cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s652h/1
title: Dataset S1. All data used for modeling in this study.

description: All datasets used for modeling in this study, including: (1) the full GLOPNET dataset with missing data, (2) GLOPNET complete cases, (3) GLOPNET complete cases for rosids, (3) GLOPNET complete cases for asterids, (4) Population means for macroevolutionary analysis across the genus Helianthus [from Mason et al., 2015 - Evolution], (5) Family means for microevolutionary analysis among populations in Helianthus anomalus [from Brouillette et al., 2014 - New Phytologist], (6) Ontogenetic data across stages in Helianthus annuus [from Mason et al., 2013 - JXB], (7) Ontogenetic data across stages in Helianthus mollis [from Mason et al., 2013 - JXB], (8) Ontogenetic data across stages in Helianthus radula [from Mason et al., 2013 - JXB].
DOI: 10.5061/dryad.t80d3/1
title: Martha_takeOut_JHBP-1
DOI: 10.5061/dryad.t80d3/2
title: Martha_takeOut_JHBP-2
DOI: 10.5061/dryad.t8n07/1
title: Aubagio_11.11.14
DOI: 10.5061/dryad.t8n07/2
title: Bosulif_11.11.14.xlsx companies
DOI: 10.5061/dryad.t8n07/3
title: Elelyso 11.11.14
DOI: 10.5061/dryad.vt966/1
title: Surfaces, volumes and landmark data of cells

description: Estimated surfaces and volumes of Micrasterias cells (sheet 1) and the landmark data of the semicells (sheet 2). The first column of both tables depicts the population affiliation of cells.
DOI: 10.5061/dryad.043tn/1
title: script and data dryade

description: Script and data for the all manuscript analysis
DOI: 10.5061/dryad.1f090/1
title: Effects of temperature, nutrients and predators on CO2 fluxes and communities in pond mesocosms

description: This data represents the independent and combined effects of increased temperatures (3 C), nutrient additions, and addition of predators (Three-Spined Stickelback) to carbon dioxide fluxes, primary producers biomass (periphyton + phytoplankton) and consumer biomass in pond mesocosms. Responses were measure after 12 and 16 months from initiation of perturbations. Study took place at the University of British Columbia's (Vancouver, Canada) experimental pond facility in 2010.
DOI: 10.5061/dryad.27g0v/1
title: Crenshaw et al data file
DOI: 10.5061/dryad.3nr2f/5
title: Input files used for Mantel tests

description: Input files for Mantel tests performed using the program ZT. These files include geographical distance, genetic differentiation (Fst), and phenotypic differentiation (Pst) between each pair of populations and for each studied species (Mioscirtus wagneri, Ramburiella hispanica, Calliptamus barbarus, Calliptamus italicus, and Oedaleus decorus).
DOI: 10.5061/dryad.46786/1
title: Face & noise single-trial ERPs from 194 recording sessions
DOI: 10.5061/dryad.4ch2c/1
title: Final_seed_data

description: the data is divided into 5 spreadsheets, for different analyses. See attached user guidance for further descriptions of column headers
DOI: 10.5061/dryad.51f00/10
title: OSM Fig S3 MCC TD full morph

description: Online Supplemental Material Figure S3. Maximum clade credibility tree from tip-dating method with 421 morphological characters and 5767 molecular characters posterior probabilities of nodes are labelled.
DOI: 10.5061/dryad.51f00/11
title: OSM Fig S4 MCC TD reduced morph

description: Maximum clade credibility tree from tip-dating method with 369 morphological characters and 5767 molecular characters posterior probabilities of nodes are labelled.
DOI: 10.5061/dryad.51f00/12
title: OSM Fig S5 Node age estimates with fixed and wide priors

description: Comparison of node age estimates for 21 select nodes, using two divergence time estimation techniques, two datasets (full and reduced morphological datasets), and wide age range or fixed age priors
DOI: 10.5061/dryad.51f00/13
title: Online Supplemental Material File S7.

