cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7m6kg/34
title: Fig. 5a: ROM 60084 — Nectocaris pteryx from the Burgess Shale

description: ROM 60084, stain lines axial cavity
DOI: 10.5061/dryad.81tr1/1
title: PAC dataset

description: Data collected in pre admission clinic, analysed using SPSS and access databases, amalgamated in to Excel spreadsheet
DOI: 10.5061/dryad.8bt72/1
title: Archive containing output files and scripts used to generate these files

description: This zip file contains output files and scripts used to generate those files from Cui et al. 2013; Evolution. See README for description of file contents.
DOI: 10.5061/dryad.8q5t4/6
title: Supplementary Table 02

description: Carbon-isotope values of pedogenic carbonate samples (n = 32) from the Morrison Formation. Values range from -6.96‰ to -3.28‰, with an average of -5.71‰. Ghost Ranch, NM; SH = Shell, WY; MD = Bridger, MT.
DOI: 10.5061/dryad.984fn/1
title: Tisaniba-ZhangMaddison2014

description: Contains alignments for 28s and 16sND1 for both the broad sample dataset and the marpissoid dataset, and trees for both.
DOI: 10.5061/dryad.9n8rh/1
title: Bee microbiome paired-end, part A

description: The paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission.  This is part A.  The file will unzip into two files containing the paired-end reads for the first 5.5M sequenced clusters.  Phred+64 quality score encoding.  Library prep details can be found in the Methods of the linked manuscript.
DOI: 10.5061/dryad.c919g/1
title: Supplemental Materials

description: List of the biofacies included in the study and literature used in the collection of morphologic and abundance data.
DOI: 10.5061/dryad.f5q32/4
title: Genebank flatfile for AB4

description: Genebank flatfile for AB4 sequences (aldolase B gene); because sequences are &lt;200bp they are not deposited to Genbank
DOI: 10.5061/dryad.g08c7/2
title: Access_Array

description: This file contains results from the 454-sequencing of 45 genomic regions amplified with the Access-Array system. We summarise analyses of differentiation and phylogenetics (see methods). Gene-specific phylogenetic trees are provided (on nexus format).
DOI: 10.5061/dryad.h8b93/1
title: Phylogenetic tree of the MhcMamu- and MhcMafa-DQB1 alleles using Neighbour-joing methods

description: Figure 3 Phylogenetic tree of the MhcMamu- and MhcMafa-DQB1 alleles using Neighbour-joing methods 23 Mamu-DQB1 sequences detected in this study are shown with a solid round spot. 46 Mamu-DQB1 alleles not detected in animals of this study are showed with a circle. 85 Mafa-DQB1 sequences are showed without anything. 2 Aona-DQB1 (Aona-DQB1*220101 and Aona-DQB1*220102) were selected as outgroup. Except for 23 Mamu-DQB1 sequences detected in this study, all other DQB1 sequences were retrieved from the IPD-MHC Database (http://www.ebi.ac.uk/ipd/mhc/). Numbers at the node are bootstrap value in statistic analysis, only values above 50% are showed. software: Mega 5.05
DOI: 10.5061/dryad.h8b93/2
title: NJTree data

description: The phylogenetic tree in Figure 3 was constructed for the 156 Mhc-DQB1 gene sequences, including 69 Mamu-DQB1, 85 Mafa-DQB1 and 2 Aona-DQB1 alleles by using the neighbor-joining method, and aona-DQB1 alleles were used as the out-group. The 156 sequences can be searched in the IPD-MHC Database (http://www.ebi.ac.uk/ipd/mhc/).
DOI: 10.5061/dryad.jc754/1
title: S_Files_140901

description: Supplementary Files - appendices 1-2, figures S1-S11, tables S1-S6
DOI: 10.5061/dryad.jc754/2
title: S_BEAST_GPI_cal

description: BEAST phylogeny for GPI - calibrated analysis - FigTree tree file
DOI: 10.5061/dryad.jc754/3
title: S_BEAST_GPI_cal

