cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5st8m/5
title: Phylogeny of lizard subfamily Phrynosomatinae

description: File containing phylogeny of lizard subfamily Phrynosomatinae. Phylogeny data from Harmon LJ, Losos JB, Davies TJ, Gillespie RG, Gittleman JL, Bryan Jennings W, Kozak KH, McPeek MA, Moreno-Roark F, Near TJ, Purvis A, Ricklefs RE, Schluter D, Schulte II JA, Seehausen O, Sidlauskas BL, Torres-Carvajal O, Weir JT, Mooers AØ (2010) Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. https://doi.org/10.5061/dryad.f660p
DOI: 10.5061/dryad.60n75dd/1
title: Number of individuals

description: Number of individuals collected for each altitude and month for all Empidinae
DOI: 10.5061/dryad.60n75dd/2
title: Number of species

description: Number of species collected for each altitude and month for all Empidinae. The numbers given in the columns and rows "Total" correspond to the total numbers of different species collected
DOI: 10.5061/dryad.61c6n05/1
title: Johnson et al RAW DATA

description: This CVS file individual dissection data
DOI: 10.5061/dryad.77hk7/4
title: Number of spores across different environments

description: Number of spores in each individual fruiting body (column 4: Logspores) per strain (column 2: Strain) in each environment(column 3: Env) per experiment (column 1: Exp)
DOI: 10.5061/dryad.7qs70/1
title: BMR, Hct, Hb, Glucose

description: Repeated measures of BMR, Hct, Hb, glucose across 3 timepoints
DOI: 10.5061/dryad.7t3s4/1
title: dryadData

description: Individual information of bighorn sheep ewes used for path analysis.
DOI: 10.5061/dryad.83bs4jd/4
title: Basic data

description: Fundamental data for the analysis of the manuscript
DOI: 10.5061/dryad.83bs4jd/5
title: Data 1

description: Data for the funnel plots
DOI: 10.5061/dryad.90kp2/1
title: ATSP
DOI: 10.5061/dryad.90kp2/2
title: Counts2sp
DOI: 10.5061/dryad.90kp2/3
title: NDVI_200
DOI: 10.5061/dryad.90kp2/4
title: NDVI_250
DOI: 10.5061/dryad.90kp2/5
title: pcovariates
DOI: 10.5061/dryad.90kp2/6
title: SAVS
DOI: 10.5061/dryad.96tt4/1
title: 160704_11loc_30pop_ImoriChugoku_structure_dryad

description: STRUCTURE file for 11 microsatellite loci
DOI: 10.5061/dryad.97cc8/1
title: simuHybrid_hybrids_w_geneflow_disperseArchi

description: Python script for simulating populations of hybrids subject to selection as a function of their genotype at two types of loci. Loci are arranged in the "dispersed architecture".
DOI: 10.5061/dryad.97cc8/2
title: simuHybrid_hybrids_w_geneflow_intersperseArchi

description: Python script to simulate populations of hybrids subject to selection on loci arranged in the "interspersed genetic architecture"
DOI: 10.5061/dryad.97cc8/3
title: simuHybrid_hybrids_w_geneflow_modularArchi

description: Python script to simulate populations of hybrids subject to selection on loci arranged in the "modular genetic architecture"
DOI: 10.5061/dryad.cq63m/10
title: phylip files for each dataset

description: Phylip format files for all 6 datasets.
DOI: 10.5061/dryad.cq63m/8
title: Table_S1

description: Gene and taxon coverage for dataset ‘i’ with species name, rogue taxa selection list for all 6 datasets.
DOI: 10.5061/dryad.cq63m/9
title: ML_tree_files

description: Maximum Likelihood bipartitions tree files for Supplementary Figs. S1-S7.
DOI: 10.5061/dryad.d1240.2
title: Data from: A century of changing flows: forest management changed flow magnitudes and warming advanced the timing of flow in a southwestern US river
DOI: 10.5061/dryad.d1240.2/5.2
title: Salt River Data Sources

description: List of data sources and data files
DOI: 10.5061/dryad.d1240.2/6.2
title: Salt River Historic and Current Forest Conditions

description: Historical and current estimates of conditions of ponderosa pine forests in the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d1240.2/7.2
title: 1916-2012 Salt River Forest Water Use History

description: Estimates of historical forest management and human water demand within the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d1240.2/8.2
title: 1914-2012 Salt River Climate

