cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1kr29/4
title: chimpAndBonobo.vcf

description: VCF files chimpAndBonobo.vcf and HGDP00222.vcf are the final filtered VCF files ( 4.2 Mb of callable sequence).
DOI: 10.5061/dryad.2d960/1
title: HusakFergusonLovern_Anolis_training_diet_alldata

description: Data for males and females included in the paper.
DOI: 10.5061/dryad.2r746/1
title: FremontiiRAD2013_rawreads_replaced
DOI: 10.5061/dryad.37312/2
title: Fox et al_Detailed reviewer data_one line per reviewer

description: This file contains lists data for each reviewer selected to review for the journal, one reviewer per line. Manuscript ID numbers are random but the manuscript ID numbers can be used to link the three files uploaded for this paper.
DOI: 10.5061/dryad.37312/3
title: Fox et al_ Author details 2010-2014_one line per paper

description: This dataset includes author details for manuscripts submitted 2010-2014, one manuscript per row. Manuscript ID numbers are random but ID numbers can be used to link the three files uploaded for this paper. Columns that could allow the dataset to be de-anonymized have been deleted.
DOI: 10.5061/dryad.37972/1
title: data_Vosteen et al. 2016_Journal of Animal Ecology
DOI: 10.5061/dryad.3836f/1
title: Oxidative state data for 85 European bird species

description: Data for: Vágási et al. 2016. Large-brained birds suffer less oxidative damage. Journal of Evolutionary Biology. Data provided: four oxidative state markers (total antioxidant status, uric acid, total glutathione and malondialdehyde), their sample sizes, other data related to sample collection, body mass and brain brain mass. For further details please see the article and the supporting information.
DOI: 10.5061/dryad.4mm12/1
title: Simulated savanna distribution

description: TTR (TTR_) and aDGVM (aDGVM_) modelled savanna presence/absence at 0.5 degree resolution (unprojected) for 1990 using an Africa model (_africa_) or a continent-specific model (_cont_), and in 2070 using a continent-specific model with changing climate (c) or changing climate and changing CO2 (cc).
DOI: 10.5061/dryad.4vg33/1
title: Supplemental Dataset
DOI: 10.5061/dryad.53n6n/4
title: R-Script: Analysis code

description: This contains the code for the analyses described in this paper. All optional settings required for analysis can be set in this script. This file also contains the code to build all the figures.
DOI: 10.5061/dryad.53n6n/5
title: R-Script: Supporting Functions

description: This file contains the R code for all of the supporting functions for the complete analysis.
DOI: 10.5061/dryad.57q6g/1
title: Microsatellite data

description: Genotype data
DOI: 10.5061/dryad.57q6g/2
title: Occurence data

description: Presence data
DOI: 10.5061/dryad.67fp5/1
title: Rossi et al. 2016 Proc B - dataset

description: The excel file contains 8 sheets. The first four sheets contain the data used for a specific figure in the manuscript. The name of the sheet identifies which figure the data represent (Fig. 1A,1B,2,3). The last four sheets contain the water chemistry data reported in table S1.
DOI: 10.5061/dryad.8g3j2/1
title: Gagic2016_EcoEvo_data

description: Seed yield, individual yield components and plant damage data
DOI: 10.5061/dryad.8gp06/1
title: Mitochondrial DNA FASTA file

description: Contains all the novel mtDNA sequence published in this study
DOI: 10.5061/dryad.8gp06/2
title: Mitochondrial DNA information

description: Contains long. lat. and archeological site information for the mtDNA sequences in mtDNA.fa
DOI: 10.5061/dryad.8gp06/3
title: Plink file (bed)

description: Contains genotype for 605 dogs
DOI: 10.5061/dryad.8gp06/4
title: Plink file (bim)

description: Contains genotype for 605 dogs
DOI: 10.5061/dryad.8gp06/5
title: Plink file (fam)

description: Contains genotype for 605 dogs
DOI: 10.5061/dryad.8gp06/6
title: Tree file (Nexus) based on Identity by State

description: Tree in Figure 1a
DOI: 10.5061/dryad.f8584/1
title: Lord_etal_2015_BupOpsinAlignmentTotal

