cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jc754/9
title: S_BEAST_SDH_cal

description: BEAST phylogeny for SDH - calibrated analysis - XML input file
DOI: 10.5061/dryad.nh6v4/1
title: WGS Variants from 556 NZ Dairy Animals Chr23:30627379-40627379
DOI: 10.5061/dryad.nh6v4/2
title: Exome Variants in Multiple Breeds Chr20:34783594-42331973
DOI: 10.5061/dryad.nh6v4/3
title: Hairy syndrome genotypes and phenotypes

description: Genotypes and phenotype used for genome-wide analysis of the hairy syndrome, Plink binary format (.bim .bed .fam)
DOI: 10.5061/dryad.nh6v4/4
title: Hairy bull progeny TaqMan results
DOI: 10.5061/dryad.nh6v4/5
title: physiological phenotypes
DOI: 10.5061/dryad.nh6v4/6
title: DFAM association results for 628,279 SNP
DOI: 10.5061/dryad.ns34t/3
title: Extended microsatellite data 4 loci from 7 populations

description: Extended microsatellite data 4 loci from 7 populations
DOI: 10.5061/dryad.ns34t/4
title: ITS2 fasta aligment
DOI: 10.5061/dryad.ns34t/5
title: B7SYM15 fasta aligment

description: Sequences for the flanking region of microsatellite B7SYM15
DOI: 10.5061/dryad.ns34t/6
title: cp23s fasta aligment
DOI: 10.5061/dryad.ns34t/7
title: psbA fasta aligment

description: Coding region of the chloroplast psbA
DOI: 10.5061/dryad.ps12h/1
title: Geographical coordinates of presence and absence points for Sicarius cariri

description: Geographical coordinates of presence and absence points used for modelling the distribution of Sicarius cariri (Araneae: Sicariidae). Presence points taken from Magalhães et al. (2011, Zootaxa 3599, 101-135). Absence points are 1) points where other species of Sicarius occur, but not S. cariri 2) localities visited during our fieldwork or localities where extensive inventories have been carried out and S. cariri has not been detected.
DOI: 10.5061/dryad.ps12h/2
title: BAYESSC-COI-1-SP

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 1, stable population
DOI: 10.5061/dryad.ps12h/3
title: BAYESSC-COI-2-GB

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 2, glacial bottleneck
DOI: 10.5061/dryad.ps12h/4
title: BAYESSC-COI-3-MR

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 3, glacial multiple refugia
DOI: 10.5061/dryad.ps12h/5
title: BAYESSC-COI-4-GE

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 4, glacial expansion
DOI: 10.5061/dryad.ps12h/6
title: BAYESSC-COI-5-WPB

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: COI. Scenario: 5, wet phase bottlenecks
DOI: 10.5061/dryad.ps12h/7
title: BAYESSC-H3-1-SP

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 1, stable population
DOI: 10.5061/dryad.ps12h/8
title: BAYESSC-H3-2-GB

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 2, glacial bottlenecks
DOI: 10.5061/dryad.qn57t/1
title: Murray_et_al_2013_alignment_and_best_tree.nex

description: Nexus format sequence alignment of 237 taxa and 5 gene regions followed by the maximum clade credibility dated phylogeny.
DOI: 10.5061/dryad.qn57t/3
title: Murray_et_al_2013_Supplementary.pdf

description: This is the supplementary information published along with the manuscript. Contains table of taxon localities of all OTUs used in matrix, dated phylogeny, ant host records, and other data.
DOI: 10.5061/dryad.sd784/1
title: Ancient Pig and modern samples primary data
DOI: 10.5061/dryad.sh53j/1
title: 1_phonotaxis_no_choice

description: Data from the no-choice phonotaxis experiment as described in the prezygotic long-range mating behaviour section of the Results and presented in Figure 2.
DOI: 10.5061/dryad.sh53j/2
title: 2_phonotaxis_two_choice

description: Data from the two-choice phonotaxis experiment as described in the Prezygotic long-range mating behaviour section of the Results and presented in Figure 2.
DOI: 10.5061/dryad.0nj49/1
title: Bee Species Trait Data