description: Monthly precipitation, temperature and potential evapotranspiration estimates from 1914-2012 for the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d8p78.1
title: Data from: Learning of salient prey traits explains Batesian mimicry evolution
DOI: 10.5061/dryad.d8p78.2/4.2
title: Color proportion measurements of butterfly wings
DOI: 10.5061/dryad.d8p78.2/5.2
title: Script to analyze discrimination learning data
DOI: 10.5061/dryad.d8p78.2/6.2
title: Script to analyze generalization test data
DOI: 10.5061/dryad.d8p78.2/7.2
title: Script to analyze salience test data
DOI: 10.5061/dryad.d8p78.2/8.2
title: Script to analyze wing data
DOI: 10.5061/dryad.d8p78.2/9.2
title: README
DOI: 10.5061/dryad.h70j3/1
title: Data indicating tree collapse over an 18 year period

description: Data for 737 trees showing their form in 1997 and again in 2015, along with landscape level covariates. Euclidean Nearest Neighbour Distance, and Interspersion & Juxtaposition Index metrics are derived from FragStats.
DOI: 10.5061/dryad.jt2jr03/1
title: Genome sizes of individual Chenopodium album aggregate species from Iran.

description: Genome sizes of individual Chenopodium album aggregate species from Iran. Population codes are taken from Table S1.
DOI: 10.5061/dryad.jt2jr03/2
title: Analysed morphological characters in Chenopodium album aggregate species from Iran.

description: Analysed morphological characters in Chenopodium album aggregate species from Iran. PL - Petiole length, LL - Lamina length, LW - Lamina width, TA - Tip angle of leaf, BA - Base angle of leaf, WV - Length from tip to widest point of the leaf (along the central vein), W1/2 - Lamina width in 1/2 of lamina length, C - Circularity of lamina, A - Area of lamina, A/A_reduced - Area of lamina/Area of lamina without teeth, PL/LL - Petiole length/Lamina length, LW/LL - Lamina width/Lamina length, WV/LL - Length from tip to widest point of the leaf/Lamina length, W1/2/LW - Lamina width in 1/2 of lamina length/Lamina length, area/LW - Area of lamina/Lamina width.
DOI: 10.5061/dryad.km42m/1
title: Review of riverine ecosystem service quantification studies

description: This file contains a database of studies that quantified riverine ecosystem services prior to April 2016, as well as quantitative data on the location of each study, the types and numbers of ecosystem services evaluated, and the methods used to quantify services.
DOI: 10.5061/dryad.m7m8n/1
title: model data

description: All numeric variables have been scaled and centered around zero.
DOI: 10.5061/dryad.q70b05k9/4
title: mtDNA used in combined analysis

description: Nexus file containing both mitochondrial  12S, 16S rRNA, NADH4 gene sequences and binary data from 298 polymorphic AFLP loci, for 36 specimens from which both sets of data were available. This was used to construct the combined mtDNA-SFLP tree.
DOI: 10.5061/dryad.r5f70/1
title: Supplementary Material

description: Supplementary Material including Figures and Table.
DOI: 10.5061/dryad.r5f70/2
title: Carnivora Fossil and Pylogenetic Empirical Data

description: The folder “empirical_data” contains the empirical data used for estimating age-dependent extinction processes. 
The folder “fossil_ Pires_et_al_2015” stores fossil data of Carnivora from the Northern Hemisphere compiled and cleansed by Pires et al. (2015). Inside the folder, “all_carnivora_SpeciesList.txt” provides a species list with extinct or extant status. The file “all_carnivora.py” is a ready for PyRate input file of the fossil data set, for more information please refer to PyRate help literature provided at https://github.com/dsilvestro/PyRate/wiki. The files “all_carnivora_combined_10_files.log” and “all_carnivora_Neogene_combined_10_files.log” are the outputs from the PyRate runs of the 10 replicated data sets for the entire fossil data set and the data set for the fossils found during the Neogene (see Fig2 for a schematic workflow).
The folder “phylogenetic_Nyakatura_Bininda-Emonds_2012” stores the dated phylogeny of 286 species extant carnivores, with crown age at about 65 Ma build by Nyakatura and Bininda-Emonds (2012)
References
- Pires M.M., Silvestro D., Quental T.B. 2015. Continental faunal exchange and the asymmetrical radiation of carnivores. Proc. R. Soc. Biol. Sci. Ser. B 282.
- Nyakatura K., Bininda-Emonds O.R.P. 2012. Updating the evolutionary history of carnivora (mammalia): A new species-level supertree complete with divergence time estimates. Bmc Biol 10.
DOI: 10.5061/dryad.r5f70/3
title: Fossil Simulations

