cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.15rs596/5
title: AT4G26610_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.4tg8530/1
title: Brood Pheromone Foraging

description: Foraging experiments conducted as described in Ma et al 2018 during Summer 2015. Camera indicates the recording equipment used to record foraging. Colony ID identifies each unique colony, that were randomly assigned Screen treatments. Repeated measures were conducted for 3 different pheromone treatments on 3 different Days. Foraging was recorded at 3 time points following pheromone treatment. The number of foaragers carrying pollen or not carrying pollen were recorded.
DOI: 10.5061/dryad.4tg8530/2
title: BPO Forage May2018

description: R code in Rmarkdown format used to analyze foraging data.
DOI: 10.5061/dryad.4tg8530/3
title: EAG_2016

description: Electroantennography (EAG) data associated with Ma et al 2018. Colony represents the source colony from which individual nurses and foragers were taken. Behavior categorizes individual bees as nurses or foragers. Four concentrations for each of two pheromones were used for the analysis. Raw values were divided by eag response to average of hexane controls to produce standardized responses. Hexane responses were taken before and after pheromone exposures
DOI: 10.5061/dryad.4tg8530/4
title: EAG May 2018

description: R code in Rmarkdown format used to anlayze EAG data.
DOI: 10.5061/dryad.7f165f6/1
title: Data_OIK05329

description: Bio = Invertebrate species data for each site in each year, Env = site coordinate + hydrological variables (see MS for full name of each variable)
DOI: 10.5061/dryad.9s1t9.2
title: Data from: North-south differentiation and a region of high diversity in European wolves (Canis lupus)
DOI: 10.5061/dryad.9s1t9.2/1.2
title: WolvesAll_22feb2012.ped

description: Single nucleotide polymorphism (SNP) raw data files for 177 individuals for use with the software PLINK: PED file.
DOI: 10.5061/dryad.9s1t9.2/2.2
title: WolvesAll_22feb2012.map

description: Single nucleotide polymorphism (SNP) raw data files for 177 individuals for use with the software PLINK: MAP file.
DOI: 10.5061/dryad.9s1t9.2/3.2
title: Italy.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.9s1t9.2/4.2
title: Dinaric-Balkan.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.bh8n5j8/1
title: field.data

description: Study species and locations (Table 1-2); interactions frequency by site (Table 3); interactions tested for their effect on recruitment (Table 4); and interaction consistency across plots (Table 5).
DOI: 10.5061/dryad.bh8n5j8/2
title: phylo.data

description: Phylip file with the sequences used to construct the phylogeny in Appendix S1.
DOI: 10.5061/dryad.cj4c2s1/1
title: Supplemental data Pedigrees_20170209_Revision Neurology

description: This file contains the pedigrees of the families described in: A family-based study into penetrance in facioscapulohumeral muscular dystrophy type 1.                                                   The file numbers refer to the family numbers in the text and supplemental data 2. All participants have a patient number that is designated in the file. Patients without number were below 18 years.
DOI: 10.5061/dryad.fg52075/1
title: Gray seal RAD loci

description: Catalog of 244,822 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 56 gray seals sampled in the Northwest Atlantic.  The gray seals selected to build the RAD catalog included 7 individuals from each of the following sampling locations and cohorts - Gulf of St Lawrence, Canada: 2015; Sable Island, NS, Canada: 1973-74, 1985, 1998, 2004, and 2015; Muskeget Island, MA, USA: 2002 and 2015-16. The details of the ddRAD protocol and bioinformatic processing are described in detail in the Methods section and Appendix S1 of Cammen et al. (2018).  In brief, ddRAD was conducted with restriction enzymes SBfI-HF and MspI, size selection by 1.5x beads, and 50-bp single-end read Illumina Hiseq 2500 sequencing.  Sequences were processed using Stacks v1.21 to build loci de novo using the following parameters, selected using the r80 optimization approach: m = 2, M = 2, and n = 2. File is in FASTA format and each sequence is identified by a numerical locus ID.
DOI: 10.5061/dryad.fg52075/2
title: Harbor seal RAD loci

description: Catalog of 195,906 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 55 bycaught harbor seals sampled in the Northeast United States between 1992 and 2015.  The details of the ddRAD protocol and bioinformatic processing are described in detail in the Methods section and Appendix S1 of Cammen et al. (2018).  In brief, ddRAD was conducted with restriction enzymes SBfI-HF and MspI, size selection by 1.5x beads, and 50-bp single-end read Illumina Hiseq 2500 sequencing.  Sequences were processed using Stacks v1.21 to build loci de novo using the following parameters, selected using the r80 optimization approach: m = 2, M = 2, and n = 2. File is in FASTA format and each sequence is identified by a numerical locus ID.
DOI: 10.5061/dryad.fg52075/3
title: Gray seal SNPs

description: Catalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 252 gray seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus.
DOI: 10.5061/dryad.g8t9240/4
title: PopulationStructure

description: apal.5x.nc2.mac4.vcf contains vcf file of genotypes for all E. pallida individuals after clone removal, but before filtering for loci with a minimum allele frequency of 5%.

