cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8c930/8
title: SNPs called from 54 individually sequenced pigs at 102.3-102.675 Mb on chromosome 13

description: This table includes the SNP data at 102.3-102.675 Mb on chromosome 13, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
DOI: 10.5061/dryad.8c930/9
title: SNPs called from 54 individually sequenced pigs at 71.775-72.15 Mb on chromosome 14

description: This table includes the SNP data at 71.775-72.15 Mb on chromosome 14, and the variants are called from 54 individually sequenced pigs from 11 populations. “00” indicates the missing genotype. column 1 & 2: chromosome and position according to Sscrofa 10.2 assembly. column 3: the reference allele according to Sscrofa 10.2 assembly. column 4: the variant allele identified from sequencing data. column 5- 8: genotypes of four Duroc pigs. column 9-12: genotypes of four Meishan pigs. column 13-19 genotypes of seven Chinese wild boars. column 20-22 genotypes of three Jinhua pigs. column 23-28 genotypes of six Landrace pigs. column 29-42 genotypes of 14 Large White pigs. column 43-45 genotypes of three Neijiang pigs. column 46-48 genotypes of three Penzhou pigs. column 49-52 genotypes of four Tongcheng pigs. column 53-55 genotypes of three Wujin pigs. column 56-58 genotypes of three Yanan pigs
DOI: 10.5061/dryad.8sm01/5
title: GWAS Results, Abundance (Sqrt(x)) of Individual OTUs

description: The square-root transformed abundances of individual OTUs were used as phenotypes in GWAS. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
DOI: 10.5061/dryad.8sm01/6
title: GWAS Results, Individual OTUs (results from P/A and Sqrt(x) combined)

description: The presence vs. absence (0/1) of individual OTUs were used as phenotypes in GWAS. In separate analyses, the abundance (sqrt(x)) of individual OTUs were also used as phenotypes. These results (p-values) were combined using Brown's (1975) approach. The Methods section of the paper describes the procedure. Please note that files labeled '16S' correspond to the bacterial community, while files labeled 'ITS' correspond to the fungal community.
DOI: 10.5061/dryad.c59q3/2
title: Rams_exp1_2

description: Data set for time series analysis of population size in experiment 1, during the first 22h. column 1: population type {clonal, diversified}; column 2: antibiotic dose; column 3: population replicate; column 4: time {hours}; column 5: log10(population size+1); column 6: future population rescue {alive, dead}
DOI: 10.5061/dryad.ct121/1
title: Dryad data
DOI: 10.5061/dryad.dm821/1
title: Data for 25933206JEB-2012-00738.R1
DOI: 10.5061/dryad.dq7ks/1
title: activity
DOI: 10.5061/dryad.j57c0/14
title: 6_README_Plot_Transitions

description: R file used to plot transition through time plots
DOI: 10.5061/dryad.j7230/2
title: Sex, captured plot# and mtDNA haplotypes of Individuals
DOI: 10.5061/dryad.jv3d2/1
title: Supplementary data

description: This file include four supplementary tables related to the paper. This data is extracted mainly from the Medicines and Healthcare products Regulatory Agency (MHRA).
DOI: 10.5061/dryad.k9g50/2
title: Geneland genotypes

description: This is the microsatellite genotypes file for Geneland analyses. There is one line per individual with 20 columns (diploid, codominant data). Missing data are represented by 000.
DOI: 10.5061/dryad.m466f/14
title: CBA28_genotypes

