cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3h4m5.2/2.2
title: A1_CharacterPartitions

description: File_A1 (Excel).  Table describing the 28 partitions (25 morphological, 3 molecular) and listing the included characters.   Character numbering is based on the matrix from [6], available as MorphoBank Project 773 (http://dx.doi.org/10.7934/P773).
DOI: 10.5061/dryad.403b2.2
title: Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
DOI: 10.5061/dryad.403b2.2/1.2
title: Scripts

description: This zip archive includes two python scripts referenced in the associated publication. Functionality includes: 1) Estimation of short and long range LD from haplotype data, 2) Identification of haplotype-blocks through singleton markers. Each script comes with an associated README file, parameter specifications and example data. See Material and Methods and a description in the Supplemental Material for more details.
DOI: 10.5061/dryad.403b2.2/2.2
title: Dmel_haplotype_fasta_base

description: This zip archive contains fasta files of 29 haploid D. melanogaster genomes associated with the experimental evolution experiment in the referenced publication. They correspond to 29 haploid genomes for the experimental starting population. Provided are the major chromosomal arms X, 2L, 2R, 3L and 3R. See Material and Methods for more details.
DOI: 10.5061/dryad.403b2.2/3.2
title: Dmel_haplotype_fasta_F67

description: This zip archive contains fasta files of 29 haploid D. melanogaster genomes associated with the experimental evolution experiment in the referenced publication. They correspond to 29 haploid genomes for a (hot) evolved population at generation 67 (2nd replicate). Provided are the major chromosomal arms X, 2L, 2R, 3L and 3R. See Material and Methods for more details.
DOI: 10.5061/dryad.45dn8/1
title: Juvenile data females

description: Development time to maturation, area at maturation and juvenile growth rate for females from development-selected lines.
DOI: 10.5061/dryad.45dn8/2
title: Juvenile data males

description: Development time to maturation, area at maturation and juvenile growth rate for males from development-selected lines.
DOI: 10.5061/dryad.45dn8/3
title: Age-specific reproduction and size - females

description: Age-specific size and reproduction for females. Day 0 = day of maturation. Size was not measured every day.
DOI: 10.5061/dryad.45dn8/4
title: Total reproduction and lambda - females

description: Total reproduction over lifespan and lambda for individual females.
DOI: 10.5061/dryad.45dn8/5
title: Heatshock resistance males and females

description: Heatshock resistance (alive/dead) per plate for both males and females
DOI: 10.5061/dryad.45dn8/6
title: Age-specific reproduction and size - males

description: Age-specific size and reproduction for development-selected males. Note that traits were not measured every day.
DOI: 10.5061/dryad.4b072/1
title: Worker movement data

description: File containing ant worker movement data within sample triplets along with distance between nests and nest volumes. For full description of labelling see readme
DOI: 10.5061/dryad.4b072/2
title: Microsatellite data

description: Data for microsatellite variation across 12 loci. Four columns preceeding mirosatellite data describing sampling (see readme), next 12 columns are variation across microsatellite data
DOI: 10.5061/dryad.4b072/3
title: Resource movement data

description: A four column file with data on the absorbance of individual ants following and ELISA assay. Arranges as follows: colony - the name of the tested triplet, n=10; nest - B, C or U for base, connected or unconnected (see paper Fig. 1 for details); sample - bl (blank, no ant), ctrl (control, known negative ant), 1-100 individual ants being tested for absorbance; absorb - absorbance value
DOI: 10.5061/dryad.57j1t/1
title: Chlamydomonas flow data files
DOI: 10.5061/dryad.62s22/16
title: Quality-filtered VCF file for treatment-replicate 2BV-I
DOI: 10.5061/dryad.62s22/17
title: Quality-filtered VCF file for treatment-replicate 2BV-II
DOI: 10.5061/dryad.62s22/18
title: Quality-filtered VCF file for treatment-replicate 2BV-III
DOI: 10.5061/dryad.67fk8/3
title: Ground-dove BEAST tree file

