cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.38f3n/2
title: comparative analysis data

description: This file consists of song data from 57 Palearctic-African migratory songbird species. Information includes species song length, versatility index, song rate, syllable repertoire size, song repertoire size, the level of sexual dichromatism, and singing intensity during the winter.
DOI: 10.5061/dryad.38f3n/3
title: summer-winter song comparison data

description: This file contains information on song parameters from great reed warblers singing during breeding and non-breeding seasons. Information includes song duration, song interval length, song rate, syllable repertoire size, and the number of syllable repeats.
DOI: 10.5061/dryad.40gd6/1
title: Figure 1-source data 1

description: Figure 1-source data 1: FPKM and fold change of all genes in rice roots and shoots upon Pi treatments.
DOI: 10.5061/dryad.40gd6/2
title: Figure 2-source data 1

description: Figure 2-source data 1: List of 175 PSI DMRs identified in the root, with DNA methylation levels and transcription levels of DMR-associated genes.
DOI: 10.5061/dryad.40gd6/3
title: Figure 2-source data 2

description: Figure 2-source data 2: Transcription levels of TEs overlapping PSI DMRS after 7 d and 21 d of Pi deprivation.
DOI: 10.5061/dryad.40gd6/4
title: Figure 2-source data 3

description: Figure 2-source data 3: List of 341 PSI DMRs identified in the shoots, with DNA methylation levels and transcription levels of DMR-associated genes.
DOI: 10.5061/dryad.40gd6/5
title: Figure 3-source data 1

description: Figure 3-source data 1: Levels of DNA methylation and FDR values for the 100 PSI DMRs associated with changes in proximal gene transcription.
DOI: 10.5061/dryad.40gd6/6
title: Figure 4-source data 1

description: Figure 4-source data 1: List of 14 root persisting PSI DMRs, despite 31 d of Pi resupply.
DOI: 10.5061/dryad.412h3/1
title: geneticdata

description: File with individual ID, geographical coordinates, microsatellite genotypes at 20 loci
DOI: 10.5061/dryad.6336b/1
title: All data files

description: Data files are associated with Table 2, Figure 1, Figure 2, Appendix C and Appendix D. Please see ReadMe.txt for further information.
DOI: 10.5061/dryad.645h2/1
title: Raw data file

description: This Excel workbook has a separate worksheet for each experiment. There are data for the treated P0 files, and F1 sons and F2 grandsons of these treated files. "w-" denotes the flies that were cured of Wolbachia prior to the experiment, while "w+" describes those that were infected at the time of experimentation. The numbers of males and females produced in each replicate is presented.
DOI: 10.5061/dryad.760sc/1
title: Analysis R Code and Full Results

description: R scripts and input data for all analyses performed in study, including full output files.
DOI: 10.5061/dryad.760sc/2
title: Dryad Supplementary Figures for Close et al. Elevated morphological rates and high disparity support a mid-Jurassic adaptive radiation in mammals

description: Dryad supplementary figures, including captions.
DOI: 10.5061/dryad.760sc/3
title: Close_et_al_Current_Biology_Mesozoic_Mammals_BEAST2

description: BEAST 2 XML file for the morphological-clock/tip-dating analysis conducted using the Zhou et al. (2013) Mesozoic mammal matrix.
DOI: 10.5061/dryad.76ph0/1
title: Xylem anatomical measurements of 82 understory woody species
DOI: 10.5061/dryad.81h12/1
title: Raw data

description: Raw Data for microbiome sequences
DOI: 10.5061/dryad.81h12/2
title: Analysis result

description: Analysis result
DOI: 10.5061/dryad.855pg/1
title: sub_c85d6m20p3

description: xml file used in BEAST analysis
DOI: 10.5061/dryad.8sc5p/1
title: S1-1
DOI: 10.5061/dryad.8sc5p/2
title: S2-1-1
DOI: 10.5061/dryad.8sc5p/3
title: S2-1-2
DOI: 10.5061/dryad.8sc5p/4
title: S2-1-3
DOI: 10.5061/dryad.906ft/1
title: Tepley&Veblen2015_transect_data

