cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.818c434/2
title: R script for finding inverted regions in a genome using population genomic data
DOI: 10.5061/dryad.8hd6764/1
title: caterpillar_performance
DOI: 10.5061/dryad.b4s71jj/1
title: Litter Chem_characteristics

description: This Excel document includes the raw data for analysed in the manuscript including leaf litter C leachates, lignin, cellulose, hemicellulose, tannin, C, N, P, Ca, K, Mg, Mn concentrations and Lignin:N, and litter decomposition rates and soil priming effect.
DOI: 10.5061/dryad.ct8p264/1
title: ENM_Filtering

description: Associated scripts and data to run all analyses and create all figures in Castellanos et al. 2019.
DOI: 10.5061/dryad.gd702q0/1
title: Kenna et al - Data Overview

description: Table shows an overview of metrics for each individual worker bumblebee that was selected for testing. If a worker did not feed it was not flown on a flight mill, and hence NA values will appear in all flight metric columns. The number of circuits each bee flew is detailed both before and after the data was cleaned. The data used in the manuscript are the cleaned data, indicated in the table by brackets stating '(after data cleaned)'. The treatment column is coded as C = Control or T = pesticide Treatment.
DOI: 10.5061/dryad.gf4f363/10
title: 12084_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/11
title: 12546_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/12
title: 12590_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/13
title: 12728_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/14
title: 12750_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/15
title: 13112_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/8
title: 11480_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/9
title: 11674_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.m8hb503/1
title: Long-term breeding data and 2D:4D measures from collared flycatchers.

description: Long-term breeding data and 2D:4D measures from a Hungarian population of collared flycatchers. Variables are detailed in the sheet named "variables".
DOI: 10.5061/dryad.nk218ht/1
title: Codes and PBDB download for Franeck and Liow 2019

description: PBDB_Ord_1.csv - downloaded data from PBDB; Franeck_and_Liow_global - global diversification and diversity dynamics; Franeck_and_Liow_PC - paleocontinental diversification and diversity dynamics; Franeck_and_Liow_onoff_ext - diversification and diversity analysis based on last occurrence in onshore or offshore areas; Franeck_and_Liow_onoff_orig - diversification and diversity analysis based on first occurrence in onshore or offshore areas; Franeck_and_Liow_globalStages - global analysis based on data assigned to global Stages only; Franeck_and_Liow_phyla - analysis of different phyla in SI; Franeck_and_Liow_classes - analysis of different classes in SI
DOI: 10.5061/dryad.pb5374s/1
title: Supplement

description: The supplementary material contains zip-archived GIS layers with data on the average plankton concentrations in mg/m3 of the following: small (Sf), medium (Mf) and large (Lf) fractions, total zooplankton (Total), different groups (Protista, Jellyfish, Copepoda, Amphipoda, Euphausia, Chaetognat, Meroplankt, Cladocera, Pteropoda, Mysida, Cumacea, Isopoda, Ostracoda, and other), as well as total concentrations obtained in the day (D) and night (N) times, different seasons (Win, Spr, Sum, Aut), and long-term periods (Y1984_1990, Y1991_1995, Y1996_2005, Y2006_2013); this material is found as shapefiles and tab-delimited txt files. These data were used to construct Figures 2-8 of the paper.
DOI: 10.5061/dryad.q88pm45/1
title: Canopy data reference

description: This is an excel sheet that contains information about each sound recording used in the bat pass analyses. Please see metadata tab for information about each column.
DOI: 10.5061/dryad.q88pm45/2
title: Canopy data outputs

description: This is an excel sheet that provides the raw amplitude in each of the tested frequency bins before, during, and after the bat pass.
DOI: 10.5061/dryad.q88pm45/3
title: Original canopy sound recordings used in analysis

description: These are the original high pass filtered wave files used in the analyses. Please see the 'Canopy data reference' sheet for information about each file, including the height and date of recording.
DOI: 10.5061/dryad.rd300kf/1
title: R-code used to run the 2-patch 2-stage vec-permutation model.
DOI: 10.5061/dryad.s11f216/1
title: Echinoidea 70% occupancy matrix

description: Contains 331,188 aligned aminoacid positions for 32 taxa, in fasta format. Output by Agalma v. 1.0.1.
DOI: 10.5061/dryad.s11f216/2
title: 70% matrix without Arbacia punctulata

