cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f4211.2/4.1
title: 4-Cinaruco CHLA Sand Exp

description: samples and calculations for chlorophyll a accumulations in sand during fish exclosure/enclosure experiments
DOI: 10.5061/dryad.fg500/1
title: Lepais-et-al_TGG_ResultsForm-4OakSpecies-ControlledCrosses
DOI: 10.5061/dryad.j4n89/1
title: Electrophysiology_Data

description: All EPG recordings
DOI: 10.5061/dryad.k41qk/15
title: IMa2_AKAM110722_9Nuc
DOI: 10.5061/dryad.k41qk/6
title: 4_Locus2_110713
DOI: 10.5061/dryad.k41qk/7
title: 5_Locus4_110713
DOI: 10.5061/dryad.kh7sc/10
title: C source code, header

description: C source code for genetic ancestry model.
DOI: 10.5061/dryad.kh7sc/11
title: R simulation code, main file
DOI: 10.5061/dryad.kh7sc/12
title: R simulation code, functions
DOI: 10.5061/dryad.kh7sc/13
title: R simulation code, parameters
DOI: 10.5061/dryad.kh7sc/14
title: R simulation code, additional script 1

description: Additional Perl script to obtain point estimates for genotype likelihoods.
DOI: 10.5061/dryad.kh7sc/15
title: R simulation code, additional script 2

description: R script to obtain starting values for q to run ancestry model.
DOI: 10.5061/dryad.kh7sc/8
title: C source code, main file

description: C source code for genetic ancestry model.
DOI: 10.5061/dryad.kh7sc/9
title: C source code, functions

description: C source code for genetic ancestry model.
DOI: 10.5061/dryad.m78fk/1
title: Veneti et al_Heredity_raw data_30may2012

description: Raw data associated with all tables presented in the manuscript
DOI: 10.5061/dryad.nm341/1
title: Apteryx owenii_microsatellite_genotypes_April 2013
DOI: 10.5061/dryad.qc603/1
title: P_dilatata plastid sequences

description: This data file contains aligned sequences from 78 samples of Platanthera dilatata and 2 samples of Platanthera aquilonis for 6 plastid regions (rpl16_intron:1-648, ndhC_trnV:649-1301, accD_psaI:1302-2005, psbC_trnS:2006-2064, atpF_atpH:2065-2220, psbA_trnK:2221-2499) and gaps coded as simple characters (2500-2566).
DOI: 10.5061/dryad.rt950/2
title: NoChoiceExperimentData_7mar13
DOI: 10.5061/dryad.s3060/3
title: Genebank accessions number of Picea likiangensis, Intraspecific divergence and range expansion in the Qinghai-Tibet Plateau
DOI: 10.5061/dryad.s33p3/1
title: Dryad Data Microsatellite genotypes
DOI: 10.5061/dryad.s33p3/2
title: Tcoer_ND1 incl internal F2 primer_reverse complement (reading frame 2)
DOI: 10.5061/dryad.s33p3/3
title: Tcoer_ND1 excl internal F2 primer_reverse complement (reading frame 2)
DOI: 10.5061/dryad.s33p3/4
title: Dryad README Tcoer_CO1 (reading frame 2)
DOI: 10.5061/dryad.s33p3/5
title: Dryad README Tcoer_CO1a
DOI: 10.5061/dryad.s33p3/6
title: Tcoer_CO1b
DOI: 10.5061/dryad.s903c/7
title: Giese et al 2013_suppl_image_Inner Mongolia grassland Xilin River

description: panorama image of the Xilingole grassland near the experimental sites
DOI: 10.5061/dryad.s903c/8
title: Giese et al 2013_suppl_image_farm heavy grazing

description: image of the heavy grazing site with farm, sheep fold and grazing sheep herd
DOI: 10.5061/dryad.vq587/6
title: Arthropod_Alignment_obo_xrefs

description: The final alignment in an OBO format Xref document.
DOI: 10.5061/dryad.0p35r/1
title: Data_PNAS
DOI: 10.5061/dryad.17bn1/1
title: ASU_Acar_v2.1.prot.fa.gz - A fasta file of the protein sequences for each transcript in ASU_Acar_v2.1
DOI: 10.5061/dryad.1cg26/1
title: Results from a microcosm experiment using nectar microbes

description: Population sizes of four species--Gluconobacter sp., Asaia sp., Metschnikowia reukaufii, and Starmarella bombicola--over 32 days. Experimental treatments were order of species arrival and temperature variability treatment. Additional experiments of changes in pH and amino acid composition of the media over the experiment also included.
DOI: 10.5061/dryad.2g43n/1
title: H7N9_linelist

description: Linelist for the 2013 (first wave) H7N9 outbreak in China. All details obtained from news reports, WHO and FluTrackers.
DOI: 10.5061/dryad.32b88/5
title: nicola.tar.gz

description: Raw RAD sequencing data in fastq format for Nicola population.
DOI: 10.5061/dryad.32b88/6
title: tepee.tar.gz

description: Raw RAD sequencing data in fastq format for Tepee population.
DOI: 10.5061/dryad.32b88/8
title: genotyped_121009.txt

description: Genotyped diagnostic SNPs across 5 westslope cutthroat trout populations.
DOI: 10.5061/dryad.35321/16
title: Diplodactylinae phylogenetic tree

description: Diplodactylinae phylogenetic tree used in community phylogenetic analyses
DOI: 10.5061/dryad.35321/3
title: Diplodactylinae species distributions

description: A zip file containing the vetted species distributions in ASCII format for all diplodactyline gecko species used in this study.
DOI: 10.5061/dryad.35321/4
title: Sminthopsine species distributions

description: A zip file containing the vetted species distributions in ASCII format for all Sminthopsinae and species used in this study, as well as maps for dasyurid outgroups (not included in analyses).
DOI: 10.5061/dryad.35321/5
title: Ctenotus species distributions

description: A zip file containing the vetted species distributions in ASCII format for all Ctenotus species used in this study.
DOI: 10.5061/dryad.35321/6
title: Ctenophorus species distributions

description: A zip file containing the vetted species distributions in ASCII format for all Ctenophorus species used in this study.
DOI: 10.5061/dryad.3p545/5
title: photos

description: Archive of photographs of each individual fish in *.jpg format.  Fish identification numbers correspond to Table S1.
DOI: 10.5061/dryad.3p545/7
title: Table S1. Sample information

description: Length, weight, smoltscale, sex and NKA activity for every fish sampled. Individuals included in the microarray analysis and incorporated into the microarray reference pool are identified. Numbers assigned to each sample during RNA purification, and names used for each sample in the Gene Expression Omnibus accession are also listed.
DOI: 10.5061/dryad.3p545/8
title: Table S2. Primer table.

description: qPCR targets, primers, amplicon sizes (bases) and efficiency percentages from Oncorhynchus mykiss standard curve.
DOI: 10.5061/dryad.3p545/9
title: Table S3. Gene Ontology enrichment in migrants or residents.

description: Trimmed GO enrichment for the day eight migrant compared to resident gene lists (GO Trimming performed with an 0.80 soft trim threshold). BP = Biological Process; CC = Cellular Component; MF = Molecular Function.
DOI: 10.5061/dryad.40pt8/1
title: Off-target sequences

description: Supplemental file with off-target sequences obtained using primers designed to specifically amplify bacterial endosymbionts. Sequences are in Fasta format.
DOI: 10.5061/dryad.5nc25/1
title: Alignment of 15 cpSSR primer pairs with Pinus plastomes

description: The published nucleotide sequences for 15 cpSSR primer pairs located within the aligned plastomes of 107 species of Pinus and six Pinaceae outgroups (TreeBase S12640).
DOI: 10.5061/dryad.5qg356qk/1
title: shiwei

description: Microsatellite data of the individuals included in the study. The first column entitled population includes the abbreviation for population affinity of the individuals, see Fig. 1 in the paper. The following columns contain allele 1 and 2 for each loci used in the analysis
DOI: 10.5061/dryad.60kk5/1
title: Microsatellite genotypes and sample locations

description: Genotype information from 14 microsatellite loci (SsaF43, Ssa14, Ssa289, Ssa171, Ssa197, Ssa202, SSsp1605, SSsp2201, SSsp2210, SSsp2216, SsspG7, SsaD144, SsaD157 and SSsp3016) for 2028 individuals collected in the field from 26 locations in Iceland.
DOI: 10.5061/dryad.6h822/1
title: Figure_3_ExperimentI

description: Data collected in the laboratory, for the number of eggs spawned per female, over the 10 day study period of Experiment I. Each spawning group (each tank) contained 1 female and 2 males (either all inbred fish or all outbred as indicated in table). Low dose refers to previous exposure to 5 ug/L clotrimazole (nominal) as detailed in manuscript.
DOI: 10.5061/dryad.733d9/1
title: butterfly
DOI: 10.5061/dryad.7c99f/1
title: Assemblies

description: Transcriptome assemblies for each of the 7 lineages studied in this paper.
DOI: 10.5061/dryad.7c99f/2
title: Pipeline

description: R and Perl scripts used in this work.
DOI: 10.5061/dryad.7gp1f/1
title: DRYAD_BaumsEtAl_2012_Plobata_Genotypes
DOI: 10.5061/dryad.7j97t/1
title: Sprattusfuegensis_msats

description: This is a zipped file that contains two fastaq files. They represent the data for microsatellite loci development for Sprattus fuegensis from using Illumina paired-end reads. The paired-end reads are in separate files and for each sequence the locus name is in the tittle with the prefix “Spfu” para Sprattus fuegensis.
DOI: 10.5061/dryad.7vs2c/2
title: Machado_et_al treefile

description: Newick format phylogenetic tree
DOI: 10.5061/dryad.8j1hb/1
title: TerrAqEggs_DRYAD

description: The data in this file are from an experiment conducted in the fall of 2010 in Gamboa, Panama. The experiment used naturally laid egg masses of the treefrog Dendropsophus ebraccatus, which were then placed above or below the surface of the water and placed inside a small cage to exclude predators or were left exposed to predators. Survival and developmental stage were recorded after 24 and 48 hours, as well as the amount of rainfall that fell, the mean and max temperature and minimum humidity during the preceeding 24 hours.
DOI: 10.5061/dryad.907p8/1
title: Tuni_et_al

description: Proportion of sperm from the second male to mate that were stored by a female cricket, Teleogryllus oceanicus, when mated by a full sibling or unrelated male and guarded by a ful sibling or unrelated male during sperm transfer
DOI: 10.5061/dryad.9tb07/1
title: Data and script files for each figure of the paper

description: Data generated using simulations with our software. See: http://chronos.isir.upmc.fr/~mouret/modularity/sferes2_modularity.tgz
DOI: 10.5061/dryad.cp6gg/2
title: Bayesian Consensus

description: This is the consensus topology resulting from Bayesian analyses.
DOI: 10.5061/dryad.cp6gg/3
title: Beast results

description: This is the consensus topology resulting from relative time analyses in Beast
DOI: 10.5061/dryad.cp6gg/4
title: Maximum Likelihood Results

description: This topology shows results from partitioned ML analyses in RAxMLHPC v7.0
DOI: 10.5061/dryad.d03nf/1
title: Jorgensen and Reilly dataset

description: Genus averages of morphological traits, size-removed residuals, and phylogenetic PCA.
DOI: 10.5061/dryad.f36h3/1
title: migration data

description: Migration data from experiment where source and number of migrants was manipulated. First column gives source of migrants (wildtype or host range mutant), second column gives number of migrants per passage, third column gives replicate of fitness estimate, and fourth column gives final titer (number of virus) for each replicate measurement.
DOI: 10.5061/dryad.f4211.2/5.1
title: 5-Cinaruco Algal Biovolume Tiles Exp

description: samples and calculations for alga taxa and their biovolumes accumulations on tiles during fish exclosure/enclosure experiments
DOI: 10.5061/dryad.f4211.2/6.1
title: 6-Cinaruco Meiofauna Density Sand Exp

description: samples and calculations for meiofauna taxa and their densities in sand during fish exclosure/enclosure experiments
DOI: 10.5061/dryad.f4ks8/1
title: Mycoplasma bovis MLST concatanate alignment

description: Mycoplasma bovis MLST concatenate alignment
DOI: 10.5061/dryad.f4ks8/2
title: Figure1

description: Mycoplasma bovis MLST phylogenetic tree
DOI: 10.5061/dryad.f4ks8/3
title: Figure2

description: Mycoplasma bovis MLVA phylogenetic tree
DOI: 10.5061/dryad.f4ks8/4
title: Figure3

description: Mycoplasma bovis MLST and MLVA phylogenetic trees
DOI: 10.5061/dryad.f4ks8/5
title: MLVA data
DOI: 10.5061/dryad.g4t8c/1
title: Evolutionary rates for multivariate traits: the database.

description: This is the repository for the `R` Code and Data for Pitchers et. al. 2014 soon to be published (July 2014) a special issue (Evolutionary Quantitative Genetics) of Philosophical Transactions of the Royal Society. We currently have a pre-print of a version of the manuscript on biorxiv (http://biorxiv.org/content/early/2014/05/05/002683). In addition to all of the code and data being here allowing you to reproduce all of the results from the paper (up to the limits of MCMC anyways), it also contains the database we generated on genetic covariance and correlation matrices that we hope will be of broad use to the Evolutionary Quantitative Genetics community. Here is a short guide to navigate this folder:1. For the analyses of evolutionary potential using measures extracted from empirical **G** matrices, you can [review](https://github.com/DworkinLab/Pitchers_PTRS2014/blob/master/Scripts/gmax_analysis.md) or reproduce our analyses. You can also download the gmax_analysis.R file to rerun it on your local machine. This folder also contains the gmax_analysis.Rmd file in case you prefer starting with the markdown + `R` code and want to use knitr.2. If you are interested in the analyses we performed examining rates of evolution or estimates of selection, these can also be found in the script folder, with the overview of the analysis and results here in the markdown file.3. If you just interested in the data for your own analyses, please find it in the data subfolder. Inside you will see additional sub-folders which contain small text files for each matrix as spelled out in the name.md file mentioned above. You can also use some of the `R` code we have set-up above, to extract the databases directly into R with the `.R` objects in that folder.
DOI: 10.5061/dryad.gd0nc/1
title: Beetle and experimental data

description: Body length and genital dimensions of Carabus maiyasanus beetles, and individual data for single and double mating experiments
DOI: 10.5061/dryad.hb653/1
title: gonorynchALL

description: interleaved alignment of all 9 nuclear genes in nexus format
DOI: 10.5061/dryad.hb653/2
title: gonorynchENC

description: alignment of ENC1 nuclear gene in nexus format
DOI: 10.5061/dryad.hb653/3
title: gonorynchGLYT

description: alignment of Glyt nuclear gene in nexus format
DOI: 10.5061/dryad.hm021/1
title: Appendix: Character data and matrix for phylogenetic analysis

description: Appendix: Character data for phylogenetic analysis of Magallanesia canaliculata gen. et sp. nov., and of other selected canaliculate forms with TABLE 1: Character matrix for selected radiolitidine rudist taxa.
DOI: 10.5061/dryad.k41qk/16
title: bpp_AMAKAP120508
DOI: 10.5061/dryad.m4fs7/1
title: Sofaer_etal_OCWAFecundityData

description: Orange-crowned warbler fecundity data.
DOI: 10.5061/dryad.m4fs7/2
title: Sofaer_etal_OCWANestSurvival

description: Orange-crowned warbler nest survival data.
DOI: 10.5061/dryad.m4fs7/3
title: Sofaer_etal_OCWA_AdultSurvival

description: Files with input and results from analysis of orange-crowned warbler adult survival in Program MARK.
DOI: 10.5061/dryad.mf1qf/1
title: Raw data
DOI: 10.5061/dryad.nh3d2/7
title: Matings_He.txt

description: Contains information on percentage of no-choice trials with females that led to matings for males from the specified populations and the expected heterozygosity of the populations. Population abbreviations are as in the manuscript.
DOI: 10.5061/dryad.nr4k8/2
title: Hepatotoxicity of Isotretinoin and Gilbert's syndrome

description: SPSS
DOI: 10.5061/dryad.ns40k/1
title: Data Archive - Robinson & Moyer

description: This zipped archive contains simulated microsatellite datasets used to assess the influence of overlapping generations on estimates of LD-based estimates of effective population size. The file contains four additional zipped directories with SPIP simulation scripts, processed genotype files, outputs from LDNe, and spreadsheets summarizing the data.
DOI: 10.5061/dryad.pb128/1
title: Ottewell 2012 Oenocarpus genetic data

description: Excel file containing microsatellite genotypes of adult Oenocarpus bataua trees and seed progeny arrays collected from a study site in northwest Ecuador
DOI: 10.5061/dryad.pj0p3/1
title: Raw Data of Mortality Observations of Replica Set Experiments
DOI: 10.5061/dryad.q2s0s/1
title: York et al_Data file

description: Data collected from the field and location-specific values obtained from http://www.usno.navy.mil/USNO/astronomical-applications/data-services
DOI: 10.5061/dryad.qq20s/1
title: Molecular, climate and functional trait data for Eucalyptus tricarpa

description: See ReadMe file.
DOI: 10.5061/dryad.s33p3/7
title: Tcoer_CO1ab
DOI: 10.5061/dryad.s4q6s/1
title: Data on species richness and genetic diversity in high-mountain vascular plants of the Alps and the Carpathians

description: (i) Floristic data of vascular high-mountain plants from the Alps and the Carpathians, with occurrences of each species with a regular grid system (ii) Species-specific AFLP data (1/0 matrices) separately for samples from Alps and Carpathians, collected along the same grid system as the floristic data
DOI: 10.5061/dryad.s706g/1
title: Phenotypic Data

description: This file contains .csv files of raw trait measurements described in the paper (growth, bleaching, PAM) in addition to processed symbiont genotyping counts data (percent mapped reads and haplotype files). The accompanying R command file opens specific trait files and calls out columns in each to perform statistical analyses and generate figures as in the accompanying paper.
DOI: 10.5061/dryad.s706g/2
title: Host Genotyping Data (microsattelite genotypes)

description: This file contains the raw data files for both the full genotyping dataset (including individuals with 3rd alleles) as well as a STRUCTURE input file that is a subset of the data containing only those individuals with diploid genotypes at all loci as described in the paper. The R command files are for completing ploidy modeling as described in supplementary file S1.
DOI: 10.5061/dryad.s706g/3
title: ITS454rawreads

description: This file contains raw .fna files from 454 sequencing of the ITS2 locus as described in the paper.  Each file contains reads for a single sample and &gt; lines give the sample name for each file.
DOI: 10.5061/dryad.s706g/4
title: White Balanced Photographs of Coral Bleaching

description: This file contains pre- and post- experiment photographs of coral fragments that were analyzed to yield intensity measures indicative of bleaching as described in the paper.
DOI: 10.5061/dryad.sd60p/1
title: morphological data

description: Morphological data for R. s. sinicus, R. s. septentrionalis, R. thomasi and R.s.ssp include specimen ID, Sex, Body mass and Forearm.
DOI: 10.5061/dryad.sd60p/2
title: mtDNA, ncDNA genes  and microsatellite data

description: The accession numbers for Cytb, Chd1 and SWs1, as well as 8 microsatellite loci for individuals from R. s. ssp and R. thomasi used in this study.
DOI: 10.5061/dryad.sj5b6/3
title: wood tox

description: Lab toxicity data: mortality data for each population when exposed to roundup and chlorpyrifos.
DOI: 10.5061/dryad.sm635/1
title: DRYAD-Smel
DOI: 10.5061/dryad.t36v1/1
title: Ruiz-Sanchez&Ornelas_IMa_NorthvsSouth_cp

description: IMa file for North versus South populations of the Trans-Mexican Volcanic Belt (TMVB) of Liquidambar styraciflua for chloroplast markers.
DOI: 10.5061/dryad.t36v1/2
title: Ruiz-Sanchez&Ornelas_IMa_MESOvsUS_cp

description: IMa file for MESO versus US populations of Liquidambar styraciflua for chloroplast markers.
DOI: 10.5061/dryad.vq587/7
title: HAO vs TGMA (mosquito)

description: Excel aligment between Hymenoptera (HAO) and Culicidae (TGMA).
DOI: 10.5061/dryad.1077n/1
title: usat_genotypes

description: Microsatellite genotypes in genepop format.
DOI: 10.5061/dryad.1077n/2
title: Species Tree

description: Species tree in Newick format.
DOI: 10.5061/dryad.1077n/3
title: usat_tree_cse

description: A Cavalli-Sforza Edwards chord distance microsatellite tree.
DOI: 10.5061/dryad.1077n/4
title: usat_tree_nei

description: Nei;s distance microsatellite tree
DOI: 10.5061/dryad.1077n/5
title: usat_tree_rey

description: Reynolds distance microsatellite tree
DOI: 10.5061/dryad.1077n/6
title: Cytb_sequence_alignments

description: Aligned Mitochondrial cytb sequences for each location
DOI: 10.5061/dryad.1077n/7
title: Nuclear_508_sequence_alignment

description: Aligned nuclear marker 508 sequences for all locations
DOI: 10.5061/dryad.1077n/8
title: Nuclear_517_sequence_alignment

description: Aligned nuclear marker 517 sequences for all locations
DOI: 10.5061/dryad.10b5v/1
title: Final data

description: Contains raw data from experiments described in article. The first spreadsheet contains data from experiments investigating the potential mating costs suffered by deceived males, including whether they found the genuine female in deceptive inflorescences, how many missed mating opportunities they experienced and how much time remained after they found the female. It also shows the ID of the male used, which floral form it was tested on and what order number that floral form was (i.e. 1 or 2 ect for males used on more than one floral form). It also shows the percentage of mating behaviour that the male exhibited on the spots of the form in question. The next spreadsheet comprises data from our learning experiments and shows the percentage mating behaviour exhibited by inexperienced males during their first and second exposure to sexually deceptive G. diffusa inflorescences. It also shows the percentage of specific mating behaviours (inspecting, changing, hopping and turning). The last spreadsheet includes data comparing the percentage of mating behaviour that inexperienced and experienced males exhibited on sexually deceptive inflorescences of G. diffusa. It also states whether these males were wild caught within natural populations, or whether they were experimental males used in our previously mentioned learning experiments. For these experimental males we also state whether the data is from their first or second exposure to sexually deceptive inflorescences.
DOI: 10.5061/dryad.187nt/1
title: suppFigure_09-17-13

description: 120 supplemental figures, with the analysis, simulation scenario and data sources labeled. See the ReadMe for more detail.
DOI: 10.5061/dryad.187nt/2
title: rdata_workspaces_12-29-13

description: A zip file containing 15 .Rdata saved workspaces, each containing the analytical results from a respective simulation scenario, as indicated in the file names. Can be used with the figure-making scripts to remake the majority of the analytical figures in the main paper and all of the figures shown in the supplement.
DOI: 10.5061/dryad.187nt/3
title: methodTest_analysis

description: The main simulation "workhorse" script, for the computer language R. Called and run with the runMethodTest R script to perform the different simulation scenarios and saves the analytical results as a workspace to an .rdata file.
DOI: 10.5061/dryad.187nt/4
title: runMethodTest_03-05-13

description: A script for the R programming language, which runs analyses in the 15 simulation scenarios described in the main paper, via calls to the methodTest script.
DOI: 10.5061/dryad.187nt/5
title: making_mainfigures_12-06-13

description: R script which, if given the 15 workspaces contained in the zip file included in this archive, will generate figures 2-9 in the main paper. (Unfortunately, the final-final figures I submitted had to be converted to a different file format and resized in GIMP, so they may not be 100% identical).
DOI: 10.5061/dryad.187nt/6
title: make_supp_files_09-15-13

description: R script which, if given the 15 workspace files contained in the zip file included in this archive, will generate the 120 supplemental figures for this paper, and save them as a single PDF file, which should be identical to the PDF file containing the supplemental figures already included here on Dryad.