cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6k939m4/1
title: ArthropodAbundances_BirdExpe_Dec2014

description: Number of individuals per quadrat for arthropod morpho-species collected on the vegetation at Jonkershoek on December 2014 for a "bird exclosure" experiment.
DOI: 10.5061/dryad.6k939m4/2
title: ArthropodTaxonomy_BirdExpe_Dec2014

description: Taxonomy of arthropods collected on the vegetation at Jonkershoek on December 2014 for a "bird exclosure" experiment.
DOI: 10.5061/dryad.6m220kd/1
title: Grooming matrices of macaques groups related to this study

description: This in an R file. To open it is needed the R statistical software program. The file contain two elements. Matrices: contains the grooming matrices used in the analysis of this study. References: contains the citation from for each group and matrix used in the study. The order of elements in each object are correspondent. To call an see the contents of an object type 'Matrices' or 'References' and hit enter.
DOI: 10.5061/dryad.7687117/10
title: GB_malesummer

description: Male grizzly bear SSF data in summer
DOI: 10.5061/dryad.7687117/11
title: GBfemale_rate

description: Female grizzly bear movement rate data
DOI: 10.5061/dryad.7687117/12
title: GBmale_rate

description: Male grizzly bear movement rate data
DOI: 10.5061/dryad.7687117/7
title: GB_femalesummer

description: Female grizzly bear SSF data in summer
DOI: 10.5061/dryad.7687117/8
title: GB_malefall

description: Male grizzly bear SSF data in fall
DOI: 10.5061/dryad.7687117/9
title: GB_malespring

description: Male grizzly bear SSF data in spring
DOI: 10.5061/dryad.7q3n51j/1
title: Pintar et al. 2018 Funct Ecol data

description: Data from Pintar, Matthew R., Jason R. Bohenek, Lauren L. Eveland, and William J. Resetarits, Jr. 2018. Colonization across gradients of risk and reward: nutrients and predators generate species-specific responses among aquatic insects. Functional Ecology. See the README for details about the data file contents.
DOI: 10.5061/dryad.c7t3810/1
title: Trait means and correlation coefficients

description: First tab is the trait means for all 5 traits measured, whereas second tab are the bootstrapped correlation coefficients and 95% confidence intervals.  Note: For intersexual correlations, haplotype BRO was removed from analyses given fitness is zero. This would skew correlation.
DOI: 10.5061/dryad.ch6b3/14
title: 9c.iBPP.Oxy.morph

description: iBPP input file (9C) with morphological data matrix for eight traits from 21 exemplars.
DOI: 10.5061/dryad.ch6b3/15
title: 9d.iBPP.Oxy

description: iBPP control file (9D) including guide tree based on analysis of four-gene data matrix for one exemplar per candidate species hypothesis, as well as run parameters and priors used for integrative species delimitation analyses.
DOI: 10.5061/dryad.ft3k3/1
title: Mitochondrial dataset

description: Concatenation of mitochondrial genes for 35 xenarthran taxa
DOI: 10.5061/dryad.ft3k3/2
title: Mitochondrial RAxML tree

description: Maximum likelihood tree for 35 xenarthran mitogenomes inferred with RAxML under a partitioned model as estimated by PartitionFinder
DOI: 10.5061/dryad.ft3k3/3
title: Mitochondrial PartitionFinder best scheme for RAxML

description: PartitionFinder best scheme for running RAxML on the mitochondrial dataset
DOI: 10.5061/dryad.ft3k3/4
title: Mitochondrial MrBayes consensus tree

description: Bayesian consensus tree for 35 xenarthran mitogenomes inferred with MrBayes under a partitioned model as estimated by PartitionFinder
DOI: 10.5061/dryad.ft3k3/5
title: Mitochondrial PartitionFinder best scheme for MrBayes

description: PartitionFinder best scheme for running MrBayes on the mitochondrial dataset
DOI: 10.5061/dryad.ft3k3/6
title: Mitochondrial PhyloBayes consensus tree

description: Bayesian consensus tree for 35 xenarthran mitogenomes inferred with PhyloBayes under the CAT-GTR+G4 mixture model. This phylogram corresponds to Figure 2a.
DOI: 10.5061/dryad.ft3k3/7
title: Mitochondrial PhyloBayes chronogram