description: The folder “fossil_simulations” contains the R and Python scripts used for the fossils simulation study. 
The folder “1.simulators” contains the R scripts adapted from (Hagen and Stadler 2014) used to simulate the initial complete phylogenies. “SimulatorScenarioIandII_ConstantOverTime.R” was used for simulating scenarios I and II, “SimulatorScenarioIII_2TimeBin.R” was used for simulating scenario III and “SimulatorScenarioIV_2TimeBin_BIGDROP.R” was used for simulating scenario IV. Please note that these files require the parameters given at “parametersage.csv” and generated by the scripts “Parametersage_Generator.R” found respectively inside each scenario folder. Please change the working directories before running the scripts.
To generate fossil data from the phylogenies the script “2.FossilSamplerRunOverFolder.py” was run, evoking “fossil_sampler.py” for all fossils inside the respective scenario. The script “3.GetPyRateEstimatesRunOverFolders.py” automates a PyRate estimation while “4.PlottingScenarios.R” is used for visualizing the result. “SummarySimulations.RData” summarizes the results and analysis conducted. Each scenario folder also contains a “summary_ScenarioX.csv” file recording the number of: sampled species, singletons, simulated extinct species, simulated extant species, fossil occurrences and several other returned values from PyRate.
References
- Hagen O., Hartmann K., Steel M., Stadler T. 2015. Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies. Syst Biol. 64 (3): 432-440. doi: 10.1093/sysbio/syv001.
- Hagen O., Stadler T. 2017. Treesimgm: Simulating phylogenetic trees under general bellman harris models with lineage-specific shifts of speciation and extinction in r. Methods Ecol. Evol. in press.
DOI: 10.5061/dryad.r5f70/4
title: Simulation of Morphospecies

description: Script used to measure the effect of anagenesis on the estimation of true ADE shape parameter (Supplementary Material Fig. S6).
DOI: 10.5061/dryad.s5n3c/3
title: ecorisk_ebm
DOI: 10.5061/dryad.v2g01/1
title: Mcav microbiome 16S assembly

description: Assembled reads for 16S pyrosequencing following quality filtering, chimera removal, and clustering at 97% similarity.
DOI: 10.5061/dryad.v2g01/2
title: Symbiodinium ITS2 Sanger reads

description: Sanger sequencing reads for 107 clones recovered from PCR amplification of ITS2 amplicons from Montastrea cavernosa samples.
DOI: 10.5061/dryad.v2g01/3
title: Metatranscriptome assembly filtered annotated

description: Transcripts from Montastrea cavernosa metatranscriptome following assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.
DOI: 10.5061/dryad.v2g01/4
title: Symbiodinium transcriptome filtered annotated

description: Transcripts classified as Symbiodinium following holobiont transcriptome assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.
DOI: 10.5061/dryad.v2g01/5
title: Mcav transcriptome assembly filtered annotated

description: Transcripts classified as Montastrea cavernosa following holobiont transcriptome assembly with Trinity/BinPacker/Tranfuse, BLAST-filtering, and annotation with Dammit.
DOI: 10.5061/dryad.v2g01/6
title: Symbiodinium transcript annotations GFF3

description: Annotation results for Symbiodinium transcripts output by Dammit
DOI: 10.17632/3s4yzj3vkk.1
title: Data for: Introduction to liquid crystals

description: Python notebooks provided with the pedagogical overview of liquid crystals
DOI: 10.17632/t2rbsbc2h6.1
title: Data for: Cut-off frequencies of circumferential horizontal shear waves in various functionally graded cylinder shells

description: The program is Maple 14 file. The relation between the cut-off frequencies and the gradient parameter are calculated based on the program.
DOI: 10.5061/dryad.08v2c/1
title: data
DOI: 10.5061/dryad.127g7/1
title: BITR-17-051 Data Suazo-Ortuño et al.

