cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4h0g0/1
title: complete data file

description: Experimental data from Huijben et al 2010, Evolution 64: 2952-2968. Given are measurements of mouse body weight, red blood cell density, asexual parasite densities of resistant clone, asexual parasite densities of susceptible clone, gametocyte densities of resistant clone, gametocyte densities of susceptible clone from day 3-21 post-infection, plus days 24,26 and 28. Measurement units are provided in excel file. Mice that died during the acute infection were excluded from the infection and are not included in the data file.
DOI: 10.5061/dryad.5ng71/1
title: sequence alignments

description: Nexus alignments of the 16 genes used in the study
DOI: 10.5061/dryad.5ng71/2
title: chrom2-3 final run

description: This folder contains the xml file used as input in BEAST analysis plus the trees and csv files from the runs
DOI: 10.5061/dryad.5ng71/3
title: LogCombined run files

description: This folder contains the xml, trees, csv and log files resulting from combining the two independent BEAST runs with LogCombiner
DOI: 10.5061/dryad.5ng71/4
title: chrom2-3 final run 2

description: This folder contains the xml file used as input in the second BEAST run plus the trees and csv output files
DOI: 10.5061/dryad.62380/2
title: Map input file for GridQTL

description: The linkage map, obtained from Crimap, of nine-spined stickleback for GridQTL analyses. Line 1: Number of chromosomes Line 2: Interval for calculation of genotype probabilities and coefficients in cM. Line 3: Name of first chromosome, number of markers on first chromosome and whether map is same for two sexes (=1) or not (=2). Line 4: For first linkage group, marker names in order separated by distances between them in cM.
DOI: 10.5061/dryad.62380/3
title: Phenotype (behavior) input file for GridQTL

description: Behavior measurements in nine-spined sticklebacks for QTL mapping analyses in GridQTL. Line 1: Numbers of fixed effects (factors), covariates and traits, respectively Line 2: Name of each fixed effect, covariate and trait. Line 3: Code for missing trait value Line 4 : Individual ID and values for fixed effects, covariates and traits for that individual. Sex: 0 female, 1 male. Feedbi, riskbi, expbi: 0 moving fish, 1 non-moving fish
DOI: 10.5061/dryad.67r03/1
title: Data matrices used in the phylogenetic analysis of Smallanthus.
DOI: 10.5061/dryad.6bs31/1
title: Journal policies

description: A file giving the data archiving policies from the journals covered in the study.
DOI: 10.5061/dryad.6v06v/2
title: 405taxa MrBayes analysis with sampled trees

description: MrBayes input and output results for the concatenated genes to determine species tree of the proteobacteria and sampled posterior trees to provide sampling for phylogenetic uncertainty in ancestral state reconstruction.
DOI: 10.5061/dryad.6v06v/3
title: Diversitree analyses

description: The diversitree analysis for ancestral state reconstruction
DOI: 10.5061/dryad.6v06v/4
title: r8s analysis to rate smooth the tree to ultrametric

description: To generate an ultrametric tree for diversitree a tree from the MrBayes posterior was rate smoothed with r8s
DOI: 10.5061/dryad.6v06v/5
title: BayesTraits input files

description: BayesTraits input files for running BT. The actual running requires specifically setting
DOI: 10.5061/dryad.73tj5/1
title: Data from: Evidence of lasting impact of the Deepwater Horizon oil spill on a deep Gulf of Mexico coral community

description: This dataset contains digital still images (*.jpg, *.png, or *.tif files) of cold-water coral colonies at Mississippi Canyon (MC) 294 in the Gulf of Mexico. They are organized into folders by the five visits to the site in November and December 2010 (2010-11 and 2010-12), March and October 2011 (2011-03 and 2011-10), and March 2012 (2012-03). Within the folders for each visit, each coral is represented by sub-folders with its ID (e.g. A10) which contains the actual image file.
DOI: 10.5061/dryad.7b37k/1
title: HITChip microarray data

description: The file contains phylogenetic microarray signal intensities for 130 intestinal genus-like bacterial groups (≥ 90% sequence similarity in the 16S rRNA gene) derived from the 55 faecal samples analysed during four different diets, for details see Supplementary Figure S1 in the article. The sample ID indicates volunteer number followed by a letter code for dietary regime as well as number of days passed from beginning of the trial. More information about the phylogenetic design of the HITChip can be found at http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01900.x/full. The data were extracted with using min-max normalisation (Bolstad et al. 2003, Bioinformatics 19:185) and log-transformed.
DOI: 10.5061/dryad.7n696/1
title: alignment_long

