cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1131/2
title: Mviol_Slatifolia_EST.fasta.zip

description: EST (Expressed Sequence tags) of Microbotryum violaceum on S. Latifolia
DOI: 10.5061/dryad.1131/3
title: Mviol_Snutans_EST.fasta.zip

description: EST (Expressed Sequence tags) of Microbotryum violaceum on S. nutans
DOI: 10.5061/dryad.1131/4
title: Mviol_Svulgaris_EST.fasta.zip

description: ESTs of Microbotryum violaceum on S. vulgaris
DOI: 10.5061/dryad.1138/1
title: GlobalVesselAnatomyDatabase.xls

description: The database is a literature compilation of angiosperms vessel anatomy measures for species distributed around the world. The first worksheet defines the data use policy. The second worksheet contains the data with column headings of family, binomial, average individual vessel size (A), vessel number (N), vessel composition (S = A/N), and vessel lumen fraction (F = AN), as well as log transformed values of these 4 variables. The third worksheet contains references for these data.
DOI: 10.5061/dryad.742j4/1
title: Dataset 1.tar

description: Zipped; raw ABI sequence data files.
DOI: 10.5061/dryad.742j4/2
title: Dataset 2.tar

description: Zipped; raw ABI sequence data files.
DOI: 10.5061/dryad.7944/2
title: TreeBase S11004 - Concatenated matrix of five loci from six closely related ophiostomatoid fungi

description: This data is based on an earlier publication (Roe et al. 2010 - Molecular Ecology Resources) and only data for Leptographium longiclavatum and Grosmannia clavigera are applicable to this study.
DOI: 10.5061/dryad.8416/2
title: Trace Files

description: Trace files of the COI sequences of all the fishes collected from Taal Lake, Philippines
DOI: 10.5061/dryad.9124/1
title: supplementary_info_revised

description: Supplementary tables and figures
DOI: 10.5061/dryad.fm0j1/1
title: Founding_phase_data

description: The data in this file describe Polistes biglumis nests at the end of the founding phase. Data were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy). To avoid pseudoreplication, one census was used for each nest.
DOI: 10.5061/dryad.fm0j1/2
title: foundress_fitness

description: This file contains data of the fitness of Polistes biglumis foundresses. They were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy).
DOI: 10.5061/dryad.fm0j1/4
title: predation

description: This file contains data on whether colonies of Polistes biglumis were killed by predators at the end of the founding phase. Data were collected in the field, in years 2004-2008, in 4 populations (Mtg: Montgenèvre, French Hautes Alpes; Fer: Ferrere, Cuneo, Italy; Carì: Canton Ticino, Switzerland; MM: Monte Mare, Isernia, Italy).
DOI: 10.5061/dryad.p515n265/4
title: Flat Holm Site

description: Earthworm prey DNA from slow worms (Anguis fragilis) amplified in PCR with earthworm-specific 12S primers and sequenced using the GS-FLX (Roche) platform. The number of identical sequences returned is indicated by the "Count" heading before each sequence.
DOI: 10.5061/dryad.1142/1
title: AFLPdata.txt

description: This is a binary data file of the 580 polymorphic AFLP peaks scored in GeneMapper. Each peak is scored with a 1 (present) or 0 (absent) and the data have been concatenated into a single string. Each line is labeled with the University of Alaska Museum voucher number and the phenotype of the individual.
DOI: 10.5061/dryad.1142/2
title: AFLPdata.txt

description: This is a binary data file of the 580 polymorphic AFLP peaks scored in GeneMapper. Each peak is scored with a 1 (present) or 0 (absent) and the data have been concatenated into a single string. Each line is labeled with the University of Alaska Museum voucher number and the phenotype of the individual.
DOI: 10.5061/dryad.1146/1
title: esn039_supp.doc

description: Table of haplotype sequences (including their frequency by population) obtained from published sequences, biopsy samples,‘‘whale meat’’ products, and GenBank sources
DOI: 10.5061/dryad.1159/1
title: WUND_DRYAD_tpslandmarkdata.tps

description: This text file is in a format compatible with F. James Rohlf’s TPS morphometrics programs (http://life.bio.sunysb.edu/morph/). The data are the raw x-y coordinates for all 147 specimens. “LM=16” indicates that 16 landmarks were scored. The left and right column of numbers reflects the x and y coordinates, respectively, in pixels. Multiply by the indicated scale factor to convert pixels to centimeters.  The “ID” reflects fishID/treatment. Treatments can be discerned from the corresponding excel file, or by considering this “ID” field. The second number (after the slash) reflects treatment. 1: limnetic fish, Artemia diet; 2 limnetic fish, bloodworm diet; 3: benthic fish, Artemia diet; 4: benthic fish, bloodworm diet; 5: marine fish, Artemia diet; 6: marine fish, bloodworm diet.
DOI: 10.5061/dryad.1159/2
title: WUND_DRYAD_proclndmrks_rakers.xlsx

description: This data file contains two types of data. First are the lengths of the 3 longest gill rakers on the first gill arch of all specimens.  Second are the Procrustes superimposed x-y coordinates for all specimens (see figure 2 in manuscript for landmark locations). Families are nested within populations, and fish are nested within families. The “TPS Picture #” column corresponds with the order of specimens in the accompanying TPS text file. Thus, if the excel data are sorted by this column, specimens will be in the same order as in the TPS file.
DOI: 10.5061/dryad.116/1
title: Graham et al Appendix 1
DOI: 10.5061/dryad.116/2
title: Graham et al Appendix 2
DOI: 10.5061/dryad.1164/1
title: Balsam Poplar nuclear genomic SNP loci

description: These data are diploid SNP genotypes for 412 nuclear genomic regions in Populus balsamifera (balsam poplar). Individuals are grouped in Col A according to population of origin (pop = ""), and each row is a unique individual (e.g., individual 1 from pop "BOY" = "BOY01"). Each biallelic SNP is represented by 2 columns per individual. Alleles symbols are the nucleotide bases at that locus; missing data are represented as "?". Loci are labeled across row 1 and are named according to the transcript I.D. from the Populus trichocarpa genome.
DOI: 10.5061/dryad.1767/1
title: Nuclear microsatellite data of western Olea europaea subsp guanchica populations

description: Matrix containing 105 Olea guanchica individuals sampled on four oceanic islands and genotyped with six nuclear microsatellites. The attached matrix has a SPAGeDI format, but please note that geographical coordinates are not included for some populations. This does not cause a problem when running the program to obtain population differentiation estimates. Also note that allele sizes are detailed without corrections after the M13 amplification technique. For more info on the study system, please contact Carlos García-Verdugo (cgarciav@bio.ucm.es)
DOI: 10.5061/dryad.8343/2
title: habitat character states for Ceanothus

description: 1 = chaparral, 2 = forest, 0 = both
DOI: 10.5061/dryad.8343/3
title: phylogenetic trees for Arctostaphylos

description: 1000 trees from the posterior set produced by BEAST
DOI: 10.5061/dryad.8343/4
title: phylogenetic trees for Ceanothus

description: 1000 trees from the posterior set produced by BEAST
DOI: 10.5061/dryad.1187/1
title: Microsatellite genotypes of Idaho giant salamanders in stream networks of eastern Idaho and western Montana

description: Individuals were sampled in 1st-order streams which were nested within catchments of confluent streams draining into a mainstem river. Catchments were nested within basins of three major rivers: the Lochsa (four catchments), the St. Joe (two catchments) and the St. Regis (two catchments).  We collected 15 individuals from three 1st-order streams within each catchment. Individuals were genotyped at 9 microsatellite loci.
DOI: 10.5061/dryad.119/1
title: Ree and Donoghue C Source Code
DOI: 10.5061/dryad.119/2
title: Source Code Readme File
DOI: 10.5061/dryad.1191/1
title: Dryad.xls
DOI: 10.5061/dryad.1194/1
title: MorjanSupplementaryMaterial.docx

description: Supplementary material for publication.  Measures of population subdivision for fungi, bacteria, plants, and animals.  Selection gradients and differentials for studies with experimentally enhanced phenotypic variation.  Effects of quantitative trait loci for animal crosses.
DOI: 10.5061/dryad.12/1
title: Apoptosis Data

description: Zip file containing 107 files
DOI: 10.5061/dryad.12/2
title: Sequences and Alignments

description: Zip file containing 11 files
DOI: 10.5061/dryad.12/3
title: Additional Table 2

description: Protein sequences for Figure 2 (phylogeny and domain organization of CED-4/Apaf-1 homologs)
DOI: 10.5061/dryad.1775/1
title: DmojFinalVersion02072007.xls

description: D. mojavensis QTL data, with cuticular hydrocarbons, courtship songs, and development times
DOI: 10.5061/dryad.1t67j57q/1
title: All Hatcheria Cytb sequences, plus outgroups

description: Fasta file containing all of the Cytochrome b sequences for Hatcheria macraei, plus outgroup samples. Unique haplotypes are labeled with the haplotype number preceding the isolate label. The isolate label usually consists of the initials of the species (HM, TA) followed by the first four letters of the locality. See readme file for which codes are associated with specific populations.
DOI: 10.5061/dryad.1t67j57q/2
title: Arlequin Analysis file for all Hatcheria Cytb sequences grouped by population

description: Arlequin file, individuals were first grouped by population in DNAsp, then grouped by river drainage in Arlequin
DOI: 10.5061/dryad.1t67j57q/3
title: Arlequin analysis file that contains all Hatcheria Cytb haplotypes

description: Arlequin haplotype file output from DNAsp. Place this file in the same directory as the Arlequin project file.
DOI: 10.5061/dryad.397
title: Data from: The virtues of gaps: xenarthran (edentate) monophyly supported by a unique deletion in αA-crystallin
DOI: 10.5061/dryad.8343/5
title: chaparral analysis script

description: Fitting the GeoSSE model with this script requires the R package diversitree, written by Rich FitzJohn.  A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (diversitreeGSE_0.4-5.tar.gz) because its GPL licence is not compatible with    Dryad's CC0 requirement.  This package is presently undergoing rapid development, so for any new applications, please use the current, improved version of the package, available from: http://cran.r-project.org/web/packages/diversitree/ and http://www.zoology.ubc.ca/prog/diversitree/.
DOI: 10.5061/dryad.8343/6
title: simulation analysis script

description: Simulating trees under the GeoSSE model requires the C program SimTreeSDD.  A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (SimTreeSDD-2009.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement.  Extensive further development is not planned, but the current version of the package is available from: http://tigger.uic.edu/~eeg/code/code.html.  The R package diversitree is also required by this script.  See Description for chaparral-analysis.R.
DOI: 10.5061/dryad.8546/1
title: Analysis1 - alignments and trees of 9 sequenced genomes
DOI: 10.5255/ukda-sn-6881-1
title: Northern Ireland Police Recorded Injury Road Traffic Collision Data, 2010
DOI: 10.5061/dryad.12/4
title: Additional Table 3

description: Protein sequences for Figure 3 (phylogeny of the multi-motif Bcl-2 family)
DOI: 10.5061/dryad.12/5
title: Additional Table 4

description: Protein sequences for Additional Figure 4 (phylogeny of the caspase family)
DOI: 10.5061/dryad.12/6
title: Additional Figure 4

description: phylogeny of the caspase family
DOI: 10.5061/dryad.120/1
title: MFCS15a2 Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/10
title: MFCS7a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/11
title: MFCS4a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/12
title: MFCS11a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/13
title: MFCS4b Data Set

description: Original ScanAlyze files
DOI: 10.5061/dryad.1563/5
title: focused12s
DOI: 10.5061/dryad.1786/1
title: SpeciesTreeAphelocomawithinstructions.xml

description: The XML file used to add fossil calibration to the species tree with some instructions for how the file should be hand-edited.
DOI: 10.5061/dryad.1786/2
title: SimulationCode.tar

description: Code for conducting coalescent simulations with a readme file.
DOI: 10.5061/dryad.1t67j57q/4
title: RAxML datafile for all Hatcheria haplotypes plus outgroups

description: Datafile used in our phylogenetic analyses. Labels consist of the haplotype number and isolate name.
DOI: 10.5061/dryad.3fb861d0/3
title: trial registration_part 1_061111

description: dataset for endorsement of trial registration in journal author instructions in relevant urology journals
DOI: 10.5061/dryad.3fb861d0/4
title: Results_trial registration_part 1_061111

description: results of endorsement of trial registration in journal author instructions in relevant urology journals
DOI: 10.5061/dryad.3fb861d0/5
title: AnalyseTrialRegistration

description: statistical code for endorsement of trial registration in journal author instructions in relevant urology journals
DOI: 10.5061/dryad.3fb861d0/6
title: trial registration_part 2_061111

description: dataset of RCTs published in journals mentioning and requiring or not mentioning trial registration in their author instructions
DOI: 10.5061/dryad.3fb861d0/7
title: Results_trial registration_part 2_061111

description: Results of RCTs published in journals mentioning and requiring or not mentioning trial registration in their author instructions
DOI: 10.5061/dryad.5rv40/5
title: raw_competition_data

description: Text file containing raw data from all competition experiments. All competitions were performed over 2 transfer cycles. Fitness values from this file are summarized in 'genotype_fitness.txt', which is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population.
DOI: 10.5061/dryad.8590/1
title: RK_LK_sexratio_rawdata_AmNat

description: This file contains the raw estimates of sex ratio for the 81 populations and 47 species used in this comparative analysis. It also includes the nexus code for the inferred phylogeny used in this paper.
DOI: 10.5061/dryad.9120/1
title: dryad_jeb_2011_00176R1
DOI: 10.5061/dryad.k9s59/1
title: Lailvaux et al. Evolution performance aging

description: These data describe weight at eclosion, maximum bite force at measured age, maximum takeoff velocity at measured age, age of performance measurement, sex, mating status, diet treatment and lifespan for T. commodus
DOI: 10.5061/dryad.120/15
title: RR Slide 10b_Cy5
DOI: 10.5061/dryad.120/16
title: SGA sig Data Set

description: Gene Expression Profiling Results
DOI: 10.5061/dryad.120/17
title: MFCS10b Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/18
title: MFCS15b2 Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/19
title: RR Slide 2a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/2
title: RR Slide 11b_Cy3
DOI: 10.5061/dryad.120/20
title: MFCS11b Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/21
title: MFCS10a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/22
title: MFCS16a2 Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.1563/6
title: focused16S
DOI: 10.5061/dryad.1817/1
title: MaanovainputCadOC.txt

description: Input file for biostatistical analysis of the microarray data using R package Maanova. ID: DNA sequence identifier for each probe on the array. DNA sequences can be retrieved from www.collembase.org.
DOI: 10.5061/dryad.1854/1
title: FoxandReed-Larvalsurvival.xls

description: Survival data for larvae from two populations (SI=South India and BF=Burkina Faso) of Callosobruchus maculatus reared at three temperature (l=17C, m=27C, h=37C) on two hosts (c=cowpea, m=mung bean). Data are presented as the stage at which larvae died (egg did not develop, egg developed but did not hatch, egg hatched but did not produce an adult, or an adult emerged) for each family. The first sheet presents data for each family. Families are grouped into blocks, with each block containing two inbred and two outbred families, as described in the paper. The additional sheets present summaries of the data, by blocks, or population/treatments. d = inbreeding depression, L = inbreeding load.
DOI: 10.5061/dryad.1978/2
title: 9-gene DNA sequence aligment of Synura petersenii

description: The concatenated 9-gene alignment of Synura petersenii (plastid: PSAA, PSBA, PSBC, RBCL; mitochondrion: COB, COX1, COX3; nuclear: ITS, 18S rDNA) with five closely related Synura and other heterokonts as outgroup taxa that used for the phylogeny analysis.
DOI: 10.5061/dryad.5rv40/3
title: Khan_etal_Fig4

description: R script to generate figure 4 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt.
DOI: 10.5061/dryad.7998/11
title: STRUCTURE .spj file for western Caribbean A. aspera populations
DOI: 10.5061/dryad.7998/12
title: STRUCTURE .spj file for all A. aspera populations
DOI: 10.5061/dryad.8343/7
title: alignment for Arctostaphylos

description: also contains habitat states and maximum clade credibility tree
DOI: 10.5061/dryad.hm06n7c0/1
title: G. bimaculatus: Immunity and life history data
DOI: 10.5061/dryad.120/23
title: RR Slide 16b_Cy5
DOI: 10.5061/dryad.120/24
title: MFCS9b Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/25
title: RR Slide 16a_Cy3
DOI: 10.5061/dryad.120/26
title: MFCS5b Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/27
title: RR Slide 10b_Cy3
DOI: 10.5061/dryad.120/28
title: RR Slide 11b_Cy5
DOI: 10.5061/dryad.120/29
title: MFCS12a2 Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/3
title: MFCS3b Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.120/30
title: MFCS3a Data Set

