cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qk26v/2
title: Western Blot CZP

description: Western blot assay for cruzipain observation
DOI: 10.5061/dryad.qk26v/3
title: in vitro

description: Raw data from T. cruzi infection assays
DOI: 10.5061/dryad.rm082/1
title: Delay discounting raw data

description: Raw data for the delay discounting manuscript.
DOI: 10.5061/dryad.t7m5v/3
title: countffrs.pl

description: This perl script was used to perform haploweb analyses on the simulated datasets.
DOI: 10.5061/dryad.t7m5v/4
title: Figure S1. Mismatch distributions computed for each simulated dataset.
DOI: 10.5061/dryad.t7m5v/5
title: Figure S2. Intra- (above) and interspecific mismatch distributions (below) computed on datasets simulated for 3 species.
DOI: 10.5061/dryad.t7m5v/6
title: Figure S3. Intra- (above) and interspecific mismatch distributions (below) computed on datasets simulated for 6 species.
DOI: 10.5061/dryad.t7m5v/7
title: Figure S4. Influence of mutation rate on the performance of GMYC-based methods.
DOI: 10.5061/dryad.v051c/5
title: effect_of_manipulated_env_deg_on_invader_fitness

description: Effect of manipulated environmental degradation on evolved invader fitness (data for Figure 3C)
DOI: 10.5061/dryad.33p91/1
title: scripts

description: The scripts used to conduct the simulations.
DOI: 10.5061/dryad.42p4q/1
title: temperature data

description: This is the data set of temperatures collected and analysed.
DOI: 10.5061/dryad.5385j/1
title: Abundance richness and evenness data VOUCHERED BEES

description: data of vouchered bees to test for differences between repeatedly sampled sites and single sample sites regarding abundance (as catch rate), rarefied richness, and evenness (as Evar).
DOI: 10.5061/dryad.5385j/2
title: Abundance richness and evenness data ALL BEES

description: data of combined bees (vouchered + released) to test for differences between repeatedly sampled sites and single sample sites regarding abundance (as catch rate), rarefied richness, and evenness (as Evar).
DOI: 10.5061/dryad.5385j/3
title: data for functional group analyses

description: data of vouchered bees to test for differences between repeatedly sampled sites and single sample sites regarding abundance functional group composition.  The four functional groups tested were diet (lecty), sociality, body size (size), and nesting substrate (nesting).  Note that sociality was tested twice, once with only Bombus considered social, and again with Bombus, Lasioglossum and Halictus as social.
DOI: 10.5061/dryad.5385j/4
title: Ready for NMDS VOUCHERED BEES ONLY

description: sample day by species matrix ready for NMDS analysis.
DOI: 10.5061/dryad.5385j/5
title: Yearly bee catch data

description: data used to calculate mean catch rates per sampling period per year by each sampling method.
DOI: 10.5061/dryad.5tq80.2
title: Data from: Longitudinal recordings of the vocalizations of immature Gombe chimpanzees for developmental studies
DOI: 10.5061/dryad.5tq80.2/2.2
title: Gombe_biography-for_1971-3

description: The Gombe_biography for the chimpanzee individuals present during the span of time that the recordings were made. The Gombe biography contains 13 columns, but the ones most useful for analyzing the vocalizations are the name of the individual (column B), the birth date (column C), the name of the mother (column H) and the sex of the individual (column I).  The columns are explained in Strier et al. [1].1.	Strier, K.B., et al., The Primate Life History Database: A unique shared ecological data resource. Methods Ecol Evol, 2010. 1(2): p. 199-211.
DOI: 10.5061/dryad.5tq80.2/3.2
title: List of names of infant vocalizations

description: A list of names of infant vocalizations as used in the Macaulay Library database notes and in the ‘All Infants’ spreadsheet.
DOI: 10.5061/dryad.5tq80.2/4.2
title: Dryad Readme file

description: Describing the Gombe chimps data package including the unparsed digital copies of the chimp tapes and the metadata for the individual sound recordings.
DOI: 10.5061/dryad.622q4/2
title: trinity_assemblies