description: The data base contains all original field data of each sampling site. The data base includes the name of the sampling site, the name of all species registered as well an number of individuals at each of the surveys.
DOI: 10.5061/dryad.12g6g/1
title: Supporting information files

description: Data file includes the analysis outputs of tables, chart and graphs to support the accepted research article.
DOI: 10.5061/dryad.1726j.2
title: Data from: The influence of climatic variability on morphological integration, evolutionary rates, and disparity in the Carnivora
DOI: 10.5061/dryad.1726j.2/1.2
title: R Scripts, TPS files, tree, and raw data

description: Zip file contains all the raw data (in csv format), jaw landmark data (in TPS format), the tree (in Newick format), and R scripts to perform all analyses described in the main text.
DOI: 10.5061/dryad.2gj34rk/1
title: final_farmer_auction_dataset_Palm-Forster

description: The file “final_farmer_auction_dataset_Palm-Forster.xlsx” consists of two worksheets that contain: (1) data on farmer preferences for conservation incentives based on bids for different types of incentive contracts in an economic experiment; and (2) a code book with the description, type, units, and range of values for each variable in the data. The  README file contains the Stata code used in the analysis of data in “final_farmer_auction_dataset_Palm-Forster.xlsx”.
DOI: 10.5061/dryad.2gj34rk/2
title: final_farmer_auction_analysis_Palm-Forster

description: The file “final_farmer_auction_analysis_Palm-Forster.dta” is a Stata data file (.dta) that contains data on farmer preferences for conservation incentives based on bids for different types of incentive contracts in an economic experiment. The code book for this file can be found in the Excel worksheet - the code book includes the description, type, units, and range of values for each variable in the data. The README file contains the Stata do file (.do) used in the analysis of data in “final_farmer_auction_analysis_Palm-Forster.dta”.
DOI: 10.5061/dryad.4c6t3/1
title: nex file for phylogeny reconstruction
DOI: 10.5061/dryad.4c6t3/2
title: Tree file
DOI: 10.5061/dryad.4c6t3/3
title: FIG. S1. A specimen with collection number J. Cavalerie 2038 in the herbarium at Royal Botanic Garden Edinburgh (E 00414276)
DOI: 10.5061/dryad.4c6t3/4
title: FIG. S2. A specimen with collection number J. Cavalerie 2038 in the herbarium at New York Botanical Garden (NY00127508)
DOI: 10.5061/dryad.4c6t3/5
title: FIG. S3. Lectotype of Pteris parviloba Christ in the herbarium at Royal Botanic Garden Edinburgh (E 00414277)
DOI: 10.5061/dryad.4k40j/1
title: Lib5_Run1_Index12_S4_L001_R2_001.fastq

description: gzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 12; Read 2
DOI: 10.5061/dryad.4k40j/2
title: Lib5_Run1_Index12_S4_L001_R1_001.fastq

description: gzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 12; Read 1
DOI: 10.5061/dryad.4k40j/3
title: Lib5_Run1_Index6_S3_L001_R2_001.fastq

description: gzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 6; Read 2
DOI: 10.5061/dryad.4k40j/4
title: Lib5_Run1_Index6_S3_L001_R1_001.fastq

description: gzipped tar file containing Illumina sequence data from: Library 5 (first run); Index 6; Read 1
DOI: 10.5061/dryad.6m4c1/1
title: Stevenson et al. 2018 Flooding_Biotropica

description: Matrix of species and plots used in the analyses. Numbers in the matrix represent the number of individual (DBH&gt; 10 cm.).
DOI: 10.5061/dryad.7m3dq/1
title: Stomach contents and morphological measurements of newts

description: Contains stomach contents (as numerical abundance), total ingested dry mass, snout-vent length and body mass of each newt.
DOI: 10.5061/dryad.7qs70/2
title: Glycerol, Triglyceride and Oxidative stress

description: Measurements of Glycerol, Triglyceride and Oxidative stress
DOI: 10.5061/dryad.7qs70/3
title: Body composition
DOI: 10.5061/dryad.83bs4jd/6
title: Data 2

description: Data for the effect size. In this data table, the data from the authors, Dobay et al. were deleted because their data showed no events both in antibiotics and control group.
DOI: 10.5061/dryad.90kp2/7
title: Appendix_S3
DOI: 10.5061/dryad.98q55/1
title: Kobuvirus time-scaled tree mapping with host traits

