cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4k40j/33
title: Sample Information for demultiplexing

description: A text file containing the following columns: Library number, Index number, barcode, sample name.  Those sample names with a trailing "_1" or "_2" indicate the same individual that was incorporated more than once into the prepared libraries.  Each of these sample replicates was run with distinct barcodes, but the resulting fastq files were eventually combined for downstream population genomic analysis.
DOI: 10.5061/dryad.505d9/1
title: Massloss of root mixtures in a subtropical forest

description: Here, we used a field experiment in a subtropical forest to investigate how species richness in root litter mixtures (air-dried fresh fine roots) affects the decomposition of root litter material. The data are the root massloss of multiple species mixtures.
DOI: 10.5061/dryad.505d9/2
title: Initial root chemicals in a subtropical forest

description: Here, we used a field experiment in a subtropical forest to investigate how species richness in root litter mixtures (air-dried fresh fine roots) affects the decomposition of root litter material. The data are the initial chemicals of these root materials.
DOI: 10.5061/dryad.7bj0f/1
title: hellbender_spleen_contigs
DOI: 10.5061/dryad.7j83s.1
title: Data from: Primate diversification inferred from phylogenies and fossils
DOI: 10.5061/dryad.7j83s.1/1.1
title: Raw data on fossil taxonomy and ages

description: Raw data on fossil taxonomy, first and last appearance dates (FAD, LAD, respectively), and number of occurrences, with ages and references from PBDB and the literature search performed in this study.
DOI: 10.5061/dryad.7j83s.1/2.1
title: Table S4. PBDB raw data

description: Raw data and references downloaded from Paleobiology Database
DOI: 10.5061/dryad.7j83s.1/3.1
title: R code for Herrera Primate diversification

description: R code to run RPANDA phylogenetic diversification analysis, and fossil data preparation for PYRATE as well as analyses with PALEOTREE
DOI: 10.5061/dryad.7j83s.1/4.1
title: Phylogenetic trees from Springer et al. 2012

description: Raw tree files of four phylogenetic trees from Springer et al. 2012 for all primates with different age calibration assumptions
DOI: 10.5061/dryad.7j83s.2/4.2
title: Phylogenetic trees from Springer et al. 2012

description: Raw tree files of four phylogenetic trees from Springer et al. 2012 for all primates with different age calibration assumptions
DOI: 10.5061/dryad.7j83s.2/5.2
title: Table S1. Model fit results

description: Table S1. Full results of RPANDA model comparisons with four different time-calibrated trees.
DOI: 10.5061/dryad.7j83s.2/6.2
title: Supplementary Materials

description: Appendix to accompany the manuscript: Primate diversification dynamics inferred from fossils and phylogenies.
DOI: 10.5061/dryad.85t2hr9/1
title: HIV_data_child
DOI: 10.5061/dryad.8m0p1/2
title: rasterstack4cov

description: This is the a raster stack of the three covariates (bio_2, bio_3 & snow) used in making the winter white probability maps. It is needed to run the R script.
DOI: 10.5061/dryad.8m0p1/3
title: global_phenology_final_script

description: This is the R script associated with the analyses from this publication. Note in order to make species maps you need to download and read into R their range maps from the IUCN red list website: http://www.iucnredlist.org/
DOI: 10.5061/dryad.9m84np6/1
title: Appendix 1 - Owl verebrate prey taxa in the souther Levant per site

description: These are the raw data of the vertebrare prey taxa and abundances (as minimum number of individuals) of owl species in Israel, The West Bank and Golan Heights, as inferred from their pellets and bone accumulations at nesting and roosting sites. Some sites were visited more than once and data were pooled. Most data are from the years 2013-2015, but some are from museum pellets and date to 1980's-2000's. Please contact the authors if you need detailed information regarding the dates of collection. Coordinates were removed in order to prevent harassment to the owls. "Prey with mass" relates to prey taxa for which we assigned mass from the literature for the predator-prey body size analysis in the article. This sheet contain all taxa in the genus or species level, while for the former mass data were averaged from measurements of local species. No mass was assigned to prey that were identified to the family level or higher.
DOI: 10.5061/dryad.dn6vr/1
title: Mating system data

description: Data from: Natural and anthropogenic influences on the mating system of the common morning glory
DOI: 10.5061/dryad.dn6vr/2
title: matsys_env_association.R

description: R script for environmental association analyses on the mating system of Ipomoea purpurea
DOI: 10.5061/dryad.g4mj2/1
title: Eugongylus_Dryad_data

description: Nucleotide data from transcriptome and anchored hybrid enriched loci, and scripts used in the analytical pipeline.
DOI: 10.5061/dryad.n24q8/28
title: RAxML_bestTree.trnH-psbA

description: Maximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the trnH-psbA dataset
DOI: 10.5061/dryad.n24q8/29
title: RAxML_bestTree.cpDNA

description: Maximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the concatenated trnL-F + trnH-psbA datasets
DOI: 10.5061/dryad.n24q8/30
title: RAxML_bestTree.ITS+cpDNA

description: Maximum likelihood tree for analyses within tribe Eudemeae generated with RAxML and using the concatenated ITS + trnL-F + trnH-psbA datasets
DOI: 10.5061/dryad.n24q8/31
title: MrBayes50_ITS

