cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bs427/1
title: arrival

description: Contains all the flycatcher arrival data used in the statistical analyses
DOI: 10.5061/dryad.bs427/2
title: swaps14

description: data of the 2014 swaps of tit broods
DOI: 10.5061/dryad.bs427/3
title: swaps15

description: Data of the 2015 tit nests used for swapping
DOI: 10.5061/dryad.bs427/4
title: replicates

description: Data of every nest box and which subplot they belonged to
DOI: 10.5061/dryad.bs427/5
title: population

description: Data of general breeding biology of the four most common nest box breeders in our study
DOI: 10.5061/dryad.bs427/6
title: arrorder

description: Data of the arrival order of flycatcher males and females in relatively "early" and "late" subplots. Used for figure 4.
DOI: 10.5061/dryad.c0kr7/1
title: Tree species traits in forest plots in Borneo and Peru

description: Specific leaf area, leaf carbon concentration, leaf nitrogen concentration, leaf C:N ratio, and mycorrhizal status of tree species under two soil conditions (less fertile sand or more fertile clay) in Borneo and Peru. The data are used for Tables 1 and 2 and Figure 6 of the paper. For more detail, see the main text of the paper.
DOI: 10.5061/dryad.d5r18/1
title: R code used for sexual dimorphism analysis

description: File contains R code for modelling alligator and rhea growth curves, including population structure and taphonomic bias, and subsampling routines.
DOI: 10.5061/dryad.d7g4c/1
title: Pairwise Relatedness Data

description: This excel file has three sheets containing pairwise relatedness data used in each of the three main analyses in the paper. 1) Relatedness between male-female dyads. 2) Relatedness between mothers and sires. 3) Relatedness in breeding and non-breeding dyads. A final sheet explains the column headings.
DOI: 10.5061/dryad.d7g4c/2
title: Chimpanzee Genotypes

description: This file includes genotyping data at 11 microsatellite loci used for paternity analyses. All genotyped individuals are included and are assigned the same code given in the pairwise relatedness file.
DOI: 10.5061/dryad.d7v27/1
title: Parentalcare

description: Raw data on parental care behaviour for 22 mother-litter sets.
DOI: 10.5061/dryad.dp005/1
title: Metadata

description: Tab-delimited text file providing the following sample information: shoot, plot, treatment, tissue, host, barcode sequence, forward and reverse primer sequences, lane
DOI: 10.5061/dryad.dp005/2
title: otu_table.txt

description: Tab-delimited text file containing OTU table with taxonomic assignments.
DOI: 10.5061/dryad.f09rh.2/10.2
title: Ctenochaetus_striatus_denovo_batch_1_filtered.vcf

description: Filtered denovo_map.pl RAD reads in .vcf format for Ctenochaetus striatus
DOI: 10.5061/dryad.f09rh.2/11.2
title: Chaetodon_austriacus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon austriacus
DOI: 10.5061/dryad.f09rh.2/12.2
title: Chaetodon_fasciatus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon fasciatus
DOI: 10.5061/dryad.f09rh.2/13.2
title: Chaetodon_larvatus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon larvatus
DOI: 10.5061/dryad.f09rh.2/14.2
title: Chaetodon_melapterus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon melapterus
DOI: 10.5061/dryad.f09rh.2/15.2
title: Chaetodon_mesoleucos_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon mesoleucos
DOI: 10.5061/dryad.f09rh.2/16.2
title: Chaetodon_paucifasciatus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon paucifasciatus
DOI: 10.5061/dryad.f09rh.2/5.2
title: Chaetodon_mesoleucos_denovo_batch_1_filtered.vcf

description: Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon mesoleucos
DOI: 10.5061/dryad.f09rh.2/9.2
title: Chaetodon_trifascialis_denovo_batch_1_filtered.vcf

description: Filtered denovo_map.pl RAD reads in .vcf format for Chaetodon trifascialis
DOI: 10.5061/dryad.g8h54/1
title: Goetz_etal_2017_data

