cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2m1n/7
title: Variation in Rh1 non-synonymous rates of evolution (dN ) across Passerines

description: Branch lengths are scaled by dN rates. Branch lengths were estimated using a free ratio model as implemented in PAML, that estimates independent dN rates for each branch in the tree.
DOI: 10.5061/dryad.dc56b/7
title: Tajima's D across all 25 kb windows of the blue tit genome

description: based on SNPs called from the transcriptome of 5 male and 5 female blue tits.
DOI: 10.5061/dryad.dc56b/8
title: iHS values across all informative scaffolds

description: based on SNPs called from the transcriptome of 5 male and 5 female blue tits.
DOI: 10.5061/dryad.ds63c/1
title: Antarctic petrels_CMR_1992-2014_Svarthamaren

description: CMR data for Antarctic petrels breeding at Svarthamaren. Capture/recapture histories for 2029 individuals, monitored between 1992 and 2014.
DOI: 10.5061/dryad.g466r/1
title: Haplotype and genepop datasets

description: All haplotype files generated by Stacks assembly and genepop files created by custom conversion. See README for additional information.
DOI: 10.5061/dryad.g466r/2
title: Outlier loci

description: Outlier loci identified using FreeNA corrected FST and He values in fdist. Each file is a fasta file with two lines - the locus identifier from the main catalogue and a consensus haplotype sequence. See README for a description of filenames.
DOI: 10.5061/dryad.g466r/3
title: fdist output

description: fdist output from each of the analyses performed in the main and supplementary text. See README file for more information.
DOI: 10.5061/dryad.g466r/4
title: Final stacks catalogue

description: Final stacks catalogue constructed using Stacks v1.21. See README for additional explanation
DOI: 10.5061/dryad.k528j/1
title: Anartia Clay Model Attack Data

description: These are the attack data for all of the models placed in the field. Each model belongs to a group of three different models. This text file lists each model and if it was not attacked (NA), missing (which were censored), and if they were attacked by an avian predator (Avian).
DOI: 10.5061/dryad.k528j/2
title: Anartia model spectra graph

description: Here are the average reflectance spectra for the color patches of the models. Each average was from several models and natural butterflies.
DOI: 10.5061/dryad.m3n87/2
title: SSR upload

description: SSR for all samples of orchardgras
DOI: 10.5061/dryad.m3n87/3
title: unigene upload

description: The unigene is the final DNA sequence assembly
DOI: 10.5061/dryad.m3n87/4
title: Genotyping results for SSR validation
DOI: 10.5061/dryad.m3n87/5
title: SNP validation
DOI: 10.5061/dryad.m3n87/6
title: The results of qRT-PCR for validated genes
DOI: 10.5061/dryad.m3n87/7
title: Readcount_FPKM
DOI: 10.5061/dryad.m3n87/8
title: Differential_analysis_results
DOI: 10.5061/dryad.0jd3t/1
title: Young&Blob_TurtleFemurStrainData_Dryad

description: Peak strain data from turtle femoral mid-shafts during swimming and terrestrial walking.
DOI: 10.5061/dryad.15v00/1
title: Genotypes_Lines_Base_Population
DOI: 10.5061/dryad.1872r/1
title: Larval environment alters amphibian immune defenses differentially across life stages and populations

description: Data includes:Larval survival (%), Larval duration, mass at sample collection, AMP production (BCA assay), AMP bioactivity as measured by the slope of the log-transformed growth curve, AMP bioactivity as measured by pathogen growth rate (r).
DOI: 10.5061/dryad.1bf13/1
title: GC-MS traces for two honey bee samples (1st page) and relative amount of each  chemical per bee or mites sample. .

