cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.60d18.2
title: Data from: Violence in the prehistoric period of Japan: the spatiotemporal pattern of skeletal evidence for violence in the Jomon period
DOI: 10.5061/dryad.60d18.2/1.2
title: ESM for Violence in Japanese prehistory

description: Definition of and sources of data for injured individuals in the Jomon period, and detailed information of all sites where skeletal remains have been recovered.
DOI: 10.5061/dryad.6gr08/1
title: hsc70-4 alignment (Messor barbarus)

description: Alignment of the hsc70-4 gene in Messor barbarus. Nucleotide ambiguity code (IUPAC) is used to signal heterozygosity: by example, a R codes for an A/G genotype, while A codes A/A and G codes for G/G.
DOI: 10.5061/dryad.6gr08/2
title: Alignment of the Catalase gene

description: Alignment of the Catalase gene (nucleotides) in 9 Messor harvester ant species (52 individuals) and Pogonomyrmex barbatus. For Messor species, sequences of the two alleles (Allele 1 and Allele 2) are provided.
DOI: 10.5061/dryad.6gr08/3
title: mitochondrial COX1 gene alignment (Messor barbarus)

description: Alignment of the COX1 gene in Messor barbarus (48 individuals) and M. capitatus.
DOI: 10.5061/dryad.7sf3g/1
title: Field predation data

description: Recorded predator attacks on artificial butterflies
DOI: 10.5061/dryad.7t4b1/1
title: Data Sets DOI10.1371journal.pone.0166648

description: Excel Table containing data given in the figures of the manuscript.
DOI: 10.5061/dryad.br14k/11
title: VVL packet 11
DOI: 10.5061/dryad.br14k/12
title: VVL packet 12
DOI: 10.5061/dryad.br14k/13
title: VVL packet 13
DOI: 10.5061/dryad.br14k/14
title: VVL packet 14
DOI: 10.5061/dryad.br14k/15
title: VVL packet 15
DOI: 10.5061/dryad.c0ss8/1
title: V.velutina alarm pheromone data
DOI: 10.5061/dryad.d4f4s/1
title: Solute concentration Data

description: This file includes all solute concentration data in stream baseflow, stormflow, rain, groundwater and throughfall.
DOI: 10.5061/dryad.gn6qb.1
title: Data from: Species distributions, quantum theory, and the enhancement of biodiversity measures
DOI: 10.5061/dryad.gn6qb.2
title: Data from: Species distributions, quantum theory, and the enhancement of biodiversity measures
DOI: 10.5061/dryad.gn6qb.2/1.2
title: onlineAppendix1

description: R functions used to calculate the geometric mean of favourabilities (equation 3) and its increment (equation 4)
DOI: 10.5061/dryad.j2t92/3
title: CLO-SWTH
DOI: 10.5061/dryad.j2t92/4
title: CLO-43SD-AUDIO
DOI: 10.5061/dryad.j2t92/5
title: CLO-WTSP-AUDIO
DOI: 10.5061/dryad.j2t92/6
title: CLO-SWTH-AUDIO
DOI: 10.5061/dryad.k3p8n/1
title: Grazing effects on soil health

description: This file provides three measures of soil health in relation to grazing by livestock and feral animals from 451 sites in eastern Australia
DOI: 10.5061/dryad.k7cr5/1
title: Chabas et al Proc B 2016 - raw data

description: raw data Chabas et al Proc B 2016
DOI: 10.5061/dryad.mg430/1
title: FronZool2016_FINZ-D-16-00043R2

description: xlsx and csv files containing bear actigraphy and light data (lux) to accompany manuscript. Also included are body temperature data.
DOI: 10.5061/dryad.ng75r/1
title: KWill leptoferonia data files

description: Mesquite NEXUS files, aligned and concatenated, MrBayes files, and TNT run files.
DOI: 10.5061/dryad.nn2h5/1
title: PreferenceExperiment1

description: Experimental assessment of nectar-inhabiting yeast impacts on pollinator foraging preference. Metadata is included in the file, outlining the experimental protocol and how preference was scored.
DOI: 10.5061/dryad.nn2h5/2
title: PreferenceExperiment2

