cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.18sg7/1
title: wyoteMeth_10x_3mil_sites_MF

description: This file contains the methylation frequency (MF, number of cytosines out of the total read coverage) per site for a coyote, wolves, and their hybrid offspring. This dataset contains ~3 million cytosines.
DOI: 10.5061/dryad.18sg7/2
title: Wyotes_15733_GBS_SNPs

description: This file contains SNP genotypes for 15,733 sites generated by GBS for a coyote, wolves, and their hybrid offspring.
DOI: 10.5061/dryad.208b1/10
title: Simulation scripts

description: R code used to simulate phylogeny and measure D.
DOI: 10.5061/dryad.208b1/2
title: Tree Sets

description: R file containing sets of cladograms timescaled with different methods that were used in the analyses of tetrapods.
DOI: 10.5061/dryad.208b1/3
title: Supplementary data

description: Age data used to timescale cladograms, sources for cladogram topologies and dates of timeslices.
DOI: 10.5061/dryad.208b1/5
title: Supplementary Figure 1

description: Example timescaled topologies for each of the three focal clades, sauropsids, synapsids and temnospondyls.
DOI: 10.5061/dryad.208b1/6
title: Supplementary Figure 2

description: Measurement of D through time on three sets of 100 phylogenies timescaled using three different timescaling algorithms.
DOI: 10.5061/dryad.208b1/7
title: Supplementary Figure 3

description: Measurement of D and Moran's I through time on a set of 100 phylogenies timescaled using the Hedman method.
DOI: 10.5061/dryad.208b1/8
title: Supplementary Figure 4

description: Measurement of D through time on a set of 100 phylogenies timescaled using the Hedman method and divided into different time bin lengths.
DOI: 10.5061/dryad.208b1/9
title: Script to measure D

description: R code that takes as input a set of timescaled phylogenies with root ages and a matrix of time bins for analysis. Calculates D and associated p-values for each tree in each time bin.
DOI: 10.5061/dryad.26h4q/1
title: tEGGS

description: Data containing information about individual eggs within all nests in the years included in the feeding experiment (to analyse hatching time, hatching asynchrony, weight, and hatching success)., as well as information about the feeding treatments of those nests.
DOI: 10.5061/dryad.26h4q/2
title: Newdat

description: Data containing all eggs in experimental years (as with data frame tEGGS), augmented with those eggs that were not laid (during interruptions in the laying sequence)
DOI: 10.5061/dryad.26h4q/4
title: tEGGSall

description: Data frame of all eggs included in main weather analyses (hatching time, hatching asynchrony, weight, and hatching success).
DOI: 10.5061/dryad.2d4t3/1
title: Menge_etal_ELE_00062_2017_Data

description: This is the R data file that contains the data and objects used for Menge et al. 2017 ELE.
DOI: 10.5061/dryad.2d4t3/2
title: Menge_etal_ELE_00062_2017_Figs

description: This is the R script that opens the data file and makes the figures.
DOI: 10.5061/dryad.31gf4/1
title: Data: Advection by ocean currents modifies phytoplankton size structure

description: Contains data of currents,
nutrients, chlorophyll and data of  concentrations of small and large particles for June and September.
DOI: 10.5061/dryad.321kr/1
title: Social_Networks_maps

description: Statistical maps for the Agents, Action, Social Interaction, Exclusive Social Interaction Network (ESIN) and Physical Interaction contrasts, on the monkey F99 cortical model of the right hemisphere, from the volume-based FFX group analysis. These metric files were generated using the freely available Caret software developed in the Van Essen Laboratory at the Washington University School of Medicine in Saint Louis, Missouri, USA, available at . The metric files can be opened with this program and overlaid on the monkey F99 cortical model of the right hemisphere. Enhanced activation is show as negative values (i.e in blue), due to the use of contrast agent for functional magnetic resonance imaging scanning.
DOI: 10.5061/dryad.44ns0/1
title: Data of phenological observations - Varronia curassavica
DOI: 10.5061/dryad.44ns0/2
title: Genotype of progenies of Varronia curassavica
DOI: 10.5061/dryad.506sg/1
title: BreedingSystemUSDA

description: This file contains the sexual system and weedy/native status for each species.
DOI: 10.5061/dryad.6k630/1
title: G-PhoCS input files for Oswald et. al 2017
DOI: 10.5061/dryad.6k630/2
title: fastsimcoal2 input files for Oswald et al. 2017
DOI: 10.5061/dryad.6k630/3
title: STRUCTURE input files for Oswald et al. 2017

description: Note that the University of Florida samples are labeled with preparator numbers. These preparator numbers and associated FLMNH collection numbers and locality information for all individuals can be found in Oswald et al. 2017 Supplementary Table 1.
DOI: 10.5061/dryad.71tv1/8
title: HTS_pipeline_scripts

description: Scripts for analysis of high-throughput sequencing data.
DOI: 10.5061/dryad.71tv1/9
title: Consensus sequence from sample ACAD2865

description: Consensus sequence generated in Geneious. Final sequence too fragmentary for upload to GenBank due to poor DNA preservation. This sequence was excluded from most analyses.
DOI: 10.5061/dryad.75g1d/1
title: Small mammal monitoring with chew cards - data and analysis

description: This zip folder contains the data and analysis code (in .R format) for three experiments conducted in Awarua wetland, Southland, New Zealand. Please read the readme file inside the folder, as this describes the folder structure and data files.
DOI: 10.5061/dryad.8m2t5/10
title: IFT122 alignment

description: IFT122 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/11
title: KIF7 alignment

description: KIF7 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/12
title: OFD1 alignment

description: OFD1 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/13
title: TALPID3 alignment

description: TALPID3 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/14
title: WDR34 alignment

description: WDR34 alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8m2t5/8
title: GLI2 alignment

description: GLI2  alignment (Fasta format) for PAML positive selection analysis
DOI: 10.5061/dryad.8p5n5/1
title: Southern New England Historical Dam Database

description: This is a historical dam database created using historical maps, town history books, county history books, existing dam databases from other agencies (The Nature Conservancy, Charles River Watershed Association, Town of Plymouth, MA) and other historical documents. Access to historical documents on google books and archive.org was integral to  compiling historical dams data.
DOI: 10.5061/dryad.8p5n5/2
title: Maine Dams Hall et al. 2011

description: These are historical dams compiled by Hall et al. (2011). This data is also available at the Gulf of Maine Historical Ecology Research website: www.GOMHER.org.
DOI: 10.5061/dryad.9cp3j/1
title: Imaging data

description: Data contains (zip format files): 1) reconstructed MRI data (General Electric MRI system) and regions-of-interests files. Excel spreadsheet is provided with signal intensity results. 2) CT whole-animal data (SIemens CT system). 3) CT angiography of placenta (Scanco CT system).
DOI: 10.5061/dryad.cb060/1
title: Bailey, Case, Caruso (2017) AJB

description: physiological data for lab-grown plants under different temperature regimes
DOI: 10.5061/dryad.cm603/10
title: Files S1-S17. Supplemental tree files.

description: Files S1-S17. This zip file contains all of the supplemental tree files. Individual tree files are described in the ReadMe file and in a text file within the zip file.
DOI: 10.5061/dryad.cm603/11
title: Files S18-S23. Zip file containing data matrices and MrBayes blocks

description: Files S18-S23. This zip file contains all of the data matrices and MrBayes blocks used for analyses. Individual files are described in the ReadMe file and in a text file within the zip file.
DOI: 10.5061/dryad.cm603/12
title: Table S1. Node calibrations included in divergence dating analyses.
DOI: 10.5061/dryad.cm603/8
title: Fig. S8. Macrostomatan phenotype reconstruction on constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny

description: Fig. S8. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa on the constrained, diversified FBD Tetrapodophis and Caldwell et al. (2015) fossils excluded phylogeny. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist.
DOI: 10.5061/dryad.cm603/9
title: Fig. S9. Macrostomatan phenotype reconstruction on constrained, diversified FBD phylogeny with madstoiids coded uncertain

description: Fig. S9. Ancestral state reconstructions from MultiState in BayesTraits showing the probability of the non-macrostomatan phenotype (blue) and macrostomatan phenotype (yellow) for each node as well as the states coded for terminal taxa. As in Fig. 4, white areas of pies at internal nodes indicate the posterior probability that a node does not exist. Madstoiids were coded as uncertain in this analysis and the analysis was performed on the phylogeny from the constrained, diversified FBD analysis.
DOI: 10.5061/dryad.g0870.1
title: Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
DOI: 10.5061/dryad.g0870.2
title: Data from: From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar
DOI: 10.5061/dryad.g0870.2/1.2
title: Aykanat et al (2016) JFB, targeted genotyping by sequencing

description: object to call genotypes of targeted SNPs in the multiplex panels from raw fastq reads, and assess genotyping quality and unspecific product reads.
DOI: 10.5061/dryad.gh225/1
title: Gambusia

description: Morphological measures of Gambusia
DOI: 10.5061/dryad.gh225/2
title: DOC

description: Measures of Dissolved organic carbon by fluorometry. Units are RFUs.
DOI: 10.5061/dryad.gh225/3
title: Transmission

description: Light transmission relative to distilled water standard
DOI: 10.5061/dryad.gp8ck/1
title: Pitcher et al, Cross-modal recognition in goats - playback data
DOI: 10.5061/dryad.h2900/1
title: List of characters utilized in the phylogenetic analysis

description: Supplemental Data 1. List of characters utilized in the phylogenetic analysis. Modified from Vera (2016).
DOI: 10.5061/dryad.h2900/2
title: Data matrix used in the phylogenetic analysis (modified from Vera, 2016).

description: Supplemental Data 2. Data matrix used in the phylogenetic analysis (modified from Vera, 2016). Abbreviations: - , inapplicable character; ?, missing data
DOI: 10.5061/dryad.h2900/3
title: Descriptive statistics for upper and lower cheek teeth of Archaeopithecus rogeri considering three levels of wear.

description: Supplemental Data 3. Descriptive statistics for upper and lower cheek teeth of Archaeopithecus rogeri considering three levels of wear. 
SW (stage of wear) = 1, little; 2, middle; 3, heavy (see text for details). CV (coefficient of variation) = 100 × (SD/mean). Measurements in mm.
DOI: 10.5061/dryad.hg600/1
title: Dataset used for the analyses

description: Mycelium growth rate data used of the linear mixed model analyses
DOI: 10.5061/dryad.hg600/2
title: Script for mixed model analyses

description: Script for the analyses with ASReml-R (see http://www.vsni.co.uk/downloads/asreml/version-3-upgrade/)
DOI: 10.5061/dryad.hg600/3
title: Script and figures from mixed model analyses

description: Output when knitting the file "Mixed_Model_Analyses.Rmd" using Rstudio (https://www.rstudio.com/)
PowerAnalyses.Rmd: Code for the power analyses
DOI: 10.5061/dryad.hg600/4
title: Script for power analyses

description: Code for power analyses
DOI: 10.5061/dryad.hg600/5
title: Script and figures from power analyses

description: Output when knitting the file "PowerAnalyses.Rmd" using Rstudio (https://www.rstudio.com/)
DOI: 10.5061/dryad.hg600/6
title: R environment for Fig. S4

description: R environment including the 1000 simulations for Fig. S4 (can be loaded using the command: "load(SimulFigS4new.R)")
DOI: 10.5061/dryad.hg600/7
title: R environment for Fig. S5

description: R environment including the 1000 simulations for Fig. S5 (can be loaded using the command: "load(SimulFigS5new.R)")
DOI: 10.5061/dryad.hg600/8
title: Estimates of the direct genetic effects

description: Estimates of the direct genetic effects of the 41 strains
DOI: 10.5061/dryad.m51q0/1
title: S1
DOI: 10.5061/dryad.n4b4c/1
title: MacGregoretal2017Oikos_Dataset

description: morphology, clutch investment, genotypes, and experimental males.
DOI: 10.5061/dryad.q2m2v/1
title: Supplementary Information for Martinelli et al

description: This file includes: the character list (1), the changes in character-states for Therioherpeton cargnini (2), the modified data matrix (3), the strict consensus trees of three different analyses (4), and photographs of the humerus of T. cargnini (5).
DOI: 10.5061/dryad.q6ft5/1
title: Glaucoma diagnosis

description: This file includes examination records of retinal nerve fiber layer (RNFL) thickness and visual field (VF) and others.
DOI: 10.5061/dryad.q7f6v/1
title: Halliwell_BEHECO-2016-0350.R1_Data
DOI: 10.5061/dryad.rp949/1
title: dpse_falcon assembly

description: We downloaded raw PacBio reads from ftp://ftp.hgsc.bcm.edu/Dpseudoobscura/Towards_finishing_the_D.pseudoobscura_genome/PacBio_Data/FastQ_files/ (these reads was generously granted by Drs. Stephen Schaeffer and Stephen Richards). We used the Falcon assembler v0.3.0 (https://github.com/PacificBiosciences/FALCON-integrate) to filter, correct and assemble reads. Then we polished the assembly using Quiver (SMRT Analysis v2.3.0)
DOI: 10.5061/dryad.rp949/2
title: dpse_falcon gtf

description: We identified exon-introns junctions by mapping annotated transcripts (r3.03; Flybase) and transcripts of Y-linked genes from NCBI (gi|295126506|gb|GU937420.1|, gi|255764727|gb|EU595397.2|, gi|295126512|gb|GU937423.1|) to our assembly using exonerate 2.4.0. To complement these data, we mapped RNA-seq reads to our assembly using Tophat v2.0.13. We annotated transcripts, eliminated small redundant isoforms with cufflinks v2.2.2 .
DOI: 10.5061/dryad.rp949/3
title: dpse expression and annotation

description: We mapped RNA-seq reads to our assembly using Tophat v2.0.13 and estimated expression level with cufflinks v2.2.2. We then searched for homologous genes using the predicted transcripts as BLAST queries to all D. melanogaster translations and transposon sequences (r6.07) with NCBIblast.
DOI: 10.5061/dryad.t7m7g/1
title: Fluorescence matrix Td ID 450-1
DOI: 10.5061/dryad.t7m7g/2
title: Fluorescence matrix Td ID 450-2
DOI: 10.5061/dryad.t7m7g/3
title: Fluorescence matrix Td ID 741-1
DOI: 10.5061/dryad.t7m7g/4
title: Fluorescence matrix Td ID 741-2
DOI: 10.5061/dryad.t7m7g/5
title: Fluorescence matrix Td ID 775-1
DOI: 10.5061/dryad.t7m7g/6
title: Fluorescence matrix Td ID 775-2
DOI: 10.5061/dryad.tj3k1/1
title: Kim et al. 2017 Harvest effects on natural enemy communities and biocontrol

description: Data summary tables and site information used in Kim et al. 2017. Harvesting biofuel grasslands has mixed effects on natural enemy communities and no effects on biocontrol services. Journal of Applied Ecology.
DOI: 10.5061/dryad.133b9/1
title: BMI & WHR

description: Body mass index (BMI) and waist-to-hip ratio (WHR) for all 49 females used in the study.
DOI: 10.5061/dryad.133b9/2
title: Procrustes shape coordinates

description: This 49 x 138 matrix contains for each of the 49 individuals the x and y coordinates of the 69 landmarks. The landmark configurations are Procrustes aligned and symmetrized.
DOI: 10.5061/dryad.133b9/3
title: PC scores of texture

description: Principal component scores of facial texture (RGB values of the pixels of the standardized images) for the 49 individuals.
DOI: 10.5061/dryad.26h4q/10
title: Weather-ORDH

description: R Script for carrying out the hatching asynchrony (ordinal hatching day) analysis on the effect of weather
DOI: 10.5061/dryad.26h4q/11
title: Weather-HATS

description: R Script for analysis of the effect of weather on hatching success
DOI: 10.5061/dryad.26h4q/12
title: Weather-WGHT

description: R Script for the analysis of the effect of weather on egg weight
DOI: 10.5061/dryad.26h4q/3
title: df

description: Nest-level data of those years included in the feeding experiment
DOI: 10.5061/dryad.26h4q/5
title: tEGGSall.aug

description: Data of all eggs included in the weather analysis, augmented to include those eggs that were not laid (in laying interruptions). Used for pausing analysis.
DOI: 10.5061/dryad.26h4q/6
title: dfall

description: Nest level data for all years included in the weather analyses.
DOI: 10.5061/dryad.26h4q/7
title: FeedingModelsScript

description: R Script for models used to analysis the feeding experiment
DOI: 10.5061/dryad.26h4q/8
title: Spline.Functions

description: R Script for setting up varying coefficient splines used in models
DOI: 10.5061/dryad.26h4q/9
title: Weather-CGH

description: R Script for carrying out the hatching time analysis on the effects of weather
DOI: 10.5061/dryad.2g7mr/1
title: Experimental data

description: The file contains 3 data tables of the traits measured at the end of the experiment on ancestral and evolved bacterial strains: one for demographic traits (maximum per capita growth rate and maximal optical density) extracted  from growth curves performed on Low-N and low-P media (with R software); one for cytometry (relative cell size data); and one for X-ray data (cell content of nitrogen and phosphorus). Data were compiled in a xls file.
DOI: 10.5061/dryad.40qt2/1
title: Overview of the R code provided in the manuscript

description: Here, we provide an overview of the R scripts and data files to accompany the main text, "Interacting livestock and fire may both threaten and increase viability of a fire-adapted Mediterranean carnivorous subshrub" and found in this depository. The .R files should be opened with an R editor (e.g., R Studio). The R code is fully commented.
DOI: 10.5061/dryad.40qt2/2
title: dataDroso

description: Demographic transitions of Drosophyllum lusitanicum populations recorded in five annual censuses (from 2011to 2015) in eight populations differing in time-since-fire (TSF) and livestock browsing (LS) in their habitats. These data are used to quantify vital rates of above-ground individuals.
DOI: 10.5061/dryad.40qt2/3
title: dataDrosoSB

description: Seed fates (in a binary format) inferred from two experiments. These data are used to quantify the transitions related to the seedbank.
DOI: 10.5061/dryad.40qt2/4
title: mcmcOUT

description: In case the reader wishes to forego the step of fitting the Bayesian models, which can be very time consuming (&gt; 24 h on 3.40 GHz processor), we provided a mcmcOUT.csv file with 600 posterior parameter values for each of the parameters estimated with Bayesian models using uninformative priors.
DOI: 10.5061/dryad.4kn05/1
title: MOTUdataset

description: This excel file presents filtered data found in the samples with the 18S_allshorts primers. It contains the number of occurrences of each MOTU in the different samples, as well as different columns related to the taxonomic identification of the MOTUs and the representative sequences of them
DOI: 10.5061/dryad.4kn05/2
title: assembled sequences

description: Fasta file containing the raw assembled sequences (singletons eliminated). For each sequence the codes of the samples where the sequence has been found are indicated, as well as the number of reads in each, the total counts of the sequence, and the sequence length
DOI: 10.5061/dryad.4kn05/3
title: code equivalences

description: This excel file provides the equivalences of sample codes between the file MOTUdataset.xlsx and the file assembled seqs.fasta
DOI: 10.5061/dryad.506sg/2
title: Tree with branch lengths

description: This file contains the tree data with branch lengths obtained via bladj. See paper for more details.
DOI: 10.5061/dryad.53d8h/1
title: Liu-eucalyptus-data
DOI: 10.5061/dryad.713q3/1
title: assembled_transcriptomes

description: Here you will find the assembled transcriptomes for the brittle star species Ophioderma longicauda C3 (broadcasting species) and Ophioderma longicauda C5 (brooding species)
DOI: 10.5061/dryad.713q3/2
title: alignments

description: Here you will find the alignments in fasta format of the 11 genes evolving under positive selection (the ones listed in Table 3 of the article) and the alignments for the genes involved in fertilization and species recognition in other marine invertebrates (the ones listed in Table 4; e.g. bindin)
DOI: 10.5061/dryad.89r82/1
title: JC_JEB_Trichome_Herbivory

description: Three sheets containing trichome and herbivory data from field studies, tests of within generation plasticity, and transgenerational effects respectively.
DOI: 10.5061/dryad.8g928/1
title: Alignments

description: Alignments and phylogenetic trees of evolutionary rate analyses
DOI: 10.5061/dryad.8g928/2
title: MGR analysis

description: Input and result files of genome rearrangement analysis with MGR.
DOI: 10.5061/dryad.8g928/3
title: SSR and repeat analysis

description: Detailed results of SSR and repeat analyses.
DOI: 10.5061/dryad.8m0k4/1
title: Complete data file for little brown myotis immune responses WNS paper

description: Data were collected from field captured animals that were hibernated in captivity and samples collected from them. See details in the paper and in the "notes" tab of this spreadsheet.
DOI: 10.5061/dryad.b4c70/1
title: Observed distances from camera traps to Maxwell's duikers

description: Filmed Maxwell's duikers were assigned to distance intervals; recorded distances are the midpoints of the intervals. "Sample.Label" references the trap location.  "Effort" is temporal effort, i.e. the number of 2-second time-steps over which the camera operated. "multiplier" describes spatial effort, as the proportion of a circle covered by the angle of view of the camera. The data is formatted as a "flatfile" suitable for use with distance sampling software including Distance and associated R packages.
DOI: 10.5061/dryad.b4c70/2
title: Observed distances from camera traps to Maxwell's duikers at times of peak activity

description: Filmed Maxwell's duikers were assigned to distance intervals; recorded distances are the midpoints of the intervals. "Sample.Label" references the trap location.  "Effort" is temporal effort, i.e. the number of 2-second time-steps over which the camera operated. "multiplier" describes spatial effort, as the proportion of a circle covered by the angle of view of the camera. The data is formatted as a "flatfile" suitable for use with distance sampling software including Distance and associated R packages. This file includes only observations recorded at times of peak activity.
DOI: 10.5061/dryad.b4c70/3
title: Start times of videos of Maxwell's duikers

description: Start times of videos of Maxwell's duikers recorded at camera traps. We included only videos recorded on days when cameras operated, and were not visited by researchers, for the entire day.
DOI: 10.5061/dryad.bb67v/1
title: 29mar17 dryad AA bird flock data

description: Spreadsheet listing all bird flocks sampled and analyzed in the study, giving dates, locations, bird species, and numbers of individuals.