cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8c30j/1
title: Keelback and Slatey-grey snake growth and reproduction data

description: Growth data for each species includes ID, initial SVL, SVL Growth Rate, Ln-transformed rainfall, Ln-transformed frog abundance and mean temperature. Female reproductive data for each species includes ln-transformed values of SVL, litter size and egg mass.
DOI: 10.5061/dryad.9vk07/1
title: KamathLososEvol_AnolissagreiPerchUse

description: Perch height and diameter of individual lizards observed from 12 June to 1 August 2014, in Possum Creek Skate Park, Gainesville FL.
DOI: 10.5061/dryad.9vk07/2
title: KamathLososEvol_AnolissagreiSVL

description: Sex and Snout vent length of individual lizards
DOI: 10.5061/dryad.9vk07/3
title: KamathLososEvol_AnolissagreiMorphAvg

description: Sex, snout vent length, and average lamellae count, toepad area, and limb length.Right and left measurements were averaged for limb length, toepad area, and lamella number on the forelimbs, as well as hindlimb length. We then took the mean of forelimb and hindlimb measurements, yielding one value per individual for limb length, toepad area, and lamella number.
DOI: 10.5061/dryad.9vk07/4
title: KamathLososEvol_AnolissagreiPerchDistAvailable

description: Counts of available perches in five diameter classes, within 50cm of three or more randomly chosen locations for each individual lizard.
DOI: 10.5061/dryad.9vk07/5
title: KamathLososEvol_AnolisSpeciesPerchUse

description: Data from Rodriguez-Schettino et al. 2010 on perch height and diameter for 10 species belonging to seven habitat specialist types of anoles from Soroa, Cuba.
DOI: 10.5061/dryad.b12kk/1
title: R scripts

description: R scripts for analyzing both sets of simulations (individual and deme level), and additional spatial coordinate files for Lotterhos & Whitlock (2015) data at http://dx.doi.org/10.5061/dryad.mh67v
DOI: 10.5061/dryad.b327c/1
title: Automated dendrometer band measurements

description: This file contains data collected by automated dendrometer bands on 119 trees in 4 different sites. The data focuses only on the 2-month study periods of each site. Included are data from 119 of 121 instrumented trees, as 2 loggers failed to record data just before the start of study period at site WFDP (see appendix 1 and 2 of paper).
DOI: 10.5061/dryad.b327c/2
title: Manual measurement data

description: These are manual measurements made with a caliper on visual marks of the automated dendrometer bands. They were used to check the validity of automatic records. They were performed in 3 out of 4 sites (SCBI, SERC, and WFDP) on a total of 87 trees.
DOI: 10.5061/dryad.b327c/3
title: Meteorological variables

description: This file contains weather data measured on each of the four study sites as well as evapotranspiration for WFDP and BCI.
DOI: 10.5061/dryad.b327c/4
title: Sap Flow Data for SCBI

description: This file contains sap flux density measured at SCBI by 28 Granier-style probes on 23 tree stems (see list of trees equipped with sap flow probes).
DOI: 10.5061/dryad.bc1v8/1
title: ENM_data
DOI: 10.5061/dryad.c494p/10
title: Fig. S10 - Scincoidea HiSSE states

description: Figure S10. Ancestral state reconstruction of viviparity for Scincoidea from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/12
title: Fig. S12 - Viperidae HiSSE states

description: Figure S12. Ancestral state reconstruction of viviparity for Viperidae from HiSSE model-averaged across all tested models. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c494p/5
title: Fig. S5 - BAMM Extinction

description: Figure S5. Maximum shift credibility tree from BAMM showing diversification rate shifts across Squamata with tip labels. Rates shown are extinction rates.
DOI: 10.5061/dryad.c494p/6
title: Fig. S6 - Gekkota Diversitree BiSSE states

description: Figure S6. Ancestral state reconstruction of gekkotan toepads using the BiSSE model from Diversitree. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black).
DOI: 10.5061/dryad.c494p/7
title: Fig. S7 - Gekkota BiSSE-like HiSSE states