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the nrITS dataset.
DOI: 10.5061/dryad.n24q8/32
title: MrBayes50_trnL-F

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnL-F dataset.
DOI: 10.5061/dryad.n24q8/33
title: MrBayes50_trnH-psbA

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the trnH-psbA dataset.
DOI: 10.5061/dryad.n24q8/34
title: MrBayes50_cpDNA

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated trnLF + trnH-psbA datasets.
DOI: 10.5061/dryad.n24q8/36
title: ITS+indel_MrBayes

description: Alignment matrix of ITS sequences for Bayesian inference with MrBayes including indel data
DOI: 10.5061/dryad.nq41m/1
title: Crocodile Egg and Hatchling Data

description: Data on saltwater crocodile eggs and hatchlings exposed to different treatments during incubation
DOI: 10.5061/dryad.rd55f/1
title: Observation data for modelling

description: The file is in a form of R data,  including all data used to fit the JSDMs, that is ,the biomass of multispecies and environmental variables of water temperature, salinity and depth.
DOI: 10.5061/dryad.rd55f/2
title: JSDM models

description: The file can be read in R, including the full structure of the fitted models, BaysComm, Boral, Mistnet, HMSC, and Gjam.
DOI: 10.5061/dryad.sf2bt/1
title: O.gothica_Dryad

description: Data from a laboratory experiment. All masses in the data file are in milligrams and growth duration is given in days. Growth rate has the unit of ln(mg/day).
DOI: 10.5061/dryad.t80gj/29
title: Supplemental File S8

description: SnpEff functional classification of the homozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/30
title: Supplemental File S9

description: Function description for the genes containing the SnpEff-annotated homozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/31
title: Supplemental File S10

description: List of SnpEff-annotated EMS-induced SNPs predicted to trigger silent stop codon lost substitutions in genes of the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/32
title: Supplemental File S11

description: SnpEff functional classification of the heterozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/33
title: Supplemental File S12

description: Function description for the genes containing the SnpEff-annotated heterozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/34
title: Supplemental File S13

description: Function description for the genes containing the SnpEff-annotated tentative false-negative homozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/35
title: Supplemental File S14

description: Function description for the genes containing the SnpEff-annotated tentative false-negative heterozygous EMS-induced SNPs in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/36
title: Supplemental File S15

description: SnpEff functional classification of the likely EMS-induced indels in all the 586 sorghum individuals.
DOI: 10.5061/dryad.t80gj/37
title: Supplemental File S16

description: Function description for the genes containing the SnpEff-annotated likely EMS-induced indels in all the 586 sorghum individuals.
DOI: 10.17632/58ng2zyyk7.1
title: Chromospheric activity of Periodic Variable stars (including Eclipsing binaries) observed in DR2 LAMOST stellar spectral survey

description: New BVRI photometric data of DY CVn, HAT-192-0001481 and LAMOST J164933.24+141255.0.
DOI: 10.17632/6rz26jzc6h.1
title: Data for: Syntheses, structures and properties of two organic-inorganic hybrid nicotinate-bridging rare-earth-containing phosphotungstates

description: Supporting Information for this paper
DOI: 10.17632/w4pht37rzp.1
title: Chromospheric activity of Periodic Variable stars (including Eclipsing binaries) observed in DR2 LAMOST stellar spectral survey
DOI: 10.17632/xdvtnzcz44.1
title: Data for: The repeatability of glucocorticoids: A review and meta-analysis

description: Data for: Taff et al. The repeatability of glucocorticoids: A review and meta-analysis.
DOI: 10.5061/dryad.31887/1
title: data_summary_dryad

description: This spreadsheet provides data on tree juvenile density, woodland structure (tree density, tree mortality, etc.), vegetation cover, and abiotic characteristics for each site. For a description of each column on this spreadsheet, please see the metadata file titled, 'data_summary_dryad_metadata'. These data were used in all structural equation modeling in the associated manuscript.
DOI: 10.5061/dryad.31887/2
title: nurse_data_dryad

