cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.326r8/125
title: Assembled scaffolds for Trachyrincus murrayi
DOI: 10.5061/dryad.4rd14/10
title: 09 - LNs 14h PBS

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/11
title: 10 - LNs 14h SGE

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/12
title: 11 - LNs 14h primary DENV

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/13
title: 12 - LNs 14h primary DENV+SGE

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/14
title: 13 - LNs 14h ADE DENV

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/15
title: 14 - LNs 14h ADE DENV+SGE

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/7
title: 06 - Dermis 14h ADE DENV

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/8
title: 07 - Dermis 14h ADE DENV+SGE.fcs

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.4rd14/9
title: 08 - LNs steady state

description: File type: The repository includes representative FSC 3.0 files that were exported from Diva software (BD Biosciences) and can be opened with FlowJo software (TreeStar). Fluorescent channels also indicate the specifically stained markers. Compensations values between fluorescence channels are included within FCS files.
DOI: 10.5061/dryad.6t6t1/1
title: Interloper - courtship vigor - R analysis - MS visit analysis - Stoffer et al Beh Eco

description: Data used for Objective 2
DOI: 10.5061/dryad.803q8/1
title: Repeat filtered VCF file

description: Subset of a previously published SNP dataset available from doi: 10.5061/dryad.qk22t. Two loci were removed due to being in a gene putatively evolving under selection. A further 1,360 SNPs were removed due to being in regions of know repetitive elements, excessive or low coverage, or low mappability in the killer whale genome. This VCF file contains the genotypes of 115 individuals at 2,316 sites.
DOI: 10.5061/dryad.803q8/2
title: Repeat and linkage filtered VCF file

description: The repeat-filtered SNP dataset was further filtered to minimise the effect of linkage by including only SNPs that were spaced &gt;100-kb apart on a scaffold, retaining the genotypes for 115 individuals at 1,346 sites.
DOI: 10.5061/dryad.803q8/3
title: Rad_orca_subsample1

description: SNAPP input file for subsample 1
DOI: 10.5061/dryad.803q8/4
title: Rad_orca_subsample2

description: SNAPP input file for subsample 2
DOI: 10.5061/dryad.803q8/5
title: Rad_orca_subsample3

description: SNAPP input file for subsample 3
DOI: 10.5061/dryad.803q8/6
title: Rad_orca_subsample4

description: SNAPP input file for subsample 4
DOI: 10.5061/dryad.803q8/7
title: Rad_orca_subsample5_10individs

description: SNAPP input file for subsample 5
DOI: 10.5061/dryad.803q8/8
title: Rad_orca_subsample1 trees

description: Trees inferred by SNAPP for subsample 1
DOI: 10.5061/dryad.803q8/9
title: Rad_orca_subsample2_1M trees

description: Trees inferred by SNAPP for subsample 2
DOI: 10.5061/dryad.8d724/10
title: Heliconius melpomene RSEM mapped count data

description: File is count data (expression level) output of Trinity contigs from RSEM for Heliconius melpomene. Column headers contain sex (M or F), tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts), and sample number. See Table S1 for specimen IDs. Samples labelled "1" are the result of merging two technical replicates (see Methods section of paper for details).
DOI: 10.5061/dryad.8d724/2
title: Eueides isabella Trinity assembly

description: This is a fasta format file containing all mRNA contigs for Eueides isabella. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.
DOI: 10.5061/dryad.8d724/3
title: Heliconius doris Trinity assembly

description: This is a fasta format file containing all mRNA contigs for Heliconius doris. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.
DOI: 10.5061/dryad.8d724/4
title: Heliconius erato Trinity assembly

description: This is a fasta format file containing all mRNA contigs for Heliconius erato. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.
DOI: 10.5061/dryad.8d724/5
title: Heliconius melpomene Trinity assembly

description: This is a fasta format file containing all mRNA contigs for Heliconius melpomene. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.
DOI: 10.5061/dryad.8d724/6
title: Heliconius sara Trinity assembly

