cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.350v2/5
title: SD4

description: Results of fitting SURFACE models allowing for regime shifts in craniodental evolution across 100 dated trees.
DOI: 10.5061/dryad.3576v/1
title: Rodent and eulipotyphlan partial cytochrome b sequences

description: FASTA file comprising 248 sequences generated during this study.
DOI: 10.5061/dryad.3hk0v/1
title: Selection experiment population dynamics

description: Details of bacterial and phage population dynamics for each of 6 replicate populations from 4 treatments evolved for 20 transfers (approx 150 bacterial generations). Data shown in figure 2 and S2. Date comprises bacterial population density, frequency of mucoid colonies, frequency of plasmid
DOI: 10.5061/dryad.3hk0v/2
title: SNPeff identifed mutations

description: Summary of mutations identified from sequenced clones taken from transfer 20 (bacterial generation ~150). Clones were sequenced on the illumina MiSeq platform and reads aligned using BWA. Small variants (SNPs and small indels) were identified using GATK HaplotypeCaller and SNPeff and structural rearrangements identified using BreakDancer. Data are shown in figure 1, S1 and table S2.
DOI: 10.5061/dryad.3mg2h/1
title: long_reads_cDNA_sequences
DOI: 10.5061/dryad.3mg2h/2
title: 4inds_gDNA_cDNA
DOI: 10.5061/dryad.3mg2h/3
title: sedge_warbler_genotyping_results
DOI: 10.5061/dryad.3rr40/1
title: Hopkins_AppendixS1

description: This appendix contains: Tables describing character matrix, with comparison to landmark data, and additional figures with 1) results when autapomorphic characters or gap-weighted characters are excluded; 2) deformation plots showing variation in cranidial shape described by the first two principal components shown in Figure 1; 3) results based on just the cranidial and just the non-cranidial characters.
DOI: 10.5061/dryad.3rr40/2
title: Hopkins_AppendixS2

description: Nexus file with character matrix for reading into Claddis in R.
DOI: 10.5061/dryad.4sd0r/1
title: Field study data-sets in Excel

description: Each of the field experiments and assays of the study, indicated by subheadings in the paper, has been given a separate Excel worksheet, with the exception of the assessment of aggression in natural encounters, which has two worksheets ('Natural encounters aggress rate' and 'Natural encounters distance').
DOI: 10.5061/dryad.5cd20/1
title: DATA for open access

description: Genotype frequencies of rs1337185, rs5275, rs5277, rs7575934, rs3213718 and rs162509 in controls and cases
DOI: 10.5061/dryad.5d781/3
title: Data.File

description: Data files and R scripts for analyses associated with M. deVries Biology Letters submission entitled “The role of feeding morphology and competition in governing the diet breadth of sympatric stomatopod crustaceans.”
DOI: 10.5061/dryad.5k05t/1
title: Nexus file

description: Nexus file with the data matix
DOI: 10.5061/dryad.5k05t/2
title: TNT file

description: Data matrix in .tnt format
DOI: 10.5061/dryad.5k303/1
title: IJO201781_Dryad data

description: Complete dataset for Seebacher et al 2017 International Journal of Obesity (IJO201781)
DOI: 10.5061/dryad.5s3b1/1
title: Table S1 Rejected Data

description: Data that was available to authors through lit review, but discarded for potential inaccuracy or age (see methodology).
DOI: 10.5061/dryad.5s3b1/2
title: Table S2 FADs

description: First Appearance Data (humans) used in paper.
DOI: 10.5061/dryad.5s3b1/3
title: Table S3 LADs

description: Last Appearance Data (Megafauna) used in paper.
DOI: 10.5061/dryad.5s3b1/4
title: Table S4 Model Comparisons

description: Model statistics as output by ArcGIS.
DOI: 10.5061/dryad.5s3b1/5
title: Emery-Wetherell_et_al_FigureS1_2col
DOI: 10.5061/dryad.5s3b1/6
title: Emery-Wetherell_et_al_FigureS2_2col
DOI: 10.5061/dryad.5s3b1/7
title: Emery-Wetherell_et_al_FigureS3_2col
DOI: 10.5061/dryad.5s3b1/8
title: Emery-Wetherell_et_al_FigureS4_2col-01
DOI: 10.5061/dryad.60326/1
title: Monthly survey data for H. cyanea (counts and environmental measurements)

