concatenation of the 13 mitochondrial protein-coding genes for 201 Cetartiodactyla species (and five outgroups).
DOI: 10.5061/dryad.0453k/4
title: completeMito_phyloBayes.tr

description: Cetartiodactyla phylogenetic tree obtained from PhyloBayes (CAT GTR Gamma 4 model). Branch lengths are given in number of substitutions per nucleotide site.
DOI: 10.5061/dryad.0453k/5
title: SuperGeneMito_Cetartio_bppml_branchLength_codon.tr

description: Cetartiodactyla phylogenetic tree after optimization of branch lengths with bppml (using the YN98 codon model). Branch lengths are given in number of substitutions per codon site.
DOI: 10.5061/dryad.1415r/1
title: discr_train_data

description: The file contains the number of attacks on rewarded (non-model) artificial prey in the discrimination training part of an experiment on imperfect mimicry.
DOI: 10.5061/dryad.1415r/2
title: generalisation_data

description: The file contains the number of attacks on rewarded (non-model) artificial prey in the generalization part of an experiment on imperfect mimicry.
DOI: 10.5061/dryad.1415r/3
title: salience_data

description: The file contains the number of attacks on rewarded artificial prey in the salience testing part of an experiment on imperfect mimicry.
DOI: 10.5061/dryad.18g80.1
title: Data from: Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae)
DOI: 10.5061/dryad.18g80.2
title: Data from: Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae)
DOI: 10.5061/dryad.18g80.2/1.1
title: DNA alignment for the genus Leucadendron phylogeny

description: This alignment is the concatenation of nine markers that were used to reconstruct the phylogeny of the genus Leucadendron in the paper cited above. Those markers were amplified for 81 Leucadendron taxa collected in natural populations in the South-African fynbos, except for three external groups which were collected in the Kirstenbosch Botanical Garden: Paranomus spathulatus, Mimetes cucullatus and Leucospermum erubescens. A detailed map of the alignment is given below: Positions 1 - 618 : AS1 marker which contains an exon of 618bp. Positions 619 - 1046 : PPR-like marker which contains an exon of 233bp and a 3'-UTR of 195bp. Positions 1047 - 1800 : SVR7 marker which contains an exon of 652bp and a 3'-UTR of 102bp. Positions 1801 - 2181 : CAF1-6 marker which only contains an exon of 381bp. Positions 2182 - 2795 : the classical ITS marker. Positions 2796 - 3591 : ATINT1 marker which contains an exon of 665bp and a 3'-UTR of 131bp. Positions 3592 - 3868 : APO2 marker which contains only an exon of 277bp. Positions 3869 - 4207 : APG6 marker which contains only an exon of 339bp.Positions 3208 - 4865 : ATPHAN marker which contains only an exon of 658bpThe methodology used to design the following markers: PPR-like, CAF1-6, ATINT1, APO2, APG6 and ATPHAN is described in (Tonnabel et al. 2013). The AS1 marker was designed in (Illing et al. 2009). Tonnabel, J., Olivieri, I., Mignot, A., Rebelo, A., Justy, F., Santoni, S., Caroli, S., Sauné, L., Bouchez, O. & Douzery, E.J.P. (2014) Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach, Molecular Phylogenetics and Evolution, 70, 37-46.Illing, N., Klak, C.,  Johnson, C., Brito, D., Negrao, N., Baine, F., van Kets, V., Ramchurn K.R., Seoighe, C. & Roden, L. (2009) Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae. Development genes and evolution, 219, 331-338.
DOI: 10.5061/dryad.18g80.2/2
title: data_sexspecific_leaf_measurements

description: This dataset corresponds to the sex-specific leaves measurements realized for the Leucadendron genus (L.) in order to assess sexual dimorphism at the leave level. Leaf area (named area), leaf length (named length) and leaf width (named width) have been assessed for several individuals (ind) of several populations (pop) of different species (species). Within the file, females are designed by 'F' and males by 'M'.
DOI: 10.5061/dryad.20r9k/17
title: myotis_reads

description: reads used to assemble little brown bat contigs
DOI: 10.5061/dryad.231g746f/5
title: Sigmodontinae and Neotominae Mitochondria Cytochrome B alignment

description: Sigmodontinae and Neotominae Mitochondria Cytochrome B alignment. 523 taxa aligned with Genbank accession number and current taxonomy indicated for each sequence.
DOI: 10.5061/dryad.231g746f/6
title: R script for phylogeneitcally informed mantel tests

description: Original R script provided by the authors of the following paper as supplementary material Harmon, L.J & Glor, R.E. (2010)  This script has been modified by O.Missa to suit working from a genetic distance Matrix
DOI: 10.5061/dryad.34jb6/16
title: 1993-SingleNote

description: Example of a 1993 single note (dash) song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/17
title: 1998-2Ch

description: Example of a 1998 two Ch note song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/19
title: 1998-DashCh

description: Example of a 1998 Dash + Ch song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/24
title: 2004-DashShortNote

description: Example of a 2004 Dash + short note song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.35db6/1
title: Weightman 2012 social determinants of infant health_data extraction & critical appraisal forms

description: Data extraction and critical appraisal information for the 36 research papers included in the review
DOI: 10.5061/dryad.47r16/1
title: DNA matrices and maximum likelihood trees

description: This is a NEXUS file containing the aligned DNA matrices, the optimal likelihood trees, and all of the original boostrap trees.  If opened in Mesquite (version 2.75 or later), you will be able to see the majority consensus trees of the bootstrap runs and other details.
DOI: 10.5061/dryad.47r16/2
title: Bembidion tetrapholeon DNA variation

description: This is a NEXUS file containing the aligned data matrices for all the sequences gathered for specimens of Bembidion tetrapholeon