description: Fasta alignment of the 'long' data set
DOI: 10.5061/dryad.7n6b8/1
title: Ishii et al. 2014 Func Ecol
DOI: 10.5061/dryad.86pr0/1
title: Sremba_AntBmu_410_52

description: Alignment of 52 Antarctic blue whale mtDNA control region haplotypes described from 410 bp in Sremba et al. 2012. File contains key for lab ID codes and GenBank codes for each haplotype not described in LeDuc et al. 2007.
DOI: 10.5061/dryad.8gh60/1
title: PGENETICS_D_13_01530R2_ReCombine_data
DOI: 10.5061/dryad.9g40d/2
title: 10562_Stapleton_DataSheet2

description: Word file containing detailed description and SAS code used for data analysis.
DOI: 10.5061/dryad.9g40d/3
title: Copy of 10562_Stapleton_DataSheet3

description: Excel file with all 3240 genetic markers, map positions, and positions of LMR and plant height QTL.
DOI: 10.5061/dryad.bn249/1
title: MEC-12-0879_DRYAD_data

description: Genotypes at 8 microsatellite loci for adult hatchery steelhead from Forks Creek Hatchery, Washington State, USA. Visualized on a MegaBACE 1000 and scored using their proprietary software.
DOI: 10.5061/dryad.bt658/1
title: Data of JEB 12087

description: Data of JEB 12087. The excel file has multiple sheets; each sheet is the database of the different analysis.
DOI: 10.5061/dryad.c32m0/2
title: Copy of PPL_1406_sm_TableS1

description: Raw and adjusted trait data for each sample for pilot and full experiment.
DOI: 10.5061/dryad.cv35b/1
title: FinWhale 43loci_Array1_fasta.txt

description: FASTA file of fin whale nuclear loci for capture array design and sequence read assembly.
DOI: 10.5061/dryad.db058/1
title: Load and displacement data for finite element models of human and pig vertebrae

description: Six porcine and four human cadaveric vertebrae were imaged using micro computed tomography (μCT) (Scanco μCT80, Scanco Medical, Switzerland) at a voxel size of 0.074 mm. Species-specific threshold values were then applied to segment the images of all of the specimens of each species. Each set of segmented images was then imported into an image processing software tool (ScanIP, Simpleware Ltd, Exeter) and downsampled to a resolution of 1 x 1 x 1 mm using an averaging method that allowed for partial volume effects. Each downsampled voxel represented the average of the binary segmented voxels within it and therefore the greyscale value of the downsampled voxel represented the BV/TV value of that region of the underlying bone. For all of the specimens, the regions were then imported into a FE meshing tool (ScanFE, Simpleware Ltd, Exeter) and a FE model of the vertebra and two end-caps was generated. An element size of approximately 1 mm was used because this had previously been shown to be sufficient for vertebral stiffness evaluation in specimens of a similar size and under similar conditions. A combination of hexahedral and tetrahedral linear elements were used to represent the vertebral geometry; in total each model contained between 200,000 and 400,000 elements. The cement region was assigned an elastic modulus of 2.45 GPa. Each element within the bone was assigned an elastic modulus based on BV/TV value derived from the downsampled voxel grayscale. All of the models were imported into a finite element software package (ABAQUS CAE version 6.9-1, Simulia Corp, USA). The models were solved and the specimen stiffness determined. To normalize for size, the ‘apparent modulus’ was also determined by multiplying the stiffness by the vertebral height and dividing by the cross sectional area. All the models were processed and the predicted vertebral stiffness was determined.
DOI: 10.5061/dryad.db058/2
title: Modelled stiffness and apparent modulus of porcine and human vertebral models for 5 loading modes