pcadapt_analysis_final.R contains code to perform PCA analysis with pcadapt. This analysis is based on a SNP matrix (SNPmat0.05.txt) of 2577 SNPs that have a minimum allele frequency of 5%. The names of the loci are in locusNames_0.05.txt and information about the population designation for each sample is in pop_file.csv.

Gene set enrichment analyses in ErmineJ used the Gene Annotation file bvpSNPS_erminej.txt and were based on the PC1 loadings in column 3 of PCloadings_final.txt. The file bvpSNPS_erminej.txt contains the AIPGENE models for all SNPs in apal.5x.nc2.mac4.vcf that were present in genic regions (5'UTR, CDS, intron or 3'UTR) as well as GO annotations from the Aiptasia genome v1.0.

out.weir.fst is a file containing Weir and Cockerham FST values output from vcftools for E. pallida from the global lineage vs. the Bocas specific lineage. This was based on the 2577 biallelic SNPs with minimum allele frequency of 5%.
DOI: 10.5061/dryad.hp370m2/1
title: Readme text file

description: Readme text file providing an overview of the data, and descriptions of what the columns in *.csv files contain.
DOI: 10.5061/dryad.hp370m2/2
title: Data_Files

description: Zip file containing all 11 data files: 10 *.csv files and 1 *.R.txt file. Please refer to the Readme.txt file (not in the zip file) for explanation.
DOI: 10.5061/dryad.hq40q06/1
title: SNP genotypes and aridity index

description: (i) SNP data for  the 1249  accessions belonging to six taxa of beets, of which 950 individuals of Beta vulgaris subsp. maritima (wild taxon) and 299 individuals of the relative cultivated varieties B. vulgaris subsp. vulgaris including all the cultivated forms (collected in Europe) and  used in genomic environment association  (ii) Aridity index  for the 950  individuals of Beta vulgaris subsp. maritima (third row )
DOI: 10.5061/dryad.j8cm402/4
title: GPS and accelerometer data for individually tracked brent geese

description: GPS and accelerometer tracking data of individual dark-bellied Brent geese during spring migration in 2012 and 2013, for birds departing from a pasture site (Terschelling island) and a saltmarsh site (Schiermonnikoog island).
DOI: 10.5061/dryad.j8cm402/5
title: GPS, accelerometer and environmental data for individually tracked brent geese

description: GPS and accelerometer tracking data of individual dark-bellied Brent geese staging on a pasture site (Terschelling island) or a saltmarsh site (Schiermonnikoog), linked to metadata on bathymetry and tidal information.
DOI: 10.5061/dryad.j8cm402/6
title: weight of brent goose excreta

description: Dry weights of brent goose excreta on a saltmarsh
DOI: 10.5061/dryad.j8cm402/7
title: sampling and chemical analysis of saltmarsh vegetation on Schiermonnikoog island

description: Sampling and chemical analysis of saltmarsh vegetation on Schiermonnikoog island. For details on sampling scheme and methods see Fokkema, Wimke, Wendy Boer, Henk P. Jeugd, Adriaan Dokter, Bart A. Nolet, Luit J. Kok, J. Theo M. Elzenga, and Han Olff. "The nature of plant adaptations to salinity stress has trophic consequences." Oikos 125, no. 6 (2016): 804-811.
DOI: 10.5061/dryad.pf550.3/14.3
title: Stacks_commands_YST_3datasets

description: Commands used for denovo analyses of "FULL", "CORE", and "OUTGROUPS" datasets in STACKS 1.20.
DOI: 10.5061/dryad.pf550.3/15.3
title: YST_EUR-AM_943loc_ABC

description: SNP data file for DIYABC analysis of YST in both Eurasia and Americas
DOI: 10.5061/dryad.pf550.3/16.3
title: YST_EUR_1069loc_ABC

description: SNP data file for DIYABC analysis of YST in three regions of Eurasia (western Europe, eastern Europe, and Asia)
DOI: 10.5061/dryad.pf550.3/17.3
title: YST_EUR-AM_943loc_BayeScan

description: SNP data file for BayeScan analysis of data set used for DIYABC analysis of YST in both Eurasia and Americas
DOI: 10.5061/dryad.pf550.3/18.3
title: YST_EUR_1069loc_BayeScan