description: Microsatellite genotypes at locus CBA28.  This is a tab-delimited text files in the format produced by Applied Biosystems GeneMapper software version 3.7.  Each sample*locus genotype is represented in one row.  The "Sample Name" column gives names of samples that directly correspond to those used in "species_chloroplast_latlong.csv".  The "Well" column indicates the location of the sample on the DNA dilution plates.  The "Marker" column indicates the microsatellite marker.  The "Panel" column indicates groups of markers that were run simultaneously on the ABI3100 capillary sequencer.  The "Dye" column indicates the fluorescent tag used to detect the PCR fragments: Y for NED, G for HEX, and B for FAM.  The "Allele" columns contain the names of all alleles detected for each genotype.  Cells are left blank if fewer alleles were detected than the number of columns.  A value of -9 for Allele 1 indicates missing data.  The "Height" columns indicate the height of the peak representing each allele, and the "Size" columns indicate the exact size of the DNA fragment as calculated by GeneMapper.  A value of "TRUE" in the "AE" column indicates that the genotype was manually edited in GeneMapper, although all genotypes were visually inspected.  The R package "polysat" can read these file directly, and will use the "Sample Name", "Marker", and "Allele" columns, and will ignore all other columns.
DOI: 10.5061/dryad.m466f/9
title: CBA15_distances

description: Pairwise genetic distances at locus CBA15 for the 579 samples analyzed.  These distances were calculated using the meandistance.matrix function in the R package "polysat" version 0.1, using the Bruvo.distance measure.  Each file contains a square matrix with row names and column names (sample names), as produced by the write.csv function in R version 2.11 under default parameters.
DOI: 10.5061/dryad.m8d1c/1
title: Jacob et al _ BMC _ Feather_bacterial_composition

description: ARISA data of feather bacterial communities
DOI: 10.5061/dryad.m8d1c/2
title: Jacob et al _ BMC _ Feather_bacterial_densities

description: Densities of cultivable bacteria on feathers
DOI: 10.5061/dryad.m8d1c/3
title: Jacob et al _ BMC _ Gland composition

description: Data of chemical compounds contained in the grand (see Table S1 for identification)
DOI: 10.5061/dryad.m8d1c/4
title: Jacob et al _ BMC _ Gland volume

description: Great tit uropygial gland and metadata
DOI: 10.5061/dryad.m8d1c/5
title: Jacob et al _ BMC _ Nest_bacterial_composition

description: ARISA data for nest bacterial communities
DOI: 10.5061/dryad.m8d1c/6
title: Jacob et al _ BMC _ Nest_bacterial_densities

description: Densities of cultivable bacteria in nests
DOI: 10.5061/dryad.mh8c1/1
title: s642c2

description: The supplied video file s661c1.avi shows the successful particle internalization event from Fig. 2 and Fig. 4 of the manuscript. The movie was recorded at 63x magnification on an Andor Neo sCMOS camera with an effective pixel size of 90 nm and at a frame rate of 7.5 Hz. The particle was actuated by a continuously rotating magnetic field at a frequency of 0.5 Hz. Camera acquisition was phase-locked to the actuation to record 15 frames per cycle. The movie file has been compressed using the Cinepak codec. Please contact the authors to obtain more information.
DOI: 10.5061/dryad.mk6g1/1
title: 1D-BoundaryLimitedRangeExpansion

description: Python script simulating the coalescence process during a boundary-limited range expansion in a linear stepping stone model.
DOI: 10.5061/dryad.nk470/2
title: HaponskiStepien_msatdata

description: Data for 7 nuclear microsatellite loci for each walleye spawning group across the range, including historic Lake Erie walleye and putative "blue pike" Sander vitreus glaucus
DOI: 10.5061/dryad.r0m2f/1
title: GBS SNP calls from Huang et al.

description: variant call file is generated originally by GATK, SNPs are filtered and phased according to the description in the paper. This is the final vcf file, and most downstream analysis are based on this file, otherwise stated in the paper.
DOI: 10.5061/dryad.s1v35/1
title: Torres-Dowdall etal. BJLS 2555.R1. Statistical niche model data

description: Data used in the construction and testing of the Statistical niche model of Poecilia reticulata and Poecilia picta. The column labeled ‘Data’ specifies if that location was used for training the model or testing it. The ‘Drainage/Area’ column indicates either the drainage or the geographic region where the river is located. The ‘Locality’ column gives more information on the location of sampling or the name of the river sampled. The ‘P.picta’ and ‘P.reticulata’ columns specify if that particular species was present or absent at that sampling locality. Then information about the sites is presented in the following order: latitude, longitude, elevation (measured in meters above sea level), salinity (measured in part per thousands), dissolved oxygen (measured in milligrams per liter), and pH.  Finally, the date of sampling is indicated.
DOI: 10.5061/dryad.t8q7t/1
title: Data for estimation of inbreeding depression