description: Bayesian chronogram for 35 xenarthran mitogenomes inferred with PhyloBayes under the CAT-GTR+G4 mixture model and a autocorrelated lognormal relaxed molecular clock. The file in nexus format can be opened in FigTree and corresponds to Figure 3a.
DOI: 10.5061/dryad.g7v1b.5
title: Data from: A framework for resolving cryptic species: a case study from the lizards of the Australian Wet Tropics
DOI: 10.5061/dryad.g7v1b.5/2.5
title: Supplementary Information
DOI: 10.5061/dryad.g7v1b.5/3.5
title: Appendix 1: Taxonomic revisions of the species groups
DOI: 10.5061/dryad.g7v1b.5/4.5
title: Pseudo-Reference Genomes (PRGs)

description: PRG.tar.gz: a tarred, gzipped directory of the pseudo-reference genomes (PRGs) for each lineage included in the study.
DOI: 10.5061/dryad.g7v1b.5/5.5
title: Variant Calls (VCFs)

description: VCFs.tar.gz: a tarred, gzipped directory of variant calls (VCFs) for each lineage included in the study
	- VCFs are filtered with respect to coverage & quality as reported in text 
	- VCFs are phased
	- this includes both variant and invariant sites
DOI: 10.5061/dryad.kp18283/1
title: Chemical Dataset

description: Labelled chemical metadata file produced by the Perl code (GCMS Parser). Columns delineate sample ID, date of sampling, zone (P = peripheral, M = Middle, C = central), distance in meters from center, and the top 100 sampled volatile organic compounds (normalized relative ratios).
DOI: 10.5061/dryad.m371v/1
title: README

description: This is the README file for all supplementary data associated with: 
Wolfe JM, Fournier GP. Horizontal gene transfer constrains the timing of methanogen evolution. Nature Ecology and Evolution.
DOI: 10.5061/dryad.m371v/2
title: 1_LUT

description: Lookup table providing the clade and full species names for truncated names used in all subsequent files (required for analysis in downstream software).
DOI: 10.5061/dryad.qg38sd1/3
title: Derivation of selection coefficients and notation used in equations 3 and 4

description: This file includes the complete derivation of the selection coefficients used to generate figures 5 and 6 in the main text of the manuscript. The file uses the notation developed by Barton and Turelli (1991; PubMedID 2016044) to separate and analyze different components of selection. These are then used to calculate the exact strength of selection from different sources in the files titles Calculation of DeltaT and DeltaH.
DOI: 10.5061/dryad.qg38sd1/4
title: Calculations of the DeltaH and figures 5

description: This files uses the coefficients derived in the "Derivation" file to get exact values for the contributions of different evolutionary forces on the evolution of female choosiness.
DOI: 10.5061/dryad.qg38sd1/5
title: Calculations of the DeltaT and figures 6

description: This files uses the coefficients derived in the "Derivation" file to get exact values for the contributions of different evolutionary forces on the evolution of male display.
DOI: 10.5061/dryad.s1v3801/2
title: Data for publication

description: This contains the data used to make Fig. 2, and all of the appendix figures.  It can be analyzed using the Matlab code in the code_for_paper document.
DOI: 10.5061/dryad.v6d9t/2
title: Figures

description: These are all data used to support the findings of this study.
DOI: 10.17632/8tj4m9snx6.1
title: Data for: A New Moving Strategy for the Sequential Monte Carlo Approach in Optimizing the Hydrological Model Parameters
DOI: 10.17632/c2m5d2mtz5.2
title: Data for: Review and Comparison of Statistical Methods for Inverse Prediction in Nuclear Forensic Applications

description: R code and data used to produce results in the data analysis section.
DOI: 10.17632/zxpj5rmsng.1
title: Data for: Association of TPMT*3C and a decreased thiopurine S-methyltransferase activity in patients with neuromyelitis optica spectrum disorders

description: Approval letter of the study. Study data of the research including patients' characteristics, TPMT activity, genotype of selected variants, et al.
DOI: 10.5061/dryad.1h73pd8/1
title: DeLisle_et_al_DATA