description: SNP data file for BayeScan analysis of data set for DIYABC analysis of YST in Eurasia
DOI: 10.5061/dryad.pf550.3/19.3
title: MEC_15-1264_Sample_Data

description: List of samples and sequencing run information
DOI: 10.5061/dryad.pf550.3/7.3
title: Sample_codes

description: Sampling sites for seeds of yellow starthistle (*Centaurea solstitialis*) and related taxa, including sampling site information (nearest city, country/state, continent, latitude, and longitude), and year of collection. Location numbers correspond to locations depicted in Fig S1. CESO = *C. solstitialis*, CENE = *C. nicaeensis*, CEPA = *C. pallescens*, CEME = *C. melitensis*.
DOI: 10.5061/dryad.qs734tp/4
title: RPI_031_GST_lambda_p22

description: Lambda N and P22 N shared with the same GST control
DOI: 10.5061/dryad.qs734tp/5
title: RPI_034_p22

description: P22 N SEQRS data
DOI: 10.5061/dryad.qt352sg/1
title: DNA sequences amplified from blue whale scats

description: Fastq files of DNA sequences amplified from blue whale scats.
DOI: 10.5061/dryad.sg4n7kb/1
title: Raw Data

description: The Raw Data including 4 tables (Table 1-4) and 3 figures (Figs. 2, 5 and 6) in the paper.
DOI: 10.5061/dryad.tt10r84/1
title: Burin_et_al_suppmat
DOI: 10.5061/dryad.0mv6t/1
title: Chemical Cross-Links in FliM homodimerization

description: Chemical Cross-links reported in literature and used to support the predicted models for FliM middle domain homodimerization.
DOI: 10.5061/dryad.0mv6t/2
title: MSA of FliM middle domain family

description: multiple sequence alignment used to compute coevolution signals in the middle domain of FliM protein from T. maritma
DOI: 10.5061/dryad.0mv6t/3
title: MSA for FliM/N c-terminal family

description: Multiple Sequence Alignment used to compute coevolution signals in FliN C-terminal and FliM C-terminal domains. These couplings were mapped to predict FliN C-terminal homodimerization in validation process and to predict a model for FliN/FliM C-terminal heterodimerization.
DOI: 10.5061/dryad.0mv6t/4
title: Prediction of FliN C-terminal homodimer

description: Prediction of FliN C-terminal homodimer through simulations with structure-based models driven by coevolution signals. The final model presented a RMSD of 0.81Å when compared to experimental X-ray structure (1O6A). This prediction was used as a validation  step to support subsequent models.
DOI: 10.5061/dryad.0mv6t/5
title: prediction of FliNM heterodimerization

description: Prediction of FliN/FliM C-terminal heterodimer through simulations with structure-based models driven by coevolution signals.
DOI: 10.5061/dryad.0mv6t/6
title: predicted FliM homodimer model I

description: Predicted homodimerization interface of FliM middle domain in a parallel configuration that is compatible to the interaction mode of one rotational state suggested by cryo-EM data fitting and chemical cross-linking experiments.
DOI: 10.5061/dryad.0mv6t/7
title: predicted FliM homodimer model II

description: Predicted homodimerization interface of FliM middle domain in a twisted configuration that is supported by chemical cross-linking experiments and can be related to an alternative conformational state of flagellum rotation.
DOI: 10.5061/dryad.0mv6t/8
title: Recurring Chemical Cross-Links in FliN/FliM C-terminal homodimerization

description: Chemical Cross-Links in FliN/FliM C-terminal dimerization that are present in both rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.
DOI: 10.5061/dryad.15rs596/10
title: AT1G02290_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.15rs596/6
title: AT3G17611_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.15rs596/7
title: AT3G10570_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.15rs596/8
title: AT1G02630_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.15rs596/9
title: AT1G17770_ahal_alyr_NGS_Sanger
DOI: 10.5061/dryad.44dr859/1
title: Becker et al 2018_AmNat_R code

description: R code for deriving threshold conditions, for numerically solving the differential equations, and for recreating key figures.
DOI: 10.5061/dryad.466k2sq/1
title: Geiger

description: File includes all original data relevant to the publication.
DOI: 10.5061/dryad.46j2nj6/1
title: Demandt_et_al_data

description: Exel table with id of tested individuals and individualised behavioural data.
DOI: 10.5061/dryad.51bp263/1
title: Piebra_SP_k55b2000_MESPAnapi

description: Draft genome of Pieris brassicae, scaffolded using MESPA.
DOI: 10.5061/dryad.51bp263/3
title: command line script

