cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sb560/4
title: Supplementary figure 2c

description: Multiple alignment of trnL-F region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB).
DOI: 10.5061/dryad.sb560/5
title: Supplementary figure 2d

description: Multiple alignment of psbM-trnD region of two accessions of Ficus krishnae (FK) and F. benghalensis (FB).
DOI: 10.5061/dryad.sd370/1
title: Behavioral and model data

description: It contains two data sets: behavioral and model data.
DOI: 10.5061/dryad.sg112/1
title: Behavioral and morphological measurements

description: Measurements of behavioral traits and morphological characteristics of threespine stickleback from a pond selection experiment.  Descriptions of the variable names are given in the READ ME file.
DOI: 10.5061/dryad.v7h28/13
title: Et.Etrach_3.final

description: Manual corrections of annotations for E. tracheiphila BuffGH reference strain, contig 3
DOI: 10.5061/dryad.v7h28/14
title: Et.Etrach_4.final

description: Manually corrected annotation file for contig 4 of E. tracheiphila reference genome BuffGH
DOI: 10.5061/dryad.v7h28/15
title: Et.Etrach_5.final

description: E. tracheiphila manual annotations of reference strain BuffGH, contig 5
DOI: 10.5061/dryad.v7h28/16
title: Et.Etrach_6.final

description: Manual annotations of E. tracheiphila reference genome BuffGH, contig 6
DOI: 10.5061/dryad.11978/1
title: 2dayCvsLD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the low dose (LD) treatment of Alexandrium fundyense for 2 days compared with the control diet Rhodomonas spp.. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.11978/2
title: 2dayCvsHD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the high dose (HD) treatment of Alexandrium fundyense for 2 days compared with the control diet Rhodomonas spp.. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.11978/3
title: 5dayCvsLD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the low dose (LD) treatment of Alexandrium fundyense for 5 days compared with the control diet Rhodomonas spp.. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.11978/4
title: 5dayCvsHD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the high dose (HD) treatment of Alexandrium fundyense for5 days compared with the control diet Rhodomonas spp.. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.11978/5
title: 2dayLDvsHD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the low dose (LD) treatment of Alexandrium fundyense for 2 days compared with the high dose (HD) treatment. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.11978/6
title: 5dayLvsHD

description: List of up- and down-regulated genes in Calanus finmarchicus adult females feeding on the low dose (LD) treatment of Alexandrium fundyense for 5 days compared with the high dose (HD) treatment. For each gene NCBI Accession No., fold change (absolute) and annotation (blastx) are listed.
DOI: 10.5061/dryad.24rj8/1
title: data_packet

description: This is a zipped folder that contains the following items: 1) alignment used to perform initial placement of the species within a broad taxon sampling (NEXUS), 2) input file for ML analysis to perform initial placement of the species within a broad taxon sampling (PHYLIP), 3) results of the initial ML analyses (PDF), 4) alignment used to perform final published molecular phylogenetic analyses of narrower taxon sampling (NEXUS), 5) input files for ML (PHYLIP) and BI (NEXUS) used to perform final published molecular phylogenetic analyses of narrower taxon sampling.
DOI: 10.5061/dryad.2jc88/1
title: S1 Table

description: S1 Table: Endosymbiotic rickettsial genes and their encoding proteins identified by the MUMmer alignment software and BLASTX in the Trace Archive of the Ixodes scapularis genome sequencing project. Column 1 and 2 are call numbers. Column 3 is the GenBank accession numbers of homologous proteins. Column 4 is the names of the homologous proteins. Column 5 is the names of the bacterial species. Column 6 and 7 are the percentage identity to top BLASTX results. Column 8 is the AT% for the DNA. Column 9 is the sequences obtained by the MUMmer alignment.
DOI: 10.5061/dryad.580bh/4
title: Guillaume at al 2015_Transgenerational plasticity_Brighton Marina temperature Mar-Sep

description: Temperature data collected at Middle Brighton Pier, Melbourne, Australia between March and September in 2013. A data logger (Onset HOBO Pendant data logger) was placed adjacent to Galeolaria caespitosa clusters used in experiments. Column headings: 'Date (MM/DD/YY) = date that data was collected in US format; ' Time' = hour, minute and second that data was collected in 12h format; 'Temp, °C' = Temperature recorded in degrees Celsius.
DOI: 10.5061/dryad.5890r/1
title: Supplementary Data

description: Image sources for functional character measurements,Skull size data specimens and sources,z transformed functional character data ,Time bin assignments,PCOa scores for all taxa - primary analysis,PCA scores for all taxa - sensitivity analyses,First and last appearance dates for all taxa,PCOa scores from individual clade analyses
DOI: 10.5061/dryad.5890r/2
title: Supplementary Text

