cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6536v/14
title: Reddy_sup_figS3_Prum_noJAR

description: This figure shows the topology of the Prum_noJAR tree (the partitioned RAxML tree for the Prum et al. 2015 dataset after excluding the data that overlap with Jarvis et al. 2014).
DOI: 10.5061/dryad.6536v/16
title: Reddy_sup_figS4_genetic_code

description: Structure of the genetic code showing the potential for the physicochemical characteristics of amino acids to lead to site-specific biases in nucleotide frequencies,
DOI: 10.5061/dryad.6536v/17
title: Reddy_sup_figS5_GCboxplot

description: Boxplot showing GC-content variation for each locus in the EB2, Prum, and Jarvis datasets. Only the parsimony informative sites were analyzed, as in Fig. 6 of the manuscript. However, this figure shows the variation when all taxa for each dataset are included in the analysis.
DOI: 10.5061/dryad.6536v/18
title: Reddy_sup_fileS2_PrumLoci

description: Information about the loci used by Prum et al. 2015. An xlsx file with two sheets ("README" and "Prum locus information").
DOI: 10.5061/dryad.6536v/19
title: Reddy_sup_fileS5_alignments.tar

description: tar.gz file with four nexus format alignments. Folder also contains a README with additional information about the sequence alignments.
DOI: 10.5061/dryad.6f052/7
title: Data7_DistancesPostHoc

description: Details of the posthoc Nemenyi tests between gopher genera (M3 shape).
DOI: 10.5061/dryad.6ph62/1
title: Manuscript data
DOI: 10.5061/dryad.96320/2
title: Original data
DOI: 10.5061/dryad.c6kj2/3
title: Microsatellite gentoypes

description: Genotypes for 11 microsatellite loci used in this study. All individuals are included with a collection site identifier.
DOI: 10.5061/dryad.d2g8v/1
title: Dama dama dama Dryad submission

description: European fallow deer (Dama dama dama) microsatellite data genotyped across 10 loci
DOI: 10.5061/dryad.d866h/1
title: Rader et al. Supplemental Data

description: This data file contains morphological and stable isotope data from 13 species of Cinclodes ovenbirds, along with museum collections metadata for each specimen.
DOI: 10.5061/dryad.dk385/1
title: MEs_Supplementary_Material

description: Explanation of Supplementary Material
DOI: 10.5061/dryad.dk385/2
title: Master Data Set

description: Master data set kindly made available by Dr Richard Bambach
DOI: 10.5061/dryad.dk385/3
title: Bambach data set

description: Most up-to-date data set used in the main analyses in paper
DOI: 10.5061/dryad.dk385/4
title: Crater data

description: Frequency of  crater occurrence, basis of analysis of impact periodicity
DOI: 10.5061/dryad.dk385/5
title: Supplementary analyses of Peters and Rohde&Muller data

description: Series of graphical analyses of periodicity in the Peters and Rohde&Muller datasets
DOI: 10.5061/dryad.f4580/1
title: BEHECO-2016-0233_Data

description: The data collected in the laboratory to test the relationship between a predator's aggressiveness level and prey-choice decision-making. The data format is for R. The R code is provided in the supplementary material.
DOI: 10.5061/dryad.hh375/10
title: 13-MI11993-04M

description: Magnetic resonance imaging data of animal 13-MI11993-04M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/11
title: 13-MI11993-05M

description: Magnetic resonance imaging data of animal 13-MI11993-05M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/12
title: 14-MI11768-01M

description: Magnetic resonance imaging data of animal 14-MI11768-01M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/13
title: 14-MI11768-02M

description: Magnetic resonance imaging data of animal 14-MI11768-02M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/14
title: 14-MI11768-03M

description: Magnetic resonance imaging data of animal 14-MI11768-03M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/15
title: 14-MI11768-04M

description: Magnetic resonance imaging data of animal 14-MI11768-04M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/16
title: 14-MI11768-05M

description: Magnetic resonance imaging data of animal 14-MI11768-05M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/9
title: 13-MI11993-03M