description: Maximum clade credibility tree and divergence time estimates from BEAST.
DOI: 10.5061/dryad.67fk8/4
title: Ground-dove BEAST xml file

description: XML file used for the BEAST analysis.
DOI: 10.5061/dryad.67fk8/5
title: Ground-dove alignment

description: Concatenated sequence alignment for the small New World ground-dove and outgroups data. Data partitions are indicated in the SETS block.
DOI: 10.5061/dryad.875kh/1
title: Supplementary Materials
DOI: 10.5061/dryad.90qb7.3
title: Data from: Effects of antibiotic resistance alleles on bacterial evolutionary responses to viral parasites
DOI: 10.5061/dryad.90qb7.3/1.3
title: Arias_Hall_BiolLett_2016_data

description: The Excel file contains population density, bacteriophage sensitivity and mutation rate estimate data. The ReadMe worksheet describes the contents in detail. ‘Main experiment’ gives population densities after 0h, 20h and 72h in the main experiment. ‘Table S1’ gives changes in bacterial sensitivity to phages in control populations against all three phages. ‘FT raw data’ gives colony counts and population sizes from fluctuation assays. ‘Falcor’ gives output from mutation rate estimation using Falcor before and after correction for partial plating (plating efficiency).
DOI: 10.5061/dryad.d2vf8/1
title: MAP analysis

description: Blood Pressure Raw Data SPSS file
DOI: 10.5061/dryad.d2vf8/2
title: HR analysis

description: Heart Rate Raw Data SPSS file
DOI: 10.5061/dryad.d2vf8/3
title: DEQ_analysis

description: Raw data for DEQ subjective measure
DOI: 10.5061/dryad.d2vf8/4
title: POMS_analysis

description: Raw data for POMS subjective measure_ SPSS file
DOI: 10.5061/dryad.d3m23/7
title: RodentPopSizeVsSeedRemoval

description: Comparison of Total Seed Removal / Number of Species Taken by Month and Small Mammal Population Size
DOI: 10.5061/dryad.d3m23/8
title: RodentPopSugarMapleRemovalWeaselPop

description: Comparison of Percent Total Sugar Maple Removed by Small Mammal Population Size and Weasel Population
DOI: 10.5061/dryad.fc8np/1
title: Data for Table 3

description: Data of survival on cotton with 3 replications per strain and cultivar.
DOI: 10.5061/dryad.fc8np/2
title: Data for Table 4

description: Data of Bt toxin concentrations in cotton cultivars.
DOI: 10.5061/dryad.h8p2r/1
title: Repository data to Reinhardt et al, PLoS ONE

description: EXCEL File. See Excel Sheet "Description of data sets" for detail.
DOI: 10.5061/dryad.qj5cr/10
title: Ravinet_et_al_Prim_Cont_Soft_Sweep

description: Computer code for a soft sweep occurring in the face of gene flow between a pair of populations under divergent selection (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/11
title: Ravinet_et_al_Prim_Cont_Hard_Sweep

description: Computer code for a hard sweep occurring in the face of gene flow between a pair of populations under divergent selection (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/4
title: data_Fig3C

description: Data used to generate Fig. 3C in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/5
title: data_Fig4A

description: Data used to generate Fig. 4A in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/6
title: data_Fig4B

description: Data used to generate Fig. 4B in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/7
title: data_Fig5

description: Data used to generate Fig. 5 in Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/8
title: Initial Conditions

description: Initial conditions used as the input for the main simulations performed by Ravinet et al. (2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.qj5cr/9
title: Ravinet_et_al_Neutral_Evolution_Phase

description: Computer code for the neutral-evolution phase (explained in detail in Ravinet et al. 2017). For further details, please refer to the separate file "ReadMeFirst".
DOI: 10.5061/dryad.vg06c/1
title: Peak amplitude of vibrations and times for measured components of thread breaking behaviour