description: Additional methods
DOI: 10.5061/dryad.5890r/3
title: Supplementary Figure 1
DOI: 10.5061/dryad.5890r/4
title: Supplementary Figure 2
DOI: 10.5061/dryad.5890r/5
title: Supplementary Figure 3
DOI: 10.5061/dryad.5890r/6
title: Supplementary Figure 4
DOI: 10.5061/dryad.5890r/7
title: Supplementary Figure 5
DOI: 10.5061/dryad.59gg3/1
title: Specimen Data Spreadsheet for PLos One

description: This Excel spreadsheet gives the raw data for the morphology measurements and mechanical testing measurement.
DOI: 10.5061/dryad.6m1m6/1
title: Data tables for Morphological drivers of trophic cascades

description: Here we provide the data files used in the article Morphological drivers of trophic cascades. The Read me document provides details about the columns of each data files.
DOI: 10.5061/dryad.6p76c3pb.2/10.2
title: makesamplingmatrix

description: This script accesses a directory, and traverses all FASTA files in it, recording the names of all taxa present in each file. Then it creates a tab-delimited file containing a matrix where the rows represent the taxa and the columns the FASTA files. The intended use is for a directory containing a set of FASTA files each corresponding to a single locus, and containing homologous sequences of that locus for different taxa. The script will record a 1 in the resulting matrix if a taxon is present in a locus file, or a 0 if not. Key point: the script does not intelligently differentiate FASTA files from other types, and it will attempt to parse any file in the directory. For this reason, you should remove all other files before you run the script. It will create (or overwrite!) a file in the passed directory called 'sampling_matrix.txt' that may be opened in any conventional spreadsheet or text-editor app. This file should be in the proper format for use in the Decisivator application. This script requires BioPython to be installed.
DOI: 10.5061/dryad.6p76c3pb.2/11.2
title: phase_1_contree_all_taxa_all_genes_all_tips
DOI: 10.5061/dryad.6p76c3pb.2/12.2
title: phase_2_contree_all_genes_stable_tips
DOI: 10.5061/dryad.6p76c3pb.2/13.2
title: phase_2.5_contree_has_ndhf_or_rbcl_all_tips
DOI: 10.5061/dryad.6p76c3pb.2/14.2
title: phase_3_contree_has_ndhf_or_rbcl_no_bad_taxa
DOI: 10.5061/dryad.6p76c3pb.2/8.2
title: filter_fasta.py

description: Usage: ./filter_fasta.py [path to input dir] [path to accepted taxon list]. Input files are expected to be in fasta format. The script will traverse all files in the input dir, so the input dir should contain only fasta files. The taxon list should be a line-delimited text file containing the names of tips as they correspond to those in the fasta alignments.
DOI: 10.5061/dryad.6p76c3pb.2/9.2
title: instability_multicore.py

description: This script will calculate I^s scores, as described in (Hinchliff, C. E. and E. H. Roalson. 2012. Using supermatrices for phylogenetic inquiry: an example using the sedges. Systematic Biology). It requires a set of trees sharing a common set of tips, to be input as a newick file (though any format readable by dendropy should be trivial to use, just change the format in the appropriate line). It outputs a comma-delimited table containing the raw instability scores (the numerator from the right side of the equation in the referenced paper), as well as the scaled I^s scores. Taxa that move more have higher scores.
DOI: 10.5061/dryad.71hp4/1
title: Outcome

description: This contains data on visual outcomes in eight secondary level eye care centers of L V Prasad Eye Institute, India
DOI: 10.5061/dryad.7205r/1
title: SSR primers designed

description: Microsatellite loci identifed for Pitcairnia staminea and P. albiflos leaf and floral transcriptomes
DOI: 10.5061/dryad.7205r/11
title: Contigs of each transcriptome

description: Files with assembled contigs of each transcriptome
DOI: 10.5061/dryad.7205r/12
title: FPKM values for each transcriptome

description: Excel files containing FPKM values for each contig
DOI: 10.5061/dryad.7205r/2
title: Table S3_List of candidate genes

description: Annotation of candidate genes of anthocyanin and flavonoid biosynthetic pathway, including FPKM (fragments per kilobase of transcript per million fragments sequenced) for each transcript.
DOI: 10.5061/dryad.7205r/3
title: Table S1_The GOs classifcation all leaves

description: GO classification of the assembled sequences into three main categories (biological function, cellular component and molecular function) at all levels (1–17). Columns list the number of transcripts corresponding to the individual species and tissues separately
DOI: 10.5061/dryad.7205r/4
title: Table S2_Keeg pathways