description: Amino acid alignment file (FASTA format) of all opsin data used in the reconstruction of the total opsin topology.
DOI: 10.5061/dryad.f8584/2
title: Lord_etal_2015_BupOpsinAlignmentUV

description: Amino acid alignment file (FASTA format) of ultraviolet-sensitive opsin data used in the reconstruction of the UVS opsin topology.
DOI: 10.5061/dryad.f8584/3
title: Lord_etal_2015_BupOpsinAlignmentLW

description: Amino acid alignment file (FASTA format) of long wavelength-sensitive opsin data used in the reconstruction of the LWS opsin topology.
DOI: 10.5061/dryad.f8584/4
title: Lord_etal_2015_Bup_OpsinAlignment_nucl_PStests

description: Nucleotide alignment file of all opsin data used in the positive selection analyses.
DOI: 10.5061/dryad.hk922/1
title: RIdata

description: Data set including the strength of Reproductive barriers to gene exchange between 3 populations of Senecio lautus. Includes Parental (pure crosses) and F1 Hybrids
DOI: 10.5061/dryad.k20ng/1
title: occ_contr

description: Data used to analyse occupied territories versus nearby control areas (not occupied by wood warblers)
DOI: 10.5061/dryad.k20ng/2
title: occ_aband

description: Data used to analyse occupied territories vs. abandoned territories. The readme file is the same as for the data set on occupied territories vs control areas.
DOI: 10.5061/dryad.k765g/1
title: Data associated with female-preference study

description: This file contains the the lab experimental data associated with the paper: “Do female Nicrophorus vespilloides reduce direct costs by choosing males that mate less frequently?” A key is included in the file.
DOI: 10.5061/dryad.mq725/1
title: Information to potential mating groups used to characterize mating system of C. testudinaria

description: Tab-delimited file. Column headers are described and explained in the ReadMe file.
DOI: 10.5061/dryad.n4r2t/1
title: Cyprogenia_DNAseq.nex

description: Cyprogenia mitochondrial sequences
DOI: 10.5061/dryad.n4r2t/2
title: Cyprogenia_Genotyping

description: Cyprogenia microsatellites data
DOI: 10.5061/dryad.pt553/1
title: Rodger & Ellis 2016 Pollen Limitation South African Data

description: South African pollen limitation data used for Rodger and Ellis 2016 Biology Letters paper
DOI: 10.5061/dryad.q2h4s/12
title: Figure S1
DOI: 10.5061/dryad.q5553/1
title: Supplementary Data

description: Data on subject identity (ID), hatching cohort (Cohort), experimental diet group (Diet), rewarded colour (Reward), discrimination level (Level), latency to choose (Latency), and whether or not a correct choice was made (Error).
DOI: 10.5061/dryad.qb74m/1
title: Bacterial archive

description: Data concerning all endophytic bacteria isolated in this work; descriptions, LOPAT and GAtta assay results, BLAST hits, plant from which isolated, site.
DOI: 10.5061/dryad.qb74m/2
title: Field HMI

description: LD50 data for all enophytic bactera isolated in this work
DOI: 10.5061/dryad.qb74m/3
title: kruskall wallis env micro

description: Kruskall Wallis testing
DOI: 10.5061/dryad.qb74m/4
title: Snowdonia high zn trial

description: Plate reader output and graphs for zinc tolerance tests
DOI: 10.5061/dryad.r9d1m/1
title: DataJEcolDryad

description: Data Focalgt: The genotype identity of focal species.Focalsp: the speceis identity of focal species, mm: medicago minima, mr: Medicago rigidula.Compgt: the genotype identity of competiting individual.Compsp: the speceis identity of competiing individual.Soil: the soil that plants were grown in, t: thyme soil (soil colelcted under thyme plants), nt: no thyme soil (soil collected away from thyme plants).Comptype: competition type, intra-,or interspecific competition. Own: refers to the competition type between identical genotypes.surv: identifies whether the focal plant survived (1) or died (0).biomass: the biomass of focal plant.potnr: The identity of the pot in which plants were grown.
DOI: 10.5061/dryad.sh2mb/7
title: TableS7