description: Experimental assessment of impacts of a nectar-inhabiting yeast on foraging behavior of naive bees. Bees were naive with respect to the yeast treatment. Metadata is included in the file, which outlines methodology used in the experiment.
DOI: 10.5061/dryad.nn2h5/3
title: PerformanceExperiment

description: No-choice feeding assay designed to assess costs and benefits of consuming a nectar yeast for bumblebee feeding and reproduction. Metadata is included in the file, outlining methodology used.
DOI: 10.5061/dryad.ns47q/1
title: Null model simulations

description: This R script was used to  simulate random mortality and then infer total selection on genotypes based on allele frequency changes while ignoring the effect of genetic drift.
DOI: 10.5061/dryad.ns47q/2
title: Simulated phenotypes based on Timema GBS data

description: This compressed folder contains the simulated data sets where Timema cristinae GBS data were used as the starting point. It contains three gemma formatted genotype files (geno_sims.txt, geno2500_sims.txt, and geno592r_sims.txt) that contain the underlying genotypic data for the base simulations, those with 2500 individuals and those with replicated genotypes, respectively. The remaining files are named based on the simulations condition (simsN): 1, h2=0.3, L = 100; 2, h2=0.3, L=10; 3, h2=0.05, L=100; 4, h2=0.05, L=10; 5, h2=0.3, L=1000; and 6, h2=0.05, L=1000. Files with 'bin' in their name correspond to results with a binary measure of fitness (e.g., alive or dead). The general file types are as follows: pheno* = gemma formatted phenotype file with one column per simulated phenotypic data set, bv* = breeding values (expected phenotypic values) for each individual based on the genotypic data, effect* = phenotypic effect sizes for causal variants, functvar* = a list of the causal variants (by SNP number, and in the same order as in effect*).
DOI: 10.5061/dryad.ns47q/3
title: Simulated phenotypes based on the Rhagoletis GBS data

description: This compressed folder contains the simulated data sets where Rhagoletis pomonella GBS data were used as the starting point. It contains two gemma formatted genotype files (geno_sims.txt and geno592r_sims.txt) that contain the underlying genotypic data for the base simulations and those with replicated genotypes, respectively. The remaining files are named based on the simulations condition (simsN): 1, h2=0.3, L = 100; 2, h2=0.3, L=10; 3, h2=0.05, L=100; 4, h2=0.05, L=10; 5, h2=0.3, L=1000; and 6, h2=0.05, L=1000. The general file types are as follows: pheno* = gemma formatted phenotype file with one column per simulated phenotypic data set, bv* = breeding values (expected phenotypic values) for each individual based on the genotypic data, effect* = phenotypic effect sizes for causal variants, functvar* = a list of the causal variants (by SNP number, and in the same order as in effect*).
DOI: 10.5061/dryad.ns47q/4
title: Timema simulation scripts

description: This compressed directory contains four R scripts. The first three sims.R, sims2500.R and sims592r.R were used to simulate the quantitative phenotypes (fitness values) from the Timema GBS data for the original genotypic data, data with 2500 individuals, and with replicated genotypes, respectively. The last script, liability2binary.R, was used to convert quantitative fitness values to binary data.
DOI: 10.5061/dryad.ns5hr/1
title: The raw data

description: The data from included studies
DOI: 10.5061/dryad.q0j90/30
title: mitochondrial BEAST tree file

description: The mitochondrial (cox1 + 16S) Beast (dating analysis) output tree
DOI: 10.5061/dryad.q0j90/31
title: CorSiM R script

description: the R script of the CorSiM analyses for simulation of missing species
DOI: 10.5061/dryad.q7274/1
title: Shonfield et al playback trial data file

description: This data file contains data from playback trials conducted in the field on red squirrels in Kluane, Yukon. This data file contains the details of each playback trial, including location, date, subject squirrel info, playback stimulus info, and response of the subject squirrel.
DOI: 10.5061/dryad.r1921/1
title: Simulation Data