description: Original ScanAlyze file
DOI: 10.5061/dryad.1563/4
title: 28S broad
DOI: 10.5061/dryad.1563/7
title: focused18
DOI: 10.5061/dryad.1563/8
title: focused 28
DOI: 10.5061/dryad.5rv40/4
title: genotype_fitness

description: Text file containing all replicate fitness measurements of each constructed genotype. Includes columns: strain, strain number; genotype, beneficial mutations present where r = rbs, t = topA, s = spoT, g = glmUS and p = pykF; mutations, number of beneficial mutations in the genotype; w, fitness estimate; block, experimental block; Plate, physical container used for the competition. This file is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population.
DOI: 10.5061/dryad.8424/1
title: Delsuc_Nature2006

description: Amino acid concatenation of 146 genes for 38 metazoans.
DOI: 10.5061/dryad.8426/2
title: Chourrout-Nature2006_92taxa

description: Alignment of the homeodomain for 92 Hox and ParaHox genes from bilaterian and the cnidarian Nematostella vectensis
DOI: 10.5061/dryad.102/1
title: Stone Data Matrix
DOI: 10.5061/dryad.1092/1
title: Presence/Absence Data on Parental Care and Pool Type in Frogs
DOI: 10.5061/dryad.1198/1
title: Rana temporaria microsatellite

description: Microsatellite data of Rana temporaria in popgen format.
DOI: 10.5061/dryad.1723/2
title: Sequences for cox1-trnM IGR

description: DNA Sequences submitted to Genbank for cox1-trnM intergenic region
DOI: 10.5061/dryad.1924/1
title: De novo contigs from RNA-Seq of the whitefish liver transcriptome

description: Excel spreadsheet with de novo contigs from RNA-Seq of the whitefish liver transcriptome. Contig consensus sequences and gene expression values (RPKM) for dwarf and normal whitefish are presented.
DOI: 10.5061/dryad.5rv40/2
title: Khan_etal_Fig1

description: R script to generate figure 1 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt.
DOI: 10.5061/dryad.8181/1
title: Segregants Gentoype

description: This file contain the genotype data of all segregants used in this study. All the yeast segregants are available at theNational Culture Yeast Collection (www.ncyc.co.uk/)Genotype keys are (Genotype,Strain,Cluster):WE,DBVPG6765,Wine/European; WA,DBVPG6044,West African; SA,Y12,Sake; NA,YPS128,North American
DOI: 10.5061/dryad.8431/1
title: data
DOI: 10.5061/dryad.8564/1
title: MunshiSouth.JOH.Nasalis.Haplotypes

description: This file includes mitochondrial d-loop haplotypes and haplotype frequencies for four populations of proboscis monkeys from Sabah, Malaysia (NE Borneo).  The haplotype file is in Arlequin format.  Original sequences are available on Genbank.
DOI: 10.5061/dryad.8621/1
title: Dreissena primer data files

description: This file contains the raw data for the paper, as well as genepop and microchecker input and output files.  File formats include excel, genepop, and microchecker.  This is compressed in a .zip file.
DOI: 10.5061/dryad.9086/2
title: Table 1

description: Sampling locations of Paracorophium from New Zealand including site codes used for sequence names.
DOI: 10.5061/dryad.p4r84/3
title: Table S2

description: Homologous DNA sequences downloaded from GenBank.
DOI: 10.5061/dryad.t99b1/1
title: Lichen-Associated Bacterial 16S Sequences & Analysis Files

description: The archive contains 5 major elements: [Clon16SFinal.fasta - A fasta-formatted file containing all cloned sequences from the order Rhizobiales generated as part of this study] [FIGS1.pdf - An image of a phylogeny of all cloned sequences from the order Rhizobiales generated as part of this study (the methodology for generating the figure is outlined in the associated publication)] [HodkinsonLichen16S_454_raw_data_archive - A directory containing archived fna + qual files of raw sequence data with associated oligos files (used for processing with Mothur 1.15)] [454_clean - A directory containing the cleaned sequence data set (in the form of a .fasta and a .groups file) after quality checks performed using Mothur 1.15] [Supporting_Information - A directory containing all of the supplementary files referenced in the text of the associated publication along with instructions for using the various scripts written for this study, all found within a system of descriptively-titled sub-directories]