description: This spreadsheet provides data on how many juveniles were found in each microsite, including units.  For a description of each column on this spreadsheet, please see the metadata file titled, 'nurse_data_dryad_metadata'. These data were used in the interaction (also referred to as electivity) analyses in the associated manuscript.
DOI: 10.5061/dryad.31887/3
title: data_summary_dryad_metadata

description: This spreadsheet provides a written description of each column in the spreadsheet titled, 'data_summary_dryad', including the units.
DOI: 10.5061/dryad.31887/4
title: nurse_data_dryad_metadata

description: This spreadsheet provides a written description of each column in the spreadsheet titled, 'nurse_data_dryad', including the units. These data also note which columns were not used in any of the analyses.
DOI: 10.5061/dryad.369n9/1
title: Gunshot data from Belize

description: CSV file giving the logarithmic ratio between a gunshots max peak amplitude and a reference amplitude at varying distances and orientation from source. We used the maximum possible magnitude for a .WAV file recorded on the device as our reference.
DOI: 10.5061/dryad.39f10/1
title: Heinen et al 2017 Journal of Ecology RAW Data Dryad Repository 02112017

description: Data file was entered in Microsoft Excel. Different tabs contain datasheets. (Data plant and insect variables per community; Plant and consumption variables per individual within communities; Environmental variables for multivariate analyses; Species variables for biomass for multivariate analyses; Species variables for consumption for multivariate analyses; PCA scores fungal diversity; PCA scores bacterial diversity.
DOI: 10.5061/dryad.3d3bq/1
title: NEE_MetaData

description: Meta data for files
DOI: 10.5061/dryad.3d3bq/2
title: PhenotypicData

description: Phenotypic data used in G-matrix analyses and QST-FST analyses
DOI: 10.5061/dryad.3d3bq/3
title: Pedigree_Driftsel

description: Pedigree format for DRIFTSEL QST-FST analyses
DOI: 10.5061/dryad.3d3bq/4
title: Microsats_Drifsel

description: Neutral marker information (microsatellite data) used in QST-FST analysis.
DOI: 10.5061/dryad.457fc/10
title: SAMDC5'UTRnwk
DOI: 10.5061/dryad.457fc/11
title: SAMDC5'UTRorignwk
DOI: 10.5061/dryad.457fc/3
title: SAMDC 3'UTRMeg
DOI: 10.5061/dryad.457fc/4
title: SAMDC 5'UTR Orthologues MEG
DOI: 10.5061/dryad.457fc/5
title: SAMDC 5'UTR Orthologues
DOI: 10.5061/dryad.457fc/6
title: SAMDC 5'UTR
DOI: 10.5061/dryad.457fc/7
title: SAMDC 5'UTRMeg
DOI: 10.5061/dryad.457fc/8
title: SAMDC3'UTRnwk
DOI: 10.5061/dryad.457fc/9
title: SAMDC3'UTRorignwk
DOI: 10.5061/dryad.6t1f2/1
title: behavior_data

description: This file contains chick anti-predator behavioral data, offspring growth and other relevant variables (treatment, foster nest, date and area of origin)
DOI: 10.5061/dryad.76gp5/1
title: Whitton et al Table S1

description: This file includes details of the cytotype designations at each site, including genome size estimates, inferred ploidy and the details of how we coded each site in our randomizations.
DOI: 10.5061/dryad.7j83s/5
title: Table S1. Model fit results

description: Table S1. Full results of RPANDA model comparisons with four different time-calibrated trees.
DOI: 10.5061/dryad.7j83s/6
title: Supplementary Materials

description: Appendix to accompany the manuscript: Primate diversification dynamics inferred from fossils and phylogenies.
DOI: 10.5061/dryad.9121q/1
title: Fungi identified from airborne spore samples in Finland

description: The zip file contains two excel files which correspond to the species x samples and covariates x samples data matrices, respectively. In the species dataset, the columns are the species and the rows are the samples. In the covariates dataset, the columns are the covariates and the rows are the samples. The sheets in the species dataset correspond to (1) species-level identifications with 0.5 reliability threshold (denoted as Species 0.5), (2) species-level identifications with 0.9 reliability threshold (denoted as Species 0.9), (3)genus-level identifications with 0.5 reliability threshold (denoted as Genus 0.5), (4) genus-level identifications with 0.9 reliability threshold (denoted as Genus 0.9), (5) wood-inhabiting fungal species-level identifications with 0.5 reliability threshold (denoted as Wood-inhabiting fungi 0.5), (6) wood-inhabiting fungal species-level identifications with 0.9 reliability threshold (denoted as Wood-inhabiting fungi 0.9).
DOI: 10.5061/dryad.9121q/2
title: Sequence data of the spore samples