description: Raw data for the modeling simulations for each of the four species (European Starling, Red-winged Blackbird, Golden Shiner and Zebrafish).
DOI: 10.5061/dryad.t3j5n/2
title: Biaggio et al BioLetters 2016 Figure 2 data

description: These data are the basis of Figure 2 in Biaggio et al BIoLetters 2016. This summarizes behavioural mating outcomes for pairs in which mating occurred; these data were tested using Fisher’s exact tests.
DOI: 10.5061/dryad.vh75r/1
title: Data for Mantel and partial Mantel tests

description: Folder containing files necessary for replicating Mantel and partial Mantel tests.
DOI: 10.5061/dryad.vh75r/2
title: Data for demographic analyses using fastsimcoal2

description: All datasets, template files, parameter files, and custom scripts needed to perform demographic analyses in fastsimcoal2, including: model choice, parameter estimation, bootstrapping, 2-population parameter estimation, and sensitivity analyses. Additional information on the input files and command lines required for each type of demographic analysis, and additional information on running custom scripts, can be found in ReadMe files within each folder.
DOI: 10.5061/dryad.vh75r/3
title: Population structure analysis using ADMIXTURE

description: PED and MAP files for population structure analysis in ADMIXTURE.
DOI: 10.5061/dryad.vh75r/4
title: Population structure analysis using DAPC

description: RAW file for analysis of population structure using DAPC.
DOI: 10.5061/dryad.vr2ns/1
title: Trimmed and aligned cytochrome b sequences, formated as .fasta, from the Centropyge J Hered Brief
DOI: 10.5061/dryad.01j61/1
title: article strains

description: The name of the directory gives the number and the strain of fish used during the experiment. Cylinder and disks gives the spots of interest used for the experiments. In the files, data are developped as: time step (first column) then x position of fish 1 (fish0x) then y position of fish 1 (fish0y)  then x position of fish 2 (fish1x) then y position of fish 2 (fish1y) then ...
DOI: 10.5061/dryad.165tm/1
title: Data matrix

description: Edited data matrix used for all statistical analyses including all 33 tested variables, # sites and time span for all SALMAs
DOI: 10.5061/dryad.165tm/2
title: File 2

description: Diversity of carnivorans throughout the Cenozoic
DOI: 10.5061/dryad.165tm/3
title: File 3

description: Diversity of different mammal lineages present in SA throughout the Cenozoic
DOI: 10.5061/dryad.165tm/4
title: File 4

description: Diversity of South American ungulates present in SA throughout the Cenozoic
DOI: 10.5061/dryad.170rb/1
title: Supplementary Figures
DOI: 10.5061/dryad.3vd6k/1
title: Pipilo genotype probability matrix

description: SNP genotype probabilities across 41,324 loci for 460 Pipilo individuals
DOI: 10.5061/dryad.3vd6k/2
title: Pipilo plumage and metadata

description: Plumage scores and voucher, tissue, field, population, and genotype ID numbers associated with 460 Pipilo individuals
DOI: 10.5061/dryad.3vd6k/3
title: Pipilo short read assembly

description: BAM (alignment) file of short reads associated with the 460 Pipilo individuals
DOI: 10.5061/dryad.5217f/1
title: Ataf Ali - Excell Data

description: It contains all data files with description of figures in the file name.
DOI: 10.5061/dryad.5632c/10
title: 56

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/11
title: 57P1

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/5
title: 59P3

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/6
title: 75P1

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/7
title: 75P3

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/8
title: 57P3

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/9
title: 65

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.62cp0/1
title: Data for Bauch et al. MEC-16-0736

description: Contains raw data used in Bauch et al. MEC-16-0736. For variable explanations see ReadMe file.
DOI: 10.5061/dryad.6f774/1
title: Fitzpatrick.et.al.2016PSF