description: Forest stand- and age-structure-data were collected across two ca. 1,340-ha study areas (Squaretop Mountain and Williams Creek) located within the San Juan National Forest of southwestern Colorado as part of a study to evaluate historical fire regimes and fire-driven forest dynamics across the moisture gradient of mixed-conifer and aspen forest. Within the data file, a separate sheet is provided for each of the following datasets: (1) transect locations, (2) overstory (&gt; 15 cm dbh) species composition and size structure, (3) ages of overstory trees, (4) sapling (1.5–15.0 cm dbh) density, (5) the forest type for each transect, and (6) codes for species used in the other datasheets.
DOI: 10.5061/dryad.b460g/1
title: OtakeoverF

description: C++ code file containing the stochastic simulation of a facultative population over taken by an obligate sub-population.
DOI: 10.5061/dryad.dn175/1
title: Genepop file for microsat data populations of Nothofagus cunninghamii

description: This is a genepop data input file for microsatellite data for populations of Nothofagus cunninghamii. Details of locations of the populations are given in Table 2 of the paper, and also in the attached csv file called "subpopulation locations.csv".
DOI: 10.5061/dryad.dn175/2
title: Genepop file for microsat data for Nothofagus cunninghamii subpopulations

description: This is a genepop data input file for microsatellite data for subpopulations of Nothofagus cunninghamii. Details of locations of the subpopulations are given in the attached csv file called "subpopulation locations.csv".
DOI: 10.5061/dryad.dn175/3
title: subpopulation locations

description: list of locations of subpopulations and populations
DOI: 10.5061/dryad.dt392/1
title: Spectral scans of reflectance for Pre-flowering spikes by pop

description: This file shows the spectral scan results (362-850nm) for reflectance of spikes (clusters) of flowers just prior to stigma emergence in any flower. Spikes were collected from plants derived from 29 European populations and that were grown in growth chambers at a warm and cool temperature. File can be read with help from the ReadMe file.
DOI: 10.5061/dryad.g7641/1
title: Fig 2 (heatmap) data files and R code

description: Data and R code needed to create Fig 2 in Hargreaves et al (2015) J Evol Biol.  One data file for each of the 6 figure panels.  Each file contains evolved D across the range in each of 500 generations of stable climate followed by 1000 generations of climate change.
DOI: 10.5061/dryad.g7641/2
title: Fig 3 (D lines) data and R code

description: Data and R code needed to create Fig 3 in Hargreaves et al (2015) J Evol Biol.  One data file for each of the 6 models shown.  Each file contains evolved D across the range after 500 generations of stable climate and after 1000 generations of climate change, averaged across 10 runs per cost per model.
DOI: 10.5061/dryad.g7641/3
title: Fig 4 (delta.D) data and R code

description: Data and R code needed to create Fig 4 in Hargreaves et al (2015) J Evol Biol.  One data file for each of the 4 models (ie figure rows) shown.  Each file contains evolved D across the range after 500 generations of stable climate and after 1000 generations of climate change for 30 runs per model.
DOI: 10.5061/dryad.g7641/4
title: Fig 6 (D vs density) data and R code

description: Data and R code needed to create Fig 6 in Hargreaves et al (2015) J Evol Biol.  Two data files (one for evolved D and one for density) for each of 2 model runs, one with dispersal (dispersal distance =1 as normal) and one run without dispersal (dispersal distance =0).
DOI: 10.5061/dryad.g7641/5
title: Appendix S1 data and R code for each figure

description: Data and R code needed to create figures in Appendix S1 in Hargreaves et al (2015) J Evol Biol. All figures remake Fig 3 while varying one parameter.  Fig S1.1 shows murate = .005; Fig S1.2 shows avshift = .01, .05, .2; Fig. S1.3 shows K=10; Fig. S1.4 shows effect of eliminating kin selection by randomizing individuals within columns before each dispersal event.  For each figure there is 1 data file per model.  Each data file contains evolved D across the range after 500 generations of stable climate and after 1000 generations of climate change, for 10 runs per cost.
DOI: 10.5061/dryad.g7641/6
title: Model code Matlab file