description: Data from 24 fields (12 putative clones per field).  Each clone was self- and cross-pollinated by hand.  These treatments were conducted at the inflorescence level.  At the time of pollination, the number of flowers per inflorescence was counted.  Later, we returned to these clones and counted the number of fruits (berries) per clone.  The data are proportion of flowers per inflorescence that set fruit (Note: if we mis-counted some flowers in the inflorescence, then proportion fruit set could be erroneously recorded as a value &gt; 1; this happened rarely).
DOI: 10.5061/dryad.v7g26/1
title: AEP files from Biosig software

description: AEP waveform data collected from 8 crabs in response to sound stimuli
DOI: 10.5061/dryad.v7g26/2
title: Predator acoustic cue experiment

description: Data on crab consumption of bivalve prey in response to predator and non-predator acoustic treatments.
DOI: 10.5061/dryad.v7g26/3
title: Predator acoustic cue experiment - day 1 only

description: Data from day 1 of an experiment on crab consumption of bivalve prey in response to predator and non-predator acoustic cues.
DOI: 10.5061/dryad.13h2q/1
title: PONE-D-14-21686R1-data

description: All clinicopathological features and immunostaining parameters of CXCL17 and immune cells data are in the SPSS file. The description of all the column headings has been written in the "label".
DOI: 10.5061/dryad.16737/10
title: Bayes_Acuclavella_Concat_All_RichartHedin_infile.nex.con

description: 28S consensus tree from Bayesian analysis.  7 Dyspnoi outgroup, 28 Acuclavella ingroup sequences.
DOI: 10.5061/dryad.16737/13
title: RAxML_Concat_All_Richart&Hedin

description: All 4 loci concatenated RAxML phylogeny in Newick tree format with bootstrap values.
DOI: 10.5061/dryad.16737/14
title: RAxML_EF1a_Richart&Hedin

description: EF1a RAxML gene tree in Newick tree format with bootstrap values.
DOI: 10.5061/dryad.1ct82/1
title: Sequence alignments

description: Sequence alignments of Platynereis genes encoding actin, colA, foxD, laminin, mhc, mox, paraxis, tropomyosin, and twist, with their orthologs from other phyla.
DOI: 10.5061/dryad.2hr40/1
title: database 2013

description: contains every data except the ones that could identify partcipants, such as gender and work location
DOI: 10.5061/dryad.2hv53/2
title: H3 alignment

description: H3 histone alignment
DOI: 10.5061/dryad.33m8k/1
title: disturbance_data

description: This file contains data of wind, bark beetle, and wildfire disturbance in Europe's ecoregions from 1971-2030.
DOI: 10.5061/dryad.33m8k/2
title: carbon_data

description: This file contains data on the carbon cycle implications of forest disturbance in Europe in the period 2021-2030.
DOI: 10.5061/dryad.3j300/1
title: Symphonia_globulifera_nSSR_data
DOI: 10.5061/dryad.41n16/2
title: Microsatellite_Data_File

description: Complete microsatellite genotypic data set.
DOI: 10.5061/dryad.41n16/3
title: StarBEAST_Data_Files

description: Zip file containing nexus files for *BEAST analysis, including one mitochondrial (ND4) and five nuclear loci (BACH1, enol, FSHR, MKL1, SLC8A1). Nuclear sequences were haplotyped using PHASE.
DOI: 10.5061/dryad.41n16/4
title: STRUCTURE_Input_Files

description: Input files for STRUCTURE analyses. The "Microsatellite" sheet corresponds to data used in Fig. 2H of the paper, and the "Nuclear Sequence Haplotypes" sheet corresponds to data used in supplementary data Fig. S4.
DOI: 10.5061/dryad.41n16/5
title: Migrate_Input_File

description: Input file for Migrate analyses. Data are microsatellite repeat numbers and populations are the adjacent Olary Ranges (OR) and Mt Lofty Ranges (LR) geographic regions.
DOI: 10.5061/dryad.41n16/6
title: MSVAR_Input_Files

description: Zip file containing input files for MSVAR analyses for two populations from the Southern Flinders Ranges (Aroona and Telowie Gorge), and one from each of the Olary Ranges (Bimbowrie), Mt Lofty Ranges (Morialta), and Kangaroo Island (Snake Lagoon) geographic regions.
DOI: 10.5061/dryad.41n16/7
title: Sequence_Data_Files

description: Zip file containing fasta files for six loci used in this study.
DOI: 10.5061/dryad.57f48/1
title: Locality Info and Genetic and Phenotypic Data for Western Scrub-Jay Museum Specimens

description: This Excel spreadsheet lists all 689 Western Scrub-Jay museum specimens used in the study. Museum abbreviations: Field Museum of Natural History (FMNH); Moore Laboratory of Zoology, Occidental College (MLZ); Museum of Vertebrate Zoology, Berkeley (MVZ). Haplotypes of the cytochrome B gene are coastal (C) or interior (I). Structure results refer to the raw results making up the different panels of Figure 3. The raw microsatellite data are listed in actual allele sizes after allele calling. For the phenotypic data: collar, vent, and eyestripe are qualitatively-scored categorical data ranging from 1 to 6. Collar is the amount of blue coming down from the shoulders under the necklace with 1 = heavy collar (coastal) and 6 = little collar (interior). Vent is the amount of blue tinging to the feathers under the tail coverts, with 1 = white feathers (coastal) and 6 = heavily blue-tinged feathers (interior). Eyestripe is the boldness of the white stripe above the eye, with 1 = bold stripe (coastal) and 6 = small stripe (interior). Other phenotypic data are in the form of continuous variables measured in millimeters. Blank cells mean there is no data taken for that individual at that variable.
DOI: 10.5061/dryad.5h52h/1
title: Segev_et_al_Dyscophus_phenology_data

description: Original field transect data indicating the number of adults, freshly laid eggs, and calls recorded from 2003-2010.
DOI: 10.5061/dryad.6nc19/1
title: LCT_Suppl_Table_B

description: SNP calls for all Oncorhynchus clarkii and O. mykiss individuals included in the study. SNPs were genotyped using Taqman assays on the Fluidigm EP1 Genotyping System. 'NC' indicates 'No Call': genotype confidence &lt; 80%. 'nr' indicates 'not run': individual not genotyped for this SNP.
DOI: 10.5061/dryad.7334t/1
title: BR_plant_trnL

description: Plant trnL sequences from the midden located at Brockman Ridge, Western Australia
DOI: 10.5061/dryad.7334t/2
title: CR_plant_trnL

description: Plant trnL sequences from the midden located at Cavenagh Range, Western Australia
DOI: 10.5061/dryad.7334t/5
title: BR_mammal_16S

description: Mammalian 16S sequences from the midden located at Brockman Ridge, Western Australia
DOI: 10.5061/dryad.7n139/1
title: Enright.etal_PrimaryDataset_PlantResponses

description: This file contains plot-by-species response as measured by abundance pre-post fire.
DOI: 10.5061/dryad.7n139/2
title: PFT_PlotScaleData_JEcol

description: Plot Locations and details of vegetation, soils, and fire histories.
DOI: 10.5061/dryad.953hv/1
title: Ion Torrent diet data

description: FASTQ sequence files and additional data described in the ReadMe file
DOI: 10.5061/dryad.953hv/2
title: 1 MER paper functions

description: Functions needed to run R code
DOI: 10.5061/dryad.953hv/3
title: 2 MER R code database

description: R code
DOI: 10.5061/dryad.b1dt2/1
title: QTL genotype and phenotype data for B x G backcross sons

description: Each row contains microsatellite genotype codes and phenotype data for male progeny produced in a backcross experiment involving the B and G populations
DOI: 10.5061/dryad.b1dt2/2
title: QTL genotype and phenotype data for S x G backcross sons