description: Performance data of focal species in conditioned soil. Block = spatial block in growth chamber. Species = numerical ID for focal plant species. Soil = numerical ID for soil conditioning plant species. See readme file for species names. AGB = aboveground biomass of focal species in particular soil treatment. BGB = belowground biomass of focal species in particular soil treatment. Species.exotic = exotic/native status of focal species. Soil.exotic = exotic/native status of soil conditioning species.
DOI: 10.5061/dryad.6f774/2
title: Trait.data

description: Trait data for every species in experiment. agb = aboveground biomass; bgb = belowground biomass; rl = root length; ra = root angle; water = leaf water content; sla = specific leaf area; rhd = root hair density; srl = specific root length. sd = standard deviation; se = standard error; n = number of independent measurements.
DOI: 10.5061/dryad.6f774/3
title: fieldsurvey

description: Co-occurence data. Population = replicate population; distance = distance between focal species and competitor; feedback = the measured feedback between each pair of focal X soil-conditioning species (see methods in paper) calculated for above-, belowground, and total biomass.
DOI: 10.5061/dryad.6f774/4
title: Phylogenetic tree

description: Phylogenetic tree including all 49 species (see methods for protocol).
DOI: 10.5061/dryad.6q1q6/1
title: Ant List

description: An Excel spreadsheet listing ant specimens used in the publication, with accompanying information on their mtDNA lineages, locality, host plant, and coccid associate (where present).
DOI: 10.5061/dryad.6q1q6/2
title: Coccus list Table S1

description: An Excel spreadsheet listing all Coccus specimens used for the publication, their morphospecies assignments and nuclear DNA clade, and including information on their host plants, host ants, and location.
DOI: 10.5061/dryad.7r10b/1
title: Phylogenetic data, scripts and results

description: ZIP archive containing the data used to conduct the phylogenetic analysis, descriptions of characters and codings, details of analytical procedures, scripts used to run analyses and visualise results, and strict consensus trees.  The README file contains the details needed to configure scripts and repeat the analysis.
DOI: 10.5061/dryad.8b5g6/1
title: Competency_Rscript

description: Statistical analysis
DOI: 10.5061/dryad.8b5g6/2
title: Bestworst_rawreads
DOI: 10.5061/dryad.8b5g6/3
title: bestwortstsurv_metadata_Competency
DOI: 10.5061/dryad.8b5g6/4
title: bestwortstsurv_norm_geom1_shiftlog_Competency
DOI: 10.5061/dryad.8b5g6/5
title: bestwortstsurv_taxonomy_Competency
DOI: 10.5061/dryad.8b5g6/6
title: foldchanges_Competency
DOI: 10.5061/dryad.8b5g6/7
title: larvalweight_Competency
DOI: 10.5061/dryad.8b5g6/8
title: Mortality_Competency
DOI: 10.5061/dryad.d4f4s/2
title: Stream Discharge Data

description: File includes annual time series of hourly discharge data for all streams in the study.
DOI: 10.5061/dryad.f8f8h/1
title: data_infectivity_for_dryad
DOI: 10.5061/dryad.f8f8h/2
title: symbiont_data_for_dryad
DOI: 10.5061/dryad.hm505/1
title: DB Lab Mate Choice

description: Mate choice behavioral assay done in the lab.
DOI: 10.5061/dryad.n4cv3/1
title: Reads and verified chimeric sequences (ITS2)

description: This contains 1) Raw reads (.fna) 2) Qual files (.qual) 3) mapping file 4) all 52 verified chimeric sequences (.fasta) 5) All fungi used in the mock communites (fasta)
DOI: 10.5061/dryad.nj811/1
title: RSPB20160841_Dryad Data

description: Gene expression values for field study and light experiments.  Each separate study/analysis is presented on new worksheet with appropriate labels.  If one has questions on data or methods used in this study, please do not hesitate to contact me at kingram@colgate.edu.
DOI: 10.5061/dryad.ns47q/5
title: Rhagoletis simulation scripts

description: This compressed directory contains two R scripts. These scripts (sims.R and sims592r.R) were used to simulate the quantitative phenotypes (fitness values) from the Rhagoletis GBS data for the original genotypic data and data with replicated genotypes, respectively.
DOI: 10.5061/dryad.ns47q/6
title: Summary scripts