description: This file contains the sequence data of the 134 spore samples. The sequence data is provided in the fasta format, the file name being coded as sample_n.seq, where n = 1...134 is the sample id (see Table S1 in the Supplemental information).
DOI: 10.5061/dryad.b31g6/1
title: Complete data
DOI: 10.5061/dryad.b31g6/3
title: R script for the evolution experiment (cf. Fig. 3)
DOI: 10.5061/dryad.b31g6/4
title: R model for the invasion dynamics of homozygous-sublethal (HS) D alleles (cf. Fig. 4)
DOI: 10.5061/dryad.b31g6/5
title: ace-1 sequences Intron2 - partial Exon3 (cf. Fig2)
DOI: 10.5061/dryad.bv5ht/1
title: Seed mass, tannin and fiber content of the 163 species used in this study.
DOI: 10.5061/dryad.cf2kd/1
title: Breeding Bird Survey trends

description: File containing the Breeding Bird Survey trends analysis results published by the Patuxent Wildlife Research Center on the following website: www.mbr-pwrc.usgs.gov/bbs/. Each trends is associated with a species' abundance and monitoring route.
DOI: 10.5061/dryad.cf2kd/2
title: Environmental variables

description: Environmental predictor variables used in analysis describing location, forest cover, and topography of BBS routes.
DOI: 10.5061/dryad.cf2kd/3
title: R code for analysis

description: This file contains annotated R code for the main analyses in the manuscript. These are 1) Determining which month for temperature change is the best predictor for each species' trend (June or July), 2) Trend ~ Temperature change * old-growth forest models for each species, 3) Global trend models for Wilson's warbler and hermit warbler that include additional interaction terms, & 4) Calculation of % change in trend per increase in June/July temperature for Wilson's warbler and hermit warbler.
DOI: 10.5061/dryad.g6f6g/1
title: Raw data of the study

description: Attached data is the raw data of the manuscript. We prepared the figure from these data.
DOI: 10.5061/dryad.gb786/2
title: Mackerel Energy Data
DOI: 10.5061/dryad.j6k37/1
title: Genotypes for genetic diversity analyses

description: Sample numbers and genotypes for juvenile steelhead trout analyzed for measures of genetic variability.  Brood year = year in which juvenile O. mykiss was produced based on scale age. Sample ID = unique sample identifier. Remaining 30 columns = 15 microsatellite loci (i.e, Locus_1 = allele 1) Locus_2 = allele 2.
DOI: 10.5061/dryad.j6k37/2
title: Redd counts and survey effort

description: Year = year of redd surveys.  Population =  River of collection. Classification = T - treatment, C - Control. Redd count = sum of redds counted per year. Period = B - before, D - During, A - after.  Distance surveyed = km.  Days = number of different days in which surveys were conducted
DOI: 10.5061/dryad.k0734/1
title: Data for Kenyan pigs

description: This Zip file has a README file that provides a complete description of the data.
DOI: 10.5061/dryad.k58fr/1
title: NESEDiveDur_V2

description: Northern elephant seal dive metrics and pregnancy status
DOI: 10.5061/dryad.k58fr/2
title: NESEwithMass

description: Northern elephant seal deployment and recovery masses with diving data
DOI: 10.5061/dryad.k5904/1
title: Data sheets and database
DOI: 10.5061/dryad.k66c0/1
title: Suwanvecho et al.Gibbon foods_2006-2011

description: This file contains data on fruit species eaten by the gibbon study group A during April-May follows for the six years 2006-2011. It contains for each visit to a fruit source: the tree species and tree number visited, date, time and fruit species code; and a summary of sources, no. of visits and no. of days for each species.  The full species names are given in a separate sheet, copied from the SI on line file associated with Suwanvecho et al. 2017 in Biotropica.
DOI: 10.5061/dryad.m605m/1
title: Species-level database of density, body mass, speed and home range size.