description: Ecological traits used in the analysis for all bee species
DOI: 10.5061/dryad.0nj49/2
title: Historical Bee Specimen Data

description: This file contains all bee specimen records included in the final analysis.
DOI: 10.5061/dryad.105c0/10
title: Duptree GlobFin1con50

description: 50% majority rule consensus tree from Gene tree parsimony analysis of post-burnin Bayesian trees from the analysis of the global data set.
DOI: 10.5061/dryad.1ph37/3
title: Raw for Figure 3

description: Data Excel file containing spatial proximity data between pair of groups when groups were within 250 m of each other.  These data were used to determine the distribution of encounters across hours of the day.
DOI: 10.5061/dryad.1ph37/4
title: Raw for Table 2

description: Data Excel file containing home range overlap data for each pair of groups at 3 time scales (monthly, biweekly, and weekly).
DOI: 10.5061/dryad.5sr48/5
title: Metadata for the presence of iridescence/eumelanic plumage patches

description: Metadata for African starling species analyzed regarding the presence of iridescent or eumelanic colors across the 10 body patches of males and females. Non-iridescent, non-eumelanic colors were not included in the analyses.
DOI: 10.5061/dryad.8fc60/2
title: parus_maj_MS_code

description: R code to run the analyses presented in the paper (including those in the supplementary online material). Also code to produce the graphs in the paper. Additional functions used in the code are provided in the file 'my.functions.R'.
DOI: 10.5061/dryad.9n815/1
title: The core pollen and age data file
DOI: 10.5061/dryad.d5f1r/1
title: Blois_etal_2013_PNAS_Data

description: Please refer to the 'README' file
DOI: 10.5061/dryad.dg380p9q/1
title: Copeland_etal_Ecosphere

description: Plant, soils, foliar chemistry, and soil moisture data for field experiment in the Brazilian Cerrado associated with manuscript (Copeland et al.) in Ecosphere
DOI: 10.5061/dryad.f5q32/12
title: Phased haplotypes MUSK-I3z

description: Phased MUSK-I3 haplotypes of 31 Eastern Yellow Robins in NEXUS format; second allele is removed for females, who are hemizygotic for this Z-linked locus
DOI: 10.5061/dryad.f5q32/6
title: Input file for TESS analysis of 11 autosomal loci

description: This file is an input file for TESS analysis of 11 autosomal loci, AB4, GAPDH, GTP, RI2, TGFb, Cpi3, Cpi8, Escmu6, HrU2, Pocc6, Smm7 (Suplementary Material S5).Genotypes for sequenced loci were assigned as haplotype number +100 for the two phased haplotypes of each individual. EYR056 was excluded from analysis restricted to 5 sequenced loci (AB4, GAPDH, GTP, RI2, TGFb).
DOI: 10.5061/dryad.f5q32/7
title: Input file for IMa2 analysis of nuclear loci
DOI: 10.5061/dryad.f5q32/8
title: Haplotype alignment of mitochondrial ND2

description: Aligned mitochondrial sequences of 100 Eastern Yellow Robins in NEXUS format
DOI: 10.5061/dryad.f5q32/9
title: Phased haplotypes AB4

description: Phased AB4 haplotypes of 44 Eastern Yellow Robins in NEXUS format
DOI: 10.5061/dryad.fj8dm/2
title: Dataset S2

description: Association tests between age and medication/neuropathology variables.
DOI: 10.5061/dryad.fj8dm/3
title: Dataset S3

description: GOTerm and Kegg Pathway analyses for probes differentially expressed by age.
DOI: 10.5061/dryad.fj8dm/4
title: Dataset S4

description: Worksheet A. GOTerm and Gene List enrichment analyses by expression level, association with age and profile types. Worksheet B. GOTerm and Gene Lists information.
DOI: 10.5061/dryad.fj8dm/5
title: Dataset S5

description: Intersection of 36 genes differentially expressed in the cerebral cortex with 	Mammalian Genome Informatics Mammalian Phenotype data.
DOI: 10.5061/dryad.gp495/2
title: spat2013_gbs_snps