description: The zip file holds six tab delimited text files that contain 1 Hz mobile lab data and accompanying local background estimates from 2012 measurements in SW PA and NE PA and 2015 measurements in  NE PA. See publication for more details. The provided local background data is derived from 20 minute 35th percentile smoothing. All time information is in military format. Date information is in mm/dd/yy. Concentration data is in units of ppbv. GPS data is in units of decimal degrees and in datum WGS84. Please contact authors if additional information is needed. All use of the provided data should be accompanied by the proper citations.
DOI: 10.5061/dryad.m066r/1
title: datasummarysuppl.

description: Excel file. One spreadsheet of samples with data, second with haplotype info.
DOI: 10.5061/dryad.mk32s/1
title: Aligned data matrices

description: all aligned, phased matrices, Nexus format
DOI: 10.5061/dryad.mn7k4/1
title: Dmagna_ME_alltraits_summary

description: Summary data file containing trait information for all individuals, for use with R scripts 1, 2, 3 and 4.
DOI: 10.5061/dryad.q2t18/2
title: Final DNA sequence assembly
DOI: 10.5061/dryad.q2t18/3
title: SSR information
DOI: 10.5061/dryad.q2t18/4
title: CDS of unigenes
DOI: 10.5061/dryad.q2t18/5
title: RPKM values of control group and treatment group
DOI: 10.5061/dryad.r99p7/5
title: BAMMOutput_v7

description: This R script analyzes the BAMM output generated by this study and includes code for generating the figures presented here.
DOI: 10.5061/dryad.r99p7/6
title: SongRates_Adams

description: This R script includes the code that was used to estimate and compare multivariate rates of trait evolution between Thraupids and Furnariids using the method developed by Adams (2014).
DOI: 10.5061/dryad.tc28h/2
title: SuppFig2-Ca vs Mn

description: Fig. S2. Manganese plotted against δ44/42Ca values for bone and enamel samples measured in this study.
DOI: 10.5061/dryad.tc28h/5
title: TableS2R1

description: Table S2. Calcium isotope values (expressed as δ44/42Ca and δ43/42Ca (in ‰) relative to standard ICP Ca-Lyon) measured on two Pleistocene assemblages as well as elemental concentrations for some major and trace elements. (1) δ13C and δ15N values from Bochoerens et al. 1997. Tooth type: capital letters refer to the upper tooth row.
DOI: 10.5061/dryad.tc28h/7
title: SuppFig3-Jaurens sampling 1-2

description: Photographs of samples analysed for this study; Canis lupus, Crocuta crocuta, Panthera spelaea, P. pardus, Ursos arctos; Jaurens, Corrèze, France.
DOI: 10.5061/dryad.tc28h/8
title: SuppFig4-Jaurens sampling 2-2

description: Figure S4. Photographs of samples analysed for this study; Ursos arctos, Coelondonta antiquitatis, Rangifer tarandus, Bison priscus; Jaurens, Corrèze, France.
DOI: 10.5061/dryad.tc28h/9
title: TableS1

description: Table S1. Data from the literature used in the model of the water/rock ratio presented in Fig. 2.
DOI: 10.5061/dryad.tc29h/4
title: Data (part 4) underpinning "Smart wing rotation and trailing-edge vortices enable high frequency mosquito flight", Bomphrey et al, 2017.

description: Flow field from computational fluid dynamic analysis at a key instant, t3. The files are in Tecplot binary format, readable using flow visualization software such as Tecplot and Paraview. Further information is available on request.
DOI: 10.5061/dryad.tc29h/5
title: Data (part 5) underpinning "Smart wing rotation and trailing-edge vortices enable high frequency mosquito flight", Bomphrey et al, 2017.