description: Six porcine and four human cadaveric vertebrae were imaged using micro computed tomography (μCT) (Scanco μCT80, Scanco Medical, Switzerland) at a voxel size of 0.074 mm. Species-specific threshold values were then applied to segment the images of all of the specimens of each species. Each set of segmented images was then imported into an image processing software tool (ScanIP, Simpleware Ltd, Exeter) and downsampled to a resolution of 1 x 1 x 1 mm using an averaging method that allowed for partial volume effects. Each downsampled voxel represented the average of the binary segmented voxels within it and therefore the greyscale value of the downsampled voxel represented the BV/TV value of that region of the underlying bone. For all of the specimens, the regions were then imported into a FE meshing tool (ScanFE, Simpleware Ltd, Exeter) and a FE model of the vertebra and two end-caps was generated. An element size of approximately 1 mm was used because this had previously been shown to be sufficient for vertebral stiffness evaluation in specimens of a similar size and under similar conditions. A combination of hexahedral and tetrahedral linear elements were used to represent the vertebral geometry; in total each model contained between 200,000 and 400,000 elements. The cement region was assigned an elastic modulus of 2.45 GPa. Each element within the bone was assigned an elastic modulus based on BV/TV value derived from the downsampled voxel grayscale. All of the models were imported into a finite element software package (ABAQUS CAE version 6.9-1, Simulia Corp, USA). The models were solved and the specimen stiffness determined. To normalize for size, the ‘apparent modulus’ was also determined by multiplying the stiffness by the vertebral height and dividing by the cross sectional area. All the models were processed and the predicted vertebral stiffness was determined. A series of virtual tests was then undertaken on the models generated with the species-specific threshold and the linear conversion factor. First, the height of the upper cement endcap was adjusted in all cases to be 40 % of the vertebral body height to ensure the loading point was always the same relative distance from the vertebra. The load was then applied to five positions equally spaced between the anterior and the posterior extent of the vertebral body. In each case, the model was solved and the vertebral stiffness determined as the load divided by the displacement at the point where the load was applied.
DOI: 10.5061/dryad.g6jm6/1
title: C. ornatus data

description: Individuals: This data file provides all the raw molecular data for each individual. The first column gives the outcrop from which each individual was taken. The second column the individual’s ID, a unique number across all outcrops.  The remaining columns give the allele sizes for each individual at each locus (listed in the first row). Each locus has 2 columns, one for each allele. Missing data are left as empty cells. Outcrops: This file provides all the outcrop level information used in the analyses. The first column gives the outcrop name, the second  gives the region where the outcrop is located. The third and fourth columns give the geographical location of the outcrop as latitude and longitude. The fifth column gives the number of outcrops within a 2km radius of the sampled outcrop and the sixth the percentage cover of granite within a 2km radius of the sampled outcrop. The seventh column indicates whether the outcrop is found in a cleared (CL) or uncleared (U) landscape and the final column provides the mean annual rainfall for the outcrop.
DOI: 10.5061/dryad.g763q/1
title: t_californicus_rqtl_file

description: File used for rqtl, including marker linkage data, individual marker data (allele by population of origin, or heterozygote), phenotypic data (measured in the lab), mitochondrial background and sex.
DOI: 10.5061/dryad.g763q/2
title: t_californicus_raw_morphodata

description: This contains the raw developmental and morphological data, as well as the transformed and mean-corrected values
DOI: 10.5061/dryad.g7j86/1
title: Eucalypt adults

description: the microsatellite genotypes of each sampled adult tree
DOI: 10.5061/dryad.g7j86/2
title: Eucalyptus progeny

description: microsatellite genotypes for all progeny
DOI: 10.5061/dryad.g8n63/1
title: Transitiva manipulation
DOI: 10.5061/dryad.g8n63/2
title: Subspecies tail length
DOI: 10.5061/dryad.g8n63/3
title: Subspecies coloration
DOI: 10.5061/dryad.mg5kv/1
title: Camera trap survey (April-July 2011) of jaguars in Belize.

description: The data are from a camera trap survey of jaguars in Cockscomb Basin Wildlife Sanctuary in Belize (UTM 0348113, 1854515 WGS84). The survey used nineteen paired camera stations and ran for 90 days (April - July 2011). Two excel worksheets are provided, one contains all the capture information (including the coordinates of each camera station) and the other one has details of trap failures.
DOI: 10.5061/dryad.ns2jn/3
title: Data_Latchetal2014MolEcol
DOI: 10.5061/dryad.p2f7c/1
title: final-ALL_Thymallus_aligned-ins.phy

description: mtDNA control region sequence alignment used to generate the phylogenetic tree presented in Fig. S1. Nexus format.
DOI: 10.5061/dryad.p2f7c/2
title: SSR_dataset

description: Microsatellite data set, with individual information about sampling location and GenBank reference for mtDNA control region
DOI: 10.5061/dryad.r07bc/1
title: Codeset information

description: CodeSet information (gene names, accession numbers, target sequences) for the NanoString probe set used in this study.
DOI: 10.5061/dryad.r07bc/2
title: Gene expression data

description: Results obtained from the NanoString analysis of gene expression during zebrafish development (raw data, normalised data, and analysis).
DOI: 10.5061/dryad.r762t/1
title: Branton and Richardson data
DOI: 10.5061/dryad.t201q/4
title: Short intron sequence alignment of the 3R chromosome arm