description: This is a fasta format file containing all mRNA contigs for Heliconius sara. The assembly was performed in Trinity version "20130216" and is a raw output that includes all assembled contigs (see Table 1 for contig counts). Assembly was carried out as described in the Methods section of the publication.
DOI: 10.5061/dryad.8d724/7
title: Eueides isabella RSEM mapped count data

description: File is count data (expression level) output of Trinity contigs from RSEM for Eueides isabella. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).
DOI: 10.5061/dryad.8d724/8
title: Heliconius doris RSEM mapped count data

description: File is count data (expression level) output of Trinity contigs from RSEM for Heliconius doris. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).
DOI: 10.5061/dryad.8sj5g/2
title: simul

description: Locations of six individuals simulated using the memory-based movement model described in details in Riotte-Lambert et al. (2015). The locations of resource patches is provided in "patches.csv". The simulation was run for 105,000 time steps. Four columns: id, time, x, y.
DOI: 10.5061/dryad.8sj5g/3
title: patches

description: Two-column matrix giving the coordinates of 400 punctual resource patches. These constitute the environment used for the simulation provided in "simul.csv".
DOI: 10.5061/dryad.b649s/1
title: Table S1. Germplasm information.

description: The parental genotypes of each hybrid are listed along with whether the line was included in the final data set (yes=1, no=0). Lines were not included if their manually-fertilized parent did not germinate.
DOI: 10.5061/dryad.b649s/2
title: Table S2. GCA, SCA, and heritability estimates.

description: Values for plots in Fig 1.
DOI: 10.5061/dryad.b649s/3
title: Table S3. Summary of significant SNPs detected in GWA analyses.

description: Number of significant SNPs detected for each trait for both within-study and across-study Bonferroni correction.
DOI: 10.5061/dryad.b649s/4
title: Table S4.  Summary of significant SNPs per trait.

description: IDs (chr_position) of all significant SNPs and their significance status in each GWA study.
DOI: 10.5061/dryad.b649s/5
title: Table S5. Summary of SConES SNPs.

description: Number of associated SNPs detected for each trait.
DOI: 10.5061/dryad.b649s/6
title: Table S6.  Summary of associated SConES SNPs per trait.

description: IDs (chr_position) of all associated SNPs and their significance status in each GWA study.
DOI: 10.5061/dryad.b649s/7
title: Table S7.  Summary of candidate genes.

description: IDs and location of all significant regions, their associated traits, genetic behavior, and candidate causal genes.
DOI: 10.5061/dryad.g60r3/10
title: OTU taxonomic assignments (97%)

description: Taxonomic assignments of OTUs (binned at 97% 16S rRNA gene sequence identity), generated by comparing representative OTU sequences to the Greengenes database using the RDP classifier in Qiime (see "Bioinformatics pipeline").
DOI: 10.5061/dryad.g60r3/11
title: Taxonomic assignments for OTUs binned at 99%

description: Taxonomic assignments of OTUs (binned at 99% 16S rRNA gene sequence identity), generated by comparing representative OTU sequences to the Greengenes database using the RDP classifier in Qiime. * Note that these are OTUs based on 99% identity, NOT the OTUs that were used for most analyses in Wagner et al. 2016 *
DOI: 10.5061/dryad.g60r3/12
title: Representative OTU 16S rRNA gene sequences

description: Representative sequence for each OTU (based on 97% sequence identity), in FASTA format. Generated from raw MiSeq reads using FLASH and UPARSE software (see "Bioinformatics pipeline")
DOI: 10.5061/dryad.g60r3/13
title: OTU table (binned at 99%)

description: OTU table (for OTUs picked based on 99% 16S rRNA gene sequence identity) that forms the basis for most analyses in Wagner et al. 2016. Generated from raw MiSeq reads. Columns are sample names (correspond to "SampleID" column in "Sample metadata" file); rows are OTUs. Decompress file using the Linux/UNIX command ' bunzip2 otuTable99.txt.bz2 '  ** note that most analyses in this paper used OTUs picked based on 97% sequence similarity-- these are in a different file (otuTable97.txt) **
DOI: 10.5061/dryad.g60r3/15
title: Key to Plant IDs