description: Flow field from computational fluid dynamic analysis at a key instant, t4. The files are in Tecplot binary format, readable using flow visualization software such as Tecplot and Paraview. Further information is available on request.
DOI: 10.5061/dryad.tc29h/6
title: Data (part 6) underpinning "Smart wing rotation and trailing-edge vortices enable high frequency mosquito flight", Bomphrey et al, 2017.

description: Flow field from computational fluid dynamic analysis at a key instant, t5. The files are in Tecplot binary format, readable using flow visualization software such as Tecplot and Paraview. Further information is available on request.
DOI: 10.5061/dryad.v103v/1
title: Seasonal wild pig habitat suitability in northern Australia: mapped results

description: This dataset contains mapped results from a resource-based, spatially-explicit and regional-scale habitat model for wild pigs in northern Australia. The modelled habitat suitability index (HSI) describes relative habitat quality for wild pig breeding and persistence during the dry (using data from March/April) and wet (using data from October/November) season. HSI values in this dataset effectively range between 11 and 81. They can be broadly classified as follows: HSI ≥ 60 = highly suitable habitat; HSI ≥ 40 = moderately suitable habitat; HSI &lt; 40 unsuitable habitat. Underlying model parameters were elicited from experts. This dataset contains results from an expert-averaged model run. The model contained a variable "Disturbance stress" for which no spatial data proxies were available. In this dataset, we assumed a uniformly “high” intensity and frequency of control activities, which likely overestimated disturbance and undervalued habitat suitability. For further detail on modelling methods and assumptions please consult the accompanying publication Froese et al. (2017). For each seasonal dataset, a georeferenced compressed .TIF file, a metadata .XML file, and an ESRI ArcGIS .LYR file visualizing an appropriate classification scheme are provided.
DOI: 10.5061/dryad.v103v/2
title: Data inputs for spatial pattern suitability analysis and model validation

description: This dataset contains input data necessary to reproduce analyses described in Froese et al. (submitted) and its supplementary information. The dataset is divided into two sub-folders. Folder "S3Appendix" contains data for spatial pattern suitability analysis, including distance-dependent response-to-pattern curves (folder "fD", .CSV format) as elicited from six wild pig experts, and raster data (folder "GIS", .TIF format) describing modelled resource quality indices. Folder "S4Appendix" contains data for model validation of each seasonal scenario (folders "dry" and "wet", .TXT format), including the expected habitat suitability index across validation backgrounds and the predicted habitat suitability index at wild pig presence records. Each "Expected" and "Predicted" folder contains 28 .TXT files because six expert models and one expert-averaged model were each validated against four independent validation data sets. For further detail about spatial analysis and validation methods and assumptions please consult the accompanying publication Froese et al. (2017).
DOI: 10.17632/v5jy3367rs.1
title: MOLECULAR-CELL-D-16-01543R1 Shetty et al

description: Data for Northerns and Westerns in the following figures: Fig 1B (Western - same panel as used in Fig S3), Fig 5B (Northern), Fig 6B (Northern), Fig S3A (Westerns), Fig S5A (Western), Fig S5B (Northern), and Fig S6B (Northerns)
DOI: 10.5061/dryad.1828q/1
title: Allele frequencies Varronia curassavica

description: Allele frequencies for eight microsatellite loci of individuals Varronia curassavica Jacq. (Boraginaceae) from four populations of Santa Catarina, Brazil.
DOI: 10.5061/dryad.41793/1
title: data and scripts

description: 1) R_ferrumequinum_Trinity_assemblies.fas is assemblies of RNAseq using Trinity;                                                                     2) Homo_cds_11158ortho_vs_RFE_Trinity.tblastx is the results from tblastx.  3) parse_results_from_tblastx.pl, extract_sequences_from_tblastx_results.pl, are scripts used to extract sequences from tblastx results
DOI: 10.5061/dryad.42s0c/4
title: Burleigh, Kimball, Braun, 2015 ML Tree, pruned

description: The tree used in this study. This is a tree from Burleigh, Kimball and Braun 2015, pruned to only include the species in this study.
DOI: 10.5061/dryad.42s0c/5
title: Diet composition full