description: The folder contains several excel files. Please refer to the titles of each excel file for a description of the specific data contained in the file. Data are either of peak amplitudes (in kU) produced when breaking or releasing threads, or of time (in seconds) elapsed between different components of thread breaking behaviour.
DOI: 10.5061/dryad.vr954/30
title: Camarasaurus posterior bite

description: Abaqus input file of a finite element model of the cranium of Camarasaurus, simulating a bite at the posteriormost four teeth.
DOI: 10.5061/dryad.vr954/31
title: Camarasaurus dentine

description: Abaqus input file of a finite element model of the cranium of Camarasaurus, with the material properties of dentine assigned to the teeth. This formed part of the sensitivity analyses testing the significance of the material properties of the teeth on results.
DOI: 10.5061/dryad.vr954/32
title: Camarasaurus enamel

description: Abaqus input file of a finite element model of the cranium of Camarasaurus, with the material properties of enamel assigned to the teeth. This formed part of the sensitivity analyses testing the significance of the material properties of the teeth on results.
DOI: 10.5061/dryad.vr954/33
title: Camarasaurus mandible anterior bite

description: Abaqus input file of a finite element model of the mandible of Camarasaurus, simulating a bilateral bite at the anteriormost four teeth.
DOI: 10.5061/dryad.vr954/34
title: Camarasaurus mandible middle bite

description: Abaqus input file of a finite element model of the mandible of Camarasaurus, simulating a bilateral bite at the middle four teeth.
DOI: 10.5061/dryad.vr954/35
title: Camarasaurus mandible posterior bite

description: Abaqus input file of a finite element model of the mandible of Camarasaurus, simulating a bilateral bite at the posteriormost four teeth.
DOI: 10.5061/dryad.vr954/36
title: Camarasaurus mandible dentine

description: Abaqus input file of a finite element model of the mandible of Camarasaurus, with the material properties of dentine assigned to the teeth. This formed part of the sensitivity analyses testing the influence of the material properties of the teeth on results.
DOI: 10.5061/dryad.vr954/37
title: Camarasaurus mandible enamel

description: Abaqus input file of a finite element model of the mandible of Camarasaurus, with the material properties of enamel assigned to the teeth. This formed part of the sensitivity analyses testing the influence of the material properties of the teeth on results.
DOI: 10.5061/dryad.vr954/38
title: Camarasaurus mandible unilateral anterior bite

description: Abaqus input file of a finite-element model of the mandible of Camarasaurus, simulating an unilateral bite at the posterior biting position.
DOI: 10.5061/dryad.vr954/39
title: Camarasaurus mandible unilateral middle bite

description: Abaqus input file of a finite-element model of the mandible of Camarasaurus, simulating an unilateral bite at the middle biting position.
DOI: 10.5061/dryad.0r9p1/1
title: Single-trial behavioral and P3 data

description: MATLAB file with single-trial behavioral/task data and P3 amplitudes. See the README file for more information.
DOI: 10.5061/dryad.2th78/10
title: Study2_3
DOI: 10.5061/dryad.2th78/2
title: Study1_1
DOI: 10.5061/dryad.2th78/3
title: Study1_2
DOI: 10.5061/dryad.2th78/4
title: Study1_3
DOI: 10.5061/dryad.2th78/5
title: Study1_4
DOI: 10.5061/dryad.2th78/6
title: Study1_5
DOI: 10.5061/dryad.2th78/7
title: Study1_6
DOI: 10.5061/dryad.3f151/1
title: TWPCO

description: Data of my results
DOI: 10.5061/dryad.3h4m5.2/10.2
title: B8_Randomised_TOLMorph25p_TOL_Gam