description: List of all KEGG pathways with the number of annotated ECs
DOI: 10.5061/dryad.7n8gc/1
title: supporting_data

description: Simulation results supporting study finding (.RData file type)
DOI: 10.5061/dryad.96818/1
title: supporting data for leopard shark navigation - raw shark tracks

description: Raw data (geographic position and mean depth between successive geographic positions) for leopard sharks that were manually acoustically tracked after being experimentally displaced offshore from the capture site off La Jolla, CA.
DOI: 10.5061/dryad.c8q11/1
title: Supplementary Table_Morphological data matrix

description: This table includes 33 morphometric characters on the bodies of two adult specimens from each of 125 species and 24 genera of Hypostominae, using 31 homologous landmarks originally proposed by Armbruster (2003): 14 of which were on the head, 5 on the mouth, and the remainder on the trunk or fins.
DOI: 10.5061/dryad.c8q11/2
title: Hypostominae Ultrametric Tree

description: Hypostominae ultrametric tree used in all macroevolutionary analysis.
DOI: 10.5061/dryad.cd62n/1
title: Anurans2010_Data.csv

description: Raw tabular data collected throughout this experiment. The data are unfiltered. All variables described within the file.
DOI: 10.5061/dryad.cd62n/2
title: Anurans2010_Rdata.csv

description: Matrix data with a header row as used by R for linear mixed models. Variables are explained in the readme.
DOI: 10.5061/dryad.cd62n/3
title: Anurans2010_MeanComparisonData.csv

description: Matrix data with a header row as used by SPSS (or R) for comparisons of anuran calling behavior between lit and unlit conditions. Includes some weather data. Variables explained in the readme. Missing data are blank cells. Rows with missing data should be removed if replicating the published analyses.
DOI: 10.5061/dryad.cd62n/4
title: Anurans2010_LogRegressionData.csv

description: Matrix data with a header row in computing the log regression between call index and number heard calling. Only non-zero data were included to accommodate the log relationship.
DOI: 10.5061/dryad.cd62n/5
title: history.txt

description: Verbatim R code with markup used to generate the linearmixed models.
DOI: 10.5061/dryad.dn048/1
title: Mundim and Bruna_AMNAT_metadata

description: Metadata describing the information used in the file "Mundim_Bruna AMNAT 2016_data".
DOI: 10.5061/dryad.dn048/2
title: Mundim_Bruna AMNAT 2016_data

description: Table with the data collected from all the publications between 1993-2013 used in the meta-analysis.
DOI: 10.5061/dryad.dn048/3
title: Mundim_Bruna AMNAT 2016_references

description: References of the studies used to extract data for the meta-analysis.
DOI: 10.5061/dryad.fc55k/1
title: AllChromosomesF2F3

description: This file contains genotype scores for 2060 specimens of the F2 and F3 generations of an intercross of inbred LG/J and SM/J mice, obtained from The Jackson Laboratory (for details see Cheverud et al. 1996; Norgard et al. 2008). Each individual was genotyped at 384 polymorphic SNPs. In our study we used only individuals without missing data and the 353 SNPs on the 19 autosomal chromosomes. Cheverud, J. M., E. J. Routman, F. A. Duarte, B. van Swinderen, K. Cothran et al., 1996 Quantitative trait loci for murine growth. Genetics 142: 1305–1319.Norgard, E. A., C. C. Roseman, G. L. Fawcett, M. Pavlicev, C. D. Morgan et al., 2008 Identification of quantitative trait loci affecting murine long bone length in a two-generation intercross of lg/j and sm/j mice. J. Bone Miner. Res. 23(6): 887–895.
DOI: 10.5061/dryad.fc55k/2
title: Chrom6_phenotypes

description: Additive and dominance genotype scores for each of the 22 screened SNPs on chromosome 6 as well as for 89 loci imputed every 1 cM. The last 11 columns comprise the phenotypic measurements: total body weight (WTN), the weights of the reproductive fat pad (FP), the heart (HT), the kidney (KD), the spleen (SP), and the liver (LV), as well as tail length (TL) and the lengths of the right set of long bones (HUM, ULN, FEM, TIB). Measurements were corrected for the effects of sex, litter size, and age at necropsy.
DOI: 10.5061/dryad.kb508/2
title: climate data
DOI: 10.5061/dryad.kb830/1
title: female productivity for control population at standard temperature

description: Female productivity for control population at standard 25 °C. Description for each column in the data sheet can be found in a separate sheet named "Variables" in the file.
DOI: 10.5061/dryad.nc66n/1
title: F0 brood ball mass