description: BEAST phylogeny for GPI - calibrated analysis - XML input file
DOI: 10.5061/dryad.jc754/4
title: S_BEAST_GPI_uncal

description: BEAST phylogeny for GPI - uncalibrated analysis - FigTree tree file
DOI: 10.5061/dryad.jc754/5
title: S_BEAST_NRPD2a_cal

description: BEAST phylogeny for NRPD2a - calibrated analysis - FigTree tree file
DOI: 10.5061/dryad.jc754/6
title: S_BEAST_NRPD2a_cal

description: BEAST phylogeny for NRPD2a - calibrated analysis - XML input file
DOI: 10.5061/dryad.m466f/10
title: CBA15_genotypes

description: Microsatellite genotypes at locus CBA15.  This is a tab-delimited text file 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/13
title: CBA28_distances

description: Pairwise genetic distances at locus CBA28 for the 579 samples that were 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.  For pairs of individuals that both had nine or more alleles at locus RhCBA28, distances were calculated manually in Microsoft Excel and then inserted into the CBA28 matrix.
DOI: 10.5061/dryad.m466f/23
title: RUB26_distances

description: Pairwise genetic distances at locus RUB26 between the 579 samples that were 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.m466f/24
title: RUB26_genotypes

description: Microsatellite genotypes at locus RUB26. This is a tab-delimited text file 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.n3jk5/2
title: 1stacks

description: Contains data directories used by scripts from the section "3Berberis_phylogeo" of this repository for running the *populations* program of *Stacks* after putative paralogous loci have been filtered.
DOI: 10.5061/dryad.n3jk5/3
title: 3Berberis_phylogeo

description: Contains scripts for paralogous loci filtering, output data from the *populations* program of *Stacks*, as well as R scripts used for analyses and plotting.
DOI: 10.5061/dryad.nd2mb/11
title: Supplementary Table 11

description: Checked errors.
DOI: 10.5061/dryad.ns34t/1
title: cp23s fragment analysis

description: Raw fragment length data for cp32s-rDNA
DOI: 10.5061/dryad.ns34t/2
title: Reduced microsatellite data 4 loci from 7 populations

description: Reduced microsatellite data 4 loci from 7 populations
DOI: 10.5061/dryad.p2p3f/1
title: Acoustic data

description: The two tables presented here contain the acoustic data for all individuals used in the cline analysis. The modern and historic datasets are presented in separate tables. The site number and distance along the transect columns correspond with Table 1 in the paper. Acoustic data is recorded as Notes per Call (NC) and Pulse Number (PN). The resulting PC1 used in cline analyses is also presented. Samples that also had a tissue sample available have Museum Victoria Registration Numbers and their mitochondrial DNA results presented in the final two columns.
DOI: 10.5061/dryad.pq87t/1
title: 513a677047258

description: Distribution of Allium sect. Spathulata according to herbarium specimens
DOI: 10.5061/dryad.pv84f/1
title: Currie_Mace_2014_ProcB_CultRates_EA_data

description: Coded Ethnographic Data from Murdock's Ethnographic Atlas matched to Bantu and Austronesian-speaking societies
DOI: 10.5061/dryad.qd08b/5
title: mPWP Climate Layers

description: Climate layers for the mPWP (~3.264–3.025 Ma) from the Hadley Climate Centre. Please see our publication for information on how GCM data were derived. Note that these layers have been clipped to the maximum study area extent.
DOI: 10.5061/dryad.qd08b/6
title: PI Climate Layers

description: Climate layers for the present-day interval from the Hadley Climate Centre. Please see our publication for information on how GCM data were derived. Note that these layers have been clipped to the maximum study area extent.
DOI: 10.5061/dryad.sb30r/2
title: HeatStressPhysiology_Data_Dryad

description: Physiological and Genetic data (Q-PCR and RNA-seq) collected by Tonia Schwartz and Anne Bronikowski between 2008-2012 from a Heat Stress Experiment on 1.2 year old lab born babies (2007) of the Western Terrestrial Garter snake (Thamnophis elegans).
DOI: 10.5061/dryad.sh53j/5
title: 5_egg_count_and_hatching_success