description: These are FASTA files containing the raw output of the Trinity RNA-Seq de novo assembler for the cDNA libraries sequenced as part of our paper in eLife, DOI: http://dx.doi.org/10.7554/eLife.05503
DOI: 10.5061/dryad.83dc2/1
title: Blair-MER-Stacksfiles

description: All output files from Stacks analyses testing for bias in whole genome amplified DNA (using multiple displacement amplification; MDA) as compared to genomic DNA. Data include both sequencing runs and assemblies with and without the Microcebus murinus reference genome. Analyses are partitioned by tissue sample (e.g. MM1812). Within a single tissue sample, MDA and gDNA sequences are represented by different barcode sequences (see paper). Comparisons between treatments (gDNA vs. MDA) were performed at the SNP level.
DOI: 10.5061/dryad.8mc79/10
title: Custom scripts and softwares

description: A link where all the custom scripts and softwares used in this paper can be found.
DOI: 10.5061/dryad.8mc79/11
title: PstI-MspI SNP table - UNEAK - 23 worldwide populations

description: Generated with mnC=0.8, minCov=1  and a MAF=0.01. Use this file as input to generate the “UNEAK-PstI/MspI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
DOI: 10.5061/dryad.8mc79/12
title: PstI-MspI SNP table - PoPoolation2 - 23 worldwide populations

description: Generated with mnC=1, minCov=5 and a MAF=0.01. Use this file as input to generate the “PoPoolation2-PstI/MspI” SNP tables with different parameters (minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
DOI: 10.5061/dryad.8mc79/13
title: ApeKI SNP table - UNEAK - 23 worldwide populations

description: Generated with mnC=0.8, minCov=1  and a MAF=0.01. Use this file as input to generate the “UNEAK-ApeKI” SNP tables with different parameters (mnC, minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
DOI: 10.5061/dryad.8mc79/14
title: ApeKI SNP table - PoPoolation2 - 23 worldwide populations

description: Generated with mnC=1, minCov=5 and a MAF=0.01. Use this file as input to generate the “PoPoolation2- ApeKI” SNP tables with different parameters (minCov and MAF) using the countCleaner script found at https://bitbucket.org/mimeeb/gbs (Windows-based software).
DOI: 10.5061/dryad.8mc79/15
title: Input file for PHYLIP - 23 worldwide populations

description: Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for phylogenetic tree analysis of the 23 Globodera rostochiensis worldwide populations.
DOI: 10.5061/dryad.8mc79/8
title: Sample description

description: Details about the origin (Country, province and field) of the samples, which experiment and figures they were used in and accession numbers (bioproject and biosample numbers).
DOI: 10.5061/dryad.8mc79/9
title: Supplemental Table 1

description: Population differentiation (Fst) of 23 worldwide populations of Globodera rostochiensis estimated from genome-wide allele frequencies at 604 loci.
DOI: 10.5061/dryad.9tm42/1
title: Liedigk Add.file-1 Alignment mtDNA 38.nex

description: Additional file 1: Basic alignment of complete mitochondrial genomes from 38 catarrhine primate taxa. (nexus format)
DOI: 10.5061/dryad.9tm42/2
title: Liedigk_Add.file-2_TabS1

description: Additional file 2: Table S1. Divergence ages among catarrhine primates in Ma (95% credibility intervals) estimated with uncorrelated and auto-correlated relaxed clock models. (docx)
DOI: 10.5061/dryad.9tm42/3
title: Liedigk_Add.file-3_FigS1

description: Additional file 3: Figure S1. Nucleotide composition among Papionini and outroup taxa. (pptx)
DOI: 10.5061/dryad.9tm42/4
title: Liedigk_Add.file-4_FigS2