description: This is a dataset compiled from bibliographic references (see Materials & Methods). Essentially, it includes information of density, body mass, speed and home range size for 44 species. Name variables (in columns) are defined as follows:  “Species” (TEXT): scientific name of each species; “BM(g)” (NUMERIC): body mass in grams; “HR(Km2)” (NUMERIC): Home range size in square kilometres; “Refs(for_BM_and_HR)” (TEXT): data source for body mass and home range size data  (see Appendix S3 in Supplementary Materials for full citations); “DENSITY(ind/Km2)” (NUMERIC): animal density in number of individuals per square kilometre; “Density_survey_method” (TEXT): details of the survey method used to estimate density (if available); “Surveyed_area” (NUMERIC+TEXT): details of the surveyed area when estimating density (if available); “Study_area” (TEXT): details of the area of study when estimating density (if available); “Refs(for_Density)” (TEXT): data source for density and density-related data  (see Appendix S3 in Supplementary Materials for full citations); “SPEED(ms-1)” (NUMERIC): speed in meters per second; “Speed_survey_method” (TEXT): details of the survey method used to estimate speed (if available); “Time_step” (NUMERIC+TEXT): time step used to estimate speed (if available); “Sampling_time” (NUMERIC+TEXT): total tracking time used to estimate speed (if available); “Refs(for_Speed)” (TEXT): data source for speed and speed-related data  (see Appendix S3 in Supplementary Materials for full citations).
DOI: 10.5061/dryad.n24q8/35
title: MrBayes_ITS+cpDNA

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated ITS+ trnLF + trnH-psbA datasets.
DOI: 10.5061/dryad.n24q8/37
title: cpDNA+indel_MrBayes

description: Alignment matrix of concatenated trnL-F + trnH-psbA datasets for Bayesian inference with MrBayes including indel data
DOI: 10.5061/dryad.n24q8/38
title: ITS+cpDNA+indel_MrBayes

description: Alignment matrix of concatenated ITS + trnL-F + trnH-psbA datasets for Bayesian inference with MrBayes including indel data
DOI: 10.5061/dryad.n24q8/39
title: MrBayes50tree_ITS+indel

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the nrITS dataset + Indel data.
DOI: 10.5061/dryad.n24q8/40
title: MrBayes50tree_cpDNA+indel

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated trnLF + trnH-psbA datasets + Indel data.
DOI: 10.5061/dryad.n24q8/41
title: MrBayes50tree_ITS+cpDNA+indel

description: Bayesian 50% majority-rule consensus trees from 6002 trees generated by Bayesian inference with MrBayes for tribe Eudemeae and the concatenated ITS+ trnLF + trnH-psbA datasets + Indel data.
DOI: 10.5061/dryad.n24q8/42
title: PrimaryConcordanceTree ITSvscpDNA Bucky

description: Primary concordance tree from the BUCKy analyses using the 6,002 trees from the ITS and the cpDNA datasets obtained in the MrBayes analyses. The discordance parameter (α) was set to 1, 10, and 100, however results from concordance analyses varying the discordance prior (α) had no effect on topology or concordance.
DOI: 10.5061/dryad.n24q8/43
title: xml BEAST for species tree analysis

description: xml file for species tree analysis under the multispecies coalescent model in BEAST 2.4.4
DOI: 10.5061/dryad.n24q8/44
title: MCC Species Tree BEAST

description: Maximum clade credibility species tree (MCCT) estimated from nuclear ribosomal ITS and two chloroplast DNA regions (trnL-F, trnH-psbA) using the multispecies coalescent method implemented in *BEAST.
DOI: 10.5061/dryad.n4b49kq/1
title: CHARLES data
DOI: 10.5061/dryad.q0rv9/1
title: Tree Data

description: This is the raw data on the 40 trees used for their project. Included are the latitude and longitude GPS coordinates for each tree, their species identity (Pinus contorta or Pinus albicaulis), their age in years, their estimated volume in m^3, their distance from the nearest forest edge (m), isolation index (number of stems within a 10m radius of the tree), and the soil chemistry information (% OM, pH, K, Mg, Na, S, cation exchange capacity, C:N ratio).
DOI: 10.5061/dryad.q0rv9/2
title: Bray Curtis rarefied dissimilarity matrix for EMF

description: This is the Bray-Curtis rarefied dissimilarity matrix for ectomycorrhizal fungal taxa for the 40 trees
DOI: 10.5061/dryad.q0rv9/3
title: Bray Curtis rarefied dissimilarity matrix for total fungi

description: This is the Bray-Curtis rarefied dissimilarity matrix for the total fungal community for the 40 trees
DOI: 10.5061/dryad.sq67g/1
title: LTEE_NonMutator_MutationList.txt
DOI: 10.5061/dryad.sq67g/2
title: LTEE_MMR_MutationList.txt
DOI: 10.5061/dryad.sq67g/3
title: LTEE_MutT_MutationList.txt
DOI: 10.5061/dryad.t7n48/1
title: PMK_Influenza_2009_2014

description: Deidentified data for individuals presenting with influenza-like illness to PMK hospital (inpatient and outpatient) from 2009-2014
DOI: 10.5061/dryad.t80gj/38
title: Supplemental File S17

description: SIFT prediction results for the missense-annotated homozygous EMS-induced SNPs in all the 586 sequenced individuals.