description: File_B8 (plain text).  The MrBayes [10] executable file to infer branch lengths for the 25 randomised morphological partitions.  The partitions were of the same size as the 25 original partitions (42-553 characters); morphological characters were randomly shuffled in Excel.   The molecular data were not randomised.  The matrix otherwise is identical to that in File B1.
DOI: 10.5061/dryad.3h4m5.2/3.2
title: B1_TreeRef6_MrBayesFile_Morph1-25

description: File_B1 (plain text).  The MrBayes [10] executable file to infer branch lengths for the 25 candidate morphological partitions, using the total-evidence Maximum Likelihood topology from [6].  The matrix consists of only the 46 extant taxa from [6], since molecular branch lengths (to which these morphological branch lengths have to be compared) cannot be ascertained for extinct taxa.
DOI: 10.5061/dryad.3h4m5.2/4.2
title: B2_TreeRef6_MrBayesFile_Codons1-3

description: File_B2 (plain text).  The MrBayes executable file to infer branch lengths for the 3 candidate molecular partitions (and overall morphological branch lengths), using the total-evidence Maximum Likelihood topology from [6].  The matrix consists of the 46 extant taxa from [6].
DOI: 10.5061/dryad.3h4m5.2/5.2
title: B3_TreeRef6_Parts1-28branchlengths_newick

description: File_B3 (newick format).  The ClockstaR [3] treefile containing the trees with the branch  lengths for the 28 candidate partitions obtained from the MrBayes analysis in files B1, B2.  Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
DOI: 10.5061/dryad.3h4m5.2/6.2
title: B4_TreeRef9_MrBayesFile_Morph1-25

description: File_B4 (plain text).  The MrBayes [10] executable file  to infer branch lengths for the 25 candidate morphological partitions, using the topology from [9].  The matrix consists of only the 46 extant taxa from [6], since molecular branch lengths (to which these morphological branch lengths have to be compared) cannot be ascertained for extinct taxa.
DOI: 10.5061/dryad.3h4m5.2/7.2
title: B5_TreeRef9_MrBayesFile_Codons1-3

description: File_B5 (plain text).  The MrBayes executable file  to infer branch lengths for the 3 candidate molecular partitions (and overall morphological branch lengths), using the topology from [9].  The matrix consists of the 46 extant taxa from [6].
DOI: 10.5061/dryad.3h4m5.2/8.2
title: B6_TreeRef9_Parts1-28branchlengths_newick

description: File_B6 (newick format).  The ClockstaR treefile containing the trees with the branch  lengths for the 28 candidate partitions obtained from the MrBayes analysis in files B4, B5.  Note: ClockstaR treats all trees as unrooted, so different rootings of trees are of no consequence.
DOI: 10.5061/dryad.3h4m5.2/9.2
title: B7_ClockstarResults

description: File_B7 (pdf). ClockstaR partition matrices and gap statistics for analyses using the guide tree from ref [6] (upper panels) and ref [9] (lower panels).  From the 28 candidate partitions, both analyses identified an optimal number of 8 clock-partitions  (pacemakers) of similar composition.  Note that the order of partitions in these tables (molecular partitions uppermost) is different to that in Fig. 1, but the same as in Fig. B10.
DOI: 10.5061/dryad.403b2.1
title: Data from: Patterns of linkage disequilibrium and long range hitchhiking in evolving experimental Drosophila melanogaster populations
DOI: 10.5061/dryad.403b2.2/4.2
title: Sync file for 3 time points for 3 replicates

description: Sync file of allele coverage counts for 1,453,774 called SNPs in the euchromatin of the *D. melanogaster* genome (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq).Bioinformatics 2011;27:3435-3436.). To the sync file a header line is added, which specifies the time points, replicates and treatment abbreviations (FX: time point at generation X, RY: replicate number Y, H: hot treatment). The sync file contains time points for generations: 0, 15, 37 and 59. For generations 0, 15 and 38 please additionally cite: Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, Schlötterer C. Adaptation of *Drosophila* to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol. 2012;21:4931-4941.
DOI: 10.5061/dryad.45dn8/10
title: Survival: matricide censored