description: Magnetic resonance imaging data of animal 13-MI11993-03M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hq67g/1
title: Parasitology Selected Course Materials

description: Selected exercises and problem sets for starting a student-centered course in undergraduate Parasitology
DOI: 10.5061/dryad.hr364/1
title: Interannual spring temperature variability

description: The standard deviation (SD) of mean minimum temperatures of the March–May period over the past 100 years (1901–2013). Spatial resolution: 5-arc minutes.
DOI: 10.5061/dryad.hr364/2
title: Interannual winter temperature variability

description: The SD of the mean minimum temperature of the coldest month over the past 100 years (1901–2013). Spatial resolution: 5-arc minutes.
DOI: 10.5061/dryad.j5v05/1
title: State Harvest Data (csv)

description: Commercial snapping turtle harvest data (in individuals) for eleven states from 1998 - 2013. States reporting are Arkansas, Delaware, Iowa, Maryland, Massachusetts, Michigan, Minnesota, New Jersey, North Carolina, Pennsylvania, and Virginia.
DOI: 10.5061/dryad.j5v05/2
title: Input and execution code for Colteaux_Johnson_2016

description: Attached R file includes the code described in the listed publication. The companion JAGS (just another Gibbs sampler) code is also stored in this repository under separate cover.
DOI: 10.5061/dryad.j5v05/3
title: JAGS model code for Colteaux_Johnson_2016

description: Attached R file includes the JAGS (just another Gibbs sampler) code described in the listed publication. The companion input and execution code is also stored in this repository under separate cover.
DOI: 10.5061/dryad.jk111/1
title: Script for CCA analysis and visualization

description: File with the script for execute the CCA analysis and visualize the results
DOI: 10.5061/dryad.jk111/2
title: environment300

description: Environmental data for the 300 m scale for the CCA analysis
DOI: 10.5061/dryad.jk111/3
title: Species

description: abundance and identity of species for the CCA analysis
DOI: 10.5061/dryad.jk111/4
title: data for SEM all

description: Data containing landscape proportion and abundance and richness (Chao-1 corrected) for the most abundant bees and for transect, pan traps and total dataset.
DOI: 10.5061/dryad.k23mq/1
title: Supplementary Data

description: Details of the datasets included in the meta-analyses and the results for individual datasets
DOI: 10.5061/dryad.p2d8h/1
title: Cannabis Genotypes

description: Reference (N=1324) and test (340) genotypes of Cannabis sativa for 13 microsatellite loci
DOI: 10.5061/dryad.pn358/1
title: Montoya et al. JEXBIO2016141325

description: Excell file with raw data and some calculated data used for all the analyses included in the article Montoya et al. Journal of Experimental Biology, where detailed description of data collected can be found.
DOI: 10.5061/dryad.pr7bk/1
title: Barn swallow data for Fulop et al. 2017 Journal of Avian Biology

description: Data file containing: (i) data of adult Barn swallows involved in the study; (ii) body mass an tarsus length data of 319 Barn swallow individuals used to calculate SMA slope for scaled-mass index; and (iii) data of Barn swallow nests involved in the study.
DOI: 10.5061/dryad.sq15g/1
title: Zhang et al FE-2016-00948.R1

description: effects of the frequency and the rate of N addition and mowing on species richness, species asynchrony, ecosystem productivity and standard deviation, and ecosystem stability.
DOI: 10.5061/dryad.tf697/1
title: Data from: Sympatry predicts spot pigmentation patterns and female association behavior in the livebearing fish "Poeciliopsis baenschi"
DOI: 10.5061/dryad.ts51k/1
title: Mt. Graham red squirrel natal dispersal distance

description: Dispersal distance (m) of radio-collared juvenile Mt. Graham red squirrels. an.id = unique animal id; sex = m,f; dist.moved = distance moved (m); year = 2010-2013; long.dist = where dispersal distance &gt; 150 m males, 100 m females
DOI: 10.5061/dryad.ts51k/2
title: Merrick_Koprowski2016_Dispersal_correlates