description: GBS genotype matrix. Output from the institute for genomic diversity pipeline in tassel. Alignment to A. lyrata was conducted as follows: bwa aln -t 8 /local/genomes/public/arabidopsis/lyrata/Alyrata_107.fa.gz mergedtagcounts/arabidopsis_CSU_boechera.fastq.fq &gt; arabidopsis_CSU_boechera.saibwa samse /local/genomes/public/arabidopsis/lyrata/Alyrata_107.fa.gz arabidopsis_CSU_boechera.sai mergedtagcounts/arabidopsis_CSU_boechera.fastq.fq &gt; 1sam
DOI: 10.5061/dryad.gp495/3
title: spat2013_8phenos_repro

description: Phenotypes of all genotypes (and replicates) including mating system.
DOI: 10.5061/dryad.gp495/4
title: spat2013_selectionfield_long

description: Genotype means of FT, GRLA and Fitness for all plants grown in the two field sites
DOI: 10.5061/dryad.gp495/5
title: spat2013_allsamples.tre

description: The full sample tree file from the R package "ape"
DOI: 10.5061/dryad.gp495/6
title: spat2014_manteltests_fordryad

description: Custom script to conduct mantel correlations on spatial subset of populations
DOI: 10.5061/dryad.h9j67/2
title: Ksepka et al. Character List

description: List of morphological characters used in phylogenetic analysis, with list of specimens examined for codings.
DOI: 10.5061/dryad.jc754/16
title: S_MrB_8cp_gene

description: MrBayes phylogeny for 8 chloroplast regions - FigTree tree file
DOI: 10.5061/dryad.jc754/17
title: S_MrB_GPI

description: MrBayes phylogeny for GPI - NEXUS input file
DOI: 10.5061/dryad.jc754/18
title: S_MrB_GPI

description: MrBayes phylogeny for GPI - FigTree tree file
DOI: 10.5061/dryad.jc754/19
title: S_MrB_NRPD2a

description: MrBayes phylogeny for NRPD2a - NEXUS input file
DOI: 10.5061/dryad.jc754/20
title: S_MrB_NRPD2a

description: MrBayes phylogeny for NRPD2a - FigTree tree file
DOI: 10.5061/dryad.jc754/21
title: S_MrB_SDH

description: MrBayes phylogeny for SDH - NEXUS input file
DOI: 10.5061/dryad.jc754/22
title: S_MrB_SDH

description: MrBayes phylogeny for SDH - FigTree tree file
DOI: 10.5061/dryad.jc754/23
title: S_MrB_trnLF

description: MrBayes phylogeny for trnL-trnF - NEXUS input file
DOI: 10.5061/dryad.jc754/24
title: S_MrB_trnLF

description: MrBayes phylogeny for trnL-trnF - FigTree tree file
DOI: 10.5061/dryad.n4mm0/1
title: Ecogeography populations_Briscoe Runquist et al

description: This file contains all known populations of both subspecies of Clarkia xantina. The file also contains numbers assigned to the populations used in manuscripts, a short description of the site and UTM coordinates (Zone 11S).
DOI: 10.5061/dryad.n4mm0/2
title: F1 pollen viab and pollen prod_Briscoe Runquist et al

description: This file contains pollen counts and pollen viability determinations for both parental subspecies and F1 reciprocal hybrids from greenhouse grown plants. Pollen was counted for 2 aliquots and summed.
DOI: 10.5061/dryad.n4mm0/3
title: F1 seed viab_Briscoe Runquist et al

description: This file contains the number of viable seeds (germinated + tetrazolium) for parental and F1 reciprocal crosses. FOr each fruit we assessed 20 seeds.
DOI: 10.5061/dryad.n4mm0/4
title: F1-growth_Briscoe Runquist et al

description: In this file, we have the growth of parentals and F1 reciprocal crosses from a greenhouse common garden. We counted the number of fully formed leaves on plants at the beginning of the initial growth phase and then 2 weeks later. Growth was determined by the number of leaves added. Plants were in different blocks which were measured on different days (noted).
DOI: 10.5061/dryad.n4mm0/5
title: Gametophyte_comp_Briscoe Runquist et al