description: Master list of all individuals originally planted in the field experiment- columns as in the Sample Metadata file (SMD.txt)
DOI: 10.5061/dryad.g60r3/6
title: Soil / environmental data

description: Data on soil & vegetation characteristics from field sites used in this experiment. "PlantDiv" = number of plant morphospecies present in each block; “Veg” = percent of each block covered by vegetation (aggregate of estimated percent cover for 50 10x10cm sub-plots per block). Units are ppm (except for pH, unitless; and conductivity, umho/cm).
DOI: 10.5061/dryad.g60r3/7
title: Sample metadata

description: Microbiome sample metadata. "SampleID" = unique identifier for a sequenced 16S rDNA amplicon pool corresponding to a single sample. "Name" = more descriptive unique sample name. "Plant_ID" = unique identifier for individual plants; may correspond to &gt;1 SampleIDs when both roots and leaves were sampled from the same plant; "Experiment" = sub-experiment that a sample belongs to (e.g., "ecotypes" = main field experiment described in Wagner et al. 2016; "ecoGH" = greenhouse experiment described in supplementary information of Wagner et al. 2016; "rilGH" and "fieldBCMA" are not presented in Wagner et al. 2016); "Cohort" = year the individual (Plant_ID) was planted, if applicable; "Harvested" = year sample was harvested; "Treatment" = type of soil the individual was planted in (only applicable to greenhouse experiments); "oldPlate" = identifier of the 96-well plate containing the sample before full randomization; "newPlate" = MiSeq run, i.e., identifier of the amplicon library into which the sample was pooled, i.e., the 96-well plate containing the sample after full randomization; "Analysis" = broadest experimental grouping of samples; either "Ecotypes" (which contains samples described in Wagner et al. 2016) or "BCMA" (containing samples not analyzed or described in Wagner et al. 2016).
DOI: 10.5061/dryad.g60r3/8
title: OTU table (97%)

description: OTU table (for OTUs picked based on 97% 16S rRNA gene sequence identity) that forms the basis for most analyses in Wagner et al. 2016. Generated from raw MiSeq reads (see "Bioinformatics pipeline"). Columns are sample names (correspond to "SampleID" column in "Sample metadata" file); rows are OTUs. Decompress file using the Linux/UNIX command ' bunzip2 otuTable97.txt.bz2 '
DOI: 10.5061/dryad.g60r3/9
title: Contaminant OTUs

description: List of OTUs identified as likely contaminants based on comparison to list of known contaminant 16S rRNA gene sequences (generated using custom scripts; see "Bioinformatics pipeline")
DOI: 10.5061/dryad.g9r36/1
title: Cissus barbeyana SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus barbeyana De Wild. & T.Durand (K Herbarium sheet collector no. 16406)
DOI: 10.5061/dryad.g9r36/2
title: Cissus bosseri SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus bosseri Desc. (K Herbarium sheet collector no. 3140)
DOI: 10.5061/dryad.g9r36/3
title: Cissus dasyantha SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus dasyantha Gilg & M.Brandt (BR Herbarium sheet collector no. 13410)
DOI: 10.5061/dryad.g9r36/4
title: Cissus dinklagei SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through the lowermost part of a herbarium fruit of Cissus dinklagei Gilg & M.Brandt (K Herbarium sheet collector no. 5207)
DOI: 10.5061/dryad.g9r36/5
title: Cissus integrifolia 1 SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus integrifolia (Baker) Planch. (K Herbarium sheet collector no. 8517, a)
DOI: 10.5061/dryad.g9r36/6
title: Cissus integrifolia 2 SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus integrifolia (Baker) Planch. (K Herbarium sheet collector no. 8517, b)
DOI: 10.5061/dryad.g9r36/7
title: Cissus lebrunii SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus lebrunii Dewit (K Herbarium sheet collector no. 1592)
DOI: 10.5061/dryad.h5r18.1
title: Data from: On the comparison of the strength of morphological integration across morphometric datasets
DOI: 10.5061/dryad.h5r18.2/3.2
title: R-PLS behavior

description: R script used to examine the behavior of R-PLS and other statistical measures as a function of sample size and number of variables
DOI: 10.5061/dryad.1225k/1
title: StarBEAST_BD_2partitions