description: The first page are two TICS (total ion chromatograms or GC-MS chromatograms) of the 2 Apis bees.  The first is a BCC, an Apis cerana that received a mite from A. cerana. The second is a BMM, an Apis mellifera that received a mite from A. mellifera. Pages after that are the relative proportions of each compound for each bee or mite sample.
DOI: 10.5061/dryad.276d6/1
title: Selwood_etal_data_2015_JANE

description: Individual species reporting rates per site, per year (worksheet= Reprates and Reprates_description for field descriptors) and measures of breeding per site, per year (worksheet = Breeding and Breeding_description for field descriptors).
DOI: 10.5061/dryad.40f6v/1
title: Experimental Data
DOI: 10.5061/dryad.446sv.1
title: Data from: Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the southeastern United States and Caribbean Islands
DOI: 10.5061/dryad.446sv.2/5.2
title: vcf SNP file from SNP calling pipeline with no additional filters
DOI: 10.5061/dryad.446sv.2/7.2
title: vcf SNP file for Fst, LD, and PCA analyses
DOI: 10.5061/dryad.4cv02/1
title: XML file for molecular calibration analysis

description: XML file used in BEAST for the molecular calibration analysis of CR H. amphibius sequences, using the split with H. liberiensis (sequence OGR) as a reference.
DOI: 10.5061/dryad.4cv02/2
title: XML for EBSP analysis

description: XML file used in BEAST for the Extended Bayesian Skyline Plot (EBSP) analysis of H. amphibius, based on control region, cytochrome-b and nuclear HMG-2 sequences
DOI: 10.5061/dryad.4rd1g/24
title: Behavioral Data - Actograms

description: This file contains activity records for the in vivo phenotyping phase of this study. To view, it is best to open them with Clocklab software.
DOI: 10.5061/dryad.54137/1
title: SUPP_INF_3

description: Site-by-species matrices for angiosperms and eudicots respectively (presence/absence data), PCA1 for temperature- and precipitation-related variables and spatial coordinates of the centroids of ecoregion polygons.
DOI: 10.5061/dryad.54137/2
title: Genus_level_Tree

description: Genus-level time-calibrated phylogeny used in the study (Newick format)
DOI: 10.5061/dryad.5g8c5/1
title: Kinematic data
DOI: 10.5061/dryad.5g8c5/2
title: Sucfion performance data
DOI: 10.5061/dryad.6b340/1
title: RAxML_COIcytB

description: Aligned COI and cytB sequences used as RAxML input file.
DOI: 10.5061/dryad.6b340/2
title: RAxML_bestTree

description: Resulting best tree with bootstrap values generated using RAxML.
DOI: 10.5061/dryad.6b340/3
title: Raw acoustic data

description: JMP raw data file used for acoustic analyses
DOI: 10.5061/dryad.6b340/4
title: Raw morphometric data

description: JMP raw data file used for morphometric analyses
DOI: 10.5061/dryad.6b340/5
title: Microsatellite genotype data

description: Raw microsatellite genotype data and input file for Genalex genetic analyses (principal coordinates)
DOI: 10.5061/dryad.6rh72/1
title: fstat-cladeF
DOI: 10.5061/dryad.73870/3
title: Sherry et al Hubbard Brook precipitation data

description: Text file for period 1983-1995, and for months of May and June, of daily average rainfall for Watersheds 5 and 6 in Hubbard Brook Experimental Forest, NH, USA.  Data used to construct annual covariates for precipitation in analyses of American redstart nesting success.
DOI: 10.5061/dryad.73870/4
title: Sherry et al Hubbard Brook temperature data

description: Text file for period 1983-1995, and for months of May and June, of daily average temperatures (deg C) for Stations 1 and 6 in Hubbard Brook Experimental Forest, NH, USA.  Data used to construct annual covariates for temperatures in analyses of American redstart nesting success.
DOI: 10.5061/dryad.7g984/7
title: md_ngo_wide_anon

description: Cleaned dataset, wide dataset by participant level data. See ReadMeFile_013015 for more information, including variable definitions (codebook).
DOI: 10.5061/dryad.7g984/8
title: md_ngo_raw_anon