description: 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (full morphological dataset) under the fossilized birth-death model in MrBayes.
DOI: 10.5061/dryad.51f00/8
title: OSM Fig S1 MCC FBD full morph

description: PDF version of Figure 3 of the main text, enlarged. Mean clade credibility tree from the fossilized birth death process, total evidence dataset with full morphological dataset
DOI: 10.5061/dryad.51f00/9
title: OSM Fig S2 MCC FBD reduced morph

description: Maximum clade credibility tree from fossilized birth-death process with 369 morphological characters and 5767 molecular characters. Posterior probabilities of nodes are labelled.
DOI: 10.5061/dryad.56bb4/1
title: README

description: Read me text file with information concerning all deposited files
DOI: 10.5061/dryad.56bb4/2
title: assay.fecundity

description: fecundity raw data
DOI: 10.5061/dryad.56bb4/3
title: assay.genotypes

description: genotypes raw data
DOI: 10.5061/dryad.56bb4/4
title: assay.growth.rate

description: fitness raw data
DOI: 10.5061/dryad.56bb4/5
title: assay.hatchability

description: hatchability raw data
DOI: 10.5061/dryad.56bb4/6
title: assay.size.glycogen

description: oocyte and embryo raw size and glycogen content data.  contains data for unstained controls
DOI: 10.5061/dryad.56bb4/7
title: ee.designation

description: experimental evolution replicate population nomenclature
DOI: 10.5061/dryad.5n0v4/1
title: lepmap input file

description: Genotypes from all five crosses formatted for the mapping program lepmap.  The SISSAQ12X03H identifier corresponds to cross GH1, the SN411X10H identifier corresponds to cross GH2, the HX6 identifier corresponds to cross D3, the HX8 identifier corresponds to cross D4, and the HX13 identifier corresponds to cross D5.
DOI: 10.5061/dryad.5n0v4/2
title: rqtl input for cross HX6

description: cross HX6 corresponds to cross D3 in the manuscript
DOI: 10.5061/dryad.5n0v4/3
title: rqtl input for cross HX8

description: Cross HX8 corresponds to cross D4 in the manuscript
DOI: 10.5061/dryad.5n0v4/4
title: rqtl input for cross HX13

description: Cross HX13 corresponds to cross D5 in the manuscript
DOI: 10.5061/dryad.603hs/7
title: MHC class II genotypes

description: Number of MHC class II reads from 454 pyrosequencing by individual and sequence.  See T. cupido MHC class II (BLB) exon 2 sequences.fasta for sequences. Tab-delimited file.
DOI: 10.5061/dryad.603hs/8
title: Sequences from 454 pyrosequencing

description: Five zipped files containing the original sequences from 454 pyrosequencing (5 runs) of MHC class I and II in prairie-chickens.  The ReadMe.csv file contains the unique 8 bp barcodes and individual identifiers used in each of the 5 files. Each individual is indicated by its two-letter state code and number. Additional birds that were sequenced in the files, but not used in this study are indicated by "not used".
DOI: 10.5061/dryad.66216/1
title: DATASET_DePasquale Cairsty et al

description: Raw data of behavioural experiments and MRI analyses described in the ms: "The influence of complex and threatening environments in early life on brain size and behaviour"
DOI: 10.5061/dryad.6824n/1
title: Gene expression of limept Cellana toreuma in different thermal and osmotic conditions
DOI: 10.5061/dryad.6m8c0/1
title: helper effect data deposited into the achieving system
DOI: 10.5061/dryad.7842r/2
title: VCF file

description: This is a .vcf file produced by calling variant genetic sites using samtools and bcftools. For each variant site identified, we required that &gt;60% of all individuals had 1 or more read at that locus.
DOI: 10.5061/dryad.7842r/3
title: entropy_variants0.6

description: Input file for analysis with the "entropy" model. This file is a filtered version of the VCF file, including genotype likelihoods for loci with MAF&gt;1%. Additionally, we randomly selected 1 SNP per contig for contigs with multiple variant sites, to ensure independence of SNPs.
DOI: 10.5061/dryad.83fb8/5
title: Distribution of haplotypes of 6 Nosema genomic loci

