cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1538f/3
title: Complete genomic sequences for the full set of non-redundant sequences

description: Genomic sequences were constructed using the genomic sequence of the reference genome and a table of SNPs.
DOI: 10.5061/dryad.1538f/4
title: SNPs used to identify redundant sequences

description: This files contains the SNPs that were used to identify redundant sequences. It is based on the file containing "SNPs for non-redundant European and North-American sequences", with missing data removed. It was analysed using DNADIST&NEIGHBOR programs in the PHYLIP Package, and a single representative of each clonal complex was kept in the dataset "SNPs for non-redundant European and North-American sequences" (clonal complex identified as groups of individuals with genetic distance &lt;0.1)
DOI: 10.5061/dryad.1538f/5
title: Mating types and Reproductive success

description: Reproductive success of 239 crosses (478 matings). Columns represent the 16 mat A strains, and rows represent the 15 mat a strains, with isolates numbers along the row and column headings of the matrix. Numbers within matrix cells indicate the reproductive success ratings (see below) of the two reciprocal matings of the cross between the corresponding isolates (mat a isolate as the perithecial parent/mat A isolate as the perithecial parent). The matrix cells have been shaded in proportion to the reproductive success of the best mating (see Figure 5B in the corresponding publication). Additional row and column headings indicate the lineage designation (see Figure 1). Isolates P581 and TX8127 are tester strains of N. discreta sensu stricto. Categories of reproductive success, corresponding to different stages in reproductive development, from the development of perithecia, to the formation of black ascospores were scored as follows: 0 & 1 if sterile, no perithecia produced; & barren perithecia, no ostiole developed; 2 if  perithecia developed ostioles, but no spores; 3 & 4 if  &lt;1% black ascospores ; & 1-15% black ascospores; 5 if  15-50% black ascospores; 6 if  &gt; 50% black ascospores.
DOI: 10.5061/dryad.1538f/6
title: Neighbor-joining tree constructed based on a matrix F84 distance computed using the full set of sequences

description: Neighbor-joining tree based on F84 distance (DNADIST, PHYLIP Package). Computations were performed on the full set of SNPs and this analysis was used to identify redundant (i.e. nearly identical, or clonal) genomic sequences.
DOI: 10.5061/dryad.18kk6/1
title: Raw Electrophysiological Data, and extracted parameters from Optic Tectum Neurons of Xenopus tadpoles

description: This dataset contains the raw electrophysiological recording data that was used to quantify cell diversity in the Optic Tectum of premetamorphic Xenopus tadpoles. The recordings were performed in pClamp, and are stored here as Matlab MAT-files. The raw data is accompanied by a summary table of measurements presented in the paper, and a "master file" that matches raw data files to cell ids from the summary table. The ZIP archive contains several folders that separately store: (1) Voltage gated current traces in response to voltage steps that were used to build Na and K IV-curves (folder "01 IV curve"); (2) Active changes in membrane potential (spiking) in response to step current injections (folder "02 Current step injections"); (3) Spiking in response to cosine current injections (folder "03 Current cosine injections"); (4) Synaptic currents recorded in voltage clamp after synaptic stimulation of the optic nerve with equally spaced impulses and with different inter-stimulus intervals (folder "04 Synaptic bursts"); (5) Miniature spontaneous excitatory postsynaptic currents (folder "05 Minis").
DOI: 10.5061/dryad.20t14/1
title: Tropheus AFLP data

description: A nexus-format file with the AFLP data of Tropheus spp. sampled from Lake Tanganyika. Sampling information is given in Egger et al. (2007; BMC Evolutionary Biology, 7, 137).
DOI: 10.5061/dryad.20t14/2
title: Canidae_SNPdata

description: This file contains SNP genotype data of North American canids used in a homoplasy excess test for hybrid signal. The data were collected by vonHoldt et al. (2011; Genome Research 21, 1294-1305). The first line contains sample names. Row names indicate SNP loci. SNP genotypes are scored as 0 (homozygous for one allele), 1 (heterozygous), 2 (homozygous for the other allele).
DOI: 10.5061/dryad.26256/1
title: Robinson_2016_spatialforest_dataset

description: Field collected data, July-August 2009. See README text file for metadata and variable descriptions.
DOI: 10.5061/dryad.30t5b/1
title: Uma Inornata microsatellite genotypes and collection coordinates

description: This is a comma delimited txt file containing individual *Uma inornata* genotypic data for 11 microsatellite markers. Fields include sample number, collection year& population name, followed by allele calls in 2 column format. 0 = missing data.  Individual collection localities are available from the authors upon request.
DOI: 10.5061/dryad.3r3v3/1
title: Bruintjes Outgroup_Raw_Data

description: Raw data
DOI: 10.5061/dryad.3rd2v/1
title: Dunlap Data Predation & Brain Efish

description: Contains data on brain cell proliferation (density of PCNA+ immunoreactive cells) and cortisol concentrations in six populations of electric fish, Brachyhypopomus occidentalis, in Panama. Also includes data on body size, body condition and gonadal size.
DOI: 10.5061/dryad.5ts48/1
title: Data

description: File includes data for calculating intraclass correlation coefficients and Fleiss' kappa shown in the article entitled "Methods for estimating causal relationships of adverse events with dietary supplements".
DOI: 10.5061/dryad.62s71/2
title: data

description: The file  contains the necesseary data to repeat the analyses presented in the article 'Resprouter fraction in Cape Restionaceae assemblages varies with climate and soil type'. The column 'siteID' lists an identifier for each of the sample sites. Columns 'long' and 'lat' give coordinates of the sites in geographic coordinates (WGS84). Columns 'resprouter_def' and 'reseeder_def' give the number of known resprouters and known reseeders at these sites. The reseeding/resprouting trait is not known for all species, we therefore give in colums 'resprouter_max' and 'reseeder_max' the maximal possible numbers of resprouting and reseeding species. The column 'mbal' gives the values used as aridity measure, 'soiltype' indicates the soil fertility classes as used in the analysis. Column 'pixelID' gives an identifier of the pixel, used to specify the random effect in the model. The remaining columns indicate the names of the recorded species, where species present at a site are given a value of 1, species absent are given a value of 0.
DOI: 10.5061/dryad.67rq6/1
title: Heterocephalus glaber microsatellite genotype data

description: Genotypes for 131 individuals of Heterocephalus glaber using 12 H. glaber specific primers.  Data is in Genepop format.
DOI: 10.5061/dryad.7nd42/1
title: Stevardiinae concatenated alignment

description: Concatenated alignment with all sequences generated to reconstruct the phylogeny of Stevardiinae. The gene partitions are: myh6 = 1 - 621; ptr = 622 - 1158; rag1 = 1159 - 2520; rag2 = 2521 - 3291; coi = 3292 - 3813; 16s = 3814 - 4387; 12s = 4388 - 4816. Also, all taxa listed are identified by its name and voucher number.
DOI: 10.5061/dryad.7nd42/2
title: Stevardiinae trees

description: Stevardiinae phylogenies reconstructed with the software's: RAxML (concatenated and gene trees), Garli, STAR and TNT. Trees were rooted in Serrasalmus sp. and bootstraps support are shown when available.
DOI: 10.5061/dryad.88755/1
title: HCMV-CCMV Alignment

description: Alignment of 41 HCMV and 1 CCMV whole genome sequences in fasta format. The alignment was used to generate figure S7 in the linked publication.
DOI: 10.5061/dryad.88755/2
title: HCMV-CCMV-RhCMV Alignment

description: Alignment of 41 HCMV, 1 CCMV and 2 RhCMV whole genome sequences in fasta format
DOI: 10.5061/dryad.8nh60/1
title: Pakkala et al_individual nestling data including body measurements and steroid concentrations

description: Hormone (corticosterone) concentrations for nestling (day 7) Savannah sparrows at baseline (within 3 minutes of disturbing the nest) and after a 30 min restraint in a cloth bag. Body measurements and precipitation values also included for each individual.
DOI: 10.5061/dryad.8nh60/2
title: Pakkala et al_Savanah Sparrow Input for MARK

description: Input table for Program MARK; capture/recapture data for juvenile Savannah sparrows before autumn migration from Kent Island, NB.
DOI: 10.5061/dryad.8qc40/1
title: Marker genotypes

description: Genotypes for 11 codominant markers—including 3 single-copy, nuclear-gene-intron-length markers and eight microsatellite markers described in Sexton et al. for 23 populations of Mimulus laciniatus in the California Sierra Nevada.
DOI: 10.5061/dryad.8qc40/3
title: Distance matrices

description: Genetic, spatial, and climate distances among 23 populations of Mimulus laciniatus
DOI: 10.5061/dryad.8qc40/4
title: Plant density data

description: Average plant density sampled in moss patches within 12 randomly assigned 0.5 square meter plots at each Mimulus laciniatus study population.
DOI: 10.5061/dryad.c2378/3
title: ReadMe file for data package
DOI: 10.5061/dryad.cg40g/1
title: 6basalBC_bams.tar.gz.splita

description: 6basalBC_bams.tar.gz, split, part a (of 16 parts, a-p, ~1GB/each). Archive contains targeted region BED file and sequencing data BAM files for 6 basal-like breast cancer cell lines (HCC38, HCC1143, HCC1187, HCC1395, HCC1954, HCC1937; each suffixed with "T") and their corresponding normal DNA sample (each suffixed with "BL"), using hg19 coordinates.
DOI: 10.5061/dryad.cg40g/2
title: 6basalBC_bams.tar.gz.splitb

description: 6basalBC_bams.tar.gz, split, part b.
DOI: 10.5061/dryad.cg40g/3
title: 6basalBC_bams.tar.gz.splitc

description: 6basalBC_bams.tar.gz, split, part c.
DOI: 10.5061/dryad.cg40g/4
title: 6basalBC_bams.tar.gz.splitd

description: 6basalBC_bams.tar.gz, split, part d.
DOI: 10.5061/dryad.cg40g/5
title: 6basalBC_bams.tar.gz.splite

description: 6basalBC_bams.tar.gz, split, part e.
DOI: 10.5061/dryad.cg40g/6
title: 6basalBC_bams.tar.gz.splitf

description: 6basalBC_bams.tar.gz, split, part f.
DOI: 10.5061/dryad.db2dd/1
title: All data

description: Data for all figures
DOI: 10.5061/dryad.g1qr6/1
title: Food web data for the Sanak Islands, Alaska

description: The food web data compiled for this study, consisting of 339 quadrats, 39 transects, five sites, four locales, and one archipelago-wide network. The table provides a unique numeric identifier per food web (WebID), the spatial scale (WebScale; distinguishing quadrats [Q], transects [T], sites [S], locales [L], and the archipelago-scale [A]), a sample number (WebUnit; to identify individual transects [quadrat- and transect-scale samples], sites, or locales), and the Integrated Taxonomic Information System's (ITIS) Taxonomic Serial Number (TSN) and name of each predator and prey (PredTSN, PreyTSN, PredName, and PreyName, respectively). Taxa lacking entries in ITIS have a unique custom TSN prepended with “san”.
DOI: 10.5061/dryad.j0bd4/1
title: Landau SupMat 1 genealogy of the plant material

description: Graphic describing the genealogy of the plant material used in this work.
DOI: 10.5061/dryad.j0bd4/2
title: Landau SupMat 2 table of primers and amplicons

description: Table of primers and amplicons used for chloroplast TILLING
DOI: 10.5061/dryad.jk7t0/1
title: Appendix 1
DOI: 10.5061/dryad.jk7t0/2
title: Appendix 2
DOI: 10.5061/dryad.jk7t0/3
title: Erik+2 Source Code
DOI: 10.5061/dryad.k1c4j/1
title: Behavioral Isolation Data

description: Spawning events across three replicate trails for each species pair.
DOI: 10.5061/dryad.k9c31/1
title: 01 Azevedo et al. 1996, Egg size and ovariole number

description: This data file contains means and 95% confidence limits of egg size (mm3) and mean ovariole number of 20 Drosophila melanogaster locations collected at 13 latitudes in 1993 (extracted from Fig 1&2). Note longitudes in data are approximate. When using this data, please cite the original publication:
Azevedo, Ricardo B. R., French, Vernon & Partridge, Linda (1996). Thermal evolution of egg size in Drosophila melanogaster. Evolution 50: 2338-2345
DOI: 10.5061/dryad.k9c31/2
title: 02 Azevedo et al. 1998, Wing traits

description: This data file contains means and 95% confidence limits of wing:thorax size ratio and mean wing-aspect ratio for 18 Drosophila melanogaster locations collected at 12 latitudes in 1993. The wing traits were measured in females and males of field collected flies and in their descendants reared under standard laboratory conditions (extracted from Fig. 1). Note longitudes in data are approximate. When using this data, please cite the original publication: Azevedo, Ricardo B. R., James, Avis C., McCabe, Jennie & Partridge, Linda (1998). Latitudinal variation of wing: thorax size ratio and wing-aspect ratio in Drosophila melanogaster. Evolution 52: 1353-1362
DOI: 10.5061/dryad.k9c31/3
title: 03 Gockel et al. 2001, Microsatellite markers

description: This data set contains raw genotypes of 19 microsatellite markers for 29 Drosophila melanogaster locations collected at 11 latitudes in 2000. When using this data, please cite the original publication:Gockel, Julia, Kennington, W. Jason, Hoffmann, Ary, Goldstein, David B., and Partridge, Linda (2001). Nonclinality of Molecular Variation Implicates Selection in Maintaining a Morphological Cline of Drosophila melanogaster. Genetics 158: 319-323
DOI: 10.5061/dryad.m8q78/2
title: Biochar pH effects on denitrification in acid soils

description: The data was generated through lab incubation. Each excel file has many sheets. The sheet labelled "Materials" has information that is important for understanding the data in other sheets in the same excel file.
DOI: 10.5061/dryad.mn5f8/1
title: List of Arboreal Plethodontid Salamanders

description: This list includes all plethodontid species known to climb plants, the general geographic region, the type of arboreality, and the sources of information.
DOI: 10.5061/dryad.mv185/1
title: Amino acid sequence of reconstructed archaeal ancestral NDK, Arc3nh

description: Amino acid sequence of Arc3nh, a last archaeal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model
DOI: 10.5061/dryad.mv185/2
title: Amino acid sequence of reconstructed archaeal ancestral NDK, Arc4nh

description: Amino acid sequence of Arc4nh, a last archaeal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
DOI: 10.5061/dryad.n08t0/2
title: Victorian Land Use Information System Data files 2006-2013

description: The Victorian Land Use Information System (VLUIS) dataset has been created by the Spatial Information Sciences Group of the Agriculture Research Division in the Department of Economic Development, Jobs, Transport, and Resources. The method used to create VLUIS is significantly different to traditional methods used to create land use information and has been designed to create regular and consistent data over time. It covers the entire landmass of Victoria and separately describes the land tenure, land use and land cover for each cadastral parcel across the state, biennially for land tenure and use and annually for land cover; for each year from 2006 to 2013. The data is in the form of a shapefile.
DOI: 10.5061/dryad.n63m4/1
title: A database to enable discovery and design of piezoelectric materials

description: This JSON-file contains metadata pertaining to the compounds studied in this work and the associated calculated piezoelectric properties.
DOI: 10.5061/dryad.pb1sb/3
title: Appendix S3- Data Matrix

description: Data Matrix
DOI: 10.5061/dryad.pb1sb/4
title: Appendix S4-Analysis of individual nodes and clades

description: Analysis of individual nodes and clades
DOI: 10.5061/dryad.pb1sb/5
title: Appendix S5-Morphometric characters considered in phylogenetic analysis

description: Morphometric characters considered in phylogenetic analysis
DOI: 10.5061/dryad.pb1sb/6
title: Appendix S6 - Plates

description: Plates
DOI: 10.5061/dryad.pb1sb/7
title: Appendix S7: analysis including Eocasea martini

description: Appendix S7: analysis including Eocasea martini
DOI: 10.5061/dryad.pb1sb/8
title: Matrix, Nexus formar

description: Matrix, Nexus format
DOI: 10.5061/dryad.pq827/4
title: Data derived from original transcriptome data
DOI: 10.5061/dryad.qb7vr/2
title: Data collected from Channel Island foxes for ear tumor risk factor analysis

description: Data collected from examinations, biopsies, ear cultures, and other for analysis regarding risk factors relating to ear tumor development in Channel Island foxes in southern California.
DOI: 10.5061/dryad.rn745/1
title: EfEmSangerSequencingForDryad

description: Sanger sequencing results for up to 16 individuals (9 blue-eyed black lemurs and 7 black lemurs from the Duke Lemur Center) sequenced at 17 amplicons throughout scaffold2503 (the scaffold containing the orthologs of HERC2/OCAs) and aligned using EBioX
DOI: 10.5061/dryad.rn745/2
title: Variable sites VCF files

description: These files contain sites with a high posterior probability (&gt; 0.8) of being polymorphic in the 8-sample dataset (4 samples from each species), along with their genotype likelihoods in these samples as estimated by ANGSD (http://popgen.dk/wiki/index.php/ANGSD). Genotype likelihoods were estimated using the GATK model (-GL 2). The probability of a site being variable was estimated using ngsStat (https://github.com/mfumagalli/ngsTools), based on posterior probabilities calculated using the genotype likelihoods and the site frequency spectrum estimated from high quality sites (minimum mapping quality 1, minimum quality 20, minimum 3 samples with data, minimum depth 9) within each species.
DOI: 10.5061/dryad.rn745/3
title: Variable sites VCF files

description: These files contain sites with a high posterior probability (&gt; 0.8) of being polymorphic in the 8-sample dataset (4 samples from each species), along with their genotype likelihoods in these samples as estimated by ANGSD (http://popgen.dk/wiki/index.php/ANGSD). Genotype likelihoods were estimated using the GATK model (-GL 2). The probability of a site being variable was estimated using ngsStat (https://github.com/mfumagalli/ngsTools), based on posterior probabilities calculated using the genotype likelihoods and the site frequency spectrum estimated from high quality sites (minimum mapping quality 1, minimum quality 20, minimum 3 samples with data, minimum depth 9) within each species.
DOI: 10.5061/dryad.t6g5t/1
title: Data on GEOGRAPHICAL RESPONSE OF CYCAD INSECTS TO CONE VOLATILE COMPOUNDS
DOI: 10.5061/dryad.0sn23/1
title: Supplementary Table S1: Characters Partitions

description: Morphological character matrix with numbers from this and the previous publication (Ronquist et al. 2012), partition assignment, and descriptions of character states.
DOI: 10.5061/dryad.0sn23/2
title: Supplementary Files S2: Scripts Simulations

description: Archive containing a bash script and several R scripts used for simulating and analyzing the data from the simulation study.
DOI: 10.5061/dryad.0sn23/3
title: Supplementary Files S3: Results Simulations

description: Pdf files containing all graphs produced in the simulation study (see ReadMe.txt for details).
DOI: 10.5061/dryad.0sn23/4
title: Supplementary File S4: Tracing the High-Rates Artefact

description: Detailed explanation of the occurrence of false positives when analyzing random or highly saturated data, and of the impact of the branch length prior.
DOI: 10.5061/dryad.1538f/7
title: Maximum likelihood genealogy representing the relationships among non-redundant genomic sequences.

description: Analyses were based on full genomic sequences (i.e. including both variant and invariant sites).
DOI: 10.5061/dryad.2j5s7/1
title: Seedling first year survival

description: Data used seedling survival analysis (see https://github.com/kunstler/indirect.effect.climaten for R code)
DOI: 10.5061/dryad.2j5s7/3
title: Seedling growth data

description: Data for seedling growth analysis (see https://github.com/kunstler/indirect.effect.climate)
DOI: 10.5061/dryad.2j5s7/5
title: Daily climatic data per plot

description: Daily climatic data per plot
DOI: 10.5061/dryad.2j5s7/7
title: Data on ground vegetation cover and light interception
DOI: 10.5061/dryad.2j5s7/9
title: Annual climatic data per site in open area
DOI: 10.5061/dryad.33553/1
title: Data&Scripts

description: All data sets and R scripts for 1) the change in the protein and sugar concentration of figs over time (FigData), 2) the response surfaces for survival, development time, and ovariole number according to the protein and carbohydrate content of the diet for Zaprionus indianus and Drosophila simulans (NutritionalGeometry), and 3) the oviposition preference for Zaprionus indianus and Drosophila simulans (Oviposition).
DOI: 10.5061/dryad.512m0/1
title: long-term database on plant observations

description: Database with plant observations for different sites (10 in total, but only those 5 with all fence types were used in the associated paper) and five different fence types, for six different years, collected in Hluhluwe-iMfolozi Park (HiP), South Africa.
DOI: 10.5061/dryad.512m0/2
title: grass trait data

description: in situ measured values of SLA, leaf N content and canopy height. This data was originally collected for the study van der Plas & Olff, 2014, Mesoherbivores affect grasshopper communities in a megaherbivore-dominated South African savannah, Oecologia 175: 639-649
DOI: 10.5061/dryad.512m0/3
title: daily rainfall values

description: rainfall data at the exclosure sites, collected on a daily basis.
DOI: 10.5061/dryad.55044/1
title: Readme, scripts and summary stats
DOI: 10.5061/dryad.55044/3
title: sp111.tar
DOI: 10.5061/dryad.55044/4
title: sp112.tar
DOI: 10.5061/dryad.55044/5
title: sp121.tar
DOI: 10.5061/dryad.67rq6/2
title: Partial Mantel test - msat

description: This is the input datafile used on the Isolation by Distance Web Service http://ibdws.sdsu.edu/~ibdws/
DOI: 10.5061/dryad.67rq6/3
title: Ingram_etal_partialMantelDloop

description: This is the input file used for the partial Mantel test- dloop on the Isolation by Distance Web Service http://ibdws.sdsu.edu/~ibdws/
DOI: 10.5061/dryad.67rq6/4
title: DIYABCparameter

description: List of the parameters used in the DIYABC analyses
DOI: 10.5061/dryad.67rq6/5
title: Ingram_etal_dloop_alignment

description: The nexus format alignment of dloop sequence of all the identified haplotypes.  Redundent haplotypes were collapsed within locality.  NCBI Accession numbers are included. Although Mtito Andei and Kathekani shared the exact same haplotype we included both sites to represent each locality.
DOI: 10.5061/dryad.67rq6/6
title: Ingram_etal_dloop_MLtree

description: Maximum Likelihood tree file for Ingram et al Dloop sequences.
DOI: 10.5061/dryad.67rq6/7
title: Ingram_etal_collecting_info

description: Additional information about the sample collection, including locality.