cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v8g60/1
title: Supporting information

description: The mean CT values of the host control P. citri 28S rDNA gene, target M. endobia 16S and 23S rDNA and target T. princeps GroEL gene from individual adult female P. citri from the populations A (n = 39) and B (n = 40), and from A♀B♂ and A♂B♀ (20 pooled offspring per mother, n = 28 mothers for A♀B♂, n = 29 mothers for A♂B♀).
DOI: 10.5061/dryad.186m0/10
title: FIRST Paired Background Survey Data

description: The associated data file contains results from the paired Teaching Background Survey which we designed to characterize the prior biology teaching experiences for the faculty participants. This data set consists of data from 18 of the pairs. For complete survey questions and scales see Supplementary Materials S1 in the associated publication (Derting et al. 2016).
DOI: 10.5061/dryad.186m0/7
title: FIRST Paired RTOP data

description: The associated data file contains results from the Reformed Teaching Observation Protocol by D. Sawada, "Reformed teacher education in science and mathematics: An evaluation of the Arizona Collaborative for Excellence in the Preparation of Teachers," (Arizona State University Document Production Services, Tempe, AZ, 2003). This data set consists of data from 17 complete pairs and two incomplete pairs from our paired study.
DOI: 10.5061/dryad.186m0/9
title: Percent Average Blooms Taxonomy for Assessments

description: The associated data file contains the average of the percent Bloom score (Bloom’s Taxonomy categories 1-6) for assessment questions. We scored individual question into cognitive skill categories and calculated the percent of points in each assessment assigned in each Bloom’s category (see Derting et al. 2016 for details). This data set consists of data from 17 FIRST Faculty and 15 non-FIRST Faculty.
DOI: 10.5061/dryad.34kt1/1
title: Muscarella_and_Uriarte_ProcB

description: Data to conduct analyses included in Muscarella & Uriarte, "Do community-weighted mean functional traits reflect optimal strategies?"  Please see metadata file for more details.
DOI: 10.5061/dryad.3ck0v/8
title: SeqFirstLocus

description: Scaffolds from the Tamalia assembly
DOI: 10.5061/dryad.3ck0v/9
title: ScaffoldSummary

description: BLAST annotations from the Tamalia assembly
DOI: 10.5061/dryad.48hq1/1
title: Spatial simulations results

description: Traditional and spatially explicit summary statistics obtained from spatial simulations under both landscape models tested: “altitudinal” (M1) and “latitudinal” (M2) models. Parameter settings associated with each simulation replicate are also provided.
DOI: 10.5061/dryad.493b7/9
title: BMGE_trimming

description: Phylip alignment for dataset 'BMGE trimming'
DOI: 10.5061/dryad.4c0s0/1
title: locust.hemolymph.ions

description: Locust hemolymph K+ concentration data
DOI: 10.5061/dryad.4c0s0/2
title: Chill coma recovery time data
DOI: 10.5061/dryad.4c0s0/3
title: locust.surv.scores

description: Locust survival score data
DOI: 10.5061/dryad.4c0s0/4
title: muscle.damage.insitu.final

description: Locust in situ muscle damage data
DOI: 10.5061/dryad.4c0s0/5
title: muscle.damage.invivo.final

description: Locust in vivo muscle damage data
DOI: 10.5061/dryad.4mr3c/1
title: Dimethylsulphoniopropionate (DMSP) and stress response metabolites in three scleractinian corals under short-term hyposalinity stress

description: Fv/Fm = maximum quantum yield ofphotosystem II DMSP = Dimethylsulphoniopropionate DMSO = dimethylsulphoxide SOD = superoxide dismutase GSx = total glutathione
DOI: 10.5061/dryad.57gj4/10
title: secondary_calibration_analyses(BEASTv2.2)

description: XML file for running the analyses with the Brassicaceae dataset (supermatrix approach) in BEASTv2.2 (Bouckaert et al., 2014) using the three secondary calibration scheme for calibration
DOI: 10.5061/dryad.57gj4/11
title: ML_RAxML_bestTree_Brassicaceae_dataset