description: Count of Roche 454 pyrosequencing haplotypes (rows) of 6 Nosema genomic loci in 31 bumble bee samples (columns). See Table S4 for geographic origins of these bee samples. Allele frequency data are used to generate Da distances and neighbor joining tree.
DOI: 10.5061/dryad.83fb8/6
title: Fasta file containing representative sequences of six Nosema genomic loci

description: Fasta file containing representative sequences of six Nosema genomic loci. Frequency of haplotypes in sampled bees can be found in genomic_loci_counts.csv.
DOI: 10.5061/dryad.83fb8/7
title: European bumble bee collection localities

description: European collection sites of bumble bees screened for Nosema
DOI: 10.5061/dryad.83fb8/8
title: Information on European bees screended for Nosema

description: Sample ID, species and collection sites of individual European bees. See european_localities.csv for locality details
DOI: 10.5061/dryad.9r295/2
title: Compressed files simulation pipeline

description: Compressed files for the simulation pipeline generates coalescent-based genealogies that comprise a mixed of current and ancestral samples. These genealogies are then converted into phylograms with branch lengths in units of substitutions per site onto which mutations are simulated. The resultant sequences serve then to estimate substitution rates in BEAST using the simulated date-calibrated data.
DOI: 10.5061/dryad.b8569/1
title: trout_stomach

description: Stomach contents of trout in each season in each treatment reach
DOI: 10.5061/dryad.b8569/2
title: trout_growth

description: Specific growth rate of individual trout in each season in each treatment reaches
DOI: 10.5061/dryad.b8569/3
title: trout_nexcretion

description: N excretion by individual trout in each season in each treatment
DOI: 10.5061/dryad.b8569/4
title: trout_pexcretion

description: P excretion by individual trout in each season in each treatment
DOI: 10.5061/dryad.c2v92/1
title: Subplot and whole-plot data

description: Data are provided in one file corresponding to subplot and whole-plot analyses of the “Prairie Restoration Heterogeneity Plots” located at the Konza Prairie Long Term Ecological Research site in Manhattan, KS USA. Subplot and whole-plot data are in different tabs (pages) labeled within the Excel file. Data include annual aboveground net primary productivity, available nitrate in soil, species diversity, species richness, and percent cover of each plant species.
DOI: 10.5061/dryad.cg7d4/1
title: Island species lists and island properties

description: First sheet is an island-species matrix of species presences (0 or 1). Second sheet includes spatial data for each island. Taxonomic nomenclature follows Haines (2011). See associated publication for details on data collection methods and supplemental appendix for additional metadata.
DOI: 10.5061/dryad.j07h2/1
title: Rocking data

description: Data on shell rocking and rapping in hermit crabs with normal and dampend shell rapping. Predictors: Treatment Group (Categorical), Outcome (Categorical), RWD (Continuous). Responses: Bouts of rocking, bouts of rapping, total rocks, total bouts, mean duration of pauses.
DOI: 10.5061/dryad.mb687/1
title: List of Conotoxins from C. vexillum

description: An excel sheet containing the list of transcripts from C. vexillum. Sequences were run on ConoPREC to predict cleavage sites.
DOI: 10.5061/dryad.mb687/2
title: Signal_DM

description: A distance matrix of the signal sequences of conotoxin transcripts from the C. vexillum venom gland.
DOI: 10.5061/dryad.mb687/3
title: C. vexillum Distal section

description: MS-file of C. vexillum distal section
DOI: 10.5061/dryad.mb687/4
title: C. vexillum Distal Central section

description: MS file of C. vexillum Distal Central section
DOI: 10.5061/dryad.mb687/5
title: C. vexillum Proximal Central section

description: MS file of C. vexillum Proximal Central section
DOI: 10.5061/dryad.mb687/6
title: C. vexillum Proximal section

description: MS of C. vexillum Proximal section
DOI: 10.5061/dryad.mb687/7
title: C. vexillum Defensive milking 1