description: A spreadsheet of diet composition for each species, including the composition from each separate study and the average (in bold) across studies for each species.
DOI: 10.5061/dryad.42s0c/6
title: Diet composition

description: A table of mean body mass and diet composition for each species.
DOI: 10.5061/dryad.4g200/1
title: Ghanizadeh et al_Dryad data file

description: All data associated with this ms.
DOI: 10.5061/dryad.55gb7/1
title: Climatic data

description: 01 - Climatic data for each site.File names in the 01_CLIM folder: climABI.csv, climBIC.csv, climD1823D1847.csv (given their geographical proximity, D1823 and D1847 received the same climatic data), climSUT.csv.These files contain climatic variables for the 1953-2013 period.Climatic variables are coded with letters:T: monthly mean temperaturesP: total monthly precipitationS: total monthly snowfallDD: total monthly degree dayDC: monthly mean drought-codeGSL: growth season length.Numbers following the variables letters indicate the number of the month associated with the variable. Negative values refer to a month of the previous year. GSL6 refers to the current GSL and GSL-6 refers to the previous GSL.
DOI: 10.5061/dryad.55gb7/3
title: Insect outbreak dates

description: 03 - Insect outbreak dates.File name: 03_outbreaks_dates.xlsx.This file contains the forest tent caterpillar and spruce budworm outbreak dates for each site.
DOI: 10.5061/dryad.55gb7/4
title: Distance among trees

description: 04 - Distances among trees on each site.File names in the 04_DIST folder: distABI.csv, distBIC.csv, distD1823.csv, distD1847.csv, distSUT.csv.These files contain the distances (&lt; 20 m) between the cored trees (rows) and all their neighbours (columns).Trees ID are coded with their species code followed by a number.
DOI: 10.5061/dryad.5sg24/1
title: DATA

description: This file contains data for the second and third objectives of the paper. Data for the first objective is presented in supplementary materials.
DOI: 10.5061/dryad.5vs40/1
title: R script to run gbs2ploidy on the aspen data

description: This script formats and summarizes the aspen data and then runs gbs2ploidy on the data set. The files needed for analysis are included in this Dryad submission.
DOI: 10.5061/dryad.5vs40/2
title: Aspen ID file

description: This csv text file contains population and individual IDs for the aspen samples, as well as ploidy levels inferred from microsatellites or flow cytometry.
DOI: 10.5061/dryad.5vs40/3
title: Simulation code

description: R script to generate the simulated data used to test gbs2ploidy.
DOI: 10.5061/dryad.5vs40/4
title: Simulation data

description: This is a R workspace object. It contains the simulation output from the allo- and autotetraploid simulations. It was generated with the ploidySims.R code also included with this Dryad submission.
DOI: 10.5061/dryad.5vs40/5
title: Allele sepecific read counts

description: This file contains the allele specific read counts for the aspen data. Each row contains the data for one SNP and each pair of columns has the data for an individual. These two columns contain the number of reads of each allele (one allele per column) if the individual was heterozygous at that SNP. Otherwise there is a NA for each column.
DOI: 10.5061/dryad.5vs40/6
title: Variant file for the aspen data

description: This vcf (variant call format) contains the filtered variant data for the aspen samples.
DOI: 10.5061/dryad.65th7/1
title: DSD27
DOI: 10.5061/dryad.772h7/1
title: Leaf trait data

description: Leaf wet weight (g), dry weight (g) and area (square cm) used to calculate leaf traits.
DOI: 10.5061/dryad.772h7/2
title: Plant height and species information
DOI: 10.5061/dryad.772h7/3
title: Soil moisure values
DOI: 10.5061/dryad.772h7/4
title: Temperature data

description: Half-hour resolution temperature data (degrees C) collected by iButtons
DOI: 10.5061/dryad.8m2t5/1
title: Cormorant gene alignment