description: Additional file 4: Figure S2. Ultrametric tree of Papionini and outgroup taxa as inferred from dataset 2. Tree topologies as inferred from Bayesian (MrBayes) as well as from ML (RAxML) estimations were mainly identical with some exceptions. All unlabelled branches show ML BP of 100% and Bayesian PP of 1.0. Values below are indicated at respective nodes. Taxa indicated with a are arranged differently in the ML (RAxML) and Bayesian tree (MrBayes): ((P. anubis west2, P. anubis west1) P. papio); ((C. torquatus, C. atys), ((C. chrysogaster, M. leucophaeus), M. sphinx)). Red ellipse indicates main difference to figure 1. * = sequences were newly generated in this study. (pptx)
DOI: 10.5061/dryad.9tm42/5
title: Liedigk_Add.file-5_FigS3

description: Additional file 5: Figure S3: Tree topology including divergence dates as estimated with an auto-correlated relaxed clock model as implemented in PhyloBayes 3.3. Time scale shows million years before present. * = sequences were newly generated in this study. (pptx)
DOI: 10.5061/dryad.9tm42/6
title: Liedigk_Add.file-6_FigS4

description: Additional file 6: Figure S4: Tree topology including divergence dates as estimated with an uncorrelated relaxed clock model as implemented in PhyloBayes 3.3. Time scale shows million years before present. * = sequences were newly generated in this study. (pptx)
DOI: 10.5061/dryad.b2q88/1
title: Eperua_falcata_AFLPs_MarkerBins

description: The file describes the AFLPs binset: the restriction enzyme used, the dye color for genotyping, and the location of the AFLPs bins.
DOI: 10.5061/dryad.b2q88/2
title: Eperua_falcata_AFLPs_Data

description: The file contains a description of the sampled trees (tree number, location) and the AFLPs data (binary)
DOI: 10.5061/dryad.bv247/7
title: Marques et al Active diet mixing, data Fig. 2c
DOI: 10.5061/dryad.fb80v/3
title: Data on experiments in pigs

description: SPSS data (.sav) file. It contains all data of the experiments in pigs. Description of the variables in the attached ReadMe file.
DOI: 10.5061/dryad.h0h90/1
title: fMRI_RT_data

description: fMRI and reaction time data from an unconscoious relational memory paradigm. All data are prepared to be processed with SPM 8 for MATLAB. Additional information about the data structure, acquisition parameters and processing instructions are included in the downloadable package (zip format). Use an archive manager such as 7-zip, winrar or similar to access data.
DOI: 10.5061/dryad.pc1th/1
title: Microsattilite genotypes for all individuals at all 16 loci

description: This file contains the microsattilite data that was attained for this study. It is in genepop format. This file contains all loci that were genotyped including those that were removed from the analysis. The 16 numbers at the top of the file represent loci names.  Each entry under a "POP" header represents an individual of that population, where A = Alaska, B = Brannen Lake, E = East Coast, M = Mayliewan (our Alberta population), and N = Norway. Each of the 16 sets of 4 digits represent diploid genotypes at each of the 16 loci for that individual.  For example, 0414 would represent a heterozygous call  for allele 4 and allele 14 for that individual for whatever locus it is under. The first column of 4 digits represents locus 51 and the last represents locus 222 (the rest are ordered accordingly). 00s represent missing data.
DOI: 10.5061/dryad.rk384/1
title: Raw PLFA data

description: Quantities of microbial biomarker phospholipid fatty acids extracted from soils under continuous corn and a restored prairie system.
DOI: 10.5061/dryad.v6b8c/1
title: Oakleyetal_2015_Heredity_JLineCross_Growout_RawData

description: Raw data
DOI: 10.5061/dryad.v6b8c/2
title: Oakleyetal_2015_Heredity_JointScale_FruitN

description: Example Python script for performing the joint scaling analyses
DOI: 10.5061/dryad.15j4j/1
title: Morphological and genetic data

description: The spreadsheet contains the morphological and genetic data presented in Langin et al. (2015), as well as supporting information used in analyses (e.g., age, family relationships, habitat information). Each row is an individual Island Scrub-Jay.
DOI: 10.5061/dryad.280m5/1
title: Hardy_etal_2015_Evolution_Archive

description: An archive containing the phylogenetic trees, trait data and R scripts used in the comparative phylogenetic analyses in Hardy et al. 2015.
DOI: 10.5061/dryad.4n2c4/23
title: mogA