description: Raw dataset, uncleaned. Note: There are some duplication of observations in the raw file. These can be noted as all variables for the observations are identical. The “cleaned” files remove these duplicates. See ReadMeFile_013015 for more information, including variable definitions (codebook).
DOI: 10.5061/dryad.8cj64/1
title: Case study LICOR data

description: WD7468 file represents the respiration data obtained while measuring CO2 from the wood debris (WD) using LICOR 820. This file was used to get the slope called deltaCO2 which is named "k" in the R script provided in the supplementary information.
DOI: 10.5061/dryad.8cj64/2
title: WD7468_measurement

description: WD7468_measurement is  the .csv file used to plot the figure FigS1 in the supplementary.
DOI: 10.5061/dryad.bg26p/1
title: eggdata CSV

description: See readme file for more information. The eggdata CSV and eggdata excel files contain the same data just in different formats.
DOI: 10.5061/dryad.bg26p/2
title: eggdata excel

description: See readme file for more information. The eggdata CSV and eggdata excel files contain the same data just in different formats.
DOI: 10.5061/dryad.bq64c/1
title: all analyses

description: Data collected in the field.  Subject is the unique identifier of each black-and-white warbler that was sampled during the study.  The study was conducted over 4 years (y1=2008, y2=2009, y3=2010, y4=2011).  Breeding (N=boreal forest, S=southeast) is based on stable hydrogen isotope values. Timing (E=Early, M=middle, L=Late) is based on the range of capture dates for each sex in a given breeding destination and in a given year.  rbc represents the stable carbon isotope value based on red blood cells collected from brachial vein puncture.  Cond is a size-specific condition index value.  Age and sex of the warbler.
DOI: 10.5061/dryad.br4rh/1
title: marmoset ontogeny data

description: Data structure for ontogeny study (Chow, Mitchell, Miller, 2015). Five family groups were collected, each with a data structure containing information for the call start and end times between pairs in the group. The five group structures are save in matlab files, as G_info4, R_info4, M_info4, O_info4, and J_info4. Each file has the same format, following as a 6 x 10 cell structure. The columns 1-10 corresponds to months, starting from month 3, so they are
in sequence months 3,4,5,6,7,8,9,10,11,12. The rows correspond to different pairs of family members conversing, # - first to second speaker. 1 - mother to baby 1, 2 - mother to baby 2, 3 - father to baby 1, 4 - father to baby 2, 5 - baby 1 to baby 2. An empty cell indicates no data was recorded that month. Each cell has the following information for conversations: DateNum: [1xN double] % identifier for the N sessions recorded that month, Animals: [1x2 double] % animal numbers %**** call times for the first speaker  Astarts: [1xM double] % times in seconds, start of first pulse in a call. Afinish: [1xM double] % times in seconds, end of the first pulse. Astarts2: [1xM double] % time in seconds, start of the second pulse in call, NaN if no second pulse. Afinish2: [1xM double] % time in seconds, end of the second pulse in call, NaN if no second pulse. Atypes: [1xM double] % type of call, 1-phee, 2-twitter, 3-trill, 4-other, 5-unidentified. %**** call times for the second speaker. Bstarts: [1xP double] % same format as above for A, but for speaker B, Bfinish: [1xP double], Bstarts2: [1xP double], Bfinish2: [1xP double], Btypes: [1x265 double]
DOI: 10.5061/dryad.c301h/1
title: Matrix of surveyed sites versus vertebrate species detected by at least one sampling technique

description: Matrix of surveyed sites versus vertebrate species detected by at least one sampling technique, including the geographical coordinate of each site.
DOI: 10.5061/dryad.c77jn/1
title: Fish_detections_UL_CH

description: Fish positions derived from acoustic telemetry contained within excel file with 5 columns. 'Record' denotes tag detection numbered consecutively in sequence; 'tag_number' denotes the fish identification number; ‘PosX’ denotes fish x coordinate in UTM; ‘PosY’ denotes fish y coordinate in UTM, ‘Treatment’ denotes experimental treatment
DOI: 10.5061/dryad.ck2d2/1
title: Aquatic gastropod phenotypic plasticity data