description: The number of eggs laid and the hatching success from pairs of three different pairing types as analysed in the section Postzygotic barriers in the Results section and depicted in Figure 5 and 6.
DOI: 10.5061/dryad.sh53j/6
title: 6_reproductive_isolation

description: The absolute contribution of sequential reproductive barriers to the total reproductive isolation between between G. bimaculatus and G. campestris for each of the two mixed-species pairing types as depicted in Figure 1B.
DOI: 10.5061/dryad.sh53j/7
title: 7_Gryllidae_barrier_overview

description: The file '7_Gryllidae_barrier_overview.csv' contains the summary data of the reproductive barriers found in the Gryllidae as depicted in Figure 7. The first column is the genus and the second the species involved in the pairing. Each subsequent column represents a different barrier. The rows should be treated in pairs(2-3, 4-5, etc (including the header as a row)), as they each contain the data of one of two possible mixed-species crosses. The Latin name in each row refers to the female in such cross, the male is the other species in the pair. In the example below, the first row (excluding the header) contains the data on the female Allonemobius fasciatus x male A. socius cross and the second row for the female A. socius x male A. fasciatus cross.
DOI: 10.5061/dryad.th4h5/1
title: Carcharhinus melanopterus - Microsats Data

description: Two sheets here - one for the 14 loci with 15 sampling location giving a total of 758 individuals, the other is for Moorea only with 380 individuals used for the Migraine analysis
DOI: 10.5061/dryad.th4h5/2
title: Carcharhinus melanopterus - Cyt B Sequence Data

description: Sequence of the Cyt B from all individual used in the paper
DOI: 10.5061/dryad.th4h5/3
title: Carcharhinus melanopterus - Dloop Sequence Data

description: Dloop Sequence Data of all individual used in the paper
DOI: 10.5061/dryad.v53h1/1
title: Maddison et al. 2014-Deep salticid phylogeny

description: Contains alignments for 8 genes for different samples of taxa, and corresponding trees
DOI: 10.7925/drs1.ucdlib_32057
title: 36 Wicklow Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_32059
title: 30 King Street South, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 3 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.5061/dryad.105c0/8
title: Hemocyanin G ortholog Group

description: Ortholog group G with Bayesian consensus trees
DOI: 10.5061/dryad.11243/1
title: Phylogenetic tree

description: The NJ tree for the Hsf proteins in grasses
DOI: 10.5061/dryad.11243/2
title: Alignment

description: The alignment of the Hsf proteins in grasses
DOI: 10.5061/dryad.11243/3
title: Summary of 125 Hsf genes identified in 5 grass genomes

description: Summary of 125 Hsf genes identified in 5 grass genomes
DOI: 10.5061/dryad.1b2q0/1
title: Teasdale et al 2013 data

description: This data was collected for male tawny dragons (Ctenophorus decresii) in the field (Flinders ranges, South Australia). Details as to how the contrast data and the pattern and colour proportion data was calculated can be found in the paper and the references there in.
DOI: 10.5061/dryad.1ph37/2
title: Raw for Figure 2 and Table 1

description: Data Excel file containing data on observed encounter days, speed, overlap area, and use of overlap area for each pair of groups.  These data were used to determine whether baboon groups encountered one another more often than expected by a null (gas) model.
DOI: 10.5061/dryad.1v8kj/1
title: Scleral ring and orbit morphology

description: This table contains linear measurements of scleral rings and orbit morphology of avians, squamates, and fossil synapsids. All measurements are in mm. Columns refer to taxon names (taxon), orbit length (ol), maximum external scleral ring diameter (ext), maximum internal scleral ring diameter (int), the geometric mean of ol, ext, and int (geomm), the optical ratio (opt), and diel activity pattern (groups).
DOI: 10.5061/dryad.1v8kj/2
title: Phylogeny