description: We analyzed whole-genome data (Langley C. et al., accepted 2012) of D. melanogaster (Release 1.0) from a sample of six inbred Malawi isofemale lines from the 50 genomes Drosophila Population Genomics Project (DPGP) (http://www.dpgp.org/ ). We downloaded (http://genome.ucsc.edu/ ) aligned single sequences of D. simulans, D. sechellia, D. erecta and D. yakuba (Release 5) (Begun et al., 2007; Clark et al., 2007) and combined them with the five D. melanogaster sequences into a multiple alignment for all autosomes. We used position 8 to 30 in short introns (less than 66 bp) as these are thought to be the least constrained sites in the Drosophila genome (Halligan and Keightley, 2006; Parsch et al., 2010). We used the D. melanogaster Flybase annotation (release 5.31) to identify these sites. Introns, which overlapped with coding regions were excluded from the analyses. Python scripts were written to concatenate all 23 considered positions per short intron into one alignment file for each chromosome arm.
DOI: 10.5061/dryad.v811c/4
title: Stimulating the Immune System PO

description: R script for Experiment 2a
DOI: 10.5061/dryad.v811c/5
title: Stimulating the Immune System PO

description: Data for Experiment 2a
DOI: 10.5061/dryad.v811c/6
title: Immune Upregulation During Breeding

description: Data for Experiment 3a
DOI: 10.5061/dryad.v811c/7
title: Wounding whilst breeding

description: R script for Experiment 3b
DOI: 10.5061/dryad.v811c/8
title: Wounding whilst breeding with control

description: Data for Experiment 3b
DOI: 10.5061/dryad.v811c/9
title: Wounding whilst breeding

description: Data for Experiment 3b
DOI: 10.5061/dryad.1s625/1
title: Field Data from 1978 and 2011/2012 sampling

description: This dataset includes the cone production data and accompanying tree and site information from the sites sampled in New Mexico and northwestern Oklahoma in 1978 and 2011/2012.
DOI: 10.5061/dryad.1s625/2
title: Annual_Whorl_and_Cone_Scar_Guide

description: This pdf file has pictures to help you understand how to distinguish an annual whorl and identify the corresponding year for each cone or cone scar. This file also provides a definition of a leader shoot (also referred to as a cone bearing branch) and accompanying diagram to further help you understand the methodology.
DOI: 10.5061/dryad.34jb6/20
title: 1998-SingleNote

description: Example of a 1998 single note (dash) song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/21
title: 2004-2Ch

description: Example of a 2004 two Ch note song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/22
title: 2004-Stutter

description: Example of a 2004 stutter song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/23
title: 2004-DashCh

description: Example of a 2004 Dash + Ch song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/25
title: 2004-SingleNote

description: Example of a 2004 single note (dash) song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/26
title: 2011-2Ch

description: Example of a 2011 two Ch song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/27
title: 2011-Stutter

description: Example of a 2011 stutter song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.34jb6/28
title: 2011-DashCh

description: Example of a 2011 Dash + Ch song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.47r16/3
title: Maximum Likelihood Trees

description: This file shows images of the maximum likelihood trees for the concatenated, 7-gene matrices as well as each individual gene.  Each figure is labeled to indicate the nature of that data analyzed for that tree.
DOI: 10.5061/dryad.47r16/4
title: Maximum Likelihood Bootstrap trees

description: This file shows images of the majority rule consensus trees from maximum likelihood bootstrap analyses for the concatenated, 7-gene matrices as well as each individual gene.  Each figure is labeled to indicate the nature of that data analyzed for that tree.  Numbers on each branch are the frequencies of that clade in the bootstrap replicates, expressed as a percentage.
DOI: 10.5061/dryad.5ng71/10
title: D_a_texana ENM

description: Maxent results for D. a. texana chromosomal form.
DOI: 10.5061/dryad.5ng71/5
title: D_americana average ENM

description: This folder contains the results from Maxent analysis for the whole species; average from 10 replicates
DOI: 10.5061/dryad.5ng71/6
title: D_americana average cold ENM

description: This folder contains mxd, csv and plots resulting from te maxent analysis using cold-related variables
DOI: 10.5061/dryad.5ng71/7
title: D_a_americana cold ENM

description: Maxent results for the D. a. americana chromosomal form using the cold-related variables
DOI: 10.5061/dryad.5ng71/8
title: D_a_americana ENM

description: Maxent modelling results for the D. a. americana chromosomal form.
DOI: 10.5061/dryad.5ng71/9
title: D_a_texana cold ENM

description: Maxent modelling results for the D. a. texana chromosomal form using cold-realted variables.
DOI: 10.5061/dryad.7d0k4/1
title: dataDryadPCR