description: Data from two cattle tank experiments with Notophthalmus viridescens
DOI: 10.5061/dryad.269pp30/1
title: Peak data for volatile wing chemicals

description: Data included are raw peak integrations from spectra of each individual. Only the components of chemical extracts discussed in the work are included. Also included are the size metrics and lab stock family identifiers for each individual. In the spreadsheet "P" indicates Pieris rapae rapae, and "J" indicates Pieris rapae crucivora.
DOI: 10.5061/dryad.2q8m903/2
title: Radial Extended MICMAC First Image Dataset

description: SfM+MVS point cloud generated from the first replicate image dataset.
DOI: 10.5061/dryad.668g444/1
title: README

description: This file describes the rest of the data for this publication.
DOI: 10.5061/dryad.668g444/2
title: Scripts

description: Simulation input files, R scripts and dataframes used for all figures and analyses in this publication.
DOI: 10.5061/dryad.668g444/4
title: Asha_G.tar.gz

description: Sample unprocessed simulation output from an experiment with a DMI (see README for experiment name key).
DOI: 10.5061/dryad.668g444/5
title: Benjen_S.tar.gz

description: Sample unprocessed neutral simulation output (see README for experiment name key).
DOI: 10.5061/dryad.6jg5g/2
title: PCA and OPLS-DA data

description: This is a simca-p type file, which contain the relavant parameters of PCA and OPLS-DA models.
DOI: 10.5061/dryad.6k939m4/3
title: ArthropodTrophicGroup_BirdExpe_Dec2014

description: Mean body length (in mm), developmental stage and trophic group of arthropod morpho-species collected on the vegetation at Jonkershoek on December 2014 for a "bird exclosure" experiment.
DOI: 10.5061/dryad.6k939m4/4
title: ExpeDesign_BirdExpe_Dec2014

description: Treatment, site and slope factors; experimental design of a "bird exclosure" experiment conducted at Jonkershoek on December 2014.
DOI: 10.5061/dryad.6k939m4/5
title: PlantCovers_m2_BirdExpe_Dec2014

description: Cover (in m2) per quadrat for plant morpho-species sampled at Jonkershoek on December 2014 for a "bird exclosure" experiment.
DOI: 10.5061/dryad.6k939m4/6
title: PlantTaxonomy_BirdExpe_Dec2014

description: Taxonomy of plants sampled at Jonkershoek on December 2014 for a "bird exclosure" experiment.
DOI: 10.5061/dryad.6k939m4/7
title: Script_BirdExpe_Ecology

description: R script
DOI: 10.5061/dryad.6k94r/1
title: Mitochondrial sequences

description: Mitochondrial sequences of 463 B. treatae individuals
DOI: 10.5061/dryad.6k94r/2
title: Wolbachia Sequences

description: Sequences of 260 Wolbachia infected B. treatae samples
DOI: 10.5061/dryad.6k94r/3
title: Cloning Sequences

description: Sequences files from 286 cloned plasmids.
DOI: 10.5061/dryad.6k94r/4
title: sample overview

description: Overview of sample codes and Wolbachia infection status of all B. treatae individuals
DOI: 10.5061/dryad.7mc7r30/1
title: Cascade Experiment Data

description: Results from the mesocosm experiment on Chl-a.
DOI: 10.5061/dryad.7mc7r30/2
title: FishExperimentData

description: Results of survivorship trials and behaviors of survivors per fish treatment.
DOI: 10.5061/dryad.7mc7r30/3
title: LatencyAnalysis

description: Data used in the latency analysis regressing time since exposure to fish predators on behavioral traits.
DOI: 10.5061/dryad.8sp77v5/1
title: Drayd species and lake conditions 4 Aug

description: Limnological field data from lakes samples and species counts from all samples.
DOI: 10.5061/dryad.9pq541j/1
title: DATA Dryad Zheng et al, Functional Ecology

description: The original data collected in the field and laboratory for the paper of "Arbuscular mycorrhizal fungal communities associated with two dominant species differ in their responses to long-term nitrogen addition in temperate grasslands"
DOI: 10.5061/dryad.bv2g720/1
title: Tar ball of genome .fq files of Mustela erminea (N=10)