description: Contains 331,188 aligned aminoacid positions for 31 taxa, in fasta format. Same as 'echinoids70.fa' but without Arbacia punctulata. Most analyses in the manuscript were performed using this matrix.
DOI: 10.5061/dryad.s11f216/3
title: 70% matrix with decontaminated Arbacia

description: All loci in the transcriptome of Arbacia punculata that are identical to those of Eucidaris tribuloides have been deleted in this version of the matrix.
DOI: 10.5061/dryad.s11f216/4
title: 70% matrix without Arbacia output by TreeShrink

description: This matrix was obtained with TreeShrink which eliminated 345 sequences that behaved as outliers with regards to branch length.
DOI: 10.5061/dryad.s11f216/5
title: Partition file

description: Contains the start and end of loci. Output by Agalma v. 1.0.1.
DOI: 10.5061/dryad.s11f216/6
title: ML phylogeny inferred under mixture model LG4X

description: Contains the tree with bootstrap support values in Newick format. Obtained using RAxML-NG v. 0.5.1 using matrix 'echinoids70_noarba.fa'.
DOI: 10.5061/dryad.s11f216/7
title: All 1,040 gene trees

description: Obtained using RAxML v8.2.1 under the model that minimizes the BIC for each loci. Individual gene sequences come from file 'echinoids70_noarba.fa'. Trees are in newick format.
DOI: 10.5061/dryad.s11f216/9
title: ML phylogeny inferred under best-fit partitioning scheme

description: Contains the tree with bootstrap support values in Newick format. Obtained using RAxML v8.2.1 using matrix 'echinoids70_noarba.fa'. Partitioning obtained using IQ-TREE v1.6.6 using the fast-relaxed clustering algorithm among the top 50% of schemes.
DOI: 10.5061/dryad.tj3bd3n/1
title: RangeMaps

description: KMZ files of range polygons used in the study along with SEINet records used to generate those polygons. Outline of Fish Slough, CA, USA also included.
DOI: 10.5061/dryad.tj3bd3n/2
title: genotypeEstimates

description: Genotype estimates for all SNPs for all individuals.
DOI: 10.5061/dryad.tj3bd3n/3
title: abioticData

description: Abiotic data corresponding to each individual sampled. Sample names correspond to those in the genotype estimate file.
DOI: 10.5061/dryad.v3t4k0m/1
title: Lopez-Uribe et al  - Raw Data

description: This text file contains all the raw data values that we used for the generalized mixed linear models. This file includes all the population genetic parameter summary statistics, body size values, level of sociality, degree of diet specialization, expected heterozygosity, mean geographic distance of each study, and other information specific to the studies that we included in the analysis.
DOI: 10.5061/dryad.v3t4k0m/2
title: Lopez-Uribe et al - R code

description: This file contains the R code used to analyze all the data. To run the code, it is necessary to use two files: (1) Lopez-Uribe_etal_data_FINAL.txt, AND (2) Lopez-Uribe_RAxML_Hedtke_bestTree.result.tre.
DOI: 10.5061/dryad.v3t4k0m/3
title: Lopez-Uribe et al - ML Phylogenetic Tree

description: This file contains the best maximum likelihood phylogenetic tree obtained from an analysis in RAxML using a modified dataset from Hedtke et al 2013.
DOI: 10.5061/dryad.v67003c/2
title: bprob
DOI: 10.5061/dryad.v67003c/3
title: fecund
DOI: 10.5061/dryad.v67003c/4
title: migrate
DOI: 10.5061/dryad.v67003c/5
title: surv
DOI: 10.5061/dryad.v67003c/6
title: scensims
DOI: 10.17632/hdxbhspv9r.1
title: Data for: Non-dioxin-like and dioxin-like polychlorinated biphenyls potentiate genotoxicity of aflatoxin B1 in a human hepatocyte line by enhancing CYP1A2 and CYP3A4 expression

description: The data contain all replicate experiments, and values used for the plots forming the figures in the manuscript.
DOI: 10.17632/r2pnm2j4vk.1
title: Confusing imaging appearance of split-tip hemodialysis catheter

description: Real time fluoroscopy shows the malaligned/fractured distal tip of the longer catheter that appears to be still attached with no large flip-flop movement.
DOI: 10.17632/zkdjfcmmbx.1
title: Data for: Fabrication of UV-curable solvent-free epoxy modified silicone resin coating with high transparency and low volume shrinkage

description: These data can be used for the research of the UV cured solvent free transparent epoxy modified silicone coatings.
DOI: 10.5061/dryad.1c9g5mm.2
title: Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)
DOI: 10.5061/dryad.1c9g5mm.2/10.2
title: min10.phy