description: MS of C. vexillum Defensive milking 1
DOI: 10.5061/dryad.mb687/8
title: C. vexillum Defensive milking 2

description: MS of C. vexillum Defensive milking 2
DOI: 10.5061/dryad.mp82q/1
title: Data file

description: All the F-, SS- and R-statistics for the calculation for the effect size for this meta analysis.  Please refer to the equations for calculating the effect sizes in OIKOS02372 and the corresponding supporting information.
DOI: 10.5061/dryad.s08f7/1
title: Data van Gils et al. 2016

description: Data collected in the field. See ReadMe file for information about used abbreviations.
DOI: 10.5061/dryad.t55gq/1
title: Maximum likelihood phylogeny based on the core genome alignment of 616 Streptococcus pneumoniae isolates

description: Newick format maximum likelihood phylogeny generated using the 106,196 polymorphic sites in a core genome alignment of 616 Streptococcus pneumoniae isolates. The tree was produced by RAxML using the general time reversible substitution model with a four category gamma distribution to correct for rate heterogeneity.
DOI: 10.5061/dryad.t55gq/2
title: Core genome codon alignment of 616 Streptococcus pneumoniae isolates

description: FASTA format 1.14 Mb codon alignment generated through concatenation of individual alignments of the 1,194 coding sequences found to be present in a single copy in each of 616 Streptococcus pneumoniae isolates sampled from Massachusetts between 2001 and 2007. File is compressed using tar and gzip.
DOI: 10.5061/dryad.t55gq/3
title: Whole genome alignments of 15 sequence clusters of similar isolates

description: Fifteen FASTA format whole genome alignments, each corresponding to one of the monophyletic sequence clusters identified through population clustering and phylogenetics as described in Croucher et al (2013) Nat. Genet. 45:656-663. Alignments were generated through mapping of paired Illumina reads to a reference sequence, itself omitted from the alignment, using SMALT. Files are compressed as a single archive using tar and gzip.
DOI: 10.5061/dryad.t55gq/4
title: Software and reference sequence for inferring serotype from Illumina sequence data

description: This software is a simple script that uses BWA mapping to identify the likely serogroup of a pneumococcal isolate based on paired end FASTQ data.
DOI: 10.5061/dryad.t55gq/6
title: Predicted protein coding sequences from 616 S. pneumoniae isolates

description: This compressed archive comprises a FASTA file containing the DNA sequences of all predicted protein coding sequences from 616 S. pneumoniae isolates collected from Massachusetts between 2001 and 2007. Each sequence is labelled with a unique identifier (of the form, “ERSX_Y”, where “ERSX” is the sample accession code in the European Nucleotide Archive and Y is an incrementing index) and, where applicable, the COG of the translated protein (of the form, “SPARC1_CLSZ” or “SPARC1_CLSTZ”, where Z is a number).
DOI: 10.5061/dryad.t55gq/7
title: Predicted protein sequences from 616 S. pneumoniae isolates

description: This compressed archive comprises a FASTA file containing the amino acid sequences translated from all predicted protein coding sequences from 616 S. pneumoniae isolates collected from Massachusetts between 2001 and 2007. Each sequence is labelled with a unique identifier (of the form, “ERSX_Y”, where “ERSX” is the sample accession code in the European Nucleotide Archive and Y is an incrementing index) and, where applicable, the COG to which the protein belongs (of the form, “SPARC1_CLSZ” or “SPARC1_CLSTZ”, where Z is a number).
DOI: 10.5061/dryad.t55gq/8
title: Draft reference genome sequences for each of the 15 sequence clusters