description: Figure S7. Ancestral state reconstruction of gekkotan toepads from HiSSE using the BiSSE-like model. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black). Branches are colored by model-averaged diversification rates.
DOI: 10.5061/dryad.c494p/8
title: Fig. S8 - Gekkota HiSSE toepad states

description: Figure S8. Ancestral state reconstruction of gekkotan toepads from HiSSE model-averaged across all tested models with tip labels. Colored circles at tips and nodes indicate the states of species and probability that ancestors were toepad-bearing (white) or padless (black). Branches are colored by model-averaged diversification rates.
DOI: 10.5061/dryad.c494p/9
title: Fig. S9 - Squamata HiSSE states

description: Figure S9. Ancestral state reconstruction of viviparity for Squamata with from HiSSE model-averaged across all tested models with tip labels. Colored circles at tips and nodes indicate the states of species and probability that ancestors were oviparous (black) or viviparous (white). The legend in the lower left shows the range of rates, as well as the distribution of rates across the tree (upper histogram) and the frequency of tips in each state (lower bars).
DOI: 10.5061/dryad.c73q1/3
title: Archive of data
DOI: 10.5061/dryad.fg220/1
title: Danise & Holland - R script - 1 nMDS & cluster

description: Script to perform NMDS ordination and cluster analysis. NOTE: run the scripts in the same order in which they are numbered (1 to 3) in order to be able to produce all the figures of the paper.
DOI: 10.5061/dryad.fg220/2
title: Danise & Holland - R script - 2 Diversity facies & biofacies

description: Script to perform diversity analyses
DOI: 10.5061/dryad.fg220/3
title: Danise & Holland - R script - 3 Similarity measures

description: Script to perform similarity analysis
DOI: 10.5061/dryad.fg220/4
title: Danise & Holland - Dataset
DOI: 10.5061/dryad.fg220/5
title: Danise & Holland - Dataset properties
DOI: 10.5061/dryad.gr1pk/1
title: for_Dryad

description: This file contains controls files and output for gene tree inference (Garli), control files for evolver simulations (evolver), control files, input files, and output for both PAML (PAML_codeml) and RELAX analyses (RELAX), and R code to make Figures 4 and 5.
DOI: 10.5061/dryad.j315n.1/16.1
title: Data XPCLR of Wine and France and Hungary Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and French (Jura) and Hungarian Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n.1/17.1
title: Combined set of SNPS including wine and flor strains and strains from other origins(Allyeast-set)

description: Data for Phylogeny and population structure (Figure 1, Figure2A and B). Compressed Vcf file containing a set of biallelic variant with less than 20 % missing position among all strains, obtained from the genotyping  of 20 flor and wine strains  compared to 82 strains with available genome sequences (obtained from Saccharomyces genome database (http://www.yeastgenome.org/), of from the SGRP project (http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html) (Liti et al. 2009, Population genomics of domestic and wild yeasts. Nature, 458, 337–41)
DOI: 10.5061/dryad.j315n.1/19.1
title: Data for differentiation based method PCA, Dxy, Da

description: - plink format files  AssembliesGenowine.raw and .map for PCA performed with adegenet   - Vcf phased data files for each chromosome of flor and wine population - R script utilising on PopGenome performing all analysis of Theta, pi, Dxy (Da = Dxy – (Piwine+piflor)/2 ) on each chromosome datafile).
DOI: 10.5061/dryad.j315n.1/20.1
title: DT FineStructure Flor Wine Champagne

description: These are the data files used for the FineStructure analysis for the hybrid nature of strains of the Champagne group (Figure S1)
DOI: 10.5061/dryad.j315n.1/21.1
title: Data for Linkage desequilibrium analysis (figureS3)

description: ped and map files  for Flor  and wine populations. Files are prepared from phased vcf file . Data used with plink  with options --ld-window 1000
  --ld-window-kb 50
  --ld-window-r2 0
  --r2
DOI: 10.5061/dryad.j315n.1/22.1
title: Data for Estimation of recombination rates  (Figure S4)

description: This data has been used for the genome scan of recombination rate (Figure S4) using a model with hotspot as inplemented in the "INTERVAL" module of LDHAT package. A global estimate of recombination rate has also been estimated for flor strain using PAIRWISE  with the module "PAIRWISE"  of the same package.
DOI: 10.5061/dryad.j315n.1/23.1
title: Data of figure4: Biofilm images used for the evaluation of the impact of each wine and flor allele on biofilm formation

description: The compress archive contains the photos and the notice indicating for image its organization.
DOI: 10.5061/dryad.j315n.1/24.1
title: de-novo draft assemblies

description: This is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study.  This data is used for  phylogenic trees and genes sequence alignments (Figures S2, S6, S8).
DOI: 10.5061/dryad.j7d32/1
title: Data used in the models

description: This file contains the basic data needed to reproduce the study, including all variables used in the models (two fragmentation and four land cover predictors; two natural landscape predictors; 10 instream habitat variables; and two taxonomic and five functional structure indicators for the fish assemblages). Description of abbreviations are provided as a metadata sheet. For a detailed description of each variable, see the main body of the manuscript and the supplementary material.
DOI: 10.5061/dryad.kj666/1
title: Query strain identities and corresponding screening set.

description: In order to obtain an IDTS-wide genetic interaction map, we modified the automated, high-density replica plating approaches previously developed for analyzing S. cerevisiae double mutants through Synthetic Genetic Array (SGA) analysis (Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368). Instead of looking at double mutants, however, we used yeast genetics to systematically assess the effects of Legionella effector co-expression on yeast growth. Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/) (Wagih O, Usaj M, Baryshnikova A, VanderSluis B, Kuzmin E, Costanzo M, Myers CL, Andrews BJ, Boone CM, Parts L (2013) SGAtools: One-stop analysis and visualization of array-based genetic interaction screens. Nucleic acids research 41: W591-596). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This spreadsheet lists all query strains and links them to one or more specific analysis set.
DOI: 10.5061/dryad.kj666/2
title: SGA output for analysis sets 1-10.

description: Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 1-10.
DOI: 10.5061/dryad.kj666/3
title: SGA output for analysis sets 11-20.

description: Query strains that express one effector were mated to an array of ~330 effectors in groups of ~10 queries at a time ("Analysis Set"). The arrays were then imaged using a high-resolution camera and the spot sizes were quantified using SGAtools (http://sgatools.ccbr.utoronto.ca/). Outlier spot sizes flagged by the Jackknife filter (JK) in SGAtools were removed and the average and standard deviation of the remaining values were calculated and normalized to the average empty vector control. This .zip archive includes spreadsheets that encompass the raw SGAtools data output from the paper for analysis sets 11-20.
DOI: 10.5061/dryad.nk35d/4
title: Responses to questionnaire

description: This datafile contains the answers to the questionnaire from all participants of the questionnaire. "Time" and "country" data was removed prior to submission. Free-form answers were altered when necessary to anonymize the data. The corresponding questionnaire can be found as a separate file in this submission.
DOI: 10.5061/dryad.nk35d/5
title: Questionnaire

description: This pdf contains all the questions from the questionnaire used to gather data about opinions of modelers and experimentalists about the collaboration between the two approaches.
DOI: 10.5061/dryad.nk35d/6
title: Bibliometric analysis

description: This file is based on Rmarkdown and contains the steps of the bibliometric analyis of the bibliometric datafiles that are part of this submission.
DOI: 10.5061/dryad.nk35d/7
title: Statistical analysis of questionnaire

description: This file is based on Rmarkdown and contains the statistical analysis and visualization code of the questionnaire answers.
DOI: 10.5061/dryad.p8t61/1
title: Effects of soil biota on plant diversity effects

description: 'nutrient' has two treatments:fertilized vs. unfertilized. 'micro' has two treatments: sterilized vs. unsterilized soil. 'comp' means species composition. 'id'means species identity. 'state' means whether the plant is alive or dead. 'shoot'means shoot dry weight. 'root' means root dry weight.
DOI: 10.5061/dryad.rs714/1
title: Island bird phylogenies

description: Island bird phylogenies, list of species added, fossil calibrations. See ReadMe file for full description
DOI: 10.5061/dryad.rv08j/1
title: Fasta files of original transcriptome assemblies for the three species