description: Brood ball (BB) mass produced by the parental generation across layers of soil in native O. illyricus and O. taurus (Italy)
DOI: 10.5061/dryad.nc66n/2
title: F1 body size

description: Pronotum width (=body size) of emerging offspring across layers of soil in native O. illyricus and O. taurus (Italy)
DOI: 10.5061/dryad.nc66n/3
title: Brood ball depth

description: Brood balls (BBs) harvested from three layers of soil (bottom, center, top) in breeding containers (BCs). The dataset includes the date each BC was set up and taken down, and the number of females and males used in each. Four populations: O. taurus (IT, IN, WA); O. illyricus (ILLY).
DOI: 10.5061/dryad.nc66n/4
title: Tibia centroid size

description: Pronotum width (=body size) and tibia centroid size (CS) of 12 randomly selected females per population analyzed: O. taurus (IT, IN, WA); O. illyricus (ILLY).
DOI: 10.5061/dryad.nc66n/5
title: Tibia landmarks

description: Coordinates of landmarks placed on each tibia specimen [12 randomly selected females per population analyzed: O. taurus (IT, IN, WA); O. illyricus (ILLY)]. Images available upon request.
DOI: 10.5061/dryad.p56mf/1
title: matlab code for generating the paper figures

description: matlab functions are named FigX corresponding to the Xth figure (figures 1 and 2 are illustrative and were not included). Some additional plotting functions are included and are needed for figure generation.
DOI: 10.5061/dryad.p56mf/2
title: dataFig3

description: .mat files for generating figures. dataFigX correspond to data required for generating figure X.
DOI: 10.5061/dryad.qd5gj/1
title: Adaptation of Phenology across Populations_dataset_Rutschmann

description: The dataset has been used to perform all statistical analyses in the manuscript: Climate and habitat interacts to shape the thermal reaction norms of breeding phenology across lizard populations. Data have been recolted in the Massif Central, France, between 2004 and 2014. #Pop (site of capture) #Id (lizard unique identity)  # R_id (lizard capture code) #alt (elevation, m) #SVL (Snout-ventral length, mm) # W1 (weight at capture, g) #Part_y (year of parturition) #Part_d (parturition date, January-1st = 1) # T_gest (mid-gestation temperatures, °C) #FCI (Forest cover coefficient)  #Region (mountain chain)
DOI: 10.5061/dryad.11978/7
title: CfinmarchicusReferenceTranscriptome

description: Annotation list for Calanus finmarchicus reference transcriptome consisting of a total of 38,104 transcripts (Lenz et al., 2014). For each transcript NCBI Accession No., sequence length (bp) and annotation results are reported. Annotation results from blastx against Non-redundant (NR) protein database (BLAST2GO) consist of: sequence description, hit description, hit accession No., e-value, similarity score, alignment length and positives. In bold transcripts that resulted annotated using BLAST2GO, but were also in silico annotated using the workflow described in Christie et al., 2013a; Christie et al., 2013b; Christie et al., 2014. In red bolded, transcripts that did not retrieve annotation using BLAST2GO, but were in silico annotated as described in Christie et al., 2013a; Christie et al., 2013b; Christie et al., 2014. For bolded transcripts (red and black) the assigned name and reference paper are listed. For more information on the transcriptome refer to Lenz et al., 2014.
DOI: 10.5061/dryad.1s4f2/1
title: Ant demography data

description: Field demographic data based on colony (nest mound) sizes of the ant Atta laevigata in a Brazilian Cerrado area. More details in the ReadMe file.
DOI: 10.5061/dryad.1s4f2/2
title: Adult distances to the nearest road

description: Field data collected during three years on the distance (in m) of adult Atta laevigata colonies (mound size &gt; 2 square metres) to the nearest road in a Brazilian Cerrado area. More details in the ReadMe file.
DOI: 10.5061/dryad.2jc88/2
title: S1 File

description: S1 File: SequenceSearch script code.
DOI: 10.5061/dryad.2jc88/3
title: S2 File

description: S2 File: NucleotideReader script code.
DOI: 10.5061/dryad.3p2j0/1
title: Simulation results: indices of sexual selection and selection differentials on the mating trait

description: Please see 'Read me' on first sheet of spreadsheet
DOI: 10.5061/dryad.3s795/1
title: Genome.tar.gz

description: A snapshot of the Hmel2 distribution available from butterflygenome.org
DOI: 10.5061/dryad.3s795/2
title: Eueides.Hmel2.vcf.gz