description: Species tree analysis file with data split into mitochondrial and nuclear partitions
DOI: 10.5061/dryad.1225k/2
title: StarBEAST_Yule_2partitions

description: Species tree analysis control file with data split into mitochondrial and nuclear partitions
DOI: 10.5061/dryad.1225k/3
title: Gono_7gene.phased

description: Concatenated alignment of 7 genes, with nuclear data phased
DOI: 10.5061/dryad.1225k/4
title: StarBEAST_BD_nuclear

description: Species tree analysis control file for nuclear data only
DOI: 10.5061/dryad.1225k/5
title: StarBEAST_Yule_nuclear

description: Species tree analysis control file for nuclear data only
DOI: 10.5061/dryad.1225k/6
title: Gono_7gene

description: Concatenated alignment of 7 loci
DOI: 10.5061/dryad.1225k/7
title: BEAST_7gene

description: Bayesian phylogenetic inference control file
DOI: 10.5061/dryad.2435k/1
title: Dryad GLOBAL Alum 18April2016

description: Alum Creek, Arkansas
DOI: 10.5061/dryad.2435k/2
title: Dryad GLOBAL Blaylock  18April2016

description: Blaylock Creek, Ouachita Mountains, Arkansas
DOI: 10.5061/dryad.326r8/126
title: Assembled unitigs for Trachyrincus murrayi
DOI: 10.5061/dryad.326r8/127
title: Assembled scaffolds for Phycis blennoides
DOI: 10.5061/dryad.326r8/128
title: Assembled unitigs for Phycis blennoides
DOI: 10.5061/dryad.326r8/129
title: Assembled scaffolds for Lesueurigobius cf. sanzoi
DOI: 10.5061/dryad.326r8/130
title: Assembled unitigs for Lesueurigobius cf. sanzoi
DOI: 10.5061/dryad.326r8/131
title: Assembled scaffolds for Gadus morhua
DOI: 10.5061/dryad.326r8/132
title: Assembled unitigs for Gadus morhua
DOI: 10.5061/dryad.44nd5/1
title: Figure Data

description: Contains the data on which the figures in the paper have been built
DOI: 10.5061/dryad.46vf8/1
title: River Wey Fish Sampling Data

description: River Wey fish sampling dataset used in species richness regression analysis (King et al. 2016).
DOI: 10.5061/dryad.46vf8/2
title: River Wey Barrier Data

description: River Wey barrier dataset used in barrier optimization analysis (King et al. 2016).
DOI: 10.5061/dryad.46vf8/3
title: OPL model

description: CPLEX Studio OPL project, including (.mod), data (.dat), settings (.ops) files, and Excel (.xlsx) files, used in performing optimization analysis (King et al. 2016).
DOI: 10.5061/dryad.4846b/1
title: de la Pena Domene et al. 2016. Oikos. Data Base

description: Data description of species, seeds number, recruit number, seeds per recruit, life history, dispersal mode and habitat
DOI: 10.5061/dryad.49m29/1
title: Foliar concentration of nitrogen and phosphorus

description: Foliar nutrient concentrations in Brosimum lactescens seedlings subject to three treatments: dung and dung beetle activity, dung without beetle activity, no dung.
DOI: 10.5061/dryad.6t6t1/2
title: Interloper trials - tuft size - MS analysis Aug 2015 - Stoffer et al Beh Eco

description: Portion of data used for Objective 1 - tuft size
DOI: 10.5061/dryad.6t6t1/3
title: Interloper trials - tuft size - MS analysis - Stoffer et al Beh Eco

description: Portion of data used in Objective 1 - tuft size
DOI: 10.5061/dryad.73q8s/1
title: Milton_Insperger_sup_material

description: Data for Figures 2b, 3 and 4.  Stick balancing data for a 0.56m stick for E1, E2, E3 and E4. Matlab programs used to estimate sensory dead zone and to generate lots shown in Figures 5 and 6.
DOI: 10.5061/dryad.7k3p2/1
title: Data from: Unpredictable Perturbation Reduces Breeding Propensity Regardless Of Pre-Laying Reproductive Readiness In A Partial Capital Breeder