description: This compressed archive contains 15 FASTA draft de novo assemblies used to generate the whole genome alignments within each sequence cluster. The files are named according to the sequence cluster and taxon identifier of the isolate to which the contigs relate.
DOI: 10.5061/dryad.t8n07/10
title: Signifor 200677
DOI: 10.5061/dryad.t8n07/11
title: Sirturo 11.20.14
DOI: 10.5061/dryad.t8n07/12
title: Stivarga 11.20.14.xlsx companies
DOI: 10.5061/dryad.t8n07/4
title: Eliquis 11.11.14
DOI: 10.5061/dryad.t8n07/5
title: Erivedge 11.11.14
DOI: 10.5061/dryad.t8n07/6
title: Inlyta 11.13.14
DOI: 10.5061/dryad.t8n07/8
title: MenHibrix_11.11.14
DOI: 10.5061/dryad.t8n07/9
title: Perjeta 11.20.14 company
DOI: 10.5061/dryad.182dv/1
title: Combined VCF for all 29 accessions for chromosome 0
DOI: 10.5061/dryad.20g8r.2
title: Data from: Asynchronous spawning in sympatric populations of a hard coral reveals cryptic species and ancient genetic lineages
DOI: 10.5061/dryad.20g8r.2/1.2
title: Microsatellite data of Acropora samoensis

description: This is the raw data from the 13 microsatellites that were genotyped in 80 individuals of Acropora samoensis in this study.
DOI: 10.5061/dryad.21q9m/1
title: Data
DOI: 10.5061/dryad.2vh04/1
title: Allele data for 16 loci for all individuals

description: Excel file with individuals in rows and locus alleles in columns
DOI: 10.5061/dryad.3j2mp/1
title: Earwigs data for Buzatto et al 2015 - Proc B

description: Two data sets with measurements and male morph information for the male dimorphic earwig Forficula auricularia. Both data sets have pedigree information, one of them (ISLANDS) with information from a half-sib common environment experiment with earwigs from three different islands; and the other one with information from a family level split environment (different diets) experiment (EXPERIMENTS) with earwigs from two different islands. All islands from the the Farne Islands group in Northumberland, UK.
DOI: 10.5061/dryad.4b18b/1
title: SSR genotypes for adults, seedlings and progeny arrays of Cariniana estrellensis

description: Genotypes of Cariniana estrellensis (Lecythidaceae) individuals (adults, seedlings and progeny arrays) based on nine microsatellite loci.
DOI: 10.5061/dryad.4p7g1/2
title: Leopard Media Reports: Spreadsheets

description: The compressed folder has two excel files. (a) NewspaperRecords.xlsx includes the list of newspapers from where data were extracted, data, type of event and the location. (b) LeopardMediaReports_DetectionMatrices.xlsx has two sheets with detection matrices; the first sheet refers to detection/non-detection of all events and the second sheet includes records of non-detection (0), detection of presence only (1), and detection of conflict incidents (2).
DOI: 10.5061/dryad.51f00/14
title: Online Supplemental Material File S8.

description: 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (reduced morphological dataset) under the fossilized birth-death model in MrBayes.
DOI: 10.5061/dryad.51f00/15
title: Online Supplemental Material File S9.

description: 1000 trees from the posterior distribution of trees inferred from the total evidence dataset (full morphological dataset) using tip-dating under the uniform clock model in MrBayes.
DOI: 10.5061/dryad.51f00/16
title: Online Supplemental Material File S10.

description: 1000 trees from the posterior distribution of trees inferred from the mtDNA dataset in MrBayes.
DOI: 10.5061/dryad.51f00/17
title: Online Supplemental Material File S11.

description: 1000 trees from the posterior distribution of trees inferred from the nDNA dataset in MrBayes.
DOI: 10.5061/dryad.51f00/18
title: Online Supplemental Material File S12.

description: 1000 trees from the posterior distribution of trees inferred from the morphological dataset in MrBayes.
DOI: 10.5061/dryad.51f00/19
title: Online Supplemental Material File S13.

description: The primary concordance tree inferred using Bayesian concordance analysis (BUCKy) of the posterior distributions of trees inferred from individual analysis of the mtDNA, nDNA and morphology.
DOI: 10.5061/dryad.51f00/20
title: Online Supplemental Material File S14.

description: Tree topology inferred from total evidence dataset and reduced morphological dataset using maximum likelihood (RaxML).
DOI: 10.5061/dryad.51f00/22
title: Online Supplemental Material File S15.