description: Maximum likelihood tree obtained using the Brassicaceae dataset (supermatrix approach) under RAxML 8.1.11
DOI: 10.5061/dryad.57gj4/8
title: nad4_Brassicaceae_dataset

description: nad4 matrix from Brassicaceae dataset
DOI: 10.5061/dryad.5t32v/10
title: framework without LD linkage map

description: This contains the cM positions for the framework linkage map. The "without LD" refers to the removal of a few markers from the original framework map that appeared to cause convergence issues during QTL mapping due to high levels of LD with neighbouring markers
DOI: 10.5061/dryad.5t32v/4
title: NL QTL mapping pedigree

description: Not all genotyped individuals could be linked into a pedigree suitable for QTL mapping, therefore these files contain only related genotyped individuals and their shared (sometimes ungenotyped) relatives. There are two sets of columns, the first column shows the QTL mapping numeric IDs (used only for QTL mapping) while the second column shows the numeric ids that relate to the genotype and trait data.
DOI: 10.5061/dryad.5t32v/5
title: NL traits

description: Separate sheets in these excel files contain trait information for the phenotyped and genotyped animals, along with important fixed and random effects fitted in the mixed models. See Supporting Information 1 for more information.
DOI: 10.5061/dryad.5t32v/6
title: UK map file

description: plink-style map file with marker locations for the UK dataset.The map file is in an amended plink format with chromosome in column 1, SNP name in column 2, cM position in column 3 (note this is different from defaul plink map files which have distances in Morgans) and genome order in column 4 (again this is different from the plink format which would usually have bp position in this column).  Chromosome codings in the map file (column 1) are as follows: Chromosomes 1-15 and 17-28 are the corresponding chromosomes 1-15 and 17-28 in the great tit genome Chromosome 29 = chromosome 1A Chromosome 30 = chromosome 4A Chromosome 31 = Z chromosome Chromosome 32 = Linkage group LGE22
DOI: 10.5061/dryad.5t32v/7
title: UK genotype file

description: Genotypes for the 2,497 UK individuals. These are standard plink files (see http://pngu.mgh.harvard.edu/~purcell/plink/) where the first column gives a family id, the second column an individual id (in this case family id = individual id), the third and fourth columns are paternal and maternal IDs (here, left blank so that ids = 0 for both parents), column five has sex (1=male; 2=female; other=unknown) and finally column 6 phenotype (here all phenotypes  = -9 for unknown). Columns 7 onwards contain genotype information for the SNPs listed (in order) in the .map file of the same name.
DOI: 10.5061/dryad.5t32v/8
title: UK QTL mapping pedigree

description: Not all genotyped individuals could be linked into a pedigree suitable for QTL mapping, therefore these files contain only related genotyped individuals and their shared (sometimes ungenotyped) relatives. There are two sets of columns, the first column shows the QTL mapping numeric IDs (used only for QTL mapping) while the second column shows the numeric ids that relate to the genotype and trait data.
DOI: 10.5061/dryad.5t32v/9
title: UK traits

description: Separate sheets in these excel files contain trait information for the phenotyped and genotyped animals, along with important fixed and random effects fitted in the mixed models. See Supporting Information 1 for more information.
DOI: 10.5061/dryad.6g181/1
title: Dryad files

description: All Bayesian analysis, TCS files and coevolution analysis files for both gene fragments are included.
DOI: 10.5061/dryad.6gb90.2
title: Data from: Analysing biodiversity and conservation knowledge products to support regional environmental assessments
DOI: 10.5061/dryad.6gb90.2/1.2
title: Total_Species_GEO

description: Total numbers of species and of threatened species occurring in each GEO region and subregion
DOI: 10.5061/dryad.6gb90.2/2.2
title: Total_Species_IPBES

description: Total numbers of species and of threatened species occurring in each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/3.2
title: Endemic_Species_GEO

description: Total numbers of species endemic and of threatened species endemic to each GEO region and subregion
DOI: 10.5061/dryad.6gb90.2/4.2
title: Endemic_Species_IPBES

description: Total numbers of species endemic and of threatened species endemic to each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/5.2
title: Red_List_Index_GEO

description: Relative annual contribution to the global Red List Index for mammals, birds, and amphibians in each GEO region and subregion
DOI: 10.5061/dryad.6gb90.2/6.2
title: Red_List_Index_IPBES

description: Relative annual contribution to the global Red List Index for mammals, birds, and amphibians in each IPBES region and subregion
DOI: 10.5061/dryad.6pr03/1
title: narG_alignment

description: Alignment of full length NarG used for phylogenetic tree. Sequences were taken from genomes included in the manuscript as well as from all publically available B. licheniformis genomes (dd June 2014) and genomes from other Bacillus species, protein ID  or locus tag is given.
DOI: 10.5061/dryad.6pr03/2
title: narK_alignment_trimmed

description: Trimmed alignment of full length NarK sequences used for phylogenetic tree. Sequences were taken from several Bacillus species, as well as reference genomes, locus tag is given.
DOI: 10.5061/dryad.74s05/1
title: Data from Okhovat et al. 2015

description: This file contains various data that was used to perform analyses and construct figures in Okhovat et al. 2015.
DOI: 10.5061/dryad.787d9/1
title: DNA sequence assembly

description: DNA sequence assembly used for the analyses, unique haplotypes (H001-H228) as in the phylogenetic tree (LTC.con). The two outgroup sequences (H227, H228) where only used for phylogeny reconstruction but not for the different species delineation and identification methods.
DOI: 10.5061/dryad.787d9/2
title: Phylogenetic tree

description: Baysian Inference (BI) phylogenetic tree used for the ABGD method.
DOI: 10.5061/dryad.80442/1
title: Arabidopsis epigenome and climate datasets

description: Epigenome and genetic maps for Eurasian and Swedish Arabidopsis accessions. Also included are climate variables at these accession sites as well as R scripts to conduct RDA analyses.
DOI: 10.5061/dryad.871db/1
title: Microsatellite genotypes for northern California tidewater goby populations

description: Microsatellite genotypes in GENEPOP format for northern California tidewater goby populations.  Definitions for site abbreviations and geographic coordinates of sampling locations can be found in the accompanying publication.
DOI: 10.5061/dryad.871db/2
title: Tidewater Goby Occupancy History Northcoast Haul  Data

description: Tidewater goby occupancy data for northern California tidewater goby populations.  Data includes presence (1) absence(0) from 94 sites between 1897 and 2014.  Primary sampling periods are years and secondary sampling sessions are repeat seine hauls within years.  For additional descriptions of the data please see accompanying publication.
DOI: 10.5061/dryad.871db/3
title: Genetic and geographic distance data for isolation by distance analysis

description: Genetic and geographic distance data for analysis of conformance to an isolation by model of gene flow.  Values above the diagonal are geographic distances (km) and values below diagonal are genetic distances (Fst).  Data are for the 19 spatially isolated locations with large sample sizes.  Only those collections with large sample sizes were included in the analysis (&gt;19).
DOI: 10.5061/dryad.871db/4
title: Input file used to construct neighbor joining tree using PHYLIP.

description: Input file used to construct neighbor joining tree using PHYLIP.  Population IDs, 1-36, defined in companion file uploaded with this data package.
DOI: 10.5061/dryad.871db/5
title: Bootstrap consensus tree from neighbor joining analysis using PHYLIP.

description: Bootstrap consensus tree from neighbor joining analysis using PHYLIP.  Population IDs, 1-36, defined in companion file uploaded with this data package.
DOI: 10.5061/dryad.871db/6
title: Project/parameter input file for Bayesian cluster analysis using STRUCTURE.

description: Project input file containing parameters for Bayesian cluster analysis using STRUCTURE.  Site IDs, 1-47, are defined in companion file with this data package.
DOI: 10.5061/dryad.87r18/1
title: Teosinte unigenes' sequences

description: Due to the lack of available reference genome, clean reads from Zea may ssp. parviglumis and Zea mays ssp. mexicana were first de novo assembled into contigs using Trans-ABySS, which can use a multiple K-mer strategy to assemble the transcriptome. After that, transcriptome from different samples were pooled to reconstruct the transcriptome using CD-HIT-EST with a word length of 8 and an identity threshold ≥ 0.98.Sequentially, CAP3 was used to discard the redundancy transcripts, and the resulting contigs and singlets were combined to represent transcriptome of teosinte.
DOI: 10.5061/dryad.9k358/1
title: GaechterSchulzDATA&CODE

description: Contains all experimental and auxiliary data (institutional and demographic variables) reported in the article and the supplementary information (in both csv and STATA format). A list of variables and their labels is in the ReadMe file.Also contains the STATA codes (do-files) of the analyses reported in the article and the Supplementary Information.
DOI: 10.5061/dryad.b1k0v/1
title: Average quantity of paracetamol and aspirin purchased in one transaction
DOI: 10.5061/dryad.c175g/1
title: Manipulative mate choice assay mean

description: Data for the manipulative mate choice assay analysis of mean offspring viability
DOI: 10.5061/dryad.c175g/2
title: Manipulative mate choice assay overyielding

description: Data for manipulative mate choice assay analysis of overyielding
DOI: 10.5061/dryad.c175g/3
title: Breeding design

description: Data for the breeding design used to estimate sire and interaction covariance matrices
DOI: 10.5061/dryad.c5n61/1
title: Group-based data

description: Group-based data underlying our results and the data points depicted in figure 2.
DOI: 10.5061/dryad.ct5q3/1
title: mergedSNPs
DOI: 10.5061/dryad.ct5q3/2
title: Sampling coordinates and site codes

description: This file lists all sampling sites, with their associated GPS coordinates.  It gives the letter and number abbreviations for the main text and all analysis files.
DOI: 10.5061/dryad.ct5q3/3
title: bayescan_input_fornicata

description: Input file for Bayescan for Crepidula fornicata.
DOI: 10.5061/dryad.ct5q3/4
title: bayescan_input_convexa

description: Input file for Bayescan with Crepidula convexa data.
DOI: 10.5061/dryad.ct5q3/5
title: bayescan_output_fornicata

description: Output from Bayescan analysis from Crepidula fornicata.
DOI: 10.5061/dryad.ct5q3/6
title: bayescan_output_convexa

description: Output from Bayescan analysis for Crepidula convexa
DOI: 10.5061/dryad.ct5q3/7
title: pairwise_distance_matrices

description: Matrices of pairwise genetic (Fst) and geographic (in kilometers) distances for populations of Crepidula fornicata and C. convexa.
DOI: 10.5061/dryad.d3459/45
title: Georeferenced locations and environmental variables

description: Georeferenced locations for Ottonia species and extracted environmental variables from WorldClim and FAO datasets
DOI: 10.5061/dryad.d3459/46
title: ITS
DOI: 10.5061/dryad.d3459/47
title: matK

description: matK sequences alignment
DOI: 10.5061/dryad.fb40c/1
title: wasp_protection_round_2_simplified070715

description: This file provides the raw data counts for each replicate (vial).
DOI: 10.5061/dryad.g4c34/1
title: EPO-predation data (T. Yuta & I. Koizumi 2015)

description: data for predation risk on extra-pair paternity in the Japanese great tit (10.1111/jav.00713)
DOI: 10.5061/dryad.h1167/1
title: Supplementary table S3_microsatellite profiles

description: Microsatellite profiles and information of origin for 30 individuals screened in this study.
DOI: 10.5061/dryad.j10r6/2
title: 2.tree_files

description: This package contains tree and xml files used in: 1) *BEAST, and 2) mtDNA phylogeny.
DOI: 10.5061/dryad.j10r6/3
title: 3.IMa2_files