description: This compressed directory contains the perl scripts used to summarize (1) the posterior distribution of genome-level genetic architecture parameters (calcpost*), and (2) SNP specific selection coefficients (summarizeSNP*pl).
DOI: 10.5061/dryad.p5cf4/1
title: Turtle Dove sequencing data

description: Single end Illumina reads for the 104 Turlte dove samples used in this study (one sample per file). All reads are 115 bp in length after trimming and removing barcodes as described in the manuscript. Reads with a single base under Phred 10 or more than 5% under Phred 20 were discarded.
DOI: 10.5061/dryad.sd64q/1
title: Penick_Beyond_thermal_limits

description: Colony survival, egg-laying rate, worker mortality rate, brood development time, brood survival, CTmax, and pupal development time.
DOI: 10.5061/dryad.t2462/1
title: Figure 1A

description: Photograph of individual 1121 taken on June 20th 2011. Image 1A taken at 0942am (GMT) showing multiple nicks on trailing edge of fin. Image 1A is considered a high quality shot. Images 1A, 1B and 1C clearly show the same fin shape, the teeth rakes and white skin lesions that show a convincing match despite the nicks.
DOI: 10.5061/dryad.t9140/1
title: Sequence_data.fasta

description: Novel DNA sequence data generated for this study from the species Glochidion lanceolarium (Phyllanthaceae) and Epicephala lanceolaria (Insecta: Lepidoptera: Gracillariidae). These data represent five loci: for Epicephala, mitochondrial COI, and nuclear EF1-α and ArgK; for Glochidion, nuclear ribosomal ITS and ETS. Sequences are the same as GenBank numbers KY078233-KY078291; however, GenBank numbers are not included in this file. For correspondences between sample numbers and GenBank sequences for Epicephala, please see Table 2 in the manuscript. Glochidion lanceolarium ITS sequence corresponds to GenBank number KY078253 and ETS sequence corresponds to GenBank number KY078252.
DOI: 10.5061/dryad.t9140/2
title: Figures_3_4

description: Data used in generating Figures 3 and 4 in the manuscript (see Excel spreadsheet tab labels). Figure 3 data represent the number of adult Epicephala lanceolaria moths found in individual Glochidion lanceolarium fruit at three sites in Guangdong Province, China. Figure 4 data represent the number of Epicephala lanceolaria pupae with and without cocoons found when dissecting Glochidion lanceolarium fruit at two sites in Guangdong Province, China.
DOI: 10.5061/dryad.t9140/3
title: MrBayes_Glochidion.nex.con

description: Phylogenetic hypothesis recovered using Bayesian inference implemented in MrBayes for Glochidion. Tip labels represent either specimen numbers or specific epithets for Glochidion species and are from the present study as well as Kawakita et al. (2004) Evolution and Hembry et al. (2013) Proc. Roy. Soc. B. Phyllanthus roseus is a very close relative to Glochidion, but is not pollinated by Epicephala (Kawakita and Kato 2009 Proc. R. Soc. B). Many tip labels follow the Supplementary Appendix in Hembry et al. (2013) Proc. R. Soc. B. This tree corresponds to Figure 5 and half of Figure 7 in the present manuscript.
DOI: 10.5061/dryad.t9140/4
title: RAxML_Glochidion

description: Phylogenetic hypothesis for Glochidion recovered using maximum likelihood inference implemented in RAxML. Tip labels represent either specimen numbers or specific epithets for Glochidion species and are from the present study as well as Kawakita et al. (2004) Evolution and Hembry et al. (2013) Proc. Roy. Soc. B. Phyllanthus roseus is a very close relative to Glochidion, but is not pollinated by Epicephala (Kawakita and Kato 2009 Proc. R. Soc. B). Many tip labels follow the Supplementary Appendix in Hembry et al. (2013) Proc. R. Soc. B. This tree corresponds to Supplementary Figure 1 in the present manuscript.
DOI: 10.5061/dryad.t9140/5
title: MrBayes_Epicephala.nex.con