description: Code to run the model simulations.
DOI: 10.5061/dryad.g830h/1
title: 8,759 multi-sequence alignments
DOI: 10.5061/dryad.n82dm/1
title: Rolshausen.etal.Guppy.oil.EvolAppl

description: The archive contains raw data from: 1. reciprocal transplant experiments; 2. geometric morphometrics; 3. microsatellite genotypes
DOI: 10.5061/dryad.p3ks4/1
title: Alignments of 18S,5.8S and 26S rDNA sequences of plants and fungal

description: The alignments were constructed using 18S, 5.8S and 26S rDNA sequences of all plants and fungal from GenBank on 9th February 2013. Multiple alignments of every group were conducted using MAFFT v6.864 (Katoh et al. 2005). The regions from NS7 priming site to the 3’ end of 18S, the 5’ end to LR3 priming site of 26S, and the complete 5.8S region were extracted for primer design and in silico tests. The "NonGreen plants" includes Rhodophytes and Glaucophytes. The "Basal fungi" includes Microsporidia and Cryptomycota.
DOI: 10.5061/dryad.q044d/2
title: PD Subsample Concordance Factors

description: Concordance factors as well as their 95% confidence intervals for all 27,405 possible 4-taxon sets of the PD subsample.
DOI: 10.5061/dryad.q044d/3
title: A. thaliana 4th Chromosome MDL Blocks

description: Gzipped archive containing the alignments of the 3,595 recombinational blocks as determined by MDL.
DOI: 10.5061/dryad.r2rn0/1
title: Sunder paper data

description: Data collected in the field. See article for details
DOI: 10.5061/dryad.r36n0/1
title: Ant assemblage species richness and PIE

description: This data file includes details of species richness and PIE from pitfall-trapped ant assemblages across the globe. The data includes the following information for 1128 assemblages: Locality_ID - A unique code for each locality; Source - Details of reference source for each dataset; Cluster - Geographic cluster used as a random factor in analyses; Latitude - Latitude provided by authors; Longitude - Longitude provided by authors; Mean annual temperature - Derived from WorldClim; Total annual precipitation - Derived from WorldClim; Temperature range - Derived from WorldClim; Disturbance - Disturbance described by authors; Hemisphere - Derived from Latitude; Continent - Continent provided by authors; Pitfall days - Number of pitfalls multiplied by trapping days; Transect length - Distance from first to last trap in transect; Species richness - Total number of species collected; PIE - Probability of Interspecific Encounter, a measure of species evenness. Further details are provided in the paper.
DOI: 10.5061/dryad.r8c3b/1
title: Illumina_Guts_Dryad_submitted_files
DOI: 10.5061/dryad.t430k/3
title: GLM code and data file

description: R code to replicate GLM construction and evaluation and database used to perform the analyses.
DOI: 10.5061/dryad.t430k/4
title: Bioclimatic data used for ENM´s

description: Bioclimatic data used for model construction and projection to the last glacial maximum was obtained from the worldclim database (worldclim.org). Both present and past layers were cropped to the study area.
DOI: 10.5061/dryad.t446r/1
title: Penguin nest days data

description: African penguin chick survival data, collected on Robben Island, South Africa. Nest identifications (ID) are unique between years; repeated nest numbers within years denote repeat clutches or multiple chicks per brood.
DOI: 10.5061/dryad.th09b/3
title: S1_Dataset

description: RNA and Protein raw data
DOI: 10.5061/dryad.th09b/4
title: S2_Figure

description: YPD 39oC t=1hr
DOI: 10.5061/dryad.tj3q6/1
title: JEcol-2014-0815_data

description: The data contain sample plot locations and all variables used in the analyses. The description for each variable is included in the data file.
DOI: 10.5061/dryad.vq33n/15
title: wordPropsProcessedData

description: Processed word properties for comparison to vocalizations.
DOI: 10.5061/dryad.vq33n/16
title: wordPropsData