description: Concatenated phylip alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/11.2
title: min20.phy

description: Concatenated phylip alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/5.2
title: min4.loci

description: Pyrad .loci file for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/6.2
title: min10.loci

description: Pyrad .loci file for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/7.2
title: min20.loci

description: Pyrad .loci file for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/8.2
title: min30.loci

description: Pyrad .loci file for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/9.2
title: min4.phy

description: Concatenated phylip alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1pc2g84/1
title: Garces_restrepo_et_al_2018_Cecropia&Coussapoa_locations

description: Cecropia obtusifolia and Coussapoa villosa locations in
an agro-ecosystem located in the Caribbean coastal plain of
northeastern Costa Rica (10.328 N, 283.598 W).
DOI: 10.5061/dryad.1pc2g84/2
title: Garces_restrepo_et_al_2018_Three-toed_sloths_resigths

description: Three-toed_sloths_resigths in an agro-ecosystem located in the Caribbean coastal plain of northeastern Costa Rica (10.328 N, 283.598 W). March 2010 and ended in March 2014.
DOI: 10.5061/dryad.1pc2g84/3
title: survival_three-toed_sloths

description: /* Adults survival three-toed sloths, Encounter occasions=49, groups=1, individual covariates=3, individual covariates names = sex (0=male, 1=female), cecropia density (tree/ha), Coussapoa density (tree/ha), number_core_area, proportion_forest_in_the_core_area. Each column corresponds to whether the individual was detected in a month, the history of capture began in March 2010 and ended in March 2014.*/ /* Juveniles survival three-toed sloths, Encounter occasions=51, groups=2 (10=year1, 01=year2), individual covariates=3, forest, cecropia, coussapoa. */ /* Juveniles 2-3 years old survival three-toed sloths, Encounter occasions=51, groups=1. Each column corresponds to whether the individual was detected in a month, the history of capture began in September 2012 and ended in December 2016.*/
DOI: 10.5061/dryad.1t2513c/1
title: Code for a dynamic model of facilitation

description: CODE TO RUN THE MODEL DESCRIBED IN DANGLES (2019) OIKOS
DOI: 10.5061/dryad.2v8rq57/1
title: Species sorting and mass effect along forest succession- evidence from taxonomic, functional, and phylogenetic diversity of amphibian communities

description: Sites characterization (sheet 1) and Number of individuals for amphibian species per site. Taxonomic, functional and phylogenetic metrics calculated per each site (sheet 2).
DOI: 10.5061/dryad.37rp8r9/1
title: urchin_data_deVriesWebbTaylor

description: This file contains the data for all of the analyses conducted in this manuscript, including urchin growth, jaw length, test diameter, and feeding efficiency, for the focal species, Strongylocentrotus purpuratus. For detailed descriptions of the data file, refer to the README file.
DOI: 10.5061/dryad.3jh80/1
title: Koch_PACD_SPI_v7

description: Collected in the field; Software: STATA (v.13) (.dta-File)
DOI: 10.5061/dryad.5g8h6f6/1
title: Population locality dat Coordinates.Status

description: This file provides location data for sites where multiple host species were present and movement of Microbotryum spores was quantified between them.
DOI: 10.5061/dryad.5ph7sm6/1
title: codes and datas20181227

description: datas and codes for experiment
DOI: 10.5061/dryad.607cq34/4
title: virgatus_volatile_analysis

description: R Script used to analyze the Sceloporus virgatus volatile response data.
DOI: 10.5061/dryad.6450hv3/11
title: AllFilesMetadata

description: Contains data description and field descriptions of all datasets.
DOI: 10.5061/dryad.6450hv3/4
title: SorensonAndDamschen2019_LightIntensity_TubeLevel

description: Light intensity was taken using a 0.7m long light intensity meter bar. Measurements were taken on cloudless days with clear skies. Six measurements were taken at each tube. Two measurements were taken at taken at 45-degree angles to the edges of the subplot edge at three different heights: 5, 15, and 25cm.
DOI: 10.5061/dryad.6450hv3/6
title: SorensonAndDamschen2019_SpeciesCodeKey