description: Field data for beetle counts by life stage across three monthly surveys in Apalachicola National Forest, FL, including environmental information (e.g., % palmetto cover and palmetto height) and fire management unit data from the US Forest Service (e.g., burn unit identifiers and months since last burn).  Formatted for reading into R.
DOI: 10.5061/dryad.74f2r.1
title: Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification
DOI: 10.5061/dryad.74f2r.1/1.1
title: Maximum clade credibility tree of FBDl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl.xml input-file.
DOI: 10.5061/dryad.74f2r.1/2.1
title: Subsample of trees from FBDl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/3.1
title: Input file for FBDl analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils (FBDl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.1/4.1
title: Maximum clade credibility tree of FBDs

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs.xml input-file
DOI: 10.5061/dryad.74f2r.2/28.2
title: Input file for NDus analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the node dating approach including 12 fossils and an uniform calibration prior (NDus). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/29.2
title: Maximum clade credibility tree of NDul

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 15 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDul.xml input-file.
DOI: 10.5061/dryad.74f2r.2/30.2
title: Subsample of trees from NDul analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis using 15 fossils and an uniform calibration prior (see NDul.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/31.2
title: Input file for NDul analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the node dating approach including 15 fossils and an uniform calibration prior (NDul). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.9t21c/1
title: Annotated HSV-2v genomes

description: Putative coding sequences were annotated with Geneious 10.0.5 using a conservative similarity threshold of 60% to coding sequences annotated in the HSV-2 reference genome (NC_001798). GFF3 format.
DOI: 10.5061/dryad.9t21c/2
title: Mutliple sequence alignments including HSV-2v sequences

description: This archive contains the following alignments: Whole genome 1, 2 and 3; Whole genome de novo 2 and 3; Non recombinant 1 to 10; UL15 non recombinant and recombinant, UL29 non recombinant and recombinant, UL30 non recombinant and recombinant, UL39 non recombinant and recombinant. Whole genome 2 and 3 and Whole genome de novo 2 and 3 are provided as NEXUS files and include site masks pinpointing the recombinant regions (Whole genome 2 and Whole genome de novo 2 and 3) and large non recombinant fragments (Whole genome 3). All other alignments are provided as FASTA files.
DOI: 10.5061/dryad.f4k24/1
title: S1 Dataset

description: Accumulated feed consumption (kg/pig) and body weight gain (kg) of pigs challenged chronically with LPS and fed an olive-oil bioactive extract (OBE)
DOI: 10.5061/dryad.f4k24/2
title: S2 Dataset

description: Immune-inflammatory response of pigs and macrophages treated with an olive-oil bioactive extract (OBE) and challenged with LPS
DOI: 10.5061/dryad.f4k24/5
title: S5 Dataset

description: Effect of an olive-oil bioactive extract on basal TEER and TNF-α induced decrease in TEER in vitro.
DOI: 10.5061/dryad.f4k24/6
title: S6_1 Dataset

description: Gut microbial composition and predicted functions in pigs chronically challenged with LPS and fed an olive-oil bioactive extract (OBE).
DOI: 10.5061/dryad.fg475/1
title: Raberg_HostSpecialization

description: This file contains qPCR and 454 amplicon sequencing data of Borrelia afzelii from tissue samples from mammals.
DOI: 10.5061/dryad.g7n7g/1
title: ScottlandSwededen combined dataset

description: The two datasets, QWIN and SHeS, were examined for comparable variables and these data were merged into a new dataset entitled QwinSHeS. A group of qualified researchers from each site evaluated the questions and defined the variables eligible for valid comparisons between the two countries. The variables included in the final Swedish – Scottish merged database were: sociodemographic characteristics, anthropometrics, lifestyle, classic risk factors for CVD, and diagnoses for CVD, general health and psychosocial distress (GHQ-questionnaire 12 items).
DOI: 10.5061/dryad.n9g60/1
title: alignment-data.tar.gz

description: Alignment data for concatenated and coalescent-based analyses.  Contents in README.
DOI: 10.5061/dryad.p2c6r/3
title: Annual projection matrices P

description: Absorbing annual matrices *P* of Cayo Santiago female rhesus macaques. Annual matrices were parameterized with demographic data of female rhesus macaques from 1973 to 2013.
DOI: 10.5061/dryad.p2c6r/4
title: Annual number of adult rhesus macaques

description: Annual number of Cayo Santiago adult rhesus macaques from 1973 to 2013.
DOI: 10.5061/dryad.q8987/1
title: Raw Data For Firth et al

description: Raw data and individual summary information for "Wild birds respond to flockmate loss by increasing their social network associations to others" (submitted). Authors: Firth*, Josh, Voelkl, Bernhard, Crates, Ross, Aplin, Lucy, Biro, Dora, Croft, Darren, Sheldon, Ben. *joshua.firth@zoo.ox.ac.uk.

The Data.RData file contains four primary objects:

1) ‘records’ contains the raw primary data for the manuscript. This is the RFID detections of visiting great tits during the study and experiment period. Each row denotes a single second RFID detection of an individual. The columns show information on (i) ’ring’ - the unique ring number of the visiting great tit, (ii) ‘time’ - the timestamp of the detection, (iii) ‘location’ - the unique feeder it was detected on and (iv) ‘week’ - a number denoting the weekend of the detection relevant to the experiment (first removals (i.e. trial 1) performed between weekends 4 and 5).

2) ‘focals’ contains summary information about which treatment category each individual fell into on each experimental weekend. Each row consists of an individual per trial. The columns show information on (i) ‘ring’ - the unique ring number of the visiting great tit, (ii) ‘trial’ - the trial number of that week’s experiment and (iii) ‘category’ which is one of 3 options: ‘fmr’ (for those who had their flockmate removed), ‘fmc’ (for those who had their flock mate captured and then released) and ‘ao’ for all other focal birds (i.e. those who appeared the weekend before and after the replica, but did not have their flock mates removed or captured). 

3) ‘info.on.caught.birds’ contains summary information regarding which birds were removed and which were caught then re-released that replica. Each row contains an individual per trial. The columns show information on (i) ‘ring’ - the unique ring number of the visiting great tit, (ii) ‘trial’ - the trial number of that week’s experiment and (iii) ‘treatment’ which is one of 2 options: ‘removed’ (for those individuals which were temporarily removed over the following weekend) and ‘re-released’ (for those individuals which were immediately re-released within 30mins of capture).

4) ‘details’ contains the ReadMe file text instructions
DOI: 10.5061/dryad.rq163/1
title: mtDNA_copy_number

description: Contains mtDNA and nuclear gene rad51 qPCR results.
DOI: 10.5061/dryad.t5800/1
title: Newton et al wolf travel on linear features data for rsf models

description: These data provide distances from wolf-points ("use" = 1) to available points ("use" = 0) within a wolf's ("ID") seasonal range. Standardized distances to each habitat feature are provided. Availability of each feature type is also provided (Feature_A). These data can be used to replicate all figures and tables in the study.
DOI: 10.5061/dryad.t5800/2
title: Newton_et_al_Tortuosity_Velocity_NorthernWolves

description: Data underlying Supplementary Figure S1,Season delineation, tortuosity and velocity of resident adult wolves in northern Ontario, Canada, 2010-2014.
DOI: 10.5061/dryad.tn36j/6
title: dragon permutations

description: R code for creation of null model for dragons
DOI: 10.5061/dryad.tn36j/7
title: hwi_functions

description: R code - custom functions for use in creation of dragon model
DOI: 10.5061/dryad.vb549/1
title: Spectra_3mm

description: Spectra obtained at a 3-mm distance of the different centre/surround colour combinations of the artificial coloured plastic plates used in Experiment 1.
DOI: 10.5061/dryad.vb549/2
title: Spectra_5mm

description: Spectra obtained at a 5-mm distance of the different colour combinations of the artificial coloured plastic sheets used in experiment 1.
DOI: 10.5061/dryad.vb549/3
title: Pmuralis_spectra_OVS