description: P-values from GWAS with highly significant SNP on chromosome 3 (position=3862256 bp) as a covariate in the model.
DOI: 10.5061/dryad.sh2mb/8
title: TableS8

description: Genes found within the 400kb haplotype block surrounding highly significant SNPs.
DOI: 10.5061/dryad.sh2mb/9
title: TableS9

description: Annotation information for all potential a posteriori candidate genes from the FAD2 haplotype block.
DOI: 10.5061/dryad.th18q/1
title: Peak RelA Nuclear Amplitude for HeLa Cells

description: Peak RelA Nuclear Amplitude for HeLa Cells following TNF stimulation arranged by virtual synchronization of cell cycle. Single cell traces upon which the peak amplitude data is based are also included
DOI: 10.5061/dryad.th18q/2
title: 020611 ALL CELLS_SK-N-AS

description: Peak RelA Nuclear Amplitude for SK-N_AS Cells following TNF stimulation arranged by virtual synchronization of cell cycle. Single cell traces upon which the peak amplitude data is based are also included
DOI: 10.5061/dryad.th18q/3
title: HeLa FUCCI ANALYSIS

description: Analysis of cell cycle transition from G1 to S using Fucci vectors in HeLa cells as well as analysis of mean Mitosis length in the cell type
DOI: 10.5061/dryad.tk5rj/1
title: Sequence alignment

description: Sequence alignement of the 1,046 DNA barcodes
DOI: 10.5061/dryad.tk5rj/2
title: Neighbour joining tree (nwk)

description: Neighbour joining tree (Newick format) of the 1,046 DNA barcodes
DOI: 10.5061/dryad.tk5rj/3
title: Neighbour joining tree (pdf)

description: Neighbour joining tree of the 1,046 DNA barcodes
DOI: 10.5061/dryad.v0nb0.1
title: Data from: Antiherbivore defenses alter natural selection on plant reproductive traits
DOI: 10.5061/dryad.v0nb0.2
title: Data from: Antiherbivore defenses alter natural selection on plant reproductive traits
DOI: 10.5061/dryad.v0nb0.2/1.2
title: Defense-Reproduction_Data

description: Data collected in the field experiment, and associated metadata, are included in the folder. For convenience, data for individual plants and data for clonal family averages are included as separate datasets.
DOI: 10.5061/dryad.v0nb0.2/2.2
title: Defense-Reproduction R Script

description: R code for all analyses and data figures included in the associated article.
DOI: 10.5061/dryad.1b1d8/1
title: Stable isotope data

description: Stable isotope data for invasive crayfish (P. clarkii) and native crabs (P. loveni) from a in situ experiment (in 2010) and a field survey (2008, 2009, 2010) in the River Malewa in Kenya.
DOI: 10.5061/dryad.26pt6.1
title: Data from: Comparative support for the expensive tissue hypothesis: big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids
DOI: 10.5061/dryad.26pt6.2
title: Data from: Comparative support for the expensive tissue hypothesis: big brains are correlated with smaller gut and greater parental investment in Lake Tanganyika cichlids
DOI: 10.5061/dryad.26pt6.2/1.2
title: data_tsuboi_etal_Evolution

description: Data on body weight, brain right, gut length of Lake Tanganyika cichlids. Other information used in the study is presented as supplementary material.
DOI: 10.5061/dryad.37972/2
title: Vosteen et al. 2016_R Skript_Fig. 2 quantitative honeydew collection

description: Fig. 2 – honeydew collection: Dry weight of honeydew collected from different pea aphid clone – host plant combinations during 24 h. Plants were infested with 50 adult pea aphids. Honeydew amount was analyzed with a one-way-ANOVA. In cases of non-homogenous variances, data were log-transformed. The Tukey Honest Significant Difference method was used for post-hoc comparison.
DOI: 10.5061/dryad.37972/3
title: Vosteen et al. 2016_R Skript_Fig. 3 honeydew attractivity