description: While collecting data we used a six-letter code system that typically is comprised of the first three letters of both the genus and specific epithet. Some codes do not match species names, but the names reported are the correct names. If species were identified only to genus, only the genus is reported with sp. For some large genera, we identified species into morphogroups within the genus. In this case, we used the first three letters of the genus followed by SP and a number. We used names from Radford, A. E., Ahles, H. E., & Bell, C. R. (1968). Manual of the vascular flora of the Carolinas. Univ of North Carolina Press. We checked spelling and current name usage using the R package taxize (Scott Chamberlain and Eduard Szocs (2013). taxize - taxonomic search and retrieval in R. F1000Research, 2:191. URL: http://f1000research.com/articles/2-191/v2.) using " iPlant_TNRS" as the source, unless otherwise noted.
DOI: 10.5061/dryad.6450hv3/7
title: SorensonAndDamschen2019_SpringPresenceAndHeight_TubeLevel

description: Late Spring Survival and height of seedlings was recorded May 27–June 5. Each tube was visited, each seedling was identified and marked with a colored pin, and seedling length was measured with a ruler to the nearest 0.1 cm. Each tube was checked for burning. Thatch level was visually recorded into categories by percent cover (and depth for level 4).
DOI: 10.5061/dryad.6450hv3/8
title: SorensonAndDamschen2019_TreeDBH_SubplotLevel

description: Surrounding canopy trees were measured for each subplot by recording species ID, distance from subplot, and diameter at breast height (DBH). Basal area was calculated from dbh. Data was recorded May 27–June 5. Each tube was visited, each seedling was identified and marked with a colored pin, and seedling length was measured with a ruler to the nearest 0.1 cm. Each tube was checked for burning. Thatch level was visually recorded into categories by percent cover (and depth for level 4).
DOI: 10.5061/dryad.6450hv3/9
title: SorensonAndDamschen2019_VegetationSurvey_SubplotLevelAndTubeLevel

description: The vegetation surrounding the root excluder tubes was recorded by measuring the plot attributes and herb community at the tube level and the shrub community at the subplot level. To measure plot attributes, a 0.5mx0.5m pvc quadrat was placed with each root excluder tube in the center and the edges aligned with the edges of the subplot. Within this quadrat, the overall %cover of: all plants from a bird’s eye view (Green), leaf litter (Litter), woody debris (Woody), bare ground (Bare), and moss and fungus (Non-Vasc) were recorded. Additionally, % cover of each species of plant that hung into the quadrat was visually estimated. %cover of each species was estimated even if a leaf of a different species overtopped it, but not for a conspecific. To measure the shrub community, a 3mx3m quadrat was placed with the subplot at the center and %cover of each species was visually estimated. This file has, admittedly poor data structure, but is easy to subset using the column data type column DT.
DOI: 10.5061/dryad.8hd6764/2
title: competition_oviposition
DOI: 10.5061/dryad.8hd6764/3
title: HPLC data
DOI: 10.5061/dryad.8hd6764/4
title: latex data
DOI: 10.5061/dryad.8hd6764/5
title: oviposition_experience
DOI: 10.5061/dryad.8hd6764/6
title: trichome data
DOI: 10.5061/dryad.b0hs8gr/1
title: Nucleomorph Nuclear Pore Data

description: A zipped folder containing all the alignments (which contain newly identified nucleoporins and reference proteins), the phylogenetic trees (used to infer figures 1 and 2), the HMM models used for the search, signal peptide predictions for all the proteins in the alignments, and a text file with the phylogenetic models used for each tree (as selected in IQTree using ModelFinder).
DOI: 10.5061/dryad.b4dn0mn/1
title: Scirpus_longii_SNPS

description: Nexus alignment of SNPs from all sequenced individuals of Scirpus long.
DOI: 10.5061/dryad.b4dn0mn/2
title: MAXENT_input_distributions

description: Species distribution data used for MAXENT species distribution modeling.
DOI: 10.5061/dryad.bm2qp7n/1
title: Transect_data

description: Data from ten 50 m by 2 m transects. Data includes all stems greater than 1 cm diameter at breast height, or greater 1 cm basal diameter for climbing plants.
DOI: 10.5061/dryad.bm2qp7n/2
title: Sample_info_1

description: Taxonomic information for root samples, derived from rbcl barcode sequences (rbcLa_root_library.fasta file).
DOI: 10.5061/dryad.bm2qp7n/3
title: Sample_info_2

description: Positions of each root tip sample. Coordinates are listed in decimal degrees.
DOI: 10.5061/dryad.bm2qp7n/4
title: otu_table_standardized

description: OTU table of all fungi. OTUs found in negative controls were removed, and read counts were standardized by median sequencing depth.
DOI: 10.5061/dryad.bm2qp7n/5
title: taxa_table

description: Taxonomