cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7625d/7
title: Supplementary Material

description: SUPPLEMENTARY 1., 2. Plant material and GenBank accessions for nuclear and chloroplast sequences respectively.SUPPLEMENTARY 3. Material and methods for sequencing the plant material with a description of all primers designed for this studySUPPLEMENTARY 4. Illustration of the clone filtering procedure for identifying putative PCR-recombinant sequences and cross taxon contamination. All clones for the octoploid F. mirabilis (specimen 13673) were used to construct a neighborNet (uncorrected p-distances) in SplitsTree4. From ploidal level, four distinct sequences are expected. Each group highlighted in green was composed of several nearly identical sequences and was retained for phylogenetic analysis. Red sequences, connected to the main frame of the network with zero-length terminal edges, were considered to be putative PCR recombinants and were therefore discarded. A sufficient number of clones was not recovered for the blue group, which was further investigated with clade specific primers.SUPPLEMENTARY 5. Description of the phylogenetic analyses deployed for inferring gene trees.SUPPLEMENTARY 6. Details of the BEAST analysis dating the Dicentra-Corydalis split.SUPPLEMENTARY 7. Description and results of the simulation that assessed the performance of the coalescent stochasticity test.SUPPLEMENTARY 8. Table that reports the result of the coalescent stochasticity test for the sets of sequences derived from the individual small Ne and large Ne analyses of coalescent stochasticity tests. Here, all the sequences in a set are analyzed together and the inference Ne is increased until the full set passes the coalescent stochasticity test.SUPPLEMENTARY 9. Tanglegram inferred with RAxML from sequences of the primary set. Nuclear (a) and chloroplast (b) topologies correspondences were visualized in Dendroscope 3 (Huson and Scornavacca 2012). SUPPLEMENTARY 10. Genome tree inferred with BEAST. The maximum clade credibility chronogram was built from all nuclear homoeologues (except sequences from F. bastardii), together with chloroplast haplotypes from the primary set plus those that passed the substitution model error test. PP ≥ 0.70 are indicated below branches. Icons indicate the chloroplast sequences that were added to the analysis at the different steps of genome tree reconstruction.
DOI: 10.5061/dryad.8hf2p/1
title: Supplementary Table 1 of manuscript

description: Morphological data from 58 cetacean species
DOI: 10.5061/dryad.dc965/1
title: suppl01_dataset bony labyrinth_Pfaff ETAL

description: Raw data and measurements of the investigated specimens
DOI: 10.5061/dryad.dc965/2
title: suppl02_taxa scan information

description: Information of the investigated specimens and the respective CT scans
DOI: 10.5061/dryad.jd2cb/1
title: Script model

description: Script with the statistical analysis.
DOI: 10.5061/dryad.jd2cb/2
title: info_samples

description: Data used to data analysis in R
DOI: 10.5061/dryad.r8tp2/1
title: Current climate and site data in Excel form
DOI: 10.5061/dryad.r8tp2/2
title: predicted 2080 plus current climate data for PCA in Excel form
DOI: 10.5061/dryad.r8tp2/3
title: Data file for multiple group PCA  current climate
DOI: 10.5061/dryad.r8tp2/4
title: Data file for PCA on  combined predicted plus current climate
DOI: 10.5061/dryad.r8tp2/5
title: Output for PCA on combined predicted and current climate
DOI: 10.5061/dryad.r8tp2/6
title: Thorpe et al phylogenetic data in nexus format

description: Zipped file containing individual data files for all species used, names by species and gene name, in nexus format
DOI: 10.5061/dryad.t3b51/1
title: Raw Eye and body size data for Megalagrion species

description: A spreadsheet of Eye size data (eye height) and body size data (thorax length) for 13 species of Megalagrion damselflies.
DOI: 10.5061/dryad.t3b51/2
title: Facet diameter data

description: A spreadsheet of facet diameters along a vertical transect of the eye for 13 species of Megalagrion damselflies.  Species codes are included.
DOI: 10.5061/dryad.t3b51/3
title: Raw interommatidial angles

description: A spreadsheet of interommatidial angles along a vertical transect of the eye for 13 species of Megalagrion damselflies.  Species codes are included.
DOI: 10.5061/dryad.tp030/1
title: NBS_peptide_sequences

description: Aminoacid sequences for the NBS domain of all genes used in the phylogenetic analysis are included in this file.
DOI: 10.5061/dryad.tp030/2
title: Figure_1_alignment

description: Raw clustalW alignment for the tree in Figure 1
DOI: 10.5061/dryad.tp030/3
title: Figure_2_and_additional_file_6_alignment

description: Raw clustalW alignment for the trees in Figure 3 and Additional File 6
DOI: 10.5061/dryad.tp030/4
title: Figure_1

description: Alignment in MEGA format used to generate the phylogenetic tree in Figure 1
DOI: 10.5061/dryad.tp030/5
title: Figure_3

description: Alignment in MEGA format used to generate the phylogenetic tree in Figure 3
DOI: 10.5061/dryad.tp030/6
title: Additional_file_6

description: Alignment in MEGA format used to generate the phylogenetic tree in Additional File 6
DOI: 10.5061/dryad.124n0/1
title: Dibble_Rudolf_2015_OIK-02373-R1

description: Microsoft excel document containing 3 tabs: 'metadata' is a description of the column headings for 2 tabs: 'sampling-data' contains all population data used in the analysis of this experiment for the current manuscript; 'simoest' is an easier-to use summary of the data that ascribes a '1' to experimental units where simocephalus were present until the end of the experiment (and a 0 otherwise). Column heading descriptions are given in 'metadata'
DOI: 10.5061/dryad.124n0/2
title: sampling-data

description: .csv version of tab 2, 'sampling-data' from the excel workbook. See 'readme.txt' or tab 1, 'metadata' of the excel workbook for column headings.
DOI: 10.5061/dryad.124n0/3
title: simoest

description: .csv version of 'simoest' tab from excel workbook. Contains data on simocephalus establishment success in experimental containers (i.e. whether simocephalus were present at the end of the experiment)
DOI: 10.5061/dryad.1pj04/12
title: CEL file for isolate IC201

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/13
title: CEL file for isolate IC311

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/14
title: CEL file for isolate IC278

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/15
title: CEL file for isolate IC1612

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/16
title: CEL file for isolate IC1616

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/17
title: CEL file for isolate IC65

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/18
title: CEL file for isolate IC1622

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/19
title: CEL file for isolate IC308

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/20
title: CEL file for isolate IC1637

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.2h5j7/1
title: Kost 3gene nuclear combined new

description: Combined nexus file for all three nuclear data sets
DOI: 10.5061/dryad.2h5j7/2
title: Kost combined 5gene plastid new

description: Combined nexus file for all 5 plastid data sets
DOI: 10.5061/dryad.2h5j7/3
title: Kost taxa for polyploid

description: Excel spreadsheet for all voucher information for each accession.  Note that each accession isidnetified by "greenhouse accession number" in matrices, which directly correspond to the voucher information presented.
DOI: 10.5061/dryad.4md11/1
title: Oxidant trade-offs in painted dragons
DOI: 10.5061/dryad.4tn05/1
title: Nexus file of 114 chloroplast genes and gene positions

description: Nexus file containing the 114 genes data set followed by the position of each gene with the matrix.
DOI: 10.5061/dryad.57fc0/1
title: Mybphylo_mts file

description: Phylogenetic tree MEGA mts file. File was generated in MEGA 4.
DOI: 10.5061/dryad.5g1k6/18
title: top_heme_oxy_optimized_charges

description: Topology file for the updated oxygen and heme parameters calculated from Quantum Mechanics calculations
DOI: 10.5061/dryad.68hp8/1
title: All data from Ecology & Evolution 2015 Newcombe et al.

description: Data on free AA in eggs from females (2 populations) reared on 2 different diets (sunflower, milkweed). Also hatching weight of offspring and egg size of mothers.
DOI: 10.5061/dryad.8hf2p/2
title: Supplementary Table 2 of manuscript

description: Characterization of mating system across 58 species of cetaceans.
DOI: 10.5061/dryad.9ph5c/1
title: Egg Phenotypes

description: Data on egg pattern, colour and luminance for Cisticolidae and Ploceidae species in Zambia.
DOI: 10.5061/dryad.bc65p/1
title: p53 haplotypes_Quina etal

description: Sequence information of the p53 haplotypes found in Microtus duodecimcostatus and Microtus lusitanicus (Quina et al, 2015).
DOI: 10.5061/dryad.bc65p/2
title: Samples Table_Quina etal

description: Information on species, sample ID, p53 genotype (with GenBank accession number) and respective cytb haplotype if known (with GenBank accession number) is provided for each specimen analysed in our study (Quina et al, 2015). Also included are sampling locality (country and location) for each specimen analysed and the source of published data.
DOI: 10.5061/dryad.bp0gv/1
title: Individual treatment, morphology and lifespan

description: Data show individual ID, treatment groups and sex for each experimental subject surviving to eclosion. DevRate = (1/days from hatching to eclosion). Weight is measured in grams. Pronotum length is measured in millimetres. SMI is calculated separately for males and females. PostEclosion is the number of days an individual survived post-eclosion.
DOI: 10.5061/dryad.bp0gv/2
title: Calling effort

description: Individual calling measurements (long format). Duration is calling effort measurement, and the time of measurement is given in time (weeks), msmt.age (days), and age.std (mean-centred and scaled days). Term denotes whether it was the final measurement taken before death; PostEclosion is number of days the individual survived after eclosion (PE.std is mean-centred and scaled)
DOI: 10.5061/dryad.bp0gv/3
title: Fecundity

description: Individual female fecundity (long format). EggCount gives a single measurement of weekly fecundity, with measurement time given as time (weeks from eclosion), msmt.age (days from eclosion), age.std (days mean-centred and scaled). PostEclosion is the number of days after eclosion that an individual survived, and PE.std is this mean-centred and scaled.
DOI: 10.5061/dryad.ft702/1
title: Raw data from Parus.Database

description: This an RData file with the raw data extract from the Parus Database that managed by Frank Adriaensen. For further information please contact frank.adriaensen@uantwerpen.be
DOI: 10.5061/dryad.h9083/1
title: Growth and functional trait data for 287 tree species

description: See read-me file
DOI: 10.5061/dryad.jd2cb/3
title: NSC_data

description: Data used to data analysis in R
DOI: 10.5061/dryad.jd2cb/4
title: spectra_data

description: Data used to data analysis in R
DOI: 10.5061/dryad.jp1mk/2
title: Blast Hits of Colobanthus quitensis transcriptome

description: All contigs were screened against Viridiplantae protein databases Nr using BLASTx (e-value&lt;10-5) (Altschul et al. 1990).
DOI: 10.5061/dryad.nk52s/1
title: Selection rates for six pairs of strains at three initial density and frequency treatments
DOI: 10.5061/dryad.r8tp2/10
title: Anolis roquet series Martinique

description: Data Set C Quantitative Traits
DOI: 10.5061/dryad.r8tp2/11
title: Anolis roquet complex Martinique

description: Data Set D Quantitative Traits
DOI: 10.5061/dryad.r8tp2/7
title: Phylogenetic trees for all species used

description: Zip file containing individual tree files names by species and the method of analysis used to produce them
DOI: 10.5061/dryad.r8tp2/8
title: Anolis marmoratus Basse Terre Guadeloupe

description: Data Set A Quantitative Traits
DOI: 10.5061/dryad.r8tp2/9
title: Anolis oculatus Dominica

description: Data Set B Quantitative Traits
DOI: 10.5061/dryad.v61m2/1
title: Double-observer data used to estimate population of Ibex and Argali in Tost Local Protected Area in South Gobi Mongolia in 2012-2013

description: Contains the sighting and detection history for all the surveys conducted
DOI: 10.5061/dryad.1pj04/21
title: CEL file for isolate IC35

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/22
title: CEL file for isolate IC36

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/23
title: CEL file for isolate IC307

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/24
title: CEL file for isolate IC1719

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/25
title: CEL file for isolate IC1722

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/26
title: CEL file for isolate IC1751

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/27
title: CEL file for isolate IC310

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/28
title: CEL file for isolate IC31

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/29
title: CEL file for isolate IC244

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.4tn05/2
title: M1 Langrange combined input and output

description: Combined Lagrange M1 model input python script followed by the results output. This includes the dispersal constraints, geographic coding for taxa, concatenated 85 genes ML tree, and inferred ancestral areas within two log-likelihoods of the most likely area with relative probabilities.
DOI: 10.5061/dryad.6nc8c/1
title: Mean annual tree diameter growth

description: Mean  annual diameter growth from a 5 year census (2008-2013) for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/2
title: Bark depth

description: Bark thickness measurements for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/3
title: Crown dimensions

description: Crown dimensions measurements for trees at SCBI, including height to base of crown, crown area, and crown volume.
DOI: 10.5061/dryad.6nc8c/4
title: Diameter growth from dendrometer bands

description: Mean diameter growth measured using dendrometer bands for trees at SCBI.
DOI: 10.5061/dryad.8239h/1
title: Gymnopus confluens and Gymnopus eneficola ITS sequences

description: Aligned ITS sequence file with Gymnopus eneficola as the outgroup.  Names are given as herbarium accession numbers and cultures with the culture collection designation.  Locations are abbreviated  following the name (see manuscript for locations).  The file is a fasta file.
DOI: 10.5061/dryad.8239h/2
title: Gymnopus confluens and G. eneficola concatinated ITS and LSU sequences

description: Gymnopus confluens (fungi) concatinated ITS + 5' part of ribosomal large subunit RNA sequence
DOI: 10.5061/dryad.88b5b/1
title: Bolnick_et_al_PLoS_One_Dryad_Submission

description: A .csv file containing all the data used for analyses and graphics in Bolnick et al 2015 PLoS One. The same data are sufficient to recreate analyses in Bolnick et al Evolution. Raw data files (.jpg photographs, spectrophotometric files, flow cytometry .fcs files) are available upon request.
DOI: 10.5061/dryad.97vt8/1
title: Supplementary_Source_Data
DOI: 10.5061/dryad.9k219/1
title: ESM 3 - complete model dataset

description: The complete model dataset used in this publication
DOI: 10.5061/dryad.9k219/2
title: Empirical data for Lasius niger ants foraging persistence

description: The raw empirical data collected for the study, and used to inform the behaviour of ants in the model.
DOI: 10.5061/dryad.9k219/3
title: ESM 2 - complete netlogo model

description: The complete Netlogo model, and all files nececcary to run it. Netlogo must be installed in order to run the model. Netlogo is available for free from https://ccl.northwestern.edu/netlogo. Note that the two .nls files must be in the same folder as the .nlogo file in order for the model to work. A full description of the model is available in the "information" tab inside the model.
DOI: 10.5061/dryad.f7301/1
title: Experiment 1a: performance of eight Aphis craccivora clones on field alfalfa

description: See ReadMe file
DOI: 10.5061/dryad.f7301/2
title: Experiment 1b: performance of eight Aphis craccivora clones on field locust

description: See ReadMe file
DOI: 10.5061/dryad.f7301/3
title: Experiment 2a: Performance of Arsenophonus-infected versus uninfected isoline of a locust-origin A. craccivora clone (LE) across 3 plant species

description: see ReadMe file
DOI: 10.5061/dryad.f7301/4
title: Experiment 2b: Performance of Arsenophonus-infected versus uninfected isoline of a locust-origin A. craccivora clone (LW) across 3 plant species

description: See ReadMe file
DOI: 10.5061/dryad.g3h22/1
title: EO raw data
DOI: 10.5061/dryad.hh63d/1
title: Raw Data for Simulation Outcomes

description: This file contains a table in which we list all outcomes for the different simulations that we performed to study the effect of life history structuring on the evolution of cooperation.
DOI: 10.5061/dryad.j54vv/1
title: False heath fritillary capture-recapture data and habitat classification maps of Sorila, Siitama and Merikarvia

description: This Zip file contains capture-recapture data and habitat classification maps of the three false heath fritillary populations in Finland that were studied in Fabritius et al. (2015).The capture-recapture data contains information on the daily search effort (i.e. areas visited on each day) and the days and locations of butterfly markings and recaptures for males and females separately. Habitat classification maps display the study landscapes categorized into breeding habitat, high-quality matrix and low-quality matrix and the locations of the search areas. Information on data collection and references to older publications where these data sets have been used are available in Fabritius et al. (2015).
DOI: 10.5061/dryad.jd627/1
title: Genotypedatadryad
DOI: 10.5061/dryad.qr20n/1
title: Table_S1 - Datasets

description: Datasets used in the main statistical analyses of the study. Details of column headings : gene : Ensembl accession number (human); Species; labs :  Species+Chromosome; chrMark : X or Autosomes; chr : Chromosome number; dN :  Number of nonsynonymous substitutions; dS:  Number of synonymous substitutions , dNdS : ratio of dN/dS; RPKM : Expression level in Reads Per Kilobase per Million sequenced Reads; Tau : Expression specificity, GC3 : GC content of the third codon position
DOI: 10.5061/dryad.qr20n/2
title: Alignments

description: Alignments were obtained from ORTHOMAM v6 (http://www.orthomam.univ-montp2.fr/) and then cleaned using Gblocks (see materials and methods for details). Alignment names correspond to Ensembl accession number and match the datasets (Table_S1).
DOI: 10.5061/dryad.r8tp2/12
title: Anolis luciae St Lucia

description: Data Set E Quantitative Traits
DOI: 10.5061/dryad.r8tp2/13
title: Anolis trinitatis St Vincent

description: Data Set F Quantitative Traits
DOI: 10.5061/dryad.r8tp2/14
title: Anolis richardii Grenada

description: Data Set G Quantitative Traits
DOI: 10.5061/dryad.r8tp2/15
title: Anolis aeneus Grenada

description: Data Set H Quantitative Traits
DOI: 10.5061/dryad.rp3g3/1
title: yil30 data

description: HML MAT and HMR positions in YIL30
DOI: 10.5061/dryad.rp3g3/2
title: yil31 data

description: HML MAT and HMR positions
DOI: 10.5061/dryad.rp3g3/3
title: yil30 with deletion of ASF

description: HML MAT and HMR positions
DOI: 10.5061/dryad.rp3g3/4
title: yil31 with deletion of ASF

description: HML MAT and HMR positions
DOI: 10.5061/dryad.rp3g3/5
title: deletion of RE in YIL30

description: HML MAT and HMR positions
DOI: 10.5061/dryad.rp3g3/6
title: deletion of RE in YIL31

description: HML MAT and HMR positions
DOI: 10.5061/dryad.sh2qf/1
title: Supporting Information

description: Six Excel spreadsheets containing raw data used for experimental and statistical analysis. Please see each Excel spreadsheet file for a brief description, in conjunction with the Methods section of the manuscript for specific details on how data was obtained and analyzed.
DOI: 10.5061/dryad.1pj04/30
title: CEL file for isolate IC2207

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/31
title: CEL file for isolate IC327

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/32
title: CEL file for isolate IC1179

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/33
title: CEL file for isolate IC1603

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/34
title: CEL file for isolate IC1650

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/35
title: CEL file for isolate IC2205

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/36
title: CEL file for isolate IC2209

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/37
title: CEL file for isolate IC640

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.1pj04/38
title: CEL file for isolate IC1566

description: aCGH raw data submitted to Gene Expression Omnibus
DOI: 10.5061/dryad.366nd/1
title: Excel file with experimentation data
DOI: 10.5061/dryad.6nc8c/10
title: SCBI_species_acronym

description: List of species and species acronym used at SCBI
DOI: 10.5061/dryad.6nc8c/5
title: Sapflow

description: Sap flow measurements for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/6
title: Sapwood

description: Sapwood measurements for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/7
title: Tree heights

description: Height measurements for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/8
title: Stem abundance

description: Count of stems within DBH class for trees at SCBI.
DOI: 10.5061/dryad.6nc8c/9
title: Tree mortality rates

description: Mortality rates from a 5 year census (2008-2013) for trees at SCBI
DOI: 10.5061/dryad.7qc3s/1
title: Tree diameter growth data of Japanse cedar

description: The individual tree growth was monitored for a long-term in a mature plantation of Japanese cedar.
DOI: 10.5061/dryad.c3g5r/1
title: Brassica SNP array data for species identification

description: SNP molecular genotyping data and marker information for Brassica accessions sourced from the Australian Grains Genebank germplasm collection.
DOI: 10.5061/dryad.f7301/5
title: Experiment 2c: Performance of Arsenophonus-infected versus uninfected isolines of two locust-origin A. craccivora clones (LE and LW) across 3 plant species

description: See ReadMe file
DOI: 10.5061/dryad.f7301/6
title: Experiment 3: Performance of Arsenophonus-transinfected versus uninfected isoline of an alfalfa-origin clone (AL) and a naturally-infected versus uninfected locust-origin clone (LW) across 3 plant species

description: See ReadMe file
DOI: 10.5061/dryad.f7301/7
title: Experiment 4: Performance of 11 Arsenophonus and Hamiltonella-infected and uninfected Aphis craccivora clones on greenhouse locust

description: See ReadMe file
DOI: 10.5061/dryad.f7301/8
title: Experiment 5a: Performance of Arsenophonus-infected, Hamiltonella-infected, and uninfected A. craccivora clones on locust in the field

description: See ReadMe file
DOI: 10.5061/dryad.f7301/9
title: Experiment 5b: Performance of Arsenophonus-infected, Hamiltonella-infected, and uninfected A. craccivora clones on locust in the field

description: See ReadMe file