description: Tar ball of genome ,fq files of Mustela erminea, representing specimens from Museum of Southwestern Biology (MSB) with catalog number: 152905 (ME01), 221783 (ME02), 199855 (ME03), 43333 (ME04), 145234 (ME05), 148962 (ME06), 149365 (ME07), 144524 (ME08), 215111 (ME09), 248153 (ME10).
DOI: 10.5061/dryad.bv2g720/9
title: Tar ball of mitochondrial genome .fq files of Mustela erminea (N=10)

description: Tar ball of mitochondrial genome ,fq files of Mustela erminea, representing specimens from Museum of Southwestern Biology (MSB) with catalog number: 152905 (ME01), 221783 (ME02), 199855 (ME03), 43333 (ME04), 145234 (ME05), 148962 (ME06), 149365 (ME07), 144524 (ME08), 215111 (ME09), 248153 (ME10).
DOI: 10.5061/dryad.ck75b2d/1
title: Matrix population models
DOI: 10.5061/dryad.ft3k3/10
title: Nuclear PartitionFinder best scheme for RAxML

description: PartitionFinder best scheme for running RAxML on the nuclear dataset
DOI: 10.5061/dryad.ft3k3/11
title: Nuclear MrBayes consensus tree

description: Bayesian consensus tree for 7 nuclear exons inferred with MrBayes under a partitioned model as estimated by PartitionFinder
DOI: 10.5061/dryad.ft3k3/12
title: Nuclear PartitionFinder best scheme for MrBayes

description: PartitionFinder best scheme for running MrBayes on the nuclear dataset
DOI: 10.5061/dryad.ft3k3/13
title: Nuclear PhyloBayes consensus tree

description: Bayesian consensus tree for 7 nuclear exons inferred with PhyloBayes under the CAT-GTR+G4 mixture model. This phylogram corresponds to Figure 2b.
DOI: 10.5061/dryad.ft3k3/14
title: Nuclear PhyloBayes chronogram

description: Bayesian chronogram for 7 nuclear exons inferred with PhyloBayes under the CAT-GTR+G4 mixture model and a autocorrelated lognormal relaxed molecular clock. The file in nexus format can be opened in FigTree and corresponds to Figure 3b.
DOI: 10.5061/dryad.ft3k3/15
title: Mylo_7exons_Final_bait_set

description: Final set of 4,381 baits of 80nt length used to capture the seven nuclear exons
DOI: 10.5061/dryad.ft3k3/8
title: Nuclear dataset

description: Concatenation of 7 nuclear exons for 28 xenarthran taxa
DOI: 10.5061/dryad.ft3k3/9
title: Nuclear RAxML tree

description: Maximum likelihood tree for 7 nuclear exons inferred with RAxML under a partitioned model as estimated by PartitionFinder
DOI: 10.5061/dryad.gk661/1
title: experiment data
DOI: 10.5061/dryad.hr804/1
title: 75oC 4hrs12

description: ZnO nanorods
DOI: 10.5061/dryad.hr804/2
title: 75oC 4hrs13

description: ZnO nanorods
DOI: 10.5061/dryad.k6r1mk8/1
title: BLUPS

description: BLUPS for the four phenotypic traits studied. Each row corresponds to one individual.
DOI: 10.5061/dryad.k6r1mk8/2
title: plink bfiles

description: Plink files (bed, bim, fam) containing genomic data for the 494 individuals.
DOI: 10.5061/dryad.k6r1mk8/3
title: PED-social

description: Pairwise relatedness obtained from social pedigree.
DOI: 10.5061/dryad.k6r1mk8/4
title: Phenotypic traits

description: Phenotypic traits for the genotyped individuals.
DOI: 10.5061/dryad.m371v/3
title: Alignment files

description: Multiple sequence alignments, containing files 2-13 (described fully in README file).
DOI: 10.5061/dryad.m371v/4
title: Phylogenetic tree topologies

description: Phylogenetic tree topologies, containing files 14-23 (described fully in README file).
DOI: 10.5061/dryad.m371v/5
title: Divergence time estimates