description: NEXUS file used to generate the Phylogram in Figure 1 using MrBayes
DOI: 10.5061/dryad.b8c4r/1
title: Thioflavin T as an amyloid dye: fibril quantification, optimal concentration, and effect on aggregation
DOI: 10.5061/dryad.b9h54/1
title: Camallanus cotti genotypes
DOI: 10.5061/dryad.b9h54/2
title: CACO-FASTA
DOI: 10.5061/dryad.bs427/7
title: arrival_early_late

description: R script in which all the results in this study can be checked and replicated, using the data files available.
DOI: 10.5061/dryad.dk6v5/1
title: Species, land use and temperature data

description: The file includes data from different sources including reports (see file for detailed references) and estimations based on these sources.
DOI: 10.5061/dryad.f09rh.1
title: Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish
DOI: 10.5061/dryad.f09rh.1/1.1
title: Chaetodon_austriacus batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon austriacus.
DOI: 10.5061/dryad.f09rh.1/2.1
title: Chaetodon_fasciatus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon fasciatus.
DOI: 10.5061/dryad.f09rh.1/3.1
title: Chaetodon_larvatus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon larvatus.
DOI: 10.5061/dryad.f09rh.1/4.1
title: Chaetodon_melapterus_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon melapterus.
DOI: 10.5061/dryad.f09rh.1/5.1
title: Chaetodon_mesoleucos_batch_1_filtered.vcf

description: Filtered RAD reads in .vcf format for Chaetodon mesoleucos.
DOI: 10.5061/dryad.f09rh.2/17.2
title: Chaetodon_pictus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon pictus
DOI: 10.5061/dryad.f09rh.2/18.2
title: Chaetodon_semilarvatus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon semilarvatus
DOI: 10.5061/dryad.f09rh.2/19.2
title: Chaetodon_trifascialis_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Chaetodon trifascialis
DOI: 10.5061/dryad.f09rh.2/20.2
title: Ctenochaetus_striatus_refmap_batch_1_filtered.vcf

description: Filtered ref_map.pl RAD reads in .vcf format for Ctenochaetus striatus
DOI: 10.5061/dryad.f5qk7.2
title: Data from: Targeted capture of complete coding regions across divergent species
DOI: 10.5061/dryad.f5qk7.2/1.2
title: Supplementary File 2 - Probe Design and Sequences

description: Complete set of probes used for cross-species targeted capture and associated data
DOI: 10.5061/dryad.f5qk7.2/2.2
title: Supplementary File 3 - Assembly and Analysis Pipelines and Scripts

description: Custom pipelines and scripts for the assembly and analysis of cross-species  targeted capture data
DOI: 10.5061/dryad.fv4b5/1
title: CalciumWater

description: Details of the individual experimental measurements made in order to extract binding energy results.
DOI: 10.5061/dryad.hg785/1
title: Stegodyphus africanus .alleles file
DOI: 10.5061/dryad.hg785/2
title: Stegodyphus dumicola .alleles file
DOI: 10.5061/dryad.hg785/3
title: Stegodyphus lineatus .alleles file
DOI: 10.5061/dryad.hg785/4
title: Stegodyphus mimosarum .alleles file
DOI: 10.5061/dryad.hg785/5
title: Stegodyphus pacificus .alleles file
DOI: 10.5061/dryad.jf402/1
title: Anopheles gambiae sensu lato fastq files - part 1

description: Individual fastq files for Anopheles gambiae sensu lato from Cameroon - part 1
DOI: 10.5061/dryad.jf402/2
title: Anopheles gambiae sensu lato fastq files - part 2

description: Individual fastq files for Anopheles gambiae sensu lato from Cameroon - part 2
DOI: 10.5061/dryad.k86m5/1
title: Vega-Trejo et al. Sperm BMC- Data