description: Survival of development-selected lines. Worms dying of matricide are censored in this dataset.
DOI: 10.5061/dryad.45dn8/7
title: Total reproduction and lambda - males

description: Total reproduction and lambda for males. Note that this is based upon the subset of times measured.
DOI: 10.5061/dryad.45dn8/8
title: Mortality-selected lines: juvenile traits

description: Development time (h), area at maturity and juvenile growth rate of females from mortality-selected lines.
DOI: 10.5061/dryad.45dn8/9
title: Survival: matricide included

description: Survival of development-selected lines. Matricide treated as dead. See other file for matricide censored.
DOI: 10.5061/dryad.4931c/1
title: Data1

description: Part 1 of Labelled EPG data from recordings of Asian Citrus Psyllid (Diaphorina citri) feeding on citrus cultivars.
DOI: 10.5061/dryad.4931c/2
title: Data2

description: Part 2 of Labelled EPG recordings of Asian Citrus Psyllid (Diaphorina citri) feeding on citrus cultivars.
DOI: 10.5061/dryad.4b072/4
title: Sample locations

description: Locations of nests used within this study along with triplet ID and their distance to forest cover historically
DOI: 10.5061/dryad.71qt7/1
title: Will82xDT2000-Soybean Rust-Genotypic Data

description: Genetic marker data generated in an RIL mapping population derived from a Williams 82 x DT2000 cross.   No. of lines: 240No. of polymorphic markers: 504
DOI: 10.5061/dryad.c9086/1
title: GenoMaiz Database
DOI: 10.5061/dryad.d2vf8/10
title: DEQ vs Outcome Measure Analysis

description: Correlation Raw Data SPSS file
DOI: 10.5061/dryad.d2vf8/11
title: Demographics Data

description: Please note that sex, height, birth control use, weight, race and ethnicity of grandparents have been removed.
DOI: 10.5061/dryad.d2vf8/5
title: ARCI analysis

description: Raw data ARCI subjective measure_SPSS file
DOI: 10.5061/dryad.d2vf8/6
title: EOG_analysis

description: Attention Bias Raw data SPSS file
DOI: 10.5061/dryad.d2vf8/7
title: VAS analysis

description: VAS Liking Raw Data SPSS file
DOI: 10.5061/dryad.d2vf8/8
title: Forced Choice Analysis

description: Behavioral Preference Raw Data SPSS file
DOI: 10.5061/dryad.d2vf8/9
title: EMG Analysis

description: Facial EMG Raw Data SPSS file
DOI: 10.5061/dryad.h61cv/1
title: igf_dataset_with_fitness

description: Juvenile IGF-1 concentrations, life history, and morphological data for female spotted hyenas from the long-term research project on spotted hyenas in the Masai Mara National Reserve in Kenya. Each row represents a unique female. Variables are described in detail in the associated manuscript.
DOI: 10.5061/dryad.hk1vv/1
title: HR, E2 & Aromatase

description: Data of heart rate, estradiol levels and relative expression of Aromatase after T3 application, at each temperature (28, 29, 30C) from Control and T3 treatments.
DOI: 10.5061/dryad.hk1vv/2
title: Incubation,growth and rate

description: First, the data of incubation, such as incubation period and hatchling size are shown here. Second, the growth rate of hatchlings are also here. In addition, the hatching success and sex ratio are listed.
DOI: 10.5061/dryad.j315n/10
title: Tableau-Genes retained  by each tests-dyad

description: This table contains all genes pointed by one list : PCA differentiating flor yeast from other strains (Allyeast-set), Dxy (VinVoile.VQSR.HighQualitybiall.vcf filtered for min genotype quality of 30 and sequence depth of 10), Da (same as Dxy), XPCLR (for Jura  and Spanish populations), 20% Best potentially damaging SNPs (according to SIFT) differentiating wine and flor PCA, codeml value. This table contains data for table S4 and for Figure 3.
DOI: 10.5061/dryad.j315n/2
title: VinVoile.VQSR.HighQualitybiall.vcf

description: Compressed (tgz) Vcf file containing a subset of high quality biallelic variant filtered out from the genotyping output file  VQSR.vcf  produced by GATK, when filtering for only variants corresponding to the best genotyping scored (Indicated with PASS).  Population analysis measures (Dxy and Da) are performed on a second subset of this file after filtering  genotypes according to allelic depth and genotyping quality with vcftools, with  parameters: --minGQ 30 --minDP 10 --maf 0.001 . This filtered data set is used for figure 2C, and Figure S7.
DOI: 10.5061/dryad.j315n/4
title: Evaluation of variant impact on protein functions according to SIFT(4G)_ High quality biallelic variant set

description: Compressed file  containing the impact of each variant  on each annotated transcript, inferred with SIFT4G, for the file including all variant (VinVoile.VQSR.HighQualitybiall.vcf).
DOI: 10.5061/dryad.j4v4b/1
title: Data associated with Snijdersetal 2016 Avian Biology

description: The file includes six sheets concerning data specifically on tagged birds before breeding, all birds before breeding, tagged birds during reproduction, all birds during reproduction, all birds during chick provisioning and data on nestbox quality. Each sheet contains a legend.
DOI: 10.5061/dryad.k1g95/1
title: FE_data_for_dryad

description: Experimental treatments as factors (run 2010-2014). Bryophyte taxa (% cover/0.09m2), bryophyte richness (spp/0.09 m2), cover and richness of short and tall vascular plants (spp/m2), biomass+litter (g DW/0.0625m2) measured in 2014.
DOI: 10.5061/dryad.mv108/1
title: 2016_Pamminger_Evolution_data
DOI: 10.5061/dryad.n4k76/1
title: Supplementary Mathematica File

description: Mathematica file deriving key results in the manuscript, including the simulations reported in the figures.
DOI: 10.5061/dryad.n4k76/2
title: Supplementary Mathematica File (PDF)

description: PDF version of the Mathematica file deriving key results in the manuscript, including the simulations reported in the figures.
DOI: 10.5061/dryad.p1442/1
title: Figure 1 Thermal sensitivity data

description: Raw data for figure 1
DOI: 10.5061/dryad.p1442/2
title: Figure 3 Isolated temperature data

description: Raw data for analysis displayed in figure 3
DOI: 10.5061/dryad.p1442/3
title: Figure 4 Fragmented temperature data

description: Raw data displayed in figure 4
DOI: 10.5061/dryad.pj032/1
title: File for test data

description: See readme file
DOI: 10.5061/dryad.pj032/2
title: Test.Data01

description: File for 01 data
DOI: 10.5061/dryad.pj032/3
title: Main.program.female.preference

description: This is the main program.  It has lines that are changed by the user
DOI: 10.5061/dryad.pj032/4
title: Functions.for.Female.preference

description: Set of functions used.
DOI: 10.5061/dryad.q3h85/1
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_1

description: Supplemental Data 1 Growth rates of Arabidopsis leaf 3, leaf 5 and leaf 7.
DOI: 10.5061/dryad.q3h85/2
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_2

description: Supplemental Data 2. Protein degradation rates of 1228 proteins and statistical analysis across samples.
DOI: 10.5061/dryad.q3h85/3
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_3

description: Supplemental Data 3. Ratios of specific protein abundances relative to a 15N fully labelled reference.
DOI: 10.5061/dryad.q3h85/4
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_4

description: Supplemental Data 4. The correlation of intrinsic properties of proteins with their protein degradation rates
DOI: 10.5061/dryad.q3h85/5
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_5

description: Supplemental Data 5. Comparison of protein degradation rate (KD) and protein abundance between selected proteins in leaf 3 and leaf 7.