description: Fig. 3 – hoverfly oviposition experiment: To test which cues elicit hoverfly oviposition under field conditions, eggs were counted on plants that were previously aphid infested, non-infested plants treated with aphid honeydew and non-treated control plants in the presence and absence of pea aphids. Plants were left for 30 h in the field and hoverfly eggs were counted afterwards. A randomized block design was used in this experiments. Each block consisted of all six treatments. Number of hoverfly eggs was analyzed with a generalized linear mixed effects model with a poisson error distribution, using blocks as random effects (random intercept) and treatments as fixed effects. P-values for explanatory variables were obtained by sequentially deleting explanatory variables and comparison of the more complex model with the simpler model with a likelihood ratio test (Zuur et al. 2009). Factor level reductions were used to reveal differences between levels of a treatment (Crawley 2013).
DOI: 10.5061/dryad.37972/4
title: Vosteen et al. 2016_R Skript_Fig. 4a relative attractivity

description: Fig. 4a – honeydew quality: Honeydew collected from 6 different pea aphid clone – host plant combinations was applied to Vicia faba. Plants were left for 30 h in the field and hoverfly eggs were counted afterwards. A randomized block design was used in this experiments. Each block consisted of all six treatments. Number of hoverfly eggs was analyzed with genaralized linear mixed effect model with poisson distribution.
DOI: 10.5061/dryad.37972/5
title: Vosteen et al. 2016_R Skript_Fig. 4b honeydew quantity

description: Fig. 4b – honeydew quantity:  Six, 12 or 18 droplets of this honeydew collected from Pisum race aphids feeding on Vicia faba were applied to uninfested Vicia faba. Plants were left for 30 h in the field and hoverfly eggs were counted afterwards. A randomized block design was used in this experiments. Each block consisted of all three treatments. Number of hoverfly eggs was analyzed with a generalized linear mixed effect model.
DOI: 10.5061/dryad.37972/6
title: Vosteen et al. 2016_R Skript_Fig. 5 less suitable plant 2014

description: Fig. 5 – less suitable plants I: Trifolium and Pisum race aphids were placed both on Trifolium pratense and Pisum sativum, so that each race was reared on its native host and a less suitable plant. Plants were left for 14 days in the field and number of hoverfly eggs, hoverfly larvae and surviving aphids was recorded several times. A randomized block design was used in this experiments. Each block consisted of all four treatments. Data was analyzed with mixed effects models using blocks as random effects (random intercept) and treatments as fixed effects. P-values for explanatory variables were obtained by sequentially deleting explanatory variables and comparison of the more complex model with the simpler model with a likelihood ratio test (Zuur et al. 2009). Factor level reductions were used to reveal differences between levels of a treatment (Crawley 2013). Number of hoverfly eggs and larvae were analyzed with generalized linear mixed models with either a Poisson error distribution, or a negative binomial error distribution (glmm with the lmer function of the lme4 package (Bates et al. 2014) whichever fitted best the data of a certain experiment. In cases were only a few hoverfly eggs or larvae were present and several plants without hoverfly eggs or larvae occurred, presence / absence data were used and analyzed with Bernoulli glmms.
DOI: 10.5061/dryad.37972/7
title: Vosteen et al. 2016_R Skript_Fig. 6 less suitable plant 2014_Aug

description: Fig. 2 – less suitable plants II: Trifolium and Pisum race aphids were placed both on Trifolium pratense and Pisum sativum, so that each race was reared on its native host and a less suitable plant. Plants were left for 6 days in the field and number of hoverfly eggs, hoverfly larvae and surviving aphids was recorded two times. A randomized block design was used in this experiments. Each block consisted of all four treatments. Survival of aphid colonies was analyzed with a generalized linear mixed effect model with a binomial distribution. Presence of hoverflz eggs and hoverflz larvae was analyzed with a generalized linear mixed effect model with poisson error distribution.
DOI: 10.5061/dryad.61d1m/1
title: 2k_table

description: Table with per 2kb window Tajima D and pi for each of the populations
DOI: 10.5061/dryad.61d1m/2
title: Pub1_parameter_means

description: Calculating chromosome means for the poopolation output of the Tajima's D, nucleotide diversity and Wattersons theta values of the five populations.
DOI: 10.5061/dryad.61d1m/3
title: Pub2_correlations