description: Data source and raw data used in the calculation and comparison of phenotypic plasticity in aquatic gastropods
DOI: 10.5061/dryad.df81n/1
title: Compressed data folder

description: Data allowing to remake all the analytical figures in the main paper
DOI: 10.5061/dryad.ds63c/2
title: Avg_HatchingDate_Productivity_AntarcticPetrels_Svarthamaren

description: Mean annual productivity and hatching dates of Antarctic petrels breeding at Svarthamaren, Dronning Maud Land.
DOI: 10.5061/dryad.g466r/5
title: Geometric morphometrics data

description: Geometric morphometrics data for Littorina ecotypes. Columns are sample, ecotype, population (island), population x ecotype. Columns with 'proc' are size adjusted procrustes coordinates. Columns with 'PC' are principle components. Columns with 'CV' are canonical variates.
DOI: 10.5061/dryad.g466r/6
title: Sample metatable

description: Metatable of all samples used in study for both RAD-seq and morphometrics. Columns are sample, population (island), ecotype, sex (NS = not sexed), whether sample was RAD-sequenced, whether sample was used in initial catalogue, whether sample was used in final catalogue, whether sample was used in morphometrics and ENA accession number for sequenced individuals.
DOI: 10.5061/dryad.g466r/7
title: vcf_files

description: VCF files for Salto, Jutholmen, Ramso and the all-island dataset.
DOI: 10.5061/dryad.g466r/8
title: Diversity statistics

description: Diversity statistics calculated from haplotype data. See README for indepth explanation.
DOI: 10.5061/dryad.hb0p4/1
title: Current management_data

description: Data regarding patients being treated for surgical oncologic emergencies
DOI: 10.5061/dryad.hr0sp/5
title: PaleocurrentDatabase

description: Database contains paleocurrent data arranged by geographic and stratigraphic content. Database is organized with each publication given a unique number that is used for all datasets derived from that publication. Each row begins with that descriptor, and includes for each unique number, one entry that gives author(s), title, date, source, volume, and pages. All entries include Period (stratigraphy), Longitude, Latitude, Direction (flow was moving toward), #Data (in each dataset), Area sq km, Dispersion, Continent, Environment, Paleocurrent indicator, Lithology, and Formation.
DOI: 10.5061/dryad.j81t3/1
title: Phylogenetic analysis of Prophyllodictya

description: 1) Character-taxon matrix used for phylogenetic analysis; 2) Characters for phylogenetic analysis
DOI: 10.5061/dryad.k4q1q/1
title: Aligned DNA sequences for CO1 and 16S genes from Colombian frogs

description: Nexus file of aligned DNA sequence data representing two mitochondrial gene fragments, 16S (bases 1-604) and CO1 (bases 605-1262) obtained for 235 frog specimens collected along the Eastern Cordillera of the Colombian Andes, South America. Alignments were accomplished using default settings in the software package, MUSCLE (Edgar, 2004).
DOI: 10.5061/dryad.n895b/1
title: Data extraction

description: Extracted data for the systematic review.
DOI: 10.5061/dryad.p610q/1
title: README

description: Description of files
DOI: 10.5061/dryad.p610q/2
title: ME-15-0114

description: Tar file containing all relevant files plus README file
DOI: 10.5061/dryad.rj7g1/1
title: Code and datasets
DOI: 10.5061/dryad.rq38c/1
title: VAS-scores
DOI: 10.5061/dryad.tk2fn/1
title: SNPs in HapMap format

description: A HapMap format file containing SNPs that were used for phylogenetic analysis.
DOI: 10.5061/dryad.tk2fn/2
title: Alignment file used for phylogenetic tree analysis

description: A phylip sequential format file that was used to reconstruct NJ tree.
DOI: 10.5061/dryad.tk2fn/3
title: Neighbor-joining tree between maize and teosinte