description: 55 most parsimonious tree topologies inferred from total evidence dataset and reduced morphological dataset using the parsimony ratchet (TNT).
DOI: 10.5061/dryad.51f00/23
title: Online Supplemental Material Figure S6.

description: Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of mtDNA in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
DOI: 10.5061/dryad.56bb4/10
title: ee.sequences

description: sequences of normoxia-anoxia environment employed for experimental evolution
DOI: 10.5061/dryad.56bb4/11
title: fix.prob.simulation

description: Wolfram Mathematica code employed to determine the probability of fixation of maternal effects
DOI: 10.5061/dryad.56bb4/8
title: ee.growth.rate

description: growth rate raw data during experimental evolution
DOI: 10.5061/dryad.56bb4/9
title: ee.sequences.code

description: QBasic code employed to design environmental sequences
DOI: 10.5061/dryad.67dg6/1
title: Oikos FA Review Dryad Data

description: Data amassed from published studies used to create figures 2 and 3
DOI: 10.5061/dryad.75ph1/1
title: female attractiveness
DOI: 10.5061/dryad.75ph1/2
title: female attractiveness replicate
DOI: 10.5061/dryad.7842r/1
title: split_scaffold_burbot_ref_long_94

description: Because there are no existing genomic resources for burbot, we constructed an artificial reference genome using smng (Seq- Man NGen, DNAstar), using 25 million reads. This artificial reference genome contains 53,789 contigs. We used this assembly as a template to for a reference-based assembly with bwa.
DOI: 10.5061/dryad.7f4p9/1
title: macaque coo calls

description: Macaque coo calls recorded from eight monkeys. The sub-folders named for each monkey's name (AL, BE, IO, MU, QU, SN, TH, TW). Each folder includes 468-1345 WAV files, each of which include one utterance of coo call.
DOI: 10.5061/dryad.8sc52/1
title: Proxy component spectra

description: This is a WiTec Project file with spectra obtained under the same conditions as for biofilm measurements, of pure proxy components with colloidal Ag. From M&M: In order to identify the individual SERS spectra of pertinent components of the S. oneidensis biofilm, we first performed SECRaM analysis on several component proxies mixed with colloidal silver (Sigma Aldrich, Hamburg, Germany). The proxy component-colloidal silver mixture was analyzed under the same working conditions as the ones applied for biofilm analysis. The same excitation wavelength, laser intensity and setup were used, however without a Ag/AgCl patch. This was done, separately, for the following expected component proxies: horse heart cytochrome c (hhcytc) (Sigma Aldrich, Hamburg, Germany) in Phosphate buffer solution (PBS) (Roth, Karlsruhe, Germany); riboflavin phosphate (Sigma Aldrich, Hamburg, Germany) in PBS; hhcytc in PBS with excess sodium dithionite (Merck, Darmstadt, Germany); hhcytc in PBS with excess potassium hexacyanoferrate (III) (Sigma Aldrich, Hamburg, Germany); riboflavin phosphate in PBS with excess sodium dithionite; riboflavin phosphate in PBS with excess potassium hexacyanoferrate; an aqueous solution of sodium alginate (Sigma Aldrich, Hamburg, Germany); pure PBS; PBS with sodium dithionite; and PBS with potassium hexacyanoferrate. Sodium dithionite and potassium hexacyanoferrate, respectively, were used to obtain reduced and oxidized cytochrome and flavin species.
DOI: 10.5061/dryad.b8569/5
title: trout_maturity

description: Maturation of trout in the spawning season
DOI: 10.5061/dryad.b8569/6
title: benthics

description: Biomasses of benthic invertebrates in each season in each treatment
DOI: 10.5061/dryad.b8569/7
title: benthic algae

description: Biomass of benthic algae in each season in each treatment reaches
DOI: 10.5061/dryad.b8569/8
title: leaf_breakdown

description: Leaf break-down rate in each season in each treatment
DOI: 10.5061/dryad.b8569/9
title: streamwater_nutrients

description: NH3-N and SRP concentrations in stream water in each season in each treatment reaches