description: Newick tree file, matching the scleral ring and orbit morphology dataset.
DOI: 10.5061/dryad.5hk2h/1
title: STT Raw Data
DOI: 10.5061/dryad.662vr/1
title: qPCR data

description: Raw and normalized starting cDNA concentrations from gill tissue for expression of 4 immune genes and 4 metabolic genes at rest and in response to challenges. Treatments are contained in separate tabs where "C" under the treatment column reflects control or resting state transcription and "T" or "P" indicates response to temperature or vaccine challenge.
DOI: 10.5061/dryad.7747n/4
title: GodaSharpWijnen2014TabS1

description: SPSS data files describing the circadian locomotor behaviour measures represented in Table S1.
DOI: 10.5061/dryad.7747n/5
title: GodaSharpWijnen2014TabS4

description: SPSS data file containing the circadian in vivo luminescence measures represented in Table S4
DOI: 10.5061/dryad.7r682/1
title: Ecological_data

description: Data on stomach contents (benthic versus limnetic) and stable isotopes for individual stickleback collected from 12 populations (six lake-stream pairs) on Vancouver Island, British Columbia, Canada.
DOI: 10.5061/dryad.84ph3/1
title: Genotypes for Iberian Wolves and Dogs

description: This file contains Iberian wolves, dogs and Barbanza individuals’ genotypes. Sheet “52 loci” contains genotypes for the whole set of markers on our dataset. Sheet “13 loci” contains genotypes for the 13 AIMs selected as the most suitable for studying wolfxdog hybridization in this project.
DOI: 10.5061/dryad.84ph3/2
title: Simulated genotypes for wolves and dogs

description: This file contains 13 sets of loci for 1000 simulated genotypes of wolves and dogs.  Sheet “52 loci” contains simulated genotypes for the whole set of markers on our dataset. Sheet “13 AIMs” contains simulated genotypes for the 13 AIMs selected as the most suitable for studying hybridization in this project. Sheet “Set Finnzymes” contains simulated genotypes for the 18 markers available on a commercial kit for dog microsatellites genotyping. Sets 1 to 10 are subsets of 13 random selected markers across the whole dataset of 52 loci.
DOI: 10.5061/dryad.9n8rh/2
title: Bee microbiome paired-end, part B

description: The paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission.  This is part B.  The file will unzip into two files containing the paired-end reads for the second 5.5M sequenced clusters.  Phred+64 quality score encoding.  Library prep details can be found in the Methods of the linked manuscript.
DOI: 10.5061/dryad.9n8rh/3
title: Bee microbiome paired-end, part C

description: The paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission.  This is part C.  The file will unzip into two files containing the paired-end reads for the third 5.5M sequenced clusters.  Phred+64 quality score encoding.  Library prep details can be found in the Methods of the linked manuscript.
DOI: 10.5061/dryad.cp405/1
title: Psychophysical adaptation data

description: Raw contrast thresholds, and threshold elevations in decibels (dB) after adaptation to either fast (13 deg/s) or slow (1.6 deg/s) motion, testing with either parallel or orthogonal low-contrast gratings. The stimuli were programmed in Matlab version 7.4, using the Psychophysics Toolbox, and thresholds were fitted using custom software written in Matlab.
DOI: 10.5061/dryad.cp405/2
title: Ranked SVM for all conditions

description: Ranked accuracies from the support vector machine analysis described in the paper for all of the classification analyses. The first column of each tab contains the subject number (1-8), the second column the number of voxels selected from each region (1 - 250), and the remaining columns give the proportion of accuracy for each region of interest.
DOI: 10.5061/dryad.d12j8/1
title: Microsatellites data of Ctenomys minutus (Rodentia: Ctenomyidae)

description: The data file comprise genotype scores of 14 microsatellite loci for 340 specimens of Ctenomys minutus, from 30 sampling sites in the southern Brazilian coastal plain. The locus names are listed in the first line of the file. The sampling sites are identified by pop = the abbreviation of the locality name, described in the Table 1 of the related manuscript. The identification of the specimens is in column 1. The genotypes for each specimen are from columns 2 to 15. The allele sizes are represented by three digits format, and they are separated by a / in the same locus. Missing genotypes are coded as 000/000.
DOI: 10.5061/dryad.f5q32/5
title: Aligned sequences of sex-linked CHDZ and CHDW

description: Aligned sequences of sex-linked loci CHD-Z and CHD-W. ANWC44930 is a sequence of two alleles of equal length and identical sequence for a male, ANWC43508 is a sequence of two alleles of equal length alleles that differ by one bp of another male, the remaining entries are sequences of a single allele cut from the agarose gel. Alleles codes are: w1-362bp, w2-366bp, z1- 329bp, z3-332bp (Supplementary material S3). Only females have w alleles.
DOI: 10.5061/dryad.fj8dm/1
title: Dataset S1

description: Probes significantly associated with age.
DOI: 10.5061/dryad.g7b05/1
title: ABx_CDI_1
DOI: 10.5061/dryad.g7b05/2
title: ABx_CDI_2
DOI: 10.5061/dryad.g7b05/3
title: ABx_CDI

description: The following R (www.r-project.org) code re-creates the analyses and output for the results section of (Brown KA, Khanafer N, Daneman N, Fisman DN. Antibiotics and the risk of community-associated Clostridium difficile infection (CDI): a meta-analysis. Antimicrob. Agents Chemother. 2013). The analyses are divided into sections A-F which correspond to the subheadings in the original article's results section.
DOI: 10.5061/dryad.gp495/1
title: spat2014_genotypematrix_inpegas

description: 15-locus SSR genotype matrix. Coded in the "pegas" R package format. Also included in the matrix is a single outgroup, "stricta4".
DOI: 10.5061/dryad.gv06d/1
title: Wilson_suppmaterial_Dec172012
DOI: 10.5061/dryad.h5nc8/1
title: On hatchery mortality during rearing density study

description: On hatchery mortality of spring Chinook salmon during the rearing density evaluation at Warm Springs National Fish Hatchery from the start of the study in April through September just prior to fall release.  Data stored in the Columbia River Information System maintained by the Columbia River Fisheries Program Office.
DOI: 10.5061/dryad.j015n/5
title: fish-probe-matches-to-uce-contigs.sqlite.gz

description: SQLITE database of LASTZ matches (from fish-lastz-probe-matches-to-uce-contigs.tar.gz) between assembled contigs in fish-contigs-from-uce-enrichments.tar.gz and the UCE probes in fish-500-loci-enrichment-probes.fasta.gz. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment.
DOI: 10.5061/dryad.jc754/10
title: S_BEAST_SDH_uncal

description: BEAST phylogeny for SDH - uncalibrated analysis - FigTree tree file
DOI: 10.5061/dryad.jc754/11
title: S_BEAST_trnLF

description: BEAST phylogeny for trnL-trnF - FigTree tree file
DOI: 10.5061/dryad.jc754/12
title: S_BEAST_trnLF

description: BEAST phylogeny for trnL-trnF - XML input file
DOI: 10.5061/dryad.jc754/13
title: S_BUGS_homoploid

description: BUGS script for estimation of homoploid speciation times - TXT file
DOI: 10.5061/dryad.jc754/14
title: S_BUGS_polyploid

description: BUGS script for estimation of polyploid speciation times - TXT file
DOI: 10.5061/dryad.jc754/15
title: S_MrB_8cp_gene

description: MrBayes phylogeny for 8 chloroplast regions - NEXUS input file
DOI: 10.5061/dryad.jc754/7
title: S_BEAST_NRPD2a_uncal

description: BEAST phylogeny for NRPD2a - uncalibrated analysis - FigTree tree file
DOI: 10.5061/dryad.jc754/8
title: S_BEAST_SDH_cal

description: BEAST phylogeny for SDH - calibrated analysis - FigTree tree file