description: Data set used to model dispersal distance and probability of non-philopatric distance dispersal in juvenile Mt. Graham red squirrels from 2010 - 2013 as a function of intrinsic and extrinsic factors.
DOI: 10.5061/dryad.v0rp5/3
title: RNAseq analysis scripts

description: zip archive of scripts used to assemble de novo transcriptome of Trifolium fucatum and assess differential expression
DOI: 10.5061/dryad.v84c2/13
title: BrIP seq peaks

description: BrIP seq peaks in WT and ORC mutant cell lines
DOI: 10.5061/dryad.052q5.2
title: Data from: Global terrestrial Human Footprint maps for 1993 and 2009
DOI: 10.5061/dryad.052q5.2/1.2
title: Human Footprint maps

description: 7-zip file including the Human Footprint maps for 1993 and 2009, individual pressures, and validation data. A full data description is included as a word file in the download.
DOI: 10.5061/dryad.1fk40/1
title: Degus data Dryad submission

description: Data for analysis of AGD and wt in Degus
DOI: 10.5061/dryad.1m0t8/1
title: Data_table 1_group1

description: Data for group 1 in Table 1
DOI: 10.5061/dryad.1m0t8/2
title: Data_table 1_group2

description: Data for group 2 in Table 1
DOI: 10.5061/dryad.1m0t8/3
title: Data_figure 3

description: Data for Figure 3
DOI: 10.5061/dryad.1m0t8/4
title: Data_figure 4

description: Data for Figure 4
DOI: 10.5061/dryad.1m0t8/5
title: ESM Video S1-S4

description: Video recording for S1-S4.
DOI: 10.5061/dryad.1nn35/1
title: Glyphosate redirects wetland vegetation trajectory following willow invasion

description: Vegetation data collected to describe the effect of glyphosate in a Salix cinerea invaded wetland. See the README file in the zip folder for further details
DOI: 10.5061/dryad.30k4v.1
title: Data from: Phylogenomics of Lophotrochozoa with consideration of systematic error
DOI: 10.5061/dryad.30k4v.2/1.2
title: Assemblies
DOI: 10.5061/dryad.30k4v.2/5.2
title: Supplementary Tables
DOI: 10.5061/dryad.30k4v.2/6.2
title: Lophotrochozoa-Kocot_core_orthologs
DOI: 10.5061/dryad.30k4v.2/7.2
title: Supplementary Figures

description: Supplementary Figures 1-70.
DOI: 10.5061/dryad.3p121/5
title: Modeling and analytic code

description: The zip file contains four folders: Data, Preliminary Code, Modeling, and Other Files. These folders correspond to sections in the READ-ME, and each contains a set of related code files.
DOI: 10.5061/dryad.4t140/1
title: Data of physiological condition,gene expression, oxidative stress for each nestling

description: See ReadMe file for description of the data
DOI: 10.5061/dryad.6536v/20
title: Reddy_sup_fileS7_ML_treefiles.tar

description: tar.gz file of four nexus format treefiles. Each contains the RAxML, IQ-TREE, MrBayes, or Exabayes trees along with additional information about the trees (this information is stored as comments in each of the nexus treefiles).
DOI: 10.5061/dryad.6536v/21
title: Reddy_sup_fileS9_EB2noJAR_nextrees

description: Nexus treefile with the results of RAxML and IQ-TREE analyses of the EB2noJAR and EB2noJARnoFGB datasets using the EB2 taxon set. The data matrices used to generate these trees correspond to the EB2 data after excluding the sites overlapping with the Jarvis et al. (2014) data. The data matrix used to generate the noJARnoFGB trees also excludes the gene encoding beta-fibrinogen (FGB). Additional information about the trees can be found as comments in the nexus treefile.
DOI: 10.5061/dryad.6536v/22
title: Reddy_sup_fileS10_Prum_noJAR.tar