description: We performed crosses using intra- and intersubspecific pollen (alternating the first pollen donor subspecies identity) in the greenhouse. We then counted the number of offspring that were hybrid from the total.
DOI: 10.5061/dryad.n4mm0/6
title: Phenology Data and RI calcs_Briscoe Runquist et al

description: This file contains the phenological and reproductive isolation calculations (using Sobel and Chen 2014) for each site at 4 different sites. We walked semi-permanent transects at each site for the flowering season and counted the number of flowers of each subspecies on the date noted.
DOI: 10.5061/dryad.n4mm0/7
title: Pollen tube growth_Briscoe Runquist et al

description: We performed intra- and intersubspecific crosses in a greenhouse for 2 sympatric populations of Clarkia xantiana. We applied single-donor pollen and noted the time that we pollinated and the time at which we fixed the style (4-6 hours). We then measured the length of the longest pollen tube and the length of the style and used the data to obtain growth rates and proportional distance.
DOI: 10.5061/dryad.nd2mb/1
title: Supplementary Table 1

description: Summary of collected samples. N is the number of specimens collected, S the number of species found, a and b the number of singletons and doubletons (respectively) amongst those species, ACE is Chao and Lee (1992)'s Abundance-based Coverage Estimator and u is Good (1953)'s coverage estimator. Depth are given in mbsf (meters below sea-floor) and age estimates are taken from the Neptune Database embedded age model (Lazarus et al. 1995), which is scaled on Berggren et al. 1995.
DOI: 10.5061/dryad.nd2mb/2
title: Supplementary Table 2

description: Antarctic Neogene radiolarian data retrieved from the Neptune dataset on the 11th of January, 2011.
DOI: 10.5061/dryad.nd2mb/3
title: Supplementary Figure 3

description: Whole-fauna dataset diversity vs untrimmed Neptune dataset subsampled diversity.  A and B: Respectively, in-sample species richness and range-through diversity in our whole-fauna dataset. C: Diversity computed from the untrimmed Neptune dataset with five different type of subsampling: UW (black line), OW (dashed black line), CR (light grey line), O2W (dashed light grey line) and SQS (bold dark grey line). Magnetostratigraphy from Berggren et al. (1995).
DOI: 10.5061/dryad.nh6v4/7
title: Phased genotypes and phenotypes for 82 Senepol crossbreeds
DOI: 10.5061/dryad.ps12h/10
title: BAYESSC-H3-4-GE

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 4, glacial expansions
DOI: 10.5061/dryad.ps12h/11
title: BAYESSC-H3-5-WPB

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 5, wet phases bottleneck
DOI: 10.5061/dryad.ps12h/12
title: Beast XML input file for COI gene tree

description: Beast XML input file for estimating the COI gene tree for Sicarius from the Brazilian Caatinga; divergence times are estimated simultaneously with the topology based on a mutation rate estimated for dysderid spiders
DOI: 10.5061/dryad.ps12h/13
title: Beast XML input file for H3 gene tree

description: Beast XML input file for estimating the H3 gene tree for Sicarius from the Brazilian Caatinga; divergence times are estimated simultaneously with the topology based on a mutation rate estimated for dysderid spiders
DOI: 10.5061/dryad.ps12h/14
title: *Beast XML input file for species delimitation analysis (hypothesis 1)

description: *Beast XML input file for species delimitation analysis (hypothesis 1). This file includes data from both markers (COI and H3) and individuals sorted into four species (Sicarius cariri, Sicarius tropicus, Sicarius ornatus, Sicarius diadorim)
DOI: 10.5061/dryad.ps12h/15
title: *Beast XML input file for species delimitation analysis (hypothesis 2)

description: *Beast XML input file for species delimitation analysis (hypothesis 1). This file includes data from both markers (COI and H3) and individuals sorted into five species (Sicarius cariri clade 1, Sicarius cariri clade 2, Sicarius tropicus, Sicarius ornatus, Sicarius diadorim)
DOI: 10.5061/dryad.ps12h/16
title: Beast XML input file for EBSP analysis of Sicarius cariri clade 1

description: Beast XML input file for the Extended Bayesian Skyline Plot (EBSP) analysis for reconstructing the demographic history of Sicarius cariri clade 1, including data from both markers (COI and H3)
DOI: 10.5061/dryad.ps12h/17
title: Beast XML input file for EBSP analysis of Sicarius cariri clade 2

description: Beast XML input file for the Extended Bayesian Skyline Plot (EBSP) analysis for reconstructing the demographic history of Sicarius cariri clade 2, including data from both markers (COI and H3)
DOI: 10.5061/dryad.ps12h/18
title: Beast XML input file for COI gene trees - preliminary runs

description: .rar file including 12 Beast XML input files with distinct population/clock models used for defining the best-fit priors for estimating the COI gene tree for Sicarius from the Brazilian Caatinga
DOI: 10.5061/dryad.ps12h/9
title: BAYESSC-H3-3-MR

description: .par input file for BAYESSC used for simulating the demographic history of Sicarius cariri (Araneae: Sicariidae). Gene: H3. Scenario: 3, glacial multiple refugia
DOI: 10.5061/dryad.r01j0/1
title: CThrelfall_DATA_Nest_Predation_2010

description: Raw data collected in the field from a nest predation experiment. The metadata tab describes more detail about when and how the data was collected.
DOI: 10.5061/dryad.sj5b6/1
title: pool data

description: Mesocosm data: data includes several life history and behavioral responses to biological stressors (competition and predation) across populations that have different land use patterns around the pond of origin.
DOI: 10.5061/dryad.tq43g/1
title: Datasets, Marie-Orleach.et.al., BMC.Evol.Biol

description: Datasets
DOI: 10.5061/dryad.v1t86/1
title: Genotype file

description: The file contains details on the age, sex, season of capture and the microsatellite genotypes used for the paternity analysis.
DOI: 10.5061/dryad.v6qj0/1
title: Full list of differentially expressed genes Kumaran.xls

description: The data file contains complete list of transcripts that are differentially expressed in Queensland fruit fly, Bactrocera tryoni male flies fed on a phytochemical, zingerone.
DOI: 10.5061/dryad.v6qj0/2
title: RT-PCR fold change expression

description: Fold change expression of candidate genes in zingerone-fed males when compared to unfed males of Bactrocera tryoni
DOI: 10.5061/dryad.v6qj0/3
title: Enriched GO terms

description: Enriched GO terms and their classes in Bactrocera tryoni transcriptome
DOI: 10.5061/dryad.v6qj0/4
title: Enriched metabolic pathways

description: KEGG Metabolic pathways in Bactrocera tryoni transcriptome
DOI: 10.5061/dryad.2qc64/1
title: All data for 14 electrodes and 30 subjects

description: one can epoch each txt file using toolbox suchas EEGLAB
DOI: 10.5061/dryad.470ft/1
title: Matsubara et al._the primary data
DOI: 10.5061/dryad.5nt3r/1
title: rawdata

description: raw data for all independent variables used (latitude, altitude, bio1, bio10, bio12)
DOI: 10.5061/dryad.5sr48/2
title: Color data for female African starling species

description: Species average color variables of measurements from female African starlings. Variables represent the first two Principal Components calculated from the relative quantum catches of the four cones involved in color vision (PC1 and PC2), and brightness (log-transformed average reflectance) for 10 body patches.
DOI: 10.5061/dryad.5sr48/3
title: Maximum Clade Credibility phyologenetic tree of African starlings

description: Maximum Clade Credibility tree for the 48 African starling species calculated from the full posterior probability distribution of the BEAST analysis, with melanosome morphology regimes for color evolution mapped on branches.
DOI: 10.5061/dryad.5sr48/4
title: sample of 500 phylogenetic trees of African starlings

description: sample of 500 trees from the posterior distribution of phylogenetic trees of the 48 African starling species from the BEAST analysis, with melanosome morphology regimes for color evolution mapped on branches.
DOI: 10.5061/dryad.6bt6k/2
title: Ord_TJ-ANBEH-D-12-00933R1_contextual-plasticity
DOI: 10.5061/dryad.6hc0f/1
title: Table S1. SSR sequences and primers (doc file)

description: Table of microsatellite repeats identified using MsatCommander and sorted by motif.  Only repeats with suitable flanking sequence for primer design were kept.  Primer sequences designed using Primer3 are also listed.
DOI: 10.5061/dryad.6hc0f/2
title: Table S2. Chromosomal order and assignment (csv file)

description: Comma-delimited spreadsheet listing contig names that were assigned to Peromyscus chromosomes.  Contigs are sorted by start of alignment in the chromosome and are displayed in typical BLAST –m6 (tabular) format.
DOI: 10.5061/dryad.6hc0f/3
title: Contig sequences for P. leucopus transcriptome (fasta file)

description: Transcriptome contigs assembled from raw SOLiD 5500 xl sequencing reads using Trinity.  Only contigs with high-quality open reading frames identified from Transdecoder and unique contigs with best match hits to Mus musculus Uniprot protein database using BLASTN were kept.
DOI: 10.5061/dryad.6hc0f/4
title: Information on SNPs identified from transcriptome data (vcf file)

description: SNPs identified from transcriptome alignment files in variant call format.  SNPs were identified using GATK. Parameters and filters for calling SNPs are listed in header.  Additional hard filters include removal of SNPs where every individual was heterozygous, overall SNP depth &gt; 10, overall SNP depth &lt; 350, and minor allele frequency (MAF) &gt; 0.025.
DOI: 10.5061/dryad.6hc0f/5
title: Annotation information, BLAST results, Gene Ontology (.dat file for Blast2GO)

description: Standard input file for BLAST2GO. This file can be loaded directly into .jnlp executable file downloaded from BLAST2GO website.  Includes BLASTX results against NCBI’s non-redundant protein database and Gene Ontology information based on best hit gene matches.
DOI: 10.5061/dryad.6hc0f/6
title: R scripts, bash scripts, and full analysis workflow (txt file)

description: This text file represents the working lab notebook of all software, scripts, and command line usage dating from when the raw data were received to when the final figures and tables were produced.
DOI: 10.5061/dryad.7cn23/1
title: Dryad DATA_Plath et al._2013_EVOLUTION

description: The file comprises data on our translocation experiments, the mate choice experiments as well as microsatellites.
DOI: 10.5061/dryad.7sq32/1
title: AFLP, Microsatellite, Morphology and Fitness data

description: The data file contains the raw data for 30 adults from a Geum urbanum x G. rivale hybrid swarm plus their open pollinated offspring (collected outside Edinburgh, Scotland). AFLP tab: scoring sheet for 202 AFLP markers of 30 adults and 5 of their open pollinated offspring each, 12 reference samples each from pure Geum urbanum and G. rivale populations and 15 controlled F1 crosses. The Microsatellite tab contains the scoring for 3 SSR loci of the same 30 adults plus 10 of their open pollinated offspring. The Morphology tab contains 9 morphological measurements taken in a common garden environment for the same samples used in the AFLP file apart from reference and controlled F1 samples. The Fitness tab contains the number of seed heads and leaf volume produced in a common garden environment for the same offspring samples used in the AFLP file.
DOI: 10.5061/dryad.80m5b/1
title: Analysis scripts from simulation study

description: The contents of this zipped file include i) the cross-validation scripts for assessing the model selection performance (modCV scripts), and ii) the PODS analysis scripts for assessing parameter estimation (POD scripts).
DOI: 10.5061/dryad.80m5b/2
title: Simulation scripts for reference table generation

description: This zipped archive file contains the 14 R scripts used to simulate data for the simulation study portion of our manuscript.  Each script corresponds to one sampling scheme, but all share the same structure and code.  The first few lines of the script (ll. 15-17) set the length of loci in the dataset ('size' scripts vary this by scaling theta), the number of individuals sampled ('ind' scripts vary this), and the number of loci sampled ('block' scripts vary this).