description: mogA nexus file; unphased
DOI: 10.5061/dryad.5tq80.2/10.2
title: Flint 1

description: First recordings of immature individual Flint
DOI: 10.5061/dryad.5tq80.2/11.2
title: Flint 2

description: Second recordings of immature individual Flint
DOI: 10.5061/dryad.5tq80.2/12.2
title: Freud 1

description: First recordings of immature individual Freud
DOI: 10.5061/dryad.5tq80.2/5.2
title: Atlas

description: All recordings of immature individual Atlas
DOI: 10.5061/dryad.5tq80.2/6.2
title: Demo Tape

description: Collection of good recordings for demonstration purposes
DOI: 10.5061/dryad.5tq80.2/7.2
title: Demo Thesis 1

description: Collection of good recordings for demonstration purposes
DOI: 10.5061/dryad.5tq80.2/8.2
title: Demo Thesis 2

description: Collection of good recordings for demonstration purposes
DOI: 10.5061/dryad.5tq80.2/9.2
title: Demo Thesis 3

description: Collection of good recordings for demonstration purposes
DOI: 10.5061/dryad.6k09k/1
title: Alignment of the sequences upload to Dryad_GYY_20141211
DOI: 10.5061/dryad.6k09k/2
title: BEAST input file and output file
DOI: 10.5061/dryad.7p9v1/1
title: Thoropa taophora microsatellite genotype data

description: This file includes genotype data for 438 individuals of the frog species Thoropa taophora. Individuals were genotyped at nine microsatellie loci. Individuals were collected at 17 sampling localities and for each individual the name and GPS point of the locality is included. Additionally, we indicate if the sampling locality was island or coastal.
DOI: 10.5061/dryad.80t07/1
title: Concurrent co-evolution of intra-organismal cheaters and resisters Data

description: This data was collected in the lab, using Ax4 Dictyostelium discoideum lines which had undergone experimental evolution for 31 generations in the Kuzdzal-Fick et al. 2011 experiment.
DOI: 10.5061/dryad.8mc79/16
title: UNEAK PstI-MspI allele frequencies - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup

description: Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for principal component analysis (PCA) of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France.
DOI: 10.5061/dryad.8mc79/17
title: Input file for PHYLIP - Validation assay - 28 Quebec populations from 2 fields + 1 outgroup

description: Allele frequencies calculated from UNEAK exact counts (mnC=1, minCov=20 and MAF=0.01) and used for phylogenetic tree analysis of Globodera rostochiensis populations from two fields of the province of Quebec, Canada and an unrelated population from France.
DOI: 10.5061/dryad.8mc79/18
title: Supplemental Figure 1

description: Relationship between the median coverage (median number of reads/locus/population supporting each SNP) and the number of SNPs retained by the two pipelines at a minimum allele frequency of 1% (MAF = 0.01) and 5% (MAF = 0.05).
DOI: 10.5061/dryad.8mc79/19
title: Supplemental Figure 2

description: Number of SNPs retained by UNEAK and PoPoolation2 pipelines at different parameter values on an ApeKI library from 23 worldwide populations of Globodera rostochiensis. ‘MAF’ is the minimum allele frequency; ‘minCov’ is the minimum number of reads/locus/population required to accept a SNP; ‘mnC’ is the minimum proportion of populations in which a locus must have been scored to be accepted. PoPoolation2 does not allow missing data (mnC = 1.0). *The number of SNPs identified by UNEAK was not influenced by the ‘mnC’ value when the minimum allele frequency was set to 5% (MAF = 0.05).
DOI: 10.5061/dryad.8mc79/20
title: Supplemental Figure 3

description: Principal component analyses of 23 worldwide populations of Globodera rostochiensis from different pathotypes (Ro1, Ro2, Ro3, Ro4, Ro5 and a mixed population of Ro2/Ro3). Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of different number of loci obtained from the PstI/MspI library supported by six different minimum coverage values (minCov = 5, 10, 20, 30, 40 or 50 reads/locus/population). Computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01) and no missing data allowed (mnC = 1.0).
DOI: 10.5061/dryad.8mc79/21
title: Supplemental Figure 4

description: Principal component analysis of 23 worldwide populations of Globodera rostochiensis. Calculated with the prcomp() function in R. Based on genome-wide allele frequencies of 1,277 loci obtained from the PstI/MspI library, and computed by the PoPoolation2 pipeline with a minimum allele frequency of 1% (MAF = 0.01), no missing data allowed (mnC = 1.0) and a minimum coverage of 20 reads/SNP/population (minCov = 20). Colors represent the different pathotypes: Black = Ro1; Yellow = Ro2; Green = Ro3; Red = Ro4; Blue = Ro5 and Grey is the mixed Ro2/3 sample.
DOI: 10.5061/dryad.90835/7
title: Acropora digitifera shannon

description: This file is a matrix with all pairwise shannon diversities values for Acropora digitifera.
DOI: 10.5061/dryad.9tm42/7
title: Liedigk_Add.file-7_TabS2

description: Additional file 7: Table S2. Studied species and individuals along with their GenBank accession numbers. (xls)
DOI: 10.5061/dryad.dt7mh/1
title: Bee specimen data

description: Please consult the ReadMe file.
DOI: 10.5061/dryad.dt7mh/2
title: Nesting habitat data (quadrats)

description: Please consult the ReadMe file.
DOI: 10.5061/dryad.dt7mh/3
title: Nesting habitat data (transects)

description: Please consult the ReadMe file.
DOI: 10.5061/dryad.k9h76/1
title: Lablab purpureus transcriptome assembly

description: Lablab purpureus transcriptome assembly
DOI: 10.5061/dryad.k9h76/2
title: Lathyrus sativus transcriptome assembly

description: Lathyrus sativus transcriptome assembly
DOI: 10.5061/dryad.k9h76/3
title: Psophocarpus tetragonolobus transcriptome assembly

description: Psophocarpus tetragonolobus transcriptome assembly
DOI: 10.5061/dryad.k9h76/4
title: Vigna subterranea transcriptome assembly

description: Vigna subterranea transcriptome assembly
DOI: 10.5061/dryad.kq1g6/1
title: Size And Shape Data

description: centroid size and landmark coordinates for individual specimens
DOI: 10.5061/dryad.kq1g6/2
title: Simulated Disparities of Size and Shape

description: results from 1000 trees simulated over 36 myr
DOI: 10.5061/dryad.3gn80/1
title: TC YASI RAW DATA PONE_D_14_40836

description: Excel spreadsheet containing three sheets: A) Reef Health and Impact Survey data from the TC Yasi impact assessment conducted in February / March 2011. The sheet includes the data used to produce figures 2 and 7. B) Size, intensity and persistence data from 44 tropical cyclones between 1985 and 2014 used to create figure 5. C) Reef Health and Impact Survey data collected in 2011 and 2013 recovery surveys used to produce figures 9a and 9b.
DOI: 10.5061/dryad.4n2c4/20
title: c7orf25

description: c7prf25 nexus file; unphased
DOI: 10.5061/dryad.4n2c4/21
title: fem1c

description: fem1c nexus file; unphased
DOI: 10.5061/dryad.4n2c4/22
title: mastl

description: mastl nexus file; unphased
DOI: 10.5061/dryad.4q7s8/1
title: Lateralization ms data
DOI: 10.5061/dryad.5tq80.2/13.2
title: Freud 2

description: Second recordings of immature individual Freud
DOI: 10.5061/dryad.5tq80.2/14.2
title: Gilka

description: All recordings of immature individual Gilka
DOI: 10.5061/dryad.5tq80.2/15.2
title: Goblin

description: All recordings of immature individual Goblin
DOI: 10.5061/dryad.5tq80.2/16.2
title: Gremlin

description: All recordings of immature individual Gremlin
DOI: 10.5061/dryad.5tq80.2/17.2
title: Kobi

description: All recordings of immature individual Kobi
DOI: 10.5061/dryad.5tq80.2/18.2
title: Little Bee

description: All recordings of immature individual Little Bee
DOI: 10.5061/dryad.5tq80.2/19.2
title: Moeza

description: All recordings of immature individual Moeza
DOI: 10.5061/dryad.5tq80.2/20.2
title: Mustard

description: All recordings of immature individual Mustard
DOI: 10.5061/dryad.5tq80.2/21.2
title: Plato

description: All recordings of immature individual Plato
DOI: 10.5061/dryad.6k09k/3
title: MP and BI tree files
DOI: 10.5061/dryad.6k09k/4
title: SplitsTree_input file
DOI: 10.5061/dryad.90835/5
title: Acropora hyacinthus Fst

description: This is a csv file is a matrix with all pairwise Fst comparisons for Acropora hyacinthus and all pairwise distances between islands.
DOI: 10.5061/dryad.90835/6
title: Island Labels

description: This is a matrix of all pairwise island labels.
DOI: 10.5061/dryad.90835/8
title: Acropora hyacinthus shannon

description: This file is a matrix with all pairwise shannon diversities values for Acropora hyacinthus.
DOI: 10.5061/dryad.g92c4/1
title: Ta2PdSe5-data.tar

description: This is a gzip tar file containing directories with input and output files from the calculations and data in the figures.
DOI: 10.5061/dryad.h5g85/1
title: Phylogenetic Uncertain Taxa

description: List of missing species in the backbone phylogeny
DOI: 10.5061/dryad.h5g85/2
title: Hummingbirds Phylogeny, with Most Derived Consensus Clades for each Phylogenetic Uncertain Taxa

description: Hummingbirds Phylogeny, with Most Derived Consensus Clades for each Phylogenetic Uncertain Taxa
DOI: 10.5061/dryad.h5g85/3
title: 25000 Phylogenies of McGuire et al. 2007, with MDCCs defined

description: 25000 Phylogenies of McGuire et al. 2007, with MDCCs defined
DOI: 10.5061/dryad.h5g85/4
title: Geographic Grid, with 2868 cells, describing New World
DOI: 10.5061/dryad.h5g85/5
title: Presence/Absence matrix of 304Spp Hummingbird in the Western Hemisphere Grid
DOI: 10.5061/dryad.h5g85/6
title: BodySize of 304 species of Hummingbirds
DOI: 10.5061/dryad.h5g85/7
title: Elevational range of 304 species of hummingbirds
DOI: 10.5061/dryad.tb08g/1
title: Pollinator Observations Data

description: This workbook contains the raw data from observations of pollinators in both two-species (sheet 1) and one-species (sheet 2) arrays. It also includes the visitation rates (visits/flower/hour) of pollinators for each observation session (sheet 3) given the number of open flowers at the time. This data was used to evaluate heterogeneity of preference between pollinator groups, differences in pollinator assemblages between yellow and white sites, differences in visitation to white and yellow flowers across sites, and floral constancy both within and between species.
DOI: 10.5061/dryad.tb08g/2
title: Local Adaptation Data

description: This workbook has data regarding the fitness characters of plants from one-species arrays (# seeds, # siliques, # total flowers). This data was used to assess the hypothesis of local adaptation by comparing the total number of seeds and mortality of white and yellow L. stylosa individuals in white and yellow populations.
DOI: 10.5061/dryad.tb08g/3
title: Leavenworthia spatial data

description: This workbook contains the population locales for L. stylosa (sheet 1), L. exigua (sheet 2), and L. torulosa (sheet 3). These raw data were utilized to estimate nearest neighbor distances from L.stylosa populations (sheet 4) and to estimate levels of geographic isolation of white and yellow L. stylosa populations from L. exigua (sheet 5) and L. torulosa (sheet 6).
DOI: 10.5061/dryad.tb08g/4
title: C code for Geographic Isolation

description: This document contains the code (written in C and compiled and executed in Microsoft Codeblocks) used to sample Leavenworthia population locality data to produce estimates of geographic isolation between white and yellow populations L. stylosa and either L. exigua or L. torulosa.