description: Spearman and Pearsons correlations of the all five populations
DOI: 10.5061/dryad.61d1m/4
title: Pub3_arabidopsis_table

description: Making the 2k table from PoPoolation output.
DOI: 10.5061/dryad.61d1m/5
title: Pub4_preliminary_parameter_plots

description: Preliminary plotting of D, pi, theta across chromosomes for all populations.
DOI: 10.5061/dryad.61d1m/6
title: Pub5_final_parameter_plots

description: Final set of Tajima D and pi plots for the publication.
DOI: 10.5061/dryad.61d1m/7
title: Pub6_populations_map

description: Publication populations map.Making the Italy part of the map.
DOI: 10.5061/dryad.61d1m/8
title: Pub7_ABC_analysis

description: This presents the code to do the ABC analysis of the msABC output files.
DOI: 10.5061/dryad.61d1m/9
title: Pub8_treemix_fourpop

description: Treemix input file generator.
DOI: 10.5061/dryad.710ng/1
title: seed sowing data
DOI: 10.5061/dryad.c96j0/1
title: MC1R alignment_Fulgione et al. 2016.fasta

description: MC1R sequences of pregnant wild boar samples collected
DOI: 10.5061/dryad.c96j0/2
title: mtDNA alignment_Fulgione et al. 2016

description: mtDNA sequences of pregnant wild boar samples collected
DOI: 10.5061/dryad.gs7j4.1
title: Data from: Unlinked Mendelian inheritance of red and black pigmentation in snakes: implications for Batesian mimicry
DOI: 10.5061/dryad.gs7j4.2
title: Data from: Unlinked Mendelian inheritance of red and black pigmentation in snakes: implications for Batesian mimicry
DOI: 10.5061/dryad.gs7j4.2/1.2
title: Compiled museum data for all Sonora sp. sampled

description: Phenotypic data (including color morph) for all Sonora sp. sampled from the 12 collections featured in this manuscript
DOI: 10.5061/dryad.gs7j4.2/2.2
title: Data input file for likelihood model

description: Data input file for running the model.R script file
DOI: 10.5061/dryad.gs7j4.2/3.2
title: Script file for likelihood model

description: Script file for generating likelihood analysis of color morph genetics
DOI: 10.5061/dryad.n4r2t/3
title: Cyprogenia_Sample

description: Cyprogenia sample information
DOI: 10.5061/dryad.pv608/1
title: Caching Trials, Willow Flats

description: Each record represents a single cache made by a kangaroo rat that had collected seeds at a bait tray in the field. Kangaroo rats were allowed to visit the tray multiple times within a trial. Fluorescent powder on the seeds aided the observer in locating the caches. Datum: WGS84
DOI: 10.5061/dryad.pv608/2
title: Rodent Trapping, Salt Valley

description: Each record is a capture of a small mammal at Salt Valley, Arches National Park, Grand Co., Utah. Trapping was conducted in 15 sessions of 2 or 3 nights each.
DOI: 10.5061/dryad.pv608/3
title: Rodent Trapping, Willow Flats

description: Each record is a capture of a small mammal at Willow Flats, Arches National Park, Grand Co., Utah. Trapping was conducted in 11 sessions of 2 or 3 nights each.
DOI: 10.5061/dryad.pv608/4
title: Telemetry, Salt Valley

description: Location records for radiocollared Ord's kangaroo rats in Salt Valley, Arches National Park, Grand Co., Utah.
DOI: 10.5061/dryad.pv608/5
title: Telemetry, Willow Flats

description: Location records for radiocollared Ord's kangaroo rats at Willow Flats, Arches National Park, Grand Co., Utah. Because sample sizes were fairly small, these data were combined with trapping data from the same time period and geographic area to produce utilization distributions for kangaroo rats. Trapping data were drawn from the companion data set "Rodent Trapping, Willow Flats.csv".
DOI: 10.5061/dryad.pv608/6
title: Randomization procedure for niche overlap

description: To investigate possible competition between D. ordii and P. flavescens at Salt Valley, we calculated the observed niche overlap for all species–time period combinations. The 163 trap stations were considered the common resource, and we used the Czechanowski index (Feinsinger et al. 1981) as an estimate of niche overlap: 1.0 – 0.5 Ʃ │pi – ri│where pi  and ri represent the proportions of captures at trap station i for D. ordii and P.flavescens, respectively. We then used a randomization procedure with 1000 trials to generate a distribution of niche overlap matrices to which the observed values could be compared (True BASIC program, S. Jenkins). The procedure generated random numbers of captures at each trapping station for each species-time period combination while keeping fixed the values of (1) the total number of captures at each station over all species-period combinations and (2) the total number of captures for each species-period combination over all stations. We could then answer the question of whether there was more or less between-species niche overlap observed within time periods (1997, 1998, and 1999-2001) than expected by chance by examining the probability of the occurrence of the observed niche overlap values relative to the distribution of values generated by the randomization procedure.
DOI: 10.5061/dryad.pv608/7
title: Food Preference Trials

description: Usable trials in a cafeteria-style design to determine a  heirarchy of preference for Ord's kangaroo rats (Dipodomys ordii) selecting to eat 4 seeds which occur at high frequencies in the plant community at Arches National Park, Grand Co., Utah: Coleogyne ramosissima, Ephedra viridis, Cowania mexicana, Wyethia scabra. Compositional analysis was used to determine preference heirarchy.
DOI: 10.5061/dryad.qb74m/5
title: Wytham strains high zinc tests

description: Plate reader output and graphs for zinc tolerance assays
DOI: 10.5061/dryad.qb74m/6
title: Metal Contents data

description: Metal concentrations in plants leaves
DOI: 10.5061/dryad.qb74m/7
title: all_rpoD_alignment.fas

description: Phylogeny - alignment
DOI: 10.5061/dryad.qb74m/8
title: all rpoD consensus

description: Consensus tree
DOI: 10.5061/dryad.qj8t3/1
title: Laskowski et al dominance clonal fish_Aggression in triads

description: The complete aggression data from which we estimated each individual's Average Dominance Index (ADI).
DOI: 10.5061/dryad.rd01s/1
title: data-Lodjak.et.al-2016-FuncEcol-IGF1

description: IGF-1 and growth rate data for pied flycatcher nestlings. IGF-1 injection study.
DOI: 10.5061/dryad.th18q/4
title: 120210 AS FUCCI O+G CTRL ANALYSIS

description: Analysis of cell cycle transition from G1 to S using Fucci vectors in SK-N-AS cells as well as analysis of mean Mitosis length in the cell type
DOI: 10.5061/dryad.th18q/5
title: Effect of TNFalpha on HeLa and SK-N-AS cell cycle length

description: Cell cycle lengths for SK-N-AS and HeLa cells without and with TNFalpha stimulation. Effect extension on cell cycle following stimulation is also shown at G1 and S phases.
DOI: 10.5061/dryad.th18q/6
title: RelA-DsRedxp E2F1-Venus BAC stables Representitive cell traces

description: RelA-DsRedexpress and E2F1-Venus BAC stables Representative cell traces separated into cell cycle phases by virtual synchronization.
DOI: 10.5061/dryad.th18q/7
title: RelA-DsRedxp E2F1-Venus BAC stables FCS molecular fluoresence Data

description: Molecular fluorescence counts in single cells of RelA-DsRedxp E2F1-Venus BAC stables and correlation data.
DOI: 10.5061/dryad.th18q/8
title: RelA-DsRedxp E2F1-Venus BAC stables FCS Autocorrolation and cross-corrolation data

description: RelA-DsRedxp E2F1-Venus BAC stables FCS autocorrolation and cross-corrolation data
DOI: 10.5061/dryad.th18q/9
title: BAC BAC Stable cell phase Meta data_Dryad

description: Traces of BAC-BAC E2F-1-Venus and Rel-A-dsRedexpress sorted into different cell cycle phases.
DOI: 10.5061/dryad.18pk7/1
title: standardized fitness scores in males and females in UU and UCL

description: Standardized fitness scores in males and in females in two populations of LHm Drosophila melanogaster: UU and UCL