description: The phylogenetic analysis was performed using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP package
DOI: 10.5061/dryad.v1d06/1
title: Data from: Disruption of memory reconsolidation erases a fear memory trace in the human amygdala:  An 18-month follow-up

description: This is data is from a fear conditioning experiment measuring skin conductance and fMRI BOLD, pertaining to the article: Björkstrand J, Agren T, Frick A,  Engman J, Larsson EM, Furmark T, Fredrikson M. Disruption of memory reconsolidation erases a fear memory trace in the human amygdala: An 18-month follow-up, yet to be published. Please consult this article and the original study:  “Agren T, Engman J, Frick A, Björkstrand J, Larsson EM, Furmark T, Fredrikson M. 2012. Disruption of reconsolidation erases a fear memory trace in the human amygdala. Science 337:1550-1552” , for details concerning the purpose and design of the study. In the folder SCRdataAndGroup you can find an excel file containing raw and range corrected skin conductance responses (SCR) for all subjects from the follow-up measurement 18 months after fear acqusition, as well as information as to which subject belongs to which group. In the folders named subject1-19 you can find  SPM8 contrast files from the renewal session three days after acquisition. The contrast shows the BOLD response to the first CSplus trial over an immediate preceding baseline for each subject. These files can be used to perform second level analysis using SPM8 for Matlab. In the folder MaskForColocalizationAnalysis you can find the SPM8 image file used to perform the colocalization analysis described in the follow-up study.
DOI: 10.5061/dryad.vh8v4/1
title: Killen et al Functional Ecology 2015 data

description: This file contains all behavioural, physiological, and morphological data used in the manuscript. Different data sets are located on different tabs within the spreadsheet. Each tab also includes descriptions of each of the data columns.
DOI: 10.5061/dryad.15v00/2
title: Genotypes_Synthetic_Populations
DOI: 10.5061/dryad.1j3s0/22
title: S3 interview.wps

description: post IDE implementation staff interview no 3
DOI: 10.5061/dryad.1j3s0/23
title: S4 interview

description: post IDE implementation staff interview no 4
DOI: 10.5061/dryad.1j3s0/24
title: s5 interview

description: post IDE implementation staff interview no 5
DOI: 10.5061/dryad.1j3s0/25
title: S6interview

description: post IDE implementation staff interview no 6
DOI: 10.5061/dryad.1j3s0/26
title: S7 interview

description: post IDE implementation staff interview no 7
DOI: 10.5061/dryad.1j3s0/27
title: S8interview.wps

description: post IDE implementation staff interview no 8
DOI: 10.5061/dryad.20k7m/1
title: Molecular dataset and phylogeny of Cycadales

description: This ZIP file contains two files. First, the molecular dataset (three genes, 5587 nucleotides, and 243 taxa) used to build the phylogeny, and to estimate origin and divergence times of the Cycadales. This is a NEXUS format, ready for MrBayes analyses. Second, the MrBayes tree obtained from the analysis described in the paper.
DOI: 10.5061/dryad.4cv02/3
title: Codes used for EBSP simulation analyses

description: Set of codes used for generating simulated datasets and performing EBSP analyses. File "ms_beast.R" runs the coalescent simulator MS (via package "phyclust" providing a R version of MS) to generate sequences from the template file "testalt_template" and create XML input files for use in BEAST. File "run.sh" runs these XML inputs in BEAST. File "plots.R" is used to visualize generated skyline plots.
DOI: 10.5061/dryad.4cv02/4
title: Sequence alignments

description: FASTA alignments of all H. amphibius' sequences included in this study: mitochondrial control region ("Hippo_CR_all.fas"), cytochome-B ("Hippo_cytB_all.fas") and nuclear HMG-2 (Hippo_Nucl_all.fas"). Taxon ID are listed in Supplementary Table S1.
DOI: 10.5061/dryad.5025v.1
title: Data from: Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships
DOI: 10.5061/dryad.5025v.2
title: Data from: Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships
DOI: 10.5061/dryad.5025v.2/1.2
title: Character_matrix_coded
DOI: 10.5061/dryad.5025v.2/5.2
title: Character_matrix
DOI: 10.5061/dryad.5025v.2/6.2
title: List_of_fossil_hypodigms
DOI: 10.5061/dryad.5025v.2/7.2
title: List_of_Characters
DOI: 10.5061/dryad.5g8c5/3
title: Kinematic R code
DOI: 10.5061/dryad.5g8c5/4
title: Suction performance R code
DOI: 10.5061/dryad.602d6/1
title: Figure files