description: Divergence time estimates, containing files 24-53 (described fully in README file).
DOI: 10.5061/dryad.m371v/6
title: Supplemental results

description: Supplemental results, containing files 54-56 (described fully in README file).
DOI: 10.5061/dryad.m371v/7
title: Effective prior files

description: Files related to the effective prior runs, containing files 57-68, related to Fig S8 in the paper (described fully in README file).
DOI: 10.5061/dryad.pf1gt/2
title: CBC reference values obtained from a healthy adult black population in Kenya

description: This data file contains reference values for CBC parameters obtained from healthy adults living in selected urban towns in Kenya. The original study was carried out by the committee of reference intervals and decision limits under the International Federation of Clinical Chemistry. We collected additional data for CBC parameter so as to determine reference intervals for our Kenyan adult population using various statistical techniques.
DOI: 10.5061/dryad.r8gd0pg/1
title: Species establishment, native status and endangerement in the Berlin flora 1990

description: The file includes data on species establishment, native status and endangerement of 1199 plant species of the Berlin flora in 1990. It is an exerpt from two original sources: a.) for endangerement: Böcker R, Auhagen A, Brockmann H, Kowarik I, Scholz H, Sukopp H, Zimmermann F (1991) Liste der wildwachsenden Farn- und Blütenpflanzen von Berlin (West) mit Angaben zur Gefährdung der Sippen, zum Zeitpunkt ihres ersten spontanen Auftretens und zu ihrer Etablierung im Gebiet sowie zur Bewertung der Gefährdung. Landschaftsentwicklung und Umweltforschung, S6, 57–88.; b.): for all other data: Kowarik I (1991) Berücksichtigung anthropogener Standort- und Florenveränderungen bei der Aufstellung Roter Listen. In: Auhagen A, Platen R, Sukopp H (Eds., 1991) Rote Listen der gefährdeten Pflanzen und Tiere in Berlin 1990. Landschaftsentwicklung und Umweltforschung, S6, 25-56.
DOI: 10.5061/dryad.s1v3801/1
title: Code for paper

description: This is a zip file that contains all of the code needed to run the simulations described in our paper, and everything needed to analyze it and recreate the figures. It includes a README.
DOI: 10.5061/dryad.t285760/1
title: Manuscript Data Embedded in SAS-ready Analysis Code.txt
DOI: 10.5061/dryad.t285760/3
title: Manuscript data embedded in SAS-ready analysis code
DOI: 10.17632/dzxj94ys3g.1
title: Data for: Detecting the effects of management regime shifts in dynamic environments using multi-population state-space models

description: All data used in Model A. These data designed to work with the JAGS code provided in Supplement 1 of the manuscript.
DOI: 10.17632/fhrnkn7pbc.1
title: Data for: Depression and Telomere Length in Colorectal Cancer Patients in Saudi Arabia

description: Dataset for depression and telomere analysis
DOI: 10.5061/dryad.221mq23/1
title: ASI_software

description: Zip file containing ASI software (Matlab scripts and functions).
DOI: 10.5061/dryad.23d8v/4
title: LOCO RepeatABEL R script

description: Implements a leave-one-chromosome-out GWAS using RepeatABEL
DOI: 10.5061/dryad.23d8v/5
title: RepeatABEL GWAS R script

description: Conducts a vanilla GWAS using RepeatABEL
DOI: 10.5061/dryad.23d8v/7
title: Field Data

description: Phenotypes for adult polar bears used for heritability calculations and GWAS
DOI: 10.5061/dryad.2q8m903/1
title: First Image Dataset

description: First replicate image dataset (50 images). Includes also 1) UAV flight log (can be viewed with the software MissionPlanner), 2) CSV file detailing image coordinates and attitude and 3) xml files containing A) ground control point information, B) image coordinates (image number and where in image a given ground control point can be seen).
DOI: 10.5061/dryad.2q8m903/3
title: Second Image Dataset

description: Second replicate image dataset (50 images). Includes also 1) UAV flight log (can be viewed with the software MissionPlanner), 2) CSV file detailing image coordinates and attitude and 3) xml files containing A) ground control point information, B) image coordinates (image number and where in image a given ground control point can be seen).
DOI: 10.5061/dryad.2q8m903/4
title: Radial Extended MICMAC Second Image Dataset