description: Bioinformatics commands used to analyse the data.
DOI: 10.5061/dryad.51bp263/4
title: Pnapi_Fst

description: Each row represents FST per base pair for all informative sites.
DOI: 10.5061/dryad.51bp263/5
title: Pnapi_TajD_pi

description: Each row represents pi and Tajima's D per gene, for all immune genes in the assembly.
DOI: 10.5061/dryad.51bp263/6
title: MK_gene_alignments

description: MK gene alignments for significant genes. This is a zipped archive containing fasta files.
DOI: 10.5061/dryad.6381477/1
title: Capture history data

description: This data file contains the capture histories of 229 individuals over a 3 year period. Data was collected using photo-identification methods with survey design to fit the Robust design. Each row is an individual, while each column is a secondary period. There were six secondary periods collected per primary period.  Data were collected over 12 primary periods (australasian seasons) resulting in 72 total secondary periods.
DOI: 10.5061/dryad.6381477/2
title: Calving event data

description: This data contains the 100 known females and any sightings of their respective calves (if any). The dataset consisted of 12 primary periods (australasian seasons), with 4 primary periods collected for each of 3 years. Calf code is a unique identifier for each individual calf.
DOI: 10.5061/dryad.6fh45/3
title: Data
DOI: 10.5061/dryad.6j6v707/1
title: Data of RSOS-171436.R3
DOI: 10.5061/dryad.8n2b32q/1
title: Kess Galindo Boulding Lsaxatilis 2018 EE Analysis Data

description: Sample metadata with sampling site and transect for each sequenced individual, Stacks output and vcf files, Genepop and Structure input files for all, neutral, and outlier loci. AMOVA and FST results from Arlequin.
DOI: 10.5061/dryad.9s1t9.1
title: Data from: North-south differentiation and a region of high diversity in European wolves (Canis lupus)
DOI: 10.5061/dryad.9s1t9.1/1.1
title: WolvesAll_22feb2012.ped

description: Single nucleotide polymorphism (SNP) raw data files for 177 individuals for use with the software PLINK: PED file.
DOI: 10.5061/dryad.9s1t9.1/2.1
title: WolvesAll_22feb2012.map

description: Single nucleotide polymorphism (SNP) raw data files for 177 individuals for use with the software PLINK: MAP file.
DOI: 10.5061/dryad.9s1t9.1/5.1
title: Carpathians.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.9s1t9.2/5.2
title: Carpathians.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.9s1t9.2/6.2
title: Northcentral_Europe.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.9s1t9.2/7.2
title: Ukrainian_Steppe.txt

description: Single nucleotide polymorphism loci not in Hardy-Weinberg equilibrium for one of the five population clusters detected in the analyses (please see Figure 1, Table 3).
DOI: 10.5061/dryad.9s1t9.2/8.2
title: WolvesAll_Sample information.xlsx

description: Excel file listing individual identification, call rate (individual
genotyping success), country, latitude and longitude.
DOI: 10.5061/dryad.9s1t9/8
title: WolvesAll_Sample information.xlsx

description: Excel file listing individual identification, call rate (individual
genotyping success), country, latitude and longitude.
DOI: 10.5061/dryad.bp26v20/1
title: PHYLACINE_1.2_Metadata

description: This text contains the metadata describing the purpose, construction, and data of PHYLACINE Version 1.2.0. Definitions for all the variables and values found in the constituent data of PHYLACINE are located here. Please read this metadata file carefully and in its entirety before attempting any analyses.
DOI: 10.5061/dryad.c67v440/1
title: Supplemental data

description: Supplemental tables 1-6
DOI: 10.5061/dryad.fg52075/4
title: Harbor seal SNPs

description: Catalog of single nucleotide polymorphisms (SNPs) identified in ddRAD loci among 55 harbor seals from the Northwest Atlantic. SNPs were identified and genotyped using a bounded maximum-likelihood model in Stacks v1.21 with no minimum minor allele frequency. LocusID refers to the locus ID in RAD loci catalog FASTA file; Column refers to the position of the variable nucleotide within the locus.
DOI: 10.5061/dryad.fg52075/5
title: Gray seal genotypes

description: A genepop file containing ddRAD genotypes for 252 gray seals from the Northwest Atlantic.  All including loci were genotyped in at least 80% of the individuals in each sample group. Gray seals samples represent three breeding colonies and up to five cohorts per colony. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus.
DOI: 10.5061/dryad.fg52075/6
title: Harbor seal genotypes

description: A genepop file containing ddRAD genotypes for 55 harbor seals from the Northeast US.  All including loci were genotyped in at least 80% of the individuals in each sample group. Harbor seals samples represent three cohorts sampled since 1992. Locus names are composed of the LocusID that corresponds to the RAD loci catalog FASTA file and the position of the variable nucleotide within the locus.
DOI: 10.5061/dryad.g14qq07/1
title: Lindgrenetal2018_data

description: Container-specific means of swimming speed variables, life-history traits and log-transformed morphology.
DOI: 10.5061/dryad.jf45095/1
title: Tadpole data

description: Number of emerged metamorphs, and remaining tadpoles of two anuran species, including wet and dry mass for both and treatment design.
DOI: 10.5061/dryad.jf45095/2
title: Primary producers

description: Density/Concentration of two primary producers : periphyton and phytoplankton
DOI: 10.5061/dryad.kc835.4
title: Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.
DOI: 10.5061/dryad.kc835.4/13.4
title: M6_v4.1_PM.fa

description: Pseudomolecules of S. chacoense M6, containing 12 chromosomes
DOI: 10.5061/dryad.kc835.4/14.4
title: Readme.txt
DOI: 10.5061/dryad.kc835.4/2.4
title: 523_3_assembly_ALLPATHS_v4.1.fasta

description: Genome assembly of S. chacoense M6, containing 8,260 scaffold sequences
DOI: 10.5061/dryad.m1h132h/1
title: Incidence matrix middle Smithian
DOI: 10.5061/dryad.m1h132h/2
title: Incidence matrix late Smithian
DOI: 10.5061/dryad.m1h132h/3
title: Table 1 SUPP. DATA
DOI: 10.5061/dryad.m1h132h/4
title: Table 2 SUPP. DATA
DOI: 10.5061/dryad.m1h132h/5
title: Table 3 SUPP. DATA
DOI: 10.5061/dryad.m1h132h/6
title: Table 4 SUPP. DATA
DOI: 10.5061/dryad.m1h132h/7
title: Table 5 SUPP. DATA
DOI: 10.5061/dryad.r8v2622/1
title: Mating success nuthatches - Dryad data

description: Dataset used in the study.
DOI: 10.5061/dryad.t6v47p1/1
title: IsonPrescottEtAl_Data&Scripts

description: This folder includes 4 data files, 3 metadata files, and 4 R scripts.
DOI: 10.5061/dryad.0mv6t/10
title: Chemical Cross-Links observed in the CCW state of FliN/FliM C-terminal dimer

description: Chemical Cross-Links in FliN/FliM C-terminal dimerization that are observed only in CCW rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.
DOI: 10.5061/dryad.0mv6t/11
title: DCA for FliM models

description: Coevolution couplings derived from Direct-Coupling Analysis used to predict FliM middle domain homodimers (parallel and twisted models).
DOI: 10.5061/dryad.0mv6t/12
title: DCA for FliM/FliN model

description: Coevolution couplings derived from Direct-Coupling Analysis used to predict the dimerization interface of FliM/FliN C-terminal domain.
DOI: 10.5061/dryad.0mv6t/13
title: DCA for FliN homodimer model

description: Coevolution couplings derived from Direct-Coupling Analysis used to predict the dimerization interface of FliN C-terminal domain (validation of methodology).
DOI: 10.5061/dryad.0mv6t/9
title: Chemical Cross-Links observed in the CW state of FliN/FliM C-terminal dimer

description: Chemical Cross-Links in FliN/FliM C-terminal dimerization that are observed only in CW rotational states of flagellar motor. This dataset from literature was used to support predicted model for FliN/FliM C-terminal heterodimer.
DOI: 10.5061/dryad.26q7j45/1
title: Aux. figure - EO measurement scales by EBV

description: Log-log plot of spatial and temporal and grain sizes for 44 current and historic satellite Earth observation (EO) sensors, colored by biodiversity pattern. Several sensors have been used to measure multiple biodiversity patterns, and the most cited or most novel were selected in these cases.
DOI: 10.5061/dryad.26q7j45/3
title: Aux. figure - Timeline of Earth observations for biodiversity monitoring by agency

description: Temporal extents of current and historic satellite sensors labeled by space agency.
DOI: 10.5061/dryad.26q7j45/5
title: Aux. table - Measurement scales of EO sensors for measuring biodiversity patterns

description: Satellite Earth observation (EO) sensors used to measure biodiversity patterns according to the Essential Biodiversity Variables framework (EBV; Pereira et al. 2013). These data were used to create the figures in the associated manuscript, and highlight which sensors have been used to measure specific patterns. These figures do not to provide a comprehensive review of all patterns measured by each sensor; in each case, the most cited or most novel studies were selected.