description: Data containing the acoustic properties of the pronounced target words.
DOI: 10.5061/dryad.vq33n/17
title: soundPropsAnalysisPraat

description: Code for measuring acoustic properties of target words.
DOI: 10.5061/dryad.21364/2
title: Matrices of Pairwise Geographic Distances for 339 Spider Species

description: Spiders were collected from locations across Canada by various collectors. GPS coordinates were obtained at the time of collection, or looked up at a later date on Google Earth based on name of collection location. Coordinate data was obtained by Sujeevan Ratnasingham from BOLD Systems and compiled as a matrix.
DOI: 10.5061/dryad.2593t/1
title: 45Markers_Hungary

description: Microsatellite information for Tisza river hybrid zone. Read the README file for informations
DOI: 10.5061/dryad.2593t/2
title: 45Markers_Italy

description: Microsatellite information for Ticino river hybrid zone. Read the README file for informations
DOI: 10.5061/dryad.2fg10/6
title: Local plant DNA reference library information

description: This file contains taxonomic information on the 1369 plant vouchers collected from Mpala Research Centre in Kenya that were used to produce the local plant DNA reference library for taxonomic assignation of dietary plant DNA sequences. The file includes (a) the project name and sample identifier required to access continuously updated data from the barcode of life datasystems (i.e., "BOLD") at boldsystems.org; (b) voucher locations and identifiers; and (c) the finest-level taxonomic identifications obtained to date. The DNA sequences associated with these specimens have been submitted to GenBank under the following accessions: KR737583 - KR738717 (trnL), KR733684 - KR734339 (ITS), KR736355 - KR737573 (rbcL), KR734343 - KR735185 (matK), and KR735186 - KR736041 (trnH-psbA). Sequence data associated with specific specimens may be obtained from GenBank by searching for the relevant BOLD Process Identifier.
DOI: 10.5061/dryad.40gd6/10
title: Figure 5-source data 2

description: Figure 5-source data 2: 11 DCL3a-dependant PSI DMRs, with methylation levels and associated gene transcription.
DOI: 10.5061/dryad.40gd6/11
title: Figure 6-source data 1

description: Figure 6-source data 1: FPKM and fold change of all genes in Arabidopsis roots upon Pi starvation.
DOI: 10.5061/dryad.40gd6/12
title: Figure 5-source data 3

description: 409 PSI DMRs in the DCL3a RNAi line, and 88 PSI DMRs in the DCL3a RNAi line, associated with significant changes in nearby gene expression
DOI: 10.5061/dryad.40gd6/7
title: Figure 4-source data 2

description: Figure 4-source data 2: List of 36 panicle PSI DMRs.
DOI: 10.5061/dryad.40gd6/8
title: Figure 4-source data 3

description: Figure 4-source data 3: Average methylation levels observed in the roots of the progeny of stressed- and non-stressed plants in all contexts and methylation levels for each replicate in CNN in the 175 root PSI DMRs.
DOI: 10.5061/dryad.40gd6/9
title: Figure 5-source data 1

description: Figure 5-source data 1: FPKM and fold change of all genes between WT +Pi and DCL3a RNAi line +Pi as well as WT -Pi and DCL3a RNAi line -Pi (FDR &lt; 0.05). List of DMRs identified between WT +Pi and DCL3a RNAi line +Pi as well as WT -Pi and DCL3a RNAi line -Pi is shown as well as the average methylation levels observed in all samples (FDR &lt; 0.05).
DOI: 10.5061/dryad.4tm8j/1
title: Nuerk_etal_age_estimation_A_completeDataset

description: BEAST v1.7.5 input file, divergence time estimations, analysis A, complete data set.
DOI: 10.5061/dryad.4tm8j/2
title: Nuerk_etal_age_estimation_A_noMissingDataset

description: BEAST v1.7.5 input file, divergence time estimations, analysis A, reduced data set that does not include missing data.
DOI: 10.5061/dryad.4tm8j/3
title: Nuerk_etal_age_estimation_B_completeDataset