description: All data associated with the figures in the publication
DOI: 10.5061/dryad.602d6/2
title: data.files

description: Microsoft excel files: Raw data for all figures in manuscript
DOI: 10.5061/dryad.6b340/6
title: Arlequin input file

description: Microsatellite data input file for Arlequin (Rst, AMOVA, Mantel Test)
DOI: 10.5061/dryad.6b340/7
title: R script for acoustic calculations

description: Two scripts for acoustic signal variable extraction. One calculates mean, sd, cv across calls for a single individual and generates a new data file with all individuals together; the other script calculates these values across waveforms for a single individual.
DOI: 10.5061/dryad.6b340/8
title: Starting file for R script

description: File required to run R script for acoustic variable calculations. See details within the script document and script ReadMe file.
DOI: 10.5061/dryad.6rh72/2
title: wsubcalde_6m_Dc_locus

description: tree description of the Figure 3
DOI: 10.5061/dryad.6rh72/3
title: figure 4

description: relationship between the allelic richness and the distance between the current location of the populations and the distance to the putative refugia (in km)
DOI: 10.5061/dryad.6tm5v/1
title: Non-Human Primate MRI Cardiac Functional Data

description: This file consists of MRI datasets from eight naive non-human primates.  The datasets are repeated twice for test and retest acquisitions.  Each dataset includes cardiac structural, tagging, and phase contrast MRI images.
DOI: 10.5061/dryad.8ck55/1
title: Experiment1_Data

description: Data from Experiment 1 (growth and fecundity).
DOI: 10.5061/dryad.bt0ns/1
title: DFE sim n = 5 dimensions
DOI: 10.5061/dryad.bt0ns/2
title: DFE sim n = 10 dimensions
DOI: 10.5061/dryad.bt0ns/3
title: DFE sim n = 25 dimensions
DOI: 10.5061/dryad.ff982/1
title: FvB Geo_Structure_all_poplns_03Feb2015

description: Nuclear microsatellite data for studied populations of Fragaria
DOI: 10.5061/dryad.hn390/1
title: Coadaptation data

description: Data description can be found in the ReadMe file.
DOI: 10.5061/dryad.jc8cp/1
title: Raw data species richness, environment, forest history
DOI: 10.5061/dryad.m5298/1
title: CaneToad_muscle_denovo_transcriptome_Australia

description: De novo transcriptome assembly of Cane toad muscle (triceps femurs) tissue using the Trinity assembler, with default settings. We filtered out any transcripts with less that 1% of the per-gene expression level using a script bundled with Trinity. Raw reads from one individual per geographic population (RM0021M, RM0094M, RM0108M and RM0169M) were pooled to produce the representative read set across all populations that was used in de novo assembly. File contains assembled sequences in fast format
DOI: 10.5061/dryad.m5298/2
title: CaneToad_West_vs_East_Differential_expression_results

description: Differential gene expression results in invasive Cane toad muscle tissue between the Western Australia range edge (West) and the Queensland range core (East). Results produced in edgeR from associated RSEM individual expression count files (See attached archive). In edgeR testing was conducted using the classic approach for two groups, CPM-filtered counts were TMM-normalised, quantile-adjusted conditional maximum likelihood method was used to estimate dispersions and the exact test was used to call differentially expressed genes and compute p-values. Columns are: transcript ID, Log Fold-change between the regions (-ve values donate down-regulation in the West and +ve the opposite), Log CPM (counts per million mapped reads), P-value of differential expression, FDR is False discovery rate.