description: Data from Are sexually selected traits affected by a poor environment early in life? by Regina Vega-Trejo, Michael D. Jennions and Megan L. Head. Excel file shows raw data on first spreadsheet and labels in the second one.
DOI: 10.5061/dryad.kv920/1
title: heliconius_speciation_inversions_dryad_repository.tar

description: This archive contains all code and data files required to replicate the analyses in this manuscript.
DOI: 10.5061/dryad.m5g71/1
title: RawPositionsBirdId

description: A data table with the time stamps from the light data as recognised by the threshold method, along with the derived lat/long for position, used for each individual bird.
DOI: 10.5061/dryad.mn7k4/2
title: Dmagna_ME_growth_coef

description: Data file for calculating growth coefficients for use with R script 1 (this is optional, as the summary of growth data is included in the Dmagna_ME_alltraits_summary.txt file).
DOI: 10.5061/dryad.mn7k4/3
title: Dmagna_ME_growth_PMRN

description: Data file for calculating and plotting probabilistic maturation reaction norms (PMRNs), for use with R scripts 5 and 6.
DOI: 10.5061/dryad.mn7k4/4
title: DaphniaME_1of6_MANOVA-ANOVA-posthoc

description: R script 1 of 6: calculating growth coefficients, followed by multivariate analysis of variance (MANOVA), analysis of variance (ANOVA)/GLMs and post-hoc tests.
DOI: 10.5061/dryad.mn7k4/5
title: DaphniaME_2of6_Univariate-figs

description: R script 2 of 6: Plotting univariate figures (those considered in the analysis of variance /GLMs from R script 1).
DOI: 10.5061/dryad.mn7k4/6
title: DaphniaME_3of6_PCA-PCV-visual

description: R script 3 of 6: Principal component analysis, together with visualisation of phenotypic change vectors in 2D sapce.
DOI: 10.5061/dryad.mn7k4/7
title: DaphniaME_4of6_PCV-stats

description: R script 4 of 6: Statistical analysis for identifying significant differences in vector lengths and angles of phenotypic change vectors (as visualised in R script 3).
DOI: 10.5061/dryad.mn7k4/8
title: DaphniaME_5of6_PMRN_GLM-selection

description: R script 5 of 6: Using GLMs to statistically model probabilistic maturation reaction norms, and comparing among models to identify the best fit.
DOI: 10.5061/dryad.mn7k4/9
title: DaphniaME_6of6_PMRN-figs

description: R script 6 of 6: Using best fitting GLM (identified in R script 5) in plots of probabilistic maturation reaction norms.
DOI: 10.5061/dryad.mv580/1
title: Porcelli et al 2016 JEB dryad

description: Data files used for data analysis presented in Porcelli et al JEB Local adaptation of reproductive performance during thermal stress
DOI: 10.5061/dryad.n82sv/1
title: Harvey & Solberg et al BMC EB

description: Data for the growth and survival analysis
DOI: 10.5061/dryad.nc69n/1
title: DATA from three experiments
DOI: 10.5061/dryad.q2t18/6
title: Differential_analysis_results
DOI: 10.5061/dryad.q2t18/7
title: The results of qRT-PCR for validated genes
DOI: 10.5061/dryad.s43c7/1
title: TableS1_primers

description: Table S1: Primer pairs used for Q-PCR on the Medicago truncatula genes
DOI: 10.5061/dryad.s43c7/2
title: Table S2. List of genes differentially regulated by NAA

description: List of genes down-regulated in the NAA condition. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.
DOI: 10.5061/dryad.s43c7/3
title: Table S3. List of genes differentially regulated by Nod Factors

description: Table S3. List of genes differently expressed in the NF treatment compared to control conditions. The first column corresponds to the NimbleGen probe ID, the second to the equivalent Mt4 coding sequence reference when available. Affy ID corresponds to the more accurate medicago affymetrix probe. LFC: Log2 fold change. CT=control condition.  NAA= 10-6M NAA; NF=10-7M NF; NAA+NF=10-6M NAA + 10-7M NF. All treatments are for 10h.