description: The data file contains information on body mass at capture (BM1) or at release (BM2), the difference between BM1 and BM2 (DIFF) the concentration of VLDL and VTG, the YEAR (2003 or 2004),the Breeding Propensity with 1 indicating a breeding bird and 0 a bird non resighted in the colony, The Treatment category (maintained 24 hours in captivity or release immediately after banding), the  release date in julian date and the band number (BAND)
DOI: 10.5061/dryad.7nk90/1
title: Stable isotope data

description: Uncorrected δ13C and δ15N stable isotope signature of Andean condor molted feathers and hair of potential relevant terrestrial food sources.
DOI: 10.5061/dryad.803q8/10
title: Rad_orca_subsample3_1M trees

description: Trees inferred by SNAPP for subsample 3
DOI: 10.5061/dryad.803q8/11
title: Rad_orca_subsample4_1Mb trees

description: Trees inferred by SNAPP for subsample 4
DOI: 10.5061/dryad.803q8/12
title: Rad_orca_subsample5_10individs_1M trees

description: Trees inferred by SNAPP for subsample 5
DOI: 10.5061/dryad.803q8/13
title: treemix input file

description: Input file for TreeMix
DOI: 10.5061/dryad.803q8/14
title: STRUCTURE input file

description: Input file for STRUCTURE analyses
DOI: 10.5061/dryad.8d724/11
title: Heliconius sara RSEM mapped count data

description: File is count data (expression level) output of Trinity contigs from RSEM for Heliconius sara. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).
DOI: 10.5061/dryad.8d724/9
title: Heliconius erato RSEM mapped count data

description: File is count data (expression level) output of Trinity contigs from RSEM for Heliconius erato. Column headers contain species name, sex (M or F), specimen ID (see Table S1 for details), and tissue type ("ant" = antennae, "leg" = legs, and "mou" = mouthparts).
DOI: 10.5061/dryad.b649s/8
title: Table S8.  Gene Ontology (GO) enrichment.

description: GO terms significantly associated with the top 1,000 associated SNPs of each trait are listed. Significance was established using a 5% FDR threshold within each trait.
DOI: 10.5061/dryad.b649s/9
title: Table S9. Genomic control (GC) values.

description: Genomic control values for all GWA analyses. Q-Q plots for GWAs with significant SNPs are shown in SI Appendix, Fig S20.
DOI: 10.5061/dryad.f1kc3/1
title: JEcol-2015-0799.R1

description: Acacia dealbata: seed weight, elaiossome weight, seedlings weight, number of seeds per pod (aborted, preyed, fully developed) for Portugal and Australia; 7 populations in each country; Acacia longifolia: seed weight, elaiossome weight, seedlings weight number of seeds per pod (aborted, preyed, fully developed) for Portugal and Australia; 10 populations in each country.
DOI: 10.5061/dryad.g3p5h/1
title: Song and mass changes data
DOI: 10.5061/dryad.g60r3/14
title: Bioinformatics pipeline

description: A description of the bioinformatics pipeline used to process raw MiSeq data, including parameter values and sample syntax.
DOI: 10.5061/dryad.g60r3/16
title: R scripts for data analysis

description: Archive of R scripts used to produce results in Wagner et al. 2016. See README file for notes on contents and recommendations for use.
DOI: 10.5061/dryad.g9r36/10
title: Cissus pileata SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus pileata Desc. (K Herbarium sheet collector no. 18981)
DOI: 10.5061/dryad.g9r36/11
title: Cissus planchoniana SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus planchoniana Gilg (K Herbarium sheet collector no. 606)
DOI: 10.5061/dryad.g9r36/12
title: Cissus polyantha 1 SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus polyantha Gilg & M.Brandt (K Herbarium sheet collector no. 5208)
DOI: 10.5061/dryad.g9r36/13
title: Cissus polyantha 2 SRXTM DTS video

description: Video of digital SRXTM tomograms in transverse section through a herbarium fruit of Cissus polyantha Gilg & M.Brandt (K Herbarium sheet collector no. 1643)