cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ff2p0/3
title: Nexus file for divergence time estimation (node-calibrated and tip-dated)

description: Nexus file used for divergence time estimation analyses. It includes molecular data from Price et al. (2014) and morphological data from de Andrade and Baroni-Urbani (1999). MrBayes blocks are included for total evidence tip-dating (Figure S3)and node-calibration (Figure S4) analyses.
DOI: 10.5061/dryad.ff2p0/4
title: BAMM control file for lineage diversification

description: This is the input file (called the control file) for lineage diversification analysis in BAMM. The file was directly adapted from the documentation on the BAMM website (http://bamm-project.org/).
DOI: 10.5061/dryad.gm7gk/1
title: Raw data for S-allele segregations, fruit set, and pollen performance analyses

description: There are 7 excel sheets: (1) meteorological data during the first 8 days after pollination. (2) fruit set analyses registered during the three year. (3) raw and summarized data of S-allele segregations for the first year. (4) raw and summarized data of S-allele segregations for the second year. (5) Summarized data of S-allele segregations for the third year. (6) Raw data of pollen tube growth kinetics and dynamics for the first and second year. (7) Raw data of pollen tube growth kinetics and dynamics for the third year.
DOI: 10.5061/dryad.h3k43/1
title: plos oneOK6

description: Data from SPSS statistical program. Abbreviations: BMI = body mass index; PSQI = Pittsburg Sleep Quality score; TST = total sleep time; PSG = polysomnography; S1 = sleep stage 1, S2 = sleep stage 2; S3 = sleep stage 3; REM = rapid eye movement; WASO = wake after sleep onset; PLM = periodic limb movement; AHI = apnea hypopnea index; SatO2 = oxyhemoglobin saturation; dessat_index  = dessaturation index, OSAS = obstructive sleep apnea syndrome. Inventories: Fatigue = Chalder; Sleepiness = Epworth; life quality = Whoqol, Beck for Anxiety and for Depression
DOI: 10.5061/dryad.hn34m/3
title: Figure 3

description: Phylogenetic distribution of ribosomal and hisDNA H3 sites in Lutjanidae species. The phylogeny and molecular clock of the divergent clades A, B and C were modified from Gold et al. (2011).
DOI: 10.5061/dryad.jv5f8/1
title: PredationBehaviours

description: Data based on in situ underwater footage of marine predators feeding on fish schools, initially shot for the film OCEANS by J. Perrin and J. Cluzaud (Galatée Films Production). Predation behaviours recorded from the observation of footage.
DOI: 10.5061/dryad.n9m02/1
title: number of flies (rover or sitters) on the refuge zone 1 or 2 as a function of time for homogenerous and mixed groups
DOI: 10.5061/dryad.nk453/1
title: Proteasomal degradation kinetics of short fluorogenic peptides

description: peptide digestions using mouse proteasome, human s- and -i proteasome. Substrates: Suc-LLVY-MCA, Z-LLE-MCA, Bz-VGR-MCA.
DOI: 10.5061/dryad.t50j5/1
title: RrContigs.fa.fasta.tar.gz

description: Sequence of Raphanus raphanistrum genomic contigs
DOI: 10.5061/dryad.t50j5/2
title: RrCDS.fa.tar.gz

description: Raphanus raphanistrum coding sequences
DOI: 10.5061/dryad.t50j5/3
title: RrPep.fa.tar.gz

description: Raphanus raphanistrum peptide sequences
DOI: 10.5061/dryad.t50j5/4
title: Rr_gene_pseu.gff.mod.tar.gz

description: Raphanus raphanistrum gene and pseudogene GFF file
DOI: 10.5061/dryad.tn888/1
title: Data used for the analysis

description: Excel file containing the data used for the analysis (GLMM)
DOI: 10.5061/dryad.vf345/2
title: Layer1_3_6_Shotgun_sequences
DOI: 10.5061/dryad.0279k/1
title: Structural Scans Used For Morphometrics

description: Included are T2-weighted structural scans in nifti format for each of the 41 sea lion subjects in this study. Scans are oblique, and were obtained perpendicular to the long axis of the hippocampus. These were the scans used in hippocampal morphometrics, using Quanta2 software, following tracing criteria detailed in the supplemental methods.
DOI: 10.5061/dryad.0279k/2
title: Functional Connectivity MRI Data Part 1

description: Included are the high-resolution structural scan used for defining thalamic ROIs, left and right thalamic ROIs in that space, and individual EPI and structural scans for two sea lion subjects. EPI data represents 15 minutes of continuous BOLD data under gas anesthesia. All scans are nifti format.
DOI: 10.5061/dryad.0279k/3
title: Functional Connectivity MRI Data Part 2

description: Individual EPI and structural scans for two sea lion subjects in nifti format. EPI data represents 15 minutes of continuous BOLD data under gas anesthesia.
DOI: 10.5061/dryad.0279k/4
title: Functional Connectivity MRI Data Part 3

description: Individual EPI and structural scans for two sea lion subjects in nifti format. EPI data represents 15 minutes of continuous BOLD data under gas anesthesia.
DOI: 10.5061/dryad.253h0/1
title: Table S3

description: Raw genotypes of 12 families for 62 microsatellite loci
DOI: 10.5061/dryad.2d4m9/17
title: Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 3

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model, with 6 subpopulations evenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 3; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/18
title: Model 3 datasets (hierarchical stepping stone model), sampling strategy No. 4

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model, with 6 subpopulations unevenly sampled (4 subpopulations not sampled) and a total of 150 individuals (sampling strategy no. 4; cf. Table 1). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/19
title: Model 4 datasets (island model), full datasets

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 4 were identical to those used for Model 1, except that the migration rate was doubled (set to 0.02) (cf. Table S1 for Fst values). The files, in Fstat format, were created by the EASYPOP program.
DOI: 10.5061/dryad.2d4m9/20
title: Model 4 datasets (island model), sampling strategy No. 1

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 4 were identical to those used for Model 1, except that the migration rate was doubled (set to 0.02) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/21
title: Model 5 datasets (hierarchical island model), full datasets

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 5 were identical to those used for Model 2, except that the migration rates between subpopulations within and between archipelagos were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values).The files, in Fstat format, were created by the EASYPOP program.
DOI: 10.5061/dryad.2d4m9/22
title: Model 5 datasets (hierarchical island model), sampling strategy No. 1

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 5 were identical to those used for Model 2, except that the migration rates between subpopulations within and between archipelagos were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.2d4m9/23
title: Model 6 datasets (hierarchical stepping stone model), full datasets

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model with 10 subpopulations and 200 individuals per subpopulation. The parameters used to simulate Model 6 were identical to those used for Model 3, except that the migration rates between subpopulations on one side versus across the contact zone were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values).The files, in Fstat format, were created by the EASYPOP program.
DOI: 10.5061/dryad.2d4m9/24
title: Model 6 datasets (hierarchical stepping stone model), sampling strategy No. 1

description: This zipped file contains 50 datasets simulated under a hierarchical  stepping stone model, with 10 subpopulations evenly sampled and a total of 620 individuals (sampling strategy no. 1; cf. Table 1). The parameters used to simulate Model 6 were identical to those used for Model 3, except that the migration rates between subpopulations on one side versus across the contact zone were doubled (set to 0.02 & 0.002 respectively) (cf. Table S1 for Fst values). The files, in Fstat format, were simulated in the EASYPOP program and sampled in R via a custom written script.
DOI: 10.5061/dryad.3jm4q/2
title: dryad_Petschenka&Agrawal 2015

description: Gravimetric data, HPLC cardenolide determinations, Na+/K+-ATPase activity data, caterpillar injections. The excel file contains seven sheets listing experimental data and a short description where necessary.
DOI: 10.5061/dryad.5c6bq/1
title: dataset
DOI: 10.5061/dryad.5hq56/1
title: Notes S1 - Population Sources, Defense Trait Data, and Aggregated Literature Data

description: Population source and locality data. Population least squares means for all leaf defense traits, secondary metabolite metrics, and environmental characteristics. Species means for all leaf defense traits and secondary metabolite metrics. Aggregated species-level data on plant interactions with herbivores and pathogens from the literature.
DOI: 10.5061/dryad.6b65r/1
title: Summary statistics for Single SNP GWAS

description: Summary statistics for Single SNP GWAS for for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG) in R Data file.
DOI: 10.5061/dryad.6b65r/2
title: Summary statistics for Regional Heritability Mapping

description: Summary statistics for Regional Heritability Mapping method  for blood lipid traits (high-density lipoprotein (HDL), low-density lipoprotein (LDL), plasma concentrations of total cholesterol (TC) and triglycerides (TG) in R Data file.
DOI: 10.5061/dryad.8tm76/1
title: Supplementary information

description: Supplementary information to ``Genealogical working distributions for Bayesian model testing with phylogenetic uncertainty'' by Guy Baele, Philippe Lemey and Marc A. Suchard
DOI: 10.5061/dryad.b786c/1
title: Stickleback Male Competition Dataset

description: This zipped file contains both the data file (Stickleback Male Comp Data.csv) and metadata explaining the data columns (Stickleback Male Comp Metadata.csv).
DOI: 10.5061/dryad.b786c/2
title: Aggression R Script

description: This is the script we used to process JWatcher files to ultimately calculate a summary aggression score for each male. The script is commented, but note that it is currently very specific to our purposes.
DOI: 10.5061/dryad.b786c/3
title: All the R Functions

description: This provides R functions to aid analysis of selection. They were written fairly generically so should be easy to utilize in your research.
DOI: 10.5061/dryad.b786c/4
title: README.txt

description: README file for Dryad Digital Repository files associated withKeagy, J., Lettieri, L., and Boughman, J.W. 2015. “Male competition fitness landscapes predict both forward and reverse speciation”. Ecology Letters.
DOI: 10.5061/dryad.c75j9/11
title: S11 Data with strain factors for studied taxa
DOI: 10.5061/dryad.c75j9/12
title: S12 Movie showing gape cycles and strain factors with a muscle resting length at 3 degrees

description: Movie showing gape cycles and strain factors with a muscle resting length at 3 degrees (.mov)
DOI: 10.5061/dryad.c75j9/13
title: S13 Movie showing gape cycles and strain factors with a muscle resting length at 6 degrees

description: Movie showing gape cycles and strain factors with a muscle resting length at 6 degrees (.mov)
DOI: 10.5061/dryad.c83j2/1
title: Occupancy data

description: This file contains two tabs with occupancy data (0 = not detected, 1 = detected) from Nebraska and from Saskatchewan. Data are from upland grassland sites using 5-minute, 100-m radius point counts. Each row specifies a single visit to a single plot.
DOI: 10.5061/dryad.c83j2/2
title: rarity sim

description: This file contains the SAS code used to simulate detection across a grid of points.
DOI: 10.5061/dryad.cr0mb/10
title: Fastq Files for H.tuberculata, egg stage

description: These are fastq files for H.tuberculata, egg stage. There are three replicates, each is 50 bp PE
DOI: 10.5061/dryad.cr0mb/11
title: Fastq Files for H.tuberculata, 4-cell stage

description: These are fastq files for H.tuberculata, 4-cell stage. There are three replicates, each is 50 bp PE
DOI: 10.5061/dryad.cr0mb/12
title: Fastq Files for H.tuberculata, 16-cell stage

description: These are fastq files for H.tuberculata, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/13
title: Fastq Files for H.tuberculata, 32-cell stage

description: These are fastq files for H.tuberculata, 32-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/4
title: Fastq Files for L. variegatus, egg stage

description: These are fastq files for L. variegatus, egg stage. There are three replicates, each is 50 bp PE
DOI: 10.5061/dryad.cr0mb/5
title: Fastq Files for L. variegatus, 16-cell stage

description: These are fastq files for L. variegatus, 16-cell stage. There are three replicates, two are 50 bp PE and one is 50bp SE
DOI: 10.5061/dryad.cr0mb/6
title: Fastq Files for L. variegatus, 32-cell stage

description: These are fastq files for L. variegatus, 4-cell stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/7
title: Fastq Files for L. variegatus, blastula stage

description: These are fastq files for L. variegatus, blastula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/8
title: Fastq Files for L. variegatus, gastrula stage

description: These are fastq files for L. variegatus, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/9
title: Fastq Files for L. variegatus, prism "early larva" stage

description: These are fastq files for L. variegatus, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.d3j00/1
title: Part 1 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/2
title: Part 2 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/3
title: Part 3 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/4
title: Part 4 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/5
title: Part 5 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/6
title: Part 6 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.d3j00/7
title: Part 7 of 11 Zip file of primary data for "A transient ischaemic environment induces reversible compaction of chromatin"

description: All image sets for the Vybrant Violet / H3K14 ac Single Molecule Localization Microscopy work (UT:9 expts; OND:12 expts; 5min:10 expts; 15min:9 expts, 60min:10 expts; 240min:9 expts).All image sets for the YOYO-1 and EdU Single Molecule Localization Microscopy work.All image sets for the DNAseI experiments (UT:11 expts; OND:11 expts).All image sets for the H2B-mCherry FRAP study, (UT:12 expts; OND:10 expts) and for H1.1-GFP FRAP study (euchromatin:10 expts; heterochromatin:11 expts; OND:11 expts).The datasets for flow cytometry: H3, panAc, K9Ac, K27ac, K4me3,K9me3 K27me3 at con, 0, 2, 5, 15 30 mins, 1 and 4 hours.
DOI: 10.5061/dryad.f94f2/1
title: Peckoltia Morphometrics

description: Morphometrics for all species examined of Peckoltia
DOI: 10.5061/dryad.ff2p0/10
title: R script for DDD settings

description: The R script loads the turtle ant data and calls the function MLkeyinnCephalotes to perform the DDD analyses. It provides all the settings which are then passed to this function.
DOI: 10.5061/dryad.ff2p0/11
title: Node-calibrated MCC tree

description: Node-calibrated maximum clade credibility (MCC) tree for Cephalotes.
DOI: 10.5061/dryad.ff2p0/12
title: Tip-dated MCC tree

description: Tip-dated maximum clade credibility (MCC) tree for Cephalotes.
DOI: 10.5061/dryad.ff2p0/5
title: BAMM control file for trait evolution

description: This is the input file (called the control file) for analysis of trait evolution in BAMM. The file was directly adapted from the documentation on the BAMM website (http://bamm-project.org/).
DOI: 10.5061/dryad.ff2p0/6
title: BAMMtools R script for lineage diversification

description: Script used in the R program BAMMtools for the analysis and visualization of lineage diversification results in BAMM. The script was adapted from documentation on the BAMM website (http://bamm-project.org/).
DOI: 10.5061/dryad.ff2p0/7
title: BAMMtools R script for trait evolution

description: Script used in the R program BAMMtools for the analysis and visualization of trait evolution, specifically body size evolution, results in BAMM. The script was adapted from documentation on the BAMM website (http://bamm-project.org/).
DOI: 10.5061/dryad.ff2p0/8
title: R script for gamma and MCCR analyses

description: Script for conducting gamma/MCCR analyses in Laser in R.
DOI: 10.5061/dryad.ff2p0/9
title: R script for DDD analyses

description: R script for performing DDD analyses on the phylogeny. It does the likelihood optimization from two different sets of starting values of the parameters, for the most parameter-rich models.
DOI: 10.5061/dryad.fk71c/1
title: Lake Erie Watersnake Growth Data Sets
DOI: 10.5061/dryad.h43c1/1
title: Androgen Receptor Genotype Data for Canada lynx Somatic Mosaicism Manuscript_2015

description: This data file contains Canada lynx genotype data that was generated for the associated manuscript, which tests for the presence of somatic mosaicism of trinucleotide repeats within the Androgen Receptor (AR) gene. The data file contains all samples analyzed for this manuscript with the exception of one sample which was determined to be contaminated and removed from the data set (see Supplementary Information document associated with the manuscript for further details). As the AR gene is X-linked, gender data is also provided for each sample.
DOI: 10.5061/dryad.jv5f8/2
title: Data per scene

description: Data based on in situ underwater footage of marine predators feeding on fish schools, initially shot for the film OCEANS by J. Perrin and J. Cluzaud (Galatée Films Production). Observations aggregated per scene.
DOI: 10.5061/dryad.jv5f8/3
title: Data per attack

description: Data based on in situ underwater footage of marine predators feeding on fish schools, initially shot for the film OCEANS by J. Perrin and J. Cluzaud (Galatée Films Production). Observations per Cape gannet attack.
DOI: 10.5061/dryad.k1f73/1
title: JAV-00771_New_York_data
DOI: 10.5061/dryad.k1f73/2
title: JAV-00771_Pennsylvania_data