description: Each row contains microsatellite genotype codes and phenotype data for male progeny produced in a backcross experiment involving the S and G populations
DOI: 10.5061/dryad.bd1s3/1
title: Latitudinal variation in thermal reaction norms of post-winter pupal development in two butterflies differing in phenological specialization

description: Excel file
DOI: 10.5061/dryad.c00b6/1
title: JAPPL_2013_01046.R2

description: Sensitivity of damselfly larvae to pesticide chlorpyrifos under global warming.
DOI: 10.5061/dryad.c4d3j/1
title: Alignment in nexus format
DOI: 10.5061/dryad.cr8sn/1
title: MAXENT data

description: Data used for MAXENT analyses. The file contains the georeferenced records of Moussonia deppeana, 19 variables of climatic data for each record, and correlation matrix between climatic variables.
DOI: 10.5061/dryad.cr8sn/5
title: IMa2 input file

description: Input file used in the Isolation with Migration analysis implemented in IMa2.
DOI: 10.5061/dryad.cr8sn/6
title: ITS alignment

description: ITS sequences alignment of Moussonia deppeana.
DOI: 10.5061/dryad.cr8sn/7
title: RPL32 alignment

description: rpl32 sequence alignment of Moussonia deppeana
DOI: 10.5061/dryad.cv910/1
title: COI Aligned sequences used for the Abyssogena southwardae network

description: Aligned sequences of COI used to construct the Abyssogena southwardae haplotype network. This file contains samples retrieved from GenBank (indicated in the file by their accession number) and samples from the West African seeps (WACS)
DOI: 10.5061/dryad.cv910/2
title: COI Aligned sequences used for the ESU 1 network

description: Aligned sequences of COI used to construct the ESU 1 haplotype network. This file contains samples from the Logatchev vent (Amrk), the Gulf of Mexico (Amu) and the West African seeps (A).
DOI: 10.5061/dryad.dc14n/1
title: MICB~HLA-B

description: The data we have uploaded includes the MICB genotypes and the HLA-B genotypes of 400 unrelated healthy Han individuals from Zhejiang province, China.
DOI: 10.5061/dryad.gd93s/4
title: Silene nutans and otites psbA

description: Alignment of chloroplastic psbA sequences
DOI: 10.5061/dryad.h0jg4/1
title: Helianthus Genespace Est Assembly

description: All genotyping was performed using a custom Affymetrix GeneChip (Affymetrix, CA, USA) designed from Helianthus expressed-sequence tags (ESTs). A total of 283,605 Sanger ESTs from 7 sunflower species (GenBank numbers: AJ318230-AJ318330, AJ412174-AJ412667, AJ437699-AJ437975, AJ539583-AJ540226, AJ541055-AJ541795, AJ542101-AJ542392, AJ827751-AJ829440, BG734514-BG734530, BG874297-BG874313, BG891021-BG891022, BQ909263-BQ917261, BQ965129-BQ980049, BU015365-BU036497, BU671782-BU672110, CD845604-CD858495, CF076145-CF099271, CX943504-CX948070, DY903733-DY959228, EE605695-EE627562, EE628472-EE661299, EL412382-EL492411, EL511146-EL515442, EL772988) were assembled using TGICL [11]. These sequences included 94,017 ESTs from H. annuus; 35,704 from H. argophyllus; 21,589 from H. ciliaris; 33,959 from H. exilis; 30,504 from H. paradoxus; 27,479 from H. petiolaris; and 40,353 from H. tuberosus. The final assembly included 87,237 “unigenes” corresponding to 27,587 contigs and 59,650 singletons.
DOI: 10.5061/dryad.j7230/1
title: Latitude and Longitude of 8 trapping plots
DOI: 10.5061/dryad.k8760/1
title: lake_whitefish_brain_transcriptome_raw
DOI: 10.5061/dryad.k8760/2
title: lake_whitefish_brain_transcriptome_normalized
DOI: 10.5061/dryad.k9g50/10
title: PartitionFinder infile

description: Input file for PartitionFinder analysis.
DOI: 10.5061/dryad.k9g50/11
title: Infile for SGoF+ analysis

description: Input file for sequential goodness-of-fit test to correct for multiple comparisons implemented in SGoF+. The file consists of an integer indicating the total number of tests (102) and after it two columns with pairs of identifiers and p-values.
DOI: 10.5061/dryad.k9g50/13
title: All SDM points

description: This file contains latitude and longitude coordinates for the 91 unique localities used to construct species distribution models.
DOI: 10.5061/dryad.k9g50/3
title: Geneland individual labels

description: This is the file of individual labels for Geneland analyses in the same order as the genotypes and coordinates files.
DOI: 10.5061/dryad.k9g50/4
title: Structure infile

description: This is the input file for Structure analyses. The second column contains sample group information used as a prior. Missing data are represented by -9.
DOI: 10.5061/dryad.k9g50/5
title: Genepop infile

description: This is the input file for Genepop v4 analyses. Individual sample names have been replaced by x and y coordinates in meters. Microsatellite and mitochondrial data are included. Missing data are represented by 000.
DOI: 10.5061/dryad.k9g50/6
title: MrBayesDir infile

description: Nexus file for modified version of MrBayes 3.1.2 with Dirichlet priors on branch lengths. Partitioning scheme and substitution models determined using PartitionFinder.
DOI: 10.5061/dryad.k9g50/9
title: Alignment phylip format

description: MtDNA alignment in phylip format for PartitionFinder analysis.
DOI: 10.5061/dryad.mg6t7/1
title: NESTS_2009_2011
DOI: 10.5061/dryad.mg6t7/2
title: COMP_HIER_EXPT
DOI: 10.5061/dryad.mg6t7/3
title: BROOD_SIZE_EXPT
DOI: 10.5061/dryad.mg6t7/4
title: RECRUITS
DOI: 10.5061/dryad.np321/1
title: Archive

description: Gene expression data and analysis. Data was collected on the Nanostring nCounter.
DOI: 10.5061/dryad.np321/2
title: CODESET-INFORMATION

description: Code set definition for the Nanostring probe set used to quantify mRNA abundance.
DOI: 10.5061/dryad.np321/3
title: CODESET-INFORMATION

description: Code set information. Excel format.
DOI: 10.5061/dryad.np321/4
title: PERTURBATION-DATA

description: Data analysis for all our expression data collected with the Nanostring nCounter under all the conditions applied in our experiments.
DOI: 10.5061/dryad.np321/5
title: PERTURBATION-DATA

description: Data analysis excel format.
DOI: 10.5061/dryad.nt4h3/1
title: Vega-Trejo et al. 2014. Behav.Ecol. Dryad

description: The file shows the data from the manuscript "The effects of familiarity and mating experience on mate choice in mosquitofish, Gambusia holbrooki" by Regina Vega-Trejo, Rose E. O’Dea, Michael D. Jennions, and Megan L. Head in Behavioral Ecology.
DOI: 10.5061/dryad.r2342/1
title: Supplemental Data Sets 1-7

description: Supplemental Data Sets 1-7
DOI: 10.5061/dryad.v7g26/4
title: Predator acoustic cue vs. chemical cue experiment

description: Data from an experiment testing the independent and interactive effects of predator (catfish) acoustic and chemical cues on crab consumption of bivalve resources.
DOI: 10.5061/dryad.vp634306/18
title: Figure S01

description: The posterior consensus topology estimated from the concatenated nuclear genomic dataset in our Bayesian analysis (left) compared to a maximum parsimony topology estimated from the same data set (right). On both trees, support for nodes (posterior support for the Bayesian consensus, bootstrap support from 500 replicates for the MP tree) is indicated: black filled circles, ≥ 0.95; gray, between 0.95 and 0.75; white, &lt; 0.75. On the right-hand tree, arrows indicate nodes in conflict with the Bayesian consensus. Scale bar indicates branch length in expected substitutions per site.