description: SfM+MVS point cloud generated from the second replicate image dataset.
DOI: 10.5061/dryad.2q8m903/5
title: Third Image Dataset

description: Third replicate image dataset (50 images). Includes also 1) UAV flight log (can be viewed with the software MissionPlanner), 2) CSV file detailing image coordinates and attitude and 3) xml files containing A) ground control point information, B) image coordinates (image number and where in image a given ground control point can be seen).
DOI: 10.5061/dryad.2q8m903/6
title: Radial Extended MICMAC Third Image Dataset

description: SfM+MVS point cloud generated from the third replicate image dataset.
DOI: 10.5061/dryad.2q8m903/7
title: Sward height correlation plots

description: Estimated sward height (SfM+MVS-based pipeline) compared to in-situ measurments of sward height using traditional agronomic techniques. These figures are the basis for the section COMPARISON OF MULTIPLE METHODS.
DOI: 10.5061/dryad.2q8m903/8
title: Relevant CSV files

description: Includes e.g. DSM as generated from SfM+MVS-based pipeline, validation DSM, validation DTM.
DOI: 10.5061/dryad.3323617/1
title: Experiment1

description: Data for experiment 1.  To test how rhizobia and nematodes impact fitness in co-infected plants, and to measure genetic variation in nematode infectivity, we used a fractional factorial design with a total of 400 M. truncatula plants from 10 genotypes across 10 blocks. We inoculated each plant with 1 of 40 nematode genotypes. Each block included 4 replicates of each plant genotype and 1 replicate of each nematode genotype, for a total of 40 replicates of each plant genotype and 10 replicates of each nematode genotype. Each nematode genotype inoculated 2 different plant genotypes, for a total of 5 replicates per nematode genotype-plant genotype combination.
DOI: 10.5061/dryad.3323617/2
title: Experiment2

description: Data for experiment 2. To measure genetic conflict between attracting rhizobia and repelling nematodes, and to test how parasitic nematodes impact the rhizobia mutualism, we used a split-plot randomized design. Each block contained two treatments: one in which we only inoculated plants with rhizobia, and one in which we inoculated plants with both rhizobia and nematodes. Plants received a total of 400 nematode eggs from a genetically variable nematode inoculum. Each treatment in each block contained one M. truncatula individual from each of 50 genotypes. We replicated this design across 10 blocks (50 plants per treatment per block × 2 treatments × 10 blocks = 1000 plants).
DOI: 10.5061/dryad.3323617/3
title: GenotypeMeans_NodulesAndGalls

description: Data used to estimate the genetic correlation between nodule and gall production.To estimate genotype means for gall number, we extracted the conditional modes of the genotype random effect from a model that included fixed effects of root mass and researcher, and random effects of genotype and block. We used estimates of nodulation from the rhizobia-only treatment to estimate the genetic correlation with gall formation. We estimated genotype means for nodule number using a model similar to the gall model, and specified a negative binomial error distribution and allowed for zero inflation in both models. We also estimated the genetic correlation between gall number and the change in nodule number between the two treatments. We estimated genotype means for nodule number in nematode-infected plants using a similar model to the one used to estimate nodule number in the rhizobia-only treatment. We subtracted the genotype mean for nodule number in nematode-infected plants from the genotype mean for nodule number in uninfected plants to calculate the change in nodule number for each genotype.
DOI: 10.5061/dryad.3323617/4
title: DataAnalysis

description: This R script contains the code used to run all the analyses presented in our manuscript.  It relies on one other script ("checkAssumptions.R") to check statistical assumptions.
DOI: 10.5061/dryad.3323617/5
title: Check regression assumptions

description: This script contains functions to check regression assumptions (normality, linearity, homoscedasticity) and calculate variance inflation factors
DOI: 10.5061/dryad.42n44/1
title: 10%susceptible

description: Time-lapse images of spread of T7 phage epidemics in Escherichia coli spatially structured populations over 48 hours. Archive contains images of the following treatment: 10% susceptible, 90% resistant cells.