description: This package contains input files for the IMa analyses concerning the five contact zones, and a summary of the replicated output files from each analysis.
DOI: 10.5061/dryad.j9k60/1
title: GPS tracking data and behavioural states

description: GPS tracking data and behavioural states of 10 breeding short-tailed shearwaters performing short foraging trips
DOI: 10.5061/dryad.mr1pt/1
title: Leopard Camera Trapping Data (for Dryad)

description: Individual identities, sex, date and location of capture for all leopards included in this study.
DOI: 10.5061/dryad.mr1pt/2
title: Leopard Camera Traps (for dryad)

description: Camera trap Identification Numbers (cam_id) and UTM easting (x) and Northing (y) coordinates for all camera stations used to detect common leopard in Royal Manas National Park, Bhutan during winter 2010-2011. The UTM coordinates are projected in UTM zone 46 with WGS84 datum.
DOI: 10.5061/dryad.q1b24/1
title: Limbodessus cox1 BDJ Paper

description: A 3' cox1 sequence dataset for New Guinea Limbodessus species
DOI: 10.5061/dryad.18pd8/1
title: The primary data and results for selection and phylogenetic analysis

description: In the manuscript, we have made a selection and phylogenetic analysis for MHC genes(DQB and DRB) in the Endangered Indo-Pacific Humpback Dolphin (Sousa chinensis).FUBAR software and CODENL program were used to test for the evidence of positive selection, and phylogenetic trees were reconstructed using MrBayes 3.1.2. The best-fit evolution model for MHC was selected on the basis of the Akaike Information Criterion(AIC) using MODELTEST 3.7. All the data underlying these analyses was submitted in a zip file(Data for Dryad).
DOI: 10.5061/dryad.1b01r/3
title: Methylation data

description: Tab-separated file containing all 1.47 M methylation level calls (rows) for CG, CHG, or CHH sequence contexts (Column 4) across all 58 samples (Columns 5-62) investigated in this study. Columns 1-5 give sequence context relative to reference genome sequence. Methylation call data were generated from BS-Seeker2 and have minimum coverage of 10×.
DOI: 10.5061/dryad.1b01r/5
title: Redundancy analysis input and output files

description: Redundancy analysis (RDA) was performed in VEGAN 2.3 in R 3.1.2 with SMVs (or SNPs) as dependent variables and climate and spatial variables as independent variables, separately for each SMV context and for SNPs. Permutation tests ('anova' function) with 999 permutations were used to assess the significance of the associations. Spatial variables included longitude ("Lon" in CLIMforRDA.txt) and latitude ("Lat") as Albers x/y coordinates, as well as elevation.
DOI: 10.5061/dryad.1b01r/6
title: PyLMM input and output files

description: We used linear mixed models implemented in PYLMM (http://genetics.cs.ucla.edu/pylmm/index.html) to test for specific SMV with significant association with climate variables after correcting for kinship. We used the methylation data to estimate the kinship matrix because we determined that it captures the relatedness of individuals, and better controls the rate of false positives than using the SNP data for estimating kinship.
DOI: 10.5061/dryad.1b01r/7
title: SNP data

description: SNP data in standard VCF format. Target genomic intervals for variant calling were identified using GATK’s CallableLoci. To avoid spurious calls at the edges of the RRBS target regions, the target intervals were trimmed by three bases on each end. Bwa-meth was used to align the reads for input to Bis-SNP. Bis-SNP’s BisulfiteGenotyper was run with the following parameters: -stand_call_conf 4 -stand_emit_conf 0 –maximum_read_cov 100000 –mm40 10 –trim5 2 –trim3 2 –mmq 10 –mbq 15 –useBAQ. GATK’s VariantFiltration and SelectVariants were used to remove calls for sites with low depth of coverage (DP &lt; 4), restrict to diallelic sites, and filter variants based on the following GATK variant annotation cutoffs, QD &lt; 2.0, MQ &lt; 40.0, MQRankSum &lt; −12.5, ReadPosRankSum &lt; −8.0, and AF &lt; 0.1.
DOI: 10.5061/dryad.1b01r/8
title: BAM files