description: tar.gz file with three files: 1) a relaxed phylip format alignment of the Prum_noJAR data (concatenated alignments of the Prum et al. 2015 loci after excluding the loci that overlap with Jarvis et al. 2014); 2) a RAxML format partitioning file for the Prum_noJAR data; and 3) a Nexus format treefile with the estimates of phylogeny for Prum_noJAR generated by RAxML and IQ-TREE analyses. Folder also contains a README with additional information about the files.
DOI: 10.5061/dryad.6536v/23
title: Reddy_sup_fileS11_backbone_trees

description: Nexus file containing: 1) the "backbone trees" (trees reduced to ordinal lineages) used for the tree clustering analysis; and 2) symmetric distances among the trees. The file contains embedded comments. If the file is executed in PAUP* it will echo this information to the screen, print the backbone trees, and conduct the tree clustering analysis.
DOI: 10.5061/dryad.6536v/24
title: Reddy_sup_fileS12_squangles_treefiles.tar

description: tar.gz file of two nexus format treefiles. Each contains squangles trees generated using different quartet amalgamation methods. One treefile is the squangles trees for all loci (concatenated) and the other is the same analyses for the BDNF locus. The BDNF locus also includes the ML tree for that locus. Additional information about the trees can be found as comments in the nexus treefiles.
DOI: 10.5061/dryad.6536v/25
title: Reddy_sup_tableS1_evolutionary_rates

description: Table showing relative rates of sequence evolution for coding regions, introns, UCEs, and a mixed alignment that includes multiple types of genomic data. The data were obtained from the trees described by Jarvis et al. (2014).
DOI: 10.5061/dryad.78ng1/1
title: Symphonia globulifera 18 SSRs in 4 populations, Spagedi format

description: Symphonia globulifera data at 18 SSR markers in four populations, in the format of Spagedi software (http://ebe.ulb.ac.be/ebe/SPAGeDi.html). Line 1: total number of individuals (125), number of populations (4), number of geographic coordinates (0), number of loci (18), number of digits per allele (3), ploidy (2). Line 2: number of distance classes (0). Line 3: column headers for rows below, including the sample identification (ID), population name (Place) and locus numbers. Following lines: ID of each sample, population of each sample (Itubera [Ituberá, Brazil], Nkong [Nkong Mekak, Cameroon], Sao_Tome [Sao Tomé island], Paracoug [morphotype S. globulifera in Paracou, French Guiana], Paracou1 [morphotype Symphonia sp.1 in Paracou, French Guiana]), SSR genotype at each locus coded by concatenation of the two alleles using 3 digits for each allele. Last line: END, to signal end of file.
DOI: 10.5061/dryad.78ng1/2
title: Symphonia globulifera genome draft in fasta format, zip compressed

description: Symphonia globulifera L.f. genome draft in fasta format, zip compressed. Final contigs and scaffolds.
DOI: 10.5061/dryad.b331s/1
title: Dianyuea turbinata_matK

description: Dianyuea turbinata maturase K (matK) gene, partial cds; chloroplast
DOI: 10.5061/dryad.b331s/2
title: Dianyuea turbinata_rbcL

description: Dianyuea turbinata ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast
DOI: 10.5061/dryad.b331s/3
title: Dianyuea turbinata_trnH-L

description: Dianyuea turbinata trnL-trnF intergenic spacer, partial sequence; chloroplast
DOI: 10.5061/dryad.b331s/4
title: MATK-F.1392427.C05

description: MatK original sequence data, forward
DOI: 10.5061/dryad.b331s/5
title: MATK-R.1392428.C06

description: MatK original sequence data, reverse
DOI: 10.5061/dryad.b331s/6
title: RBCL-F.1392429.C07

description: rbcL original sequence data, forward
DOI: 10.5061/dryad.b331s/7
title: RBCL-R.1392430.C08

description: MatK original sequence data, reverse
DOI: 10.5061/dryad.b331s/8
title: TRNL-F.YP01513957.E05

description: trnL-trnF original sequence data, forward
DOI: 10.5061/dryad.b331s/9
title: TRNL-R.YP01513958.E06

description: trnL-trnF original sequence data, reverse
DOI: 10.5061/dryad.d3q4q/1
title: Fisher detection–non-detection data

description: This text file contains an R-formatted list of data objects for fitting occupancy models in the "unmarked" package.
DOI: 10.5061/dryad.dc409/1
title: Master ZIP file containing data, analysis script, and metadata.