description: BEAST v1.7.5 input file, divergence time estimations, analysis B, complete data set
DOI: 10.5061/dryad.4tm8j/4
title: Nuerk_etal_age_estimation_B_noMissingDataset

description: BEAST v1.7.5 input file, divergence time estimations, analysis B, reduced data set that does not include missing data.
DOI: 10.5061/dryad.521h5/1
title: Additional file Table S1

description: SNP allelic profile of 43 grapevine cultivars and 28 putative wild individuals from Georgia at 15,317 SNP loci. Nucleotides were scored with Genotyping Module 1.9.4 of the GenomeStudio Data Analysis V2011.1 software (Illumina Inc.). Dataset was filtered based on SNP call quality and GenTrain score: samples with low SNP call quality (p50GC&lt;0.54) were removed from the analysis and only SNPs with a GenTrain score higher than 0.6 were retained. Markers with a number of NCs (non-call) higher than 20%, as well as the 100% NC markers, were removed.
DOI: 10.5061/dryad.6nt0d/1
title: individual_accessions

description: individual accession numbers for all the dataset sequences
DOI: 10.5061/dryad.6nt0d/17
title: Pmarina_IMa2_input

description: Input datafile for IMa2 analysis (includes both the mitochondrial and nuclear loci)
DOI: 10.5061/dryad.6nt0d/2
title: Pmarina_STRUCTURE_input

description: Input file for structure (nuclear loci only)
DOI: 10.5061/dryad.6nt0d/4
title: Pmarina_NJtree_newick

description: NJ tree resulting from the POFAD analysis, in newick format
DOI: 10.5061/dryad.6nt0d/5
title: PmarinaCR

description: aligned fasta file with all control region sequences.
DOI: 10.5061/dryad.6nt0d/7
title: Pema3

description: fasta file for anonymous nuclear locus Pema3
DOI: 10.5061/dryad.707g2/1
title: Biological motion individual ERP files

description: These are the ERP files of every subject in each condition, used in the paper entitled  "Direction of biological motion affects early brain ativation: a link with social cognition", by Pegna, Gehring, Meyer & Del Zotto, and published in PLoS-One. Data for each of the 4 experimental conditions (radial iological motion -rBM- ; lateral biological motion -lBM-; radial scrambled motion -rSM-; and lateral scrmbled motion -lSM-)  are placed in separate folders named for the condition. Within each folder, the ERP of each subject is given under the subject number; i.e.,  1s for the first subject, 2s for the second subjects and so forth, followed by the abberviation  of the experimental condition. Thus for example, the ERP of the 1st subject in the lateral scrambled motion condition is given the name "1s_lSM.txt". The data within the each file is given in ASCII format with each column corresponding to a given electrode and each row to a time frame. There are 64 columns corresponding to the following electrodes (in order) from left to right:  Fp1, AF7; AF3; F1; F3; F5; F7; FT7; FC5; FC3; FC1; C1; C3; C5; T7; TP7; CP5; CP3; CP1; P1; P3; P5; P7; P9; PO7; PO3; O1; Iz; Oz; POz; Pz; CPz; Fpz; Fp2; AF8; AF4; Afz; Fz; F2; F4; F6; F8; FT8; FC6; FC4; FC2; FCz; Cz; C2; C4; C6; T8; TP8; CP6; CP4; CP2; P2; P4; P6; P8; P10; PO8; PO4; O2. There are 1126 rows corresponding to the successive time frames over time beginning 100ms before the appearance  of the stimulus at the top row. As the sampling rate was of 1024 Hz, each time frame corresponds to 0.976ms. The total duration of the epochs is consequently of 1098.632 ms (1126 time frames). A separate file named Biosemi_64.els is included containing the names of the electrodes as well as their cartesian coordinates.
DOI: 10.5061/dryad.7g02r/1
title: Arena fight and venom usage

description: The table "Arena fight and venom usage.csv" corresponds to the  manuscript sections of the same name. It contains the mortality of Argentine ant and workers of four Monomorium ant species after 1, 4 and 24 hours, as well as behavioural responses and observed venom usage of ant workers in the arena trials. It furthermore contains data derived from this raw data (for example relative occurence of behaviours). The experimental design is explained in the publication in the methods section with the same name as the datafile, further description of this and the other datafiles associated with this publication can be found in the ReadMe.txt
DOI: 10.5061/dryad.7g02r/2
title: Arena fight and venom usage Argentine ant Survival

description: The table "Arena fight and venom usage Argentine ant Survival.csv" corresponds to the manuscript section "Arena fight and venom usage". It contains data represented in the Argentine ant Mortality column in table "Arena fight and venom usage.csv" formatted for a survival analysis. The experimental design is explained in the publication in the methods section with the same name as the datafile, further description of this and the other datafiles associated with this publication can be found in the ReadMe.txt
DOI: 10.5061/dryad.7g02r/3
title: Arena fight and venom usage Monomorium Survival

description: The table "Arena fight and venom usage Monomorium Survival.csv" corresponds to the manuscript section "Arena fight and venom usage". It contains data represented in the Monomorium Mortality column in table "Arena fight and venom usage.csv" formatted for a survival analysis. The experimental design is explained in the publication in the methods section with the same name as the datafile, further description of this and the other datafiles associated with this publication can be found in the ReadMe.txt
DOI: 10.5061/dryad.7g02r/4
title: Venom survivability

description: The table "Venom survivability.csv" corresponds to the manuscript sections of the same name. It contains the responses of Argentine ants after 1 and 4 hours when treated with different concentrations of venom of four different Monomorium ant species and can be used to calculate the LD 50 of these venoms on Argentine ants. The experimental design is explained in the publication in the methods section with the same name as the datafile, further description of this and the other datafiles associated with this publication can be found in the ReadMe.txt
DOI: 10.5061/dryad.7q5c7/1
title: KarachiFishing_PlosOne

description: Quality of Cataract Surgery in The Karachi Marine Fishing Communities Eye and General Health Survey
DOI: 10.5061/dryad.855pg/10
title: All Virentes SSRs in Structure format

description: Dinucleotide nuclear microsatellites (ZAG36, ZAG11, ZAG1/5, ZAG1/2, ZAG102, ZAG9, ZAG15, ZAG30, ZAG46, ZAG16, ZAG110) for seven Virentes species and 672 individuals, including source location information and geographic coordinates. This is the input file used for the Structure analysis.
DOI: 10.5061/dryad.855pg/2
title: sub_c85d6m20p3b

description: xml file used in BEAST analysis.
DOI: 10.5061/dryad.855pg/3
title: sub_c85d6m20p3c

description: xml file used in BEAST analysis
DOI: 10.5061/dryad.855pg/4
title: Freezing vulnerability

description: Predicted vulnerability to freezing at -15oC are given as a percentage between 0 and 100 for individuals of each of seven Virentes species based on Bioclim 6 data (mean minimum temperature of the coldest month) for each geographic location. The equation for predicting vulnerability to freezing (FV) was based on empirical relationships from Koehler, Center and Cavender Bares 2012 using the electrolyte leakage method of freezing injury to stems at -15oC: FV =100-[81.202 - 1.4075*X], where X is the mean minimum temperature in the coldest month. Any negative values were assumed to indicate zero vulnerability to freezing at -15oC.
DOI: 10.5061/dryad.855pg/5
title: Tree height (m) for Virentes species

description: Data show tree height data in meters for mature trees for seven Virentes species, including source locations and geographic coordinates.
DOI: 10.5061/dryad.855pg/6
title: Leaf area and shape for Virentes species

description: Leaf laminar area (mm2) and shape variables based on the first six principal components from analysis of leaf shape for 5,818 scanned leaves from 695 individual trees of seven Virentes species. The approach is based on a quantitative evaluation of the contour shape of each leaf with elliptic Fourier descriptors using the Shape 1.2 imaging software (Iwata & Ukai 2002). The data file also includes source location information of each tree, geographic coordinates, and Bioclim variables associated with each location.