description: Data with information on the carrier status of Pasteurella multocida labelled "PCR CARRIER STATUS" and several immune traits of Common eiders
DOI: 10.5061/dryad.7d0k4/2
title: dataDryadIF

description: Data on measured immune traits of Common eiders during the pre-breeding and incubation stages
DOI: 10.5061/dryad.7d0k4/3
title: dataDryad15052014

description: Dataset used to test for directional selection on immune traits. Body size and mass measurements are provided as well as data for the 8 immune traits. The LIVEDEAD column provides information on the fate of individuals (1 is dead, 0 alive). BLEEDING.TIME is in min.
DOI: 10.5061/dryad.7h65f/1
title: Genome-wide admixture in the Picea glauca x P. engelmannii hybrid zone_311SNPs

description: This file contains Illumina genomic data for 311 candidate gene single nucleotide polymorphisms (SNPs) tested in 700 individuals of P.glauca, P.engelmannii and their hybrids in British Columbia (Canada). The file has a format similar to the "Structure" (Pritchard et al.2000) program, in which the first column is the genotype ID, second column is the population ID and all other columns are the SNP IDs. Please note that each SNP is described by two columns, each containing one allele. Missing values are denoted by "-9", according to the Structure format requirements.
DOI: 10.5061/dryad.7h65f/2
title: Genome-wide admixture in the Picea glauca x P. engelmannii hybrid zone_Small data set
DOI: 10.5061/dryad.7h65f/3
title: Climate_data

description: This file contains the location (latitude, longitude and elevation) of the 771 sampled individuals (white spruce, Engelmann spruce and their hybrids). It also contains the climatic variables used in the environmental association analysis. 21 different climatic variables are included for each of the sampled individuals.
DOI: 10.5061/dryad.7n696/2
title: alignment_short

description: Fasta alignment for the 'short' data set
DOI: 10.5061/dryad.7n696/3
title: beast_fig1

description: XML file for beast analysis visualised in figure 1
DOI: 10.5061/dryad.7n696/4
title: beast_fig2&3

description: XML file for beast analysis depicted in figures 2 and 3
DOI: 10.5061/dryad.7n696/5
title: MCC_fig1

description: Nexus file of MCC tree in figure 1
DOI: 10.5061/dryad.7n696/6
title: MCC_fig3

description: Nexus file for MCC tree in figure 3
DOI: 10.5061/dryad.7th55/1
title: OTU sequences 454 data cp23s HVR gene

description: 33 OTUs identified from samples based on clustering at 97% similarity using average neighbor algorithm in mothur
DOI: 10.5061/dryad.7th55/2
title: HAI cp23s sanger sequences

description: Abrolhos Islands sanger sequences cp23s
DOI: 10.5061/dryad.7th55/3
title: KIM cp23s sanger sequences

description: Kimberley sanger sequences cp23s
DOI: 10.5061/dryad.7th55/4
title: OTU sequences 454 data ITS2 gene

description: 454 data from Acropora clustered into OTUs based on 97% similarity using average neighbour algorithm
DOI: 10.5061/dryad.8m8r1/1
title: Protonemura gevi nymphs data
DOI: 10.5061/dryad.8m8r1/2
title: Protonemura gevi environment data
DOI: 10.5061/dryad.8m8r1/3
title: Protonemura gevi adults data
DOI: 10.5061/dryad.9fk1s/1
title: ALIGNMENTS_DRYAD

description: Alignments for 1,534 1:1 orthologous genes across lice and their primate hosts. There are 4 alignment folders each with 1,534 genes in them. 1. Lice DNA alignments. 2. Lice protein alignments 3. Primate DNA alignments. 4. Primate protein alignments.
DOI: 10.5061/dryad.c32m0/3
title: Copy of PPL_1406_sm_TableS2

description: Expression-QTL genes under leaf nitrate reductase activity QTL. Markers within the nitrate reductase activity QTL region were used to select markers that had significant linkage to expression differences in genes that mapped to the same chromosomal bin. The MZ_IDs for the array oligonucleotides have only been mapped to bin in the B73 Refgen1 sequence, not to the exact genomic location, so some of these eQTL may not be within the nitrate reductase activity QTL region within that bin.
DOI: 10.5061/dryad.c32m0/4
title: Copy of PPL_1406_sm_TableS3

description: Genes located in the same chromosomal region as nitrate reductase activity QTL regions. Flanking genetic markers were localized on the B73 sequence and all genes in the filtered gene set that had genomic locations between those co-ordinates were selected.