description: Variant calls for Eueides isabella cross aligned to Hmel2.fa
DOI: 10.5061/dryad.3s795/3
title: GitHub.tar.gz

description: A snapshot of the bespoke code written to reassemble the genome, available from https://github.com/johnomics/Heliconius_melpomene_version_2, commit f826fd1 from Dec 10, 2015
DOI: 10.5061/dryad.3s795/4
title: Hmel_cross.Hmel_haplotype_scaffolds.vcf.gz

description: Variant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 haplotype scaffolds (Hmel_haplotype_scaffolds.fas)
DOI: 10.5061/dryad.3s795/5
title: Hmel_cross.Hmel1-1_primaryScaffolds.vcf.gz

description: Variant calls for Heliconius melpomene mapping cross aligned to Hmel1-1 primary scaffolds (Hmel1-1_primaryScaffolds.fa)
DOI: 10.5061/dryad.3s795/6
title: Hmel_cross.linkage_map.clean.db.gz

description: SQLite3 database containing scaffold_map and chromosome_map tables used to reassemble genome, fixing all identified linkage errors, recalculating cM values and reversing chromosomes where necessary
DOI: 10.5061/dryad.3s795/7
title: Hmel_cross.linkage_map.db.gz

description: SQLite3 database containing marker information for linkage map (see README.txt for table descriptions)
DOI: 10.5061/dryad.40j0j/1
title: COP Fixed Floor

description: COP data of human subjects on a fixed floor.
DOI: 10.5061/dryad.40j0j/2
title: COP Rotational Floor

description: COP data of human subjects on a rotational floor.
DOI: 10.5061/dryad.4gn47/1
title: Model analyses

description: Mathematica 8.0 file in which we derive and analyze the model equations in the paper.
DOI: 10.5061/dryad.5890r/10
title: Supplementary Table 1
DOI: 10.5061/dryad.5890r/11
title: Supplementary Table 2
DOI: 10.5061/dryad.5890r/12
title: Supplementary Table 3
DOI: 10.5061/dryad.5890r/13
title: Supplementary Table 4
DOI: 10.5061/dryad.5890r/8
title: Supplementary Figure 6
DOI: 10.5061/dryad.5890r/9
title: Supplementary Figure 7
DOI: 10.5061/dryad.5ks03/1
title: fasta alignments: 11 genetic markers

description: This folder contains the fasta alignments of the 11 genetic markers used in this study, for the Ophioderma longicauda clusters C3, C5 and C6. The sequences were obtained using Miseq sequencing.
DOI: 10.5061/dryad.5ks03/2
title: raw_miseq_data_1

description: this folder contains the raw Miseq data for the wells A1 to B10 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplified
DOI: 10.5061/dryad.5ks03/3
title: raw_miseq_data_2

description: this folder contains the raw Miseq data for the wells B11 to D9 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplified
DOI: 10.5061/dryad.5ks03/4
title: raw_miseq_data_3

description: this folder contains the raw Miseq data for the wells D10 to F11 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplified
DOI: 10.5061/dryad.5ks03/5
title: raw_miseq_data_4

description: this folder contains the raw Miseq data for the wells F12 to H12 (two fastq files per well, read 1 and read 2). each well corresponds to 3 individuals, for which 38 markers were amplified
DOI: 10.5061/dryad.5ks03/6
title: sample sheet - individuals and position on the plate

description: this excel file shows the pooling of PCR amplicons (38 markers used) for 288 individuals in a 96-well plate. In each well, the amplicons of three individuals were pooled. Each well was sequenced using a Miseq sequencer.
DOI: 10.5061/dryad.5q67v/1
title: Soudi_et_al_data_survival

description: Survival of individuals from both willow and birch host races of L. capreae leaf beetles and hybrids between them on willow and birch
DOI: 10.5061/dryad.6p76c3pb.1
title: Data from: Using supermatrices for phylogenetic inquiry: an example using the sedges
DOI: 10.5061/dryad.6p76c3pb.2/15.2
title: phase_4_contree_has_ndhf_or_rbcl_stable_tips
DOI: 10.5061/dryad.6p8p0/1
title: CAC.Mimulus.2012.phenology.by.plot

description: This file contains data on flowering phenology from mixed populations of Mimulus guttatus, Mimulus nasutus, and hybrids, from Catherine Creek in Wasthington State, USA during 2012. Flowering data was collected from each of 20 0.5 meter squared plots. The number of open flowers in each plot was recorded on 31 days throughout the 2012 flowering season. Each row in the datasheet is a date; plots are represented in columns. Each data point is the number of open flowers recorded within a plot on a single day. See Kenney and Sweigart 2016 for detailed information on species composition per plot.