description: Phylogenetic hypothesis for Epicephala, recovered using Bayesian inference implemented in MrBayes. Tip labels represent either specimen numbers and/or host species (in the genera Flueggea, Phyllanthus, Breynia, and Glochidion) from which specimens were reared, and are from the present study as well as Kawakita et al. (2004) Evolution, Kawakita et al. (2009) Proc. R. Soc. B, and Hembry et al. (2013) Proc. Roy. Soc. B. Many tip labels follow the Supplementary Appendix in Hembry et al. (2013) Proc. R. Soc. B. For E. lanceolaria OTUs, numbers refer to particular specimens; two-letter codes indicate collection localities (GB: Gaobangshan, LD: South China Botanical Garden, QA: Qiao Island, WT: Wutongshan); C = pupa with cocoon, NC = pupa with no cocoon. This tree corresponds to Figure 6 in the present manuscript.
DOI: 10.5061/dryad.vh75r/5
title: Raw VCF files.

description: Raw VCF files exported from STACKS.
DOI: 10.5061/dryad.vv29r/1
title: Duncan_JEB

description: This data file comprises 3 data sheets. One with bacteria and phage densities, another with bacteria resistance data from bacteria and phage time-shift curves and another with the coevolution score.
DOI: 10.5061/dryad.0t407/1
title: Data_archive_part2

description: This contains the second part of the data (too large for a single file upload)
DOI: 10.5061/dryad.0t407/2
title: Data_archive_part1

description: This archive contains all of the intermediate data files and R-scripts needed to generate the main figures and most of the supplementary materials. The original sequence data are stored on the Short Read Archive.
DOI: 10.5061/dryad.165tm/5
title: File 5

description: Diversity of phorusrhacid birds throughout the Cenozoic
DOI: 10.5061/dryad.165tm/6
title: File 6

description: Diversity of rodents throughout the Cenozoic
DOI: 10.5061/dryad.165tm/7
title: File 8

description: Statistical results of the 264 computed multiple linear regressions
DOI: 10.5061/dryad.165tm/8
title: File 7

description: Number of LADs for different body-size sparassodontans throughout the Cenozoic
DOI: 10.5061/dryad.165tm/9
title: Additional references and occurences' list
DOI: 10.5061/dryad.5632c/12
title: 63P3

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/13
title: 63P1

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/14
title: 41_60

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/15
title: 64P3

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/16
title: 64P1

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/17
title: 58

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/18
title: 45

description: Barcode file for AftrRAD
DOI: 10.5061/dryad.5632c/19
title: Dryad- microsats

description: Microsatellite data for comparison with RADseq data
DOI: 10.5061/dryad.5632c/20
title: Dryad- RADdatafile for comparison with microsats

description: Reduced RADseq dataset for comparison with microsatellites
DOI: 10.5061/dryad.5cb5b/1
title: DATA FILE

description: Departure fuel loads were regressed against fuel deposition rates. For each species, 3 separate regressions were performed: 1) All individuals, 2) only individuals of known sex regardless of age (sex was a factor), and 3) only individuals of the more specific age classes regardless of sex (age was a factor). All analyses, including the resampling process, were performed in R 3.1.2 (R Core Team 2015).
DOI: 10.5061/dryad.6q1q6/3
title: Ant Plant Coccus counts for binomial tests

description: An Excel spreadsheet showing how counts for the binomial tests were tallied, relying on information in the other two accompanying files in this data package (Ant list.xlsx & Coccus list Table S1.xlsx). Each of the six sets of tests has its own sheet.
DOI: 10.5061/dryad.7hh20/1
title: mutation_data

description: Summary of mutates genes identified in evolved clones isolated from replay populations
DOI: 10.5061/dryad.871pc/1
title: JAGS model code

description: Code, in JAGS language, for dynamic community occupancy model
DOI: 10.5061/dryad.871pc/2
title: Covariates

description: Relevant covariates and meta-data used in occupancy model fitting. Rdata file contains a list of objects.