description: This .ZIP file contains data (.csv) for each milkweed plant included in the experiment, with information about treatments and measurements. It also includes analysis script (.R), and a  readme file (.txt) containing metadata.
DOI: 10.5061/dryad.dc409/2
title: Dataset only (.csv)

description: Download only the data
DOI: 10.5061/dryad.dc409/3
title: Analysis script only (.R)

description: Download only the R script.
DOI: 10.5061/dryad.dr71n/1
title: Microsatellite Genotype Data

description: This file includes raw genotype scores for 21 microsatellite loci across 82 Greater Prairie Chicken sampled from Jasper and Marion Counties in Illinois from 2010-2012.
DOI: 10.5061/dryad.hh375/17
title: 14-MI11768-07M

description: Magnetic resonance imaging data of animal 14-MI11768-07M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/18
title: 14-MI12026-01M

description: Magnetic resonance imaging data of animal 14-MI12026-01M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/19
title: 14-MI12026-02M

description: Magnetic resonance imaging data of animal 14-MI12026-02M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/20
title: 14-MI12026-03M

description: Magnetic resonance imaging data of animal 14-MI12026-03M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/21
title: 14-MI12026-04M

description: Magnetic resonance imaging data of animal 14-MI12026-04M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/22
title: 14-MI12026-05M

description: Magnetic resonance imaging data of animal 14-MI12026-05M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/23
title: 14-MI12026-06M

description: Magnetic resonance imaging data of animal 14-MI12026-06M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/24
title: 14-MI12026-07M

description: Magnetic resonance imaging data of animal 14-MI12026-07M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/25
title: 14-MI12026-08M

description: Magnetic resonance imaging data of animal 14-MI12026-08M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.hh375/26
title: 14-MI12026-09M

description: Magnetic resonance imaging data of animal 14-MI12026-09M, acquired with a Bruker 7 T magnet, with ParaVision 5.1 software. Each subfolder contains a ParaVisions study. The name of the subfolder refers to the date of data acquisition. An overview of all animals is provided in 'animal_overview.xlsx'.
DOI: 10.5061/dryad.j315n.2
title: Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts
DOI: 10.5061/dryad.j315n.2/10.2
title: Tableau-Genes retained  by each tests-dyad

description: This table contains all genes pointed by one list : PCA differentiating flor yeast from other strains (Allyeast-set), Dxy (VinVoile.VQSR.HighQualitybiall.vcf filtered for min genotype quality of 30 and sequence depth of 10), Da (same as Dxy), XPCLR (for Jura  and Spanish populations), 20% Best potentially damaging SNPs (according to SIFT) differentiating wine and flor PCA, codeml value. This table contains data for table S4 and for Figure 3.
DOI: 10.5061/dryad.j315n.2/11.2
title: DTdadi

description: Demographic  inferences (Figure S5a and b): SNP data set for wine and Jura/Hungary flor strains, and wine and Spain/Italy flor strains at dadi format for demographic inference. Obtained with script Vcf-to-dadi.pl
DOI: 10.5061/dryad.j315n.2/12.2
title: Vcf-to-dadi perl  script

description: Demographic  inferences (Figure S5a and b): Perl script that converts a vcf file including 2 or 3 pop with Ancestral Allele field (not necessary if folded)  to a file for diffusion approximation demographic inference (dadi,  Gutenkunst 2015, PLoS Genetics). Requires Bioperl, reference sequence fasta file, and variant file at VCF format (only with strains required for the analysis)
DOI: 10.5061/dryad.j315n.2/13.2
title: TranslocationsCompilation_outputs_delly

description: Compilation of delly  V 0.1.1 outputs  for each strain. This file contrains only events that occured more than 40 times.
DOI: 10.5061/dryad.j315n.2/14.2
title: XPCLR selection test: Script prepares ms data and runs XPLCR