description: Maximum Clade Credibility (MCC) tree representing the time-scale phylogeny of kobuvirus from all hosts based on the VP1 gene (n=416). Tree was genereated using Beast V1.8.2.The best fitting model was a general time-reversible (GTR) model with a gamma distribution (G) across sites as the substitution model, with an uncorrelated log-normal relaxed molecular clock model and with a constant size coalescent process prior over the phylogenies. The MCMC chains were run for 100 million iterations with sub-sampling every 10,000 iterations and 10% burn-in.we applied a strong prior of substitution rate using a normal distribution (mean rate = 2×10-3 substitutions/site/year; Standard Deviation =5×10-4).An asymmetric model with Bayesian Stochastic Search Variable selection (BSSVS) was applied to identify statistically significant transition rates between host species and geographic locations.The tree file was viewed and edited in Figtree V1.4.2.
DOI: 10.5061/dryad.99dc0/1
title: Studies applying Community Level Models

description: Summary table of empirical studies applying Community Level Models (CLMs). The studies have been grouped by CLM algorithm.
DOI: 10.5061/dryad.99dc0/3
title: Community Level Modeling vignette

description: Rmarkdown file with code for the Community Level Modeling tutorial: Fitting multispecies models in R
DOI: 10.5061/dryad.9sn26/1
title: Decomposition_chemistry_microbial_McTee

description: These data include soil temperature, pH, and decomposition rates of root and shoot litter placed in the field. It also includes Terminal restriction fragment length polymorphism (T-RFLP) of fungi and bacteria that inhabited the litter. The file includes seven sheets. The TRFLP data that is suffixed with "fun" in the sheet name means that plant species were grouped based on whether they were a forb or grass. We provide a supplement in the manuscript that includes code for different analyses using R Software.
DOI: 10.5061/dryad.d1240.1
title: Data from: A century of changing flows: forest management changed flow magnitudes and warming advanced the timing of flow in a southwestern US river
DOI: 10.5061/dryad.d1240.1/10.1
title: 1914_2012 SaltRiverChangeMagnitudesFlowClimate Apr 2017

description: Estimated magnitudes of change in monthly flows in Salt River near Roosevelt, Arizona from 1914-2012.
DOI: 10.5061/dryad.d1240.1/5.1
title: SaltRiverDataSources Apr2017

description: List of data sources and data files
DOI: 10.5061/dryad.d1240.1/6.1
title: SaltRiverHistoricCurrentForestConditions Apr 2017

description: Historical and current estimates of conditions of ponderosa pine forests in the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d1240.1/7.1
title: 1916_2012 SaltRiverForestWaterUseHistory Apr 2017

description: Estimates of historical forest management and human water demand within the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d1240.1/8.1
title: 1914_2012 SaltRiverClimate Apr 2017

description: Monthly precipitation, temperature and potential evapotranspiration estimates from 1914-2012 for the Salt River watershed in central Arizona.
DOI: 10.5061/dryad.d1240.2/10.2
title: 1914-2012 Salt River Magnitudes of Change in Flow Climate

description: Estimated magnitudes of change in monthly flows in Salt River near Roosevelt, Arizona from 1914-2012.
DOI: 10.5061/dryad.d1240.2/11.2
title: 1914-2012 Salt River Changes in Flow Timing

description: Changes in timing of peak spring flows in Salt River near Roosevelt, Arizona.
DOI: 10.5061/dryad.d1240.2/9.2
title: 1914-2012 Salt River Streamflow

description: Monthly flows and trend estimates from 1914-2012 for the Salt River near Roosevelt in central Arizona.
DOI: 10.5061/dryad.f1h1t/1
title: Ketz_et_al_2018_RMNP_Data.zip

description: The zipped folder contains all data used for the analysis, including 12 comma separated value files, that are to be used with the R code provided in the supplemental materials DataS1 and DataS2.
DOI: 10.15468/dl.ubxeck
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hyloxalus anthracinus (Edwards, 1971))",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087838-240626123714530/datasets/export for details.
DOI: 10.15468/dl.pbxp5m
title: Occurrence Download

description: A dataset containing 1960 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Aleucis distinctata (Herrich-Schäffer, 1839)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1960 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087837-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phft9b
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Sitophilus zeamais Motschulsky & V.de, 1855",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 230 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087839-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hutzd9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ectopoglossus atopoglossus (Grant, Humphrey & Myers, 1997))",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 100",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087841-240626123714530/datasets/export for details.