description: Spectra of the UV outer-ventral scale (OVS) displayed by Podarcis muralis, spectra of their orange ventral coloration, and spectra of their black coloration. We also took chimeric spectra including UV-OVS with the orange ventral coloration and with the black coloration
DOI: 10.5061/dryad.2g343/1
title: Mammal registers

description: Register of mammals sampled with camera traps in six Brazilian Atlantic Forest reserves
DOI: 10.5061/dryad.2g343/2
title: Variables for modeling occupancy and detection of mammals

description: Variables used to model occupancy and detection of mammals in six reserves of Brazilian Atlantic Forest
DOI: 10.5061/dryad.31048.1/15.1
title: test_which_parsimony_informative_01-16-17

description: Revised script for testing whether characters are parsimony informative.
DOI: 10.5061/dryad.31048.1/18.1
title: runFiles.zip

description: Zipped directory containing output from phylogenetic analyses, necessary for use with analyses in Rmd file. All tree files are contained in this zipped directory.
DOI: 10.5061/dryad.31048.1/19.1
title: run_coding_12-15-16a.pdf

description: PDF table explaining how the identifiers, labels and conditions of the different phylogenetic analyses as given in the main text and in the supplemental data materials relate.
DOI: 10.5061/dryad.31048.1/21.1
title: raw_morphMat_MrBayes_04-21-17.nex

description: The raw morphological matrix, as used in the Bayesian analyses, as a Nexus-formatted text file.
DOI: 10.5061/dryad.31048/1
title: Appendix_1_05-11-17

description: List of 66 morphological characters used, revised from Schreiber et al. (2013).
DOI: 10.5061/dryad.31048/14
title: Appendix_4_05-11-17

description: Table giving the number of taxa having each character state (or coded as missing) for each morphological character in the revised matrix.
DOI: 10.5061/dryad.31048/16
title: Appendix_5_05-11-17

description: List of the 40 extant rhynchonellide species (modified from Logan 2007; Bitner 2009).
DOI: 10.5061/dryad.31048/2
title: Appendix_2_05-11-17

description: Morphological character matrix used for parsimony analyses, revised from Schreiber et al. (2013), for 25 genera and 66 characters (the codings for the two Basiliola species are not repeated).
DOI: 10.5061/dryad.31048/6
title: Appendix_3_05-11-17

description: Information on DNA specimens used in Cohen and Bitner (2013) and their respective Genbank accession numbers, taken from their Table 1.
DOI: 10.5061/dryad.350v2/6
title: SD5

description: Results of fitting SURFACE models allowing for regime shifts in craniodental evolution across 100 dated trees, after the omission of poorly-known taxa.
DOI: 10.5061/dryad.37882/1
title: Virtual species

description: The virtual species used in the manuscript, which were generated in NicheA 3.0.
DOI: 10.5061/dryad.5s3b1/9
title: Emery-Wetherell et al.gdb
DOI: 10.5061/dryad.61n4k/1
title: Behavioral isolation assay data

description: Behavioral data used to measure behavioral isolation between species of Etheostoma darters in the laboratory. Data is included for measurements of male aggression, male choice, and female choice. Each behavioral trial included a focal male, a rival male, and a female.
DOI: 10.5061/dryad.6c886/1
title: Environmental variables

description: Date were collected in 70 beech-fir montane forests of the French Northern Alps, in 2014 (stand measurements) and 2015 (soil measurements). Abbreviated headlines are as follows: "H_index" = Humus index (based on humus form); "pH" = pH-H2O (topsoil); "CN_ratio" = Total carbon / total nitrogen ratio (topsoil); "Canop" = Mean canopy openness (%); "Tree_Compo" = Coniferous proportion; "Tree_Struc" = Number of diameter classes of standing trees ; "Alpha_LU" = Land-use diversity (500 m radius); "Dist_Forest" = Distance to forest edge in meters; "Prop_Forest" = Forest proportion (500 m radius).
DOI: 10.5061/dryad.6c886/2
title: Herbaceous plants data

description: Site by species matrix of herbaceous plants (presence/absence).
DOI: 10.5061/dryad.6c886/3
title: Springtails data

description: Site by species matrix of springtail MOTUs (presence/absence).
DOI: 10.5061/dryad.6d159/1
title: Mandatory Reporting Meta-Synthesis - Extracted Data Coded

description: All data extracted and coded data for this meta-synthesis is found in this excel file.
DOI: 10.5061/dryad.74f2r.1/10.1
title: Subsample of trees from NDbs analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 12 fossils (see NDbs.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/11.1
title: Maximum clade credibility tree of NDbs

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities) using 12 fossils, resulting from the beast2 analysis using the NDbs.xml input-file.
DOI: 10.5061/dryad.74f2r.1/12.1
title: Input file NDbs analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 12 calibration constraints based on fossil information (NDbs). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.1/13.1
title: Subsample of trees from NDnl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 15 fossils (see NDnl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/5.1
title: Subsample of trees from FBDs analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/6.1
title: Input file for FBDs analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils (FBDs). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.1/7.1
title: Maximum clade credibility tree of NDbl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities), using 15 fossils; resulting from the beast2 analysis using the NDbl.xml input-file.
DOI: 10.5061/dryad.74f2r.1/8.1
title: Subsample of trees from NDbl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 15 fossils (see NDbl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/9.1
title: Input file NDbl analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 15 calibration constraints based on fossil information (NDbl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.7j660/1
title: verbal autopsy data ballabgarh 2008-2012
DOI: 10.5061/dryad.7qj20/1
title: Stipa Seedling Survivorship

description: Stipa pulchra seedling survivorship and stem counts of Stipa seedlings and adults and Avena adults across two community types (Stipa pulchra or Avena fatua), three Nitrogen treatments (low, ambient, and high), and three light treatments (low, ambient, and high) within study conducted at the University of California South Coast Research and Extension Center.
DOI: 10.5061/dryad.7qj20/2
title: Stipa adult survivorship

description: The number of Stipa pulchra adults at each sampling point and the proportion of adults that survived across seven blocks of paired grazed and ungrazed plots over two years at the Vasco Caves Regional Park
DOI: 10.5061/dryad.7qj20/3
title: Stipa adult fecundity

description: Reproductive data for Stipa pulchra at Vasco Caves Regional Park. These data include total number of individuals within a plot, whether a given individual reproduced and the number of culms per plant if it did. These data span multiple years and grazed treatments.
DOI: 10.5061/dryad.7qj20/4
title: Stipa pulchra recruitment data

description: Recruitment data for Stipa pulchra across three nitrogen treatments at the Irvine Ranch Natural Landmark
DOI: 10.5061/dryad.7qj20/5
title: Data to assess Avena seed production

description: Avena fatua stem counts and per capita seed production data, as well as Stipa pulchra seedling and adult stem counts across two community types (Stipa pulchra or Avena fatua), three Nitrogen treatments (low, ambient, and high), and three light treatments (low, ambient, and high) within study conducted at the University of California South Coast Research and Extension Center.
DOI: 10.5061/dryad.7qj20/6
title: Avena recruitment

description: Germination and recruitment stem data for Avena barbata across a density and precipitation experiment conducted at the University of California Sierra Foothills Research and Extension Center.
DOI: 10.5061/dryad.80p28/1
title: Control file for M8 model in PAML

description: Control file for the positive selection M8 PAML model used to analyze Toll-like receptors (Table 1)
DOI: 10.5061/dryad.80p28/2
title: Control file for M7 model in PAML

description: Control file for the selection null (M7) PAML model used to analyze Toll-like receptors (Table 1).
DOI: 10.5061/dryad.80p28/3
title: SLR raw data for TLR2

description: TLR2 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.9tn73/1
title: dataset 1

description: dataset 1, Savannah Sparrow (biological variable) x Grassland (landscape variable)
DOI: 10.5061/dryad.9tn73/2
title: dataset 2

description: dataset 2, Bobolink (biological variable) x Grassland (landscape variable)
DOI: 10.5061/dryad.9tn73/3
title: dataset 3

description: dataset 3, Bobolink (biological variable) x Forest (landscape variable)