description: BAM files generated from BS-Seeker2 with bowtie aligner
DOI: 10.5061/dryad.1n70s/1
title: Data associated with figures in the paper

description: Data for figures 1a, 1c, 1d, 1e, 2b and 3c. The columns in each file correspond to the axes and groups in the graph for the respective figure. For more explanation, please consult the figure captions and the Electronic Supplementary Material.
DOI: 10.5061/dryad.2f0j5/1
title: Alignments

description: Alignments of haplotype data for three genes used in analysis
DOI: 10.5061/dryad.2f0j5/2
title: Trees

description: All trees generated for the publication in editable formats (nexus and newick). Fig. 2  The history of diversification within the G. balcanicus group. Maximum clade credibility chronogram generated with a Bayesian inference, based on the full multimarker data. Figure S1 Topology of Maximum Likelihood reconstruction of phylogeny based on the mitochondrial COI DNA marker. Figure S2 Topology of Maximum Likelihood reconstruction of phylogeny based on the mitochondrial 16S rRNA marker. Figure S3 Topology of Maximum Likelihood reconstruction of phylogeny based on the nuclear 28S rRNA marker. Figure S4 Maximum clade credibility chronogram generated using Bayesian inference and based on the full multimarker data set. Figure S5 Time calibrated phylogeny of the G. balcanicus group based on the reduced multimarker data set
DOI: 10.5061/dryad.4c0s0/6
title: in.situ.images

description: Muscle tissue damage images from in situ experiment
DOI: 10.5061/dryad.4c0s0/7
title: in.vivo.muscle.images

description: Images from in vivo muscle damage experiment
DOI: 10.5061/dryad.57gj4/12
title: fossil_calibration_MCCT_Brassicaceae_dataset

description: Maximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "four Brassicales fossil scheme" for calibration.
DOI: 10.5061/dryad.57gj4/13
title: secondary_calibration_MCCT_Brassicaceae_dataset

description: Maximum clade credibility tree obtained in BEASTv2.2 using the Brassicaceae dataset (supermatrix approach) and the "secondary calibration scheme" for calibration.
DOI: 10.5061/dryad.57gj4/14
title: ITS_CES_dataset

description: ITS matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
DOI: 10.5061/dryad.57gj4/15
title: trnLF_CES_dataset

description: trnLF matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
DOI: 10.5061/dryad.57gj4/16
title: trnH_CES_dataset

description: trnH matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
DOI: 10.5061/dryad.57gj4/17
title: rps16_CES_dataset

description: rps16 matrix from CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset
DOI: 10.5061/dryad.57gj4/18
title: CES_analyses(BEASTv2.2)

description: XML file for running the analyses with the CES dataset (Cremolobeae, Eudemeae, Schizopetaleae) in BEASTv2.2 (Bouckaert et al., 2014).
DOI: 10.5061/dryad.57gj4/9
title: fossil_calibration_analyses(BEASTv2.2)

description: XML file for running the analyses with the Brassicaceae dataset (supermatrix approach) in BEASTv2.2 (Bouckaert et al., 2014) using the four Brassicales fossil scheme for calibration.
DOI: 10.5061/dryad.5t32v/11
title: GWAS results

description: This folder contains the GWAS results for the UK and NL traits, as estimated using the mmscore function in GenABEL
DOI: 10.5061/dryad.6gb90.2/10.2
title: PAs_IPBES

description: Percentage protected area coverage of land and sea, for each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/11.2
title: Protected_IBAs_GEO

description: Percentage of IBAs wholly covered by protected areas, over time, for each GEO region and subregion
DOI: 10.5061/dryad.6gb90.2/12.2
title: Protected_IBAs_IPBES

description: Percentage of IBAs wholly covered by protected areas, over time, for each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/13.2
title: Protected_AZEs_GEO

description: Percentage of AZE sites wholly covered by protected areas, over time, for each GEO region and subregion