description: These are the original transcriptome assembly files prior to the filtering and ORF prediction described in the paper.
DOI: 10.5061/dryad.rv08j/2
title: Functional Annotation Table

description: Gene annotation of the 2010 orthologous genes for each species.  The table includes best blast hit to NCBI nr database, Gene Ontology (GO) categories, and pfam domains.
DOI: 10.5061/dryad.rv08j/4
title: Pairwise dN, dS, dN/dS data for the 2010 orthologs

description: Pairwise dN, dS, and dN/dS were calculated for each ortholog using PAML.  See paper and the scripts and commands for additional details.
DOI: 10.5061/dryad.rv08j/5
title: Scripts and commands for the generation of the PAML results
DOI: 10.5061/dryad.s6c68/1
title: Medicago traits and fitness

description: Primary data file containing data on Medicago height, flowering date, herbivore damage, and fruit number.
DOI: 10.5061/dryad.sm72f/1
title: Mouchet et al., 2016, Proc. R. Soc. B, Primary Data

description: Reflectance spectra; Excitation spectra; Emission spectra; Time-resolved Fluorescence Intensity - Further information: see related article.
DOI: 10.5061/dryad.v1c16/1
title: Cat Activity

description: This folder contains files necessary to replicate the analysis presented in Gruen, M.E., et al (2016). "The Use of Functional Data Analysis to Evaluate Activity in a Spontaneous Model of Degenerative Joint Disease Associated Pain in Cats". PLOSone, under revision. The code was created by Marcela Alfaro-Cordoba and Ana-Maria Staicu.
DOI: 10.5061/dryad.02f6r/1
title: Reporter gene expression data

description: For all of the reporter genes tested in the paper, the genomic location of the transgene insertion is provided, along with the relevant annotations. The mean expression (measured as beta-galactosidase activity) and standard deviation of each reporter gene in whole males, whole females, or carcass is provided in units on mOD/min.
DOI: 10.5061/dryad.1g98m/1
title: Mathematica notebook containing model and analysis

description: Mathemetica Notebook with the model description and analysis to create the Figures presented in the manuscript.
DOI: 10.5061/dryad.1g98m/2
title: R Script for sensitivity analysis

description: R script for the sensitivity analysis as described in the manuscript
DOI: 10.5061/dryad.21j0n/2
title: Plestiodon RAxML data set

description: Phylip file with concatenated UCE sequences. UCE loci specified in partition file. See ReadMe file to match sample names with species and locality.
DOI: 10.5061/dryad.21j0n/3
title: Plestiodon UCE loci partitions file

description: UCE loci partitions.
DOI: 10.5061/dryad.2k0s6/1
title: Apical length measurements of Didymosphenia geminata from South Boulder Creek, Colorado USA

description: This apical length dataset was collected using a Fluid Imaging FlowCam in 2013. Length measurements (in micrometers) of D. geminata valves were exported from VisualSpreadsheet, Fluid Imaging, Inc.'s proprietary FlowCam software. This .csv file contains (in long format) all the length measurements analyzed for this study along with their collection date, the accessioned sample at INSTAAR from which they derive, the collection locality, and that locality's latitude and longitude in decimal degrees (WGS84 datum).
DOI: 10.5061/dryad.3264f/1
title: FC lifespan and snapshots
DOI: 10.5061/dryad.32r30/1
title: Virulence data

description: Virulence data for the confection experiment
DOI: 10.5061/dryad.32r30/2
title: culturedata

description: Bacterial growth parameters in the co-culture experiments
DOI: 10.5061/dryad.3418j/3
title: HPLC-S.canadensis

description: HPLC characterization of leaves of S. canadensis grown in various soil microbial communities
DOI: 10.5061/dryad.3418j/4
title: HPLC-S.rugosa

description: HPLC characterization of leaves of Solidago rugosa grown in various soil microbial communities
DOI: 10.5061/dryad.34k42/1
title: 1.Total_Number_of_Submissive_interactions_in_dog_packs

description: This file contains six tables. Each table is a squared matrix reporting the total number of submissive gestures exchanged among dogs belonging to the same pack. So, each table corresponds to a different dog pack. Performers of submissive gestures are reported on the vertical axis on the left side of each table, in which each individual dog is identified using a 2-3 letters code. Recipients of submissive gestures are reported on the upper horizontal axis of each table, and again each individual dog is identified using a 2-3 letter code. Note that the data reported for the Curva pack are not statistically independent from those reported for the Fused pack, since the latter originated from the fusion of the Curva pack with another one and the data collected before and after the fusion event were combined (see Bonanni et al. 2017, Behav Ecol, for additional explanations). In the original paper, the data reported in these tables were used to calculate the statistical parameters reported in Table 3, i.e. hierarchy linearity, directional consistency of submissive behaviour, hierarchy steepness, as well as percentage of unknown, 1-way, 2-ways, and tied dyadic relationships. Moreover, these data were also used to arrange pack members in the rank order that was most consistent with a linear hierachy.
DOI: 10.5061/dryad.34k42/2
title: 2.Gender_Age_DominanceRank_of_Individual_Dogs

description: This file contains data concerning gender, age and dominance rank of all individual dogs studied. Note that “age” is reported as “age class”, i.e. individual dogs of each pack were assigned to age classes that were ranked from the youngest to the oldest one, based on their actual or estimated year of birth (which is also reported in the table). So, “age class” does not express the actual age of dogs in years. Note that empty cells refer to missing values, i.e. dogs whose ages could not be estimated relative to that of other dogs. Dominance rank was standardized by distributing ranks evenly between the highest (+1) and the lowest (-1), with the median rank being scored as 0, to allow comparison across packs. In the original paper these data were used to: 1) assess the correlation between dominance rank and age for each pack separately; 2) assess the effect of gender on dominance rank, as well as the effect of gender on age.
DOI: 10.5061/dryad.34k42/3
title: 3.Gender_DominanceRank_Age_Body_Size_of_Individual_Dogs

description: This files contains data concerning gender, dominance rank, age and body size for some of the dogs studied. In particular, body measurements were collected for members of two dog packs, one studied during the period 2005-2006 (most behaviorual data analyses concerning this group were published by Cafazzo et al. 2010, Behav Ecol 21, 443-455), and another one studied during 2007-2008 (most behavioural data analyses concerning this one are included in Bonanni et al. 2017). As said above, the variable “age class” does not express the actual age of dogs in years, but rather it ranks pack members from the youngest (lowest rank) to the oldest one (highest rank). All body measurements are espressed in cm. Head size was obtained by summing up three distances: nose-occipital bone, temporal-temporal, mandible-forehead. Empty cells refer to missing values. In the original paper by Bonanni et al. (2017), these data were used to: 1) assess the correlation between standardized dominance rank and body measurements (separately for each pack); 2) assess the partial correlation between dominance  rank and age, after controlling for body size (it was feasible only for the Corridoio pack); 3) assess the partial correlation between dominance rank and body measurements after controlling for age (it was feasible only for the Corridoio pack; 4) assess the effect of gender on the body measurements (all measured individuals taken together). Note that one female dog was a member of both packs at different times, and her body measurements were used in the statistical tests concerning both packs since she was already fully adult/grown during the study period 2005-2006.
DOI: 10.5061/dryad.37jg4/1
title: single participant behavioral data files

description: .mat files for single participants. README.txt file in each zipped folder describes columns
DOI: 10.5061/dryad.4cs45/1
title: Hydromantes.data

description: Measurement data for Hydromantes salamanders
DOI: 10.5061/dryad.4cs45/2
title: Rcode

description: R script for running analyses
DOI: 10.5061/dryad.4qb79/1
title: Meyer Science 2016 Fig 1A

description: Data collected for results shown in figure 1a, see notes within the file and the manuscript for further guidance.
DOI: 10.5061/dryad.4qb79/2
title: Meyer Science 2016 Fig 1B

description: Data collected for results shown in figure 1b, see notes within the file and the manuscript for further guidance.
DOI: 10.5061/dryad.4qb79/3
title: Meyer Science 2016 Fig 2

description: Data collected for results shown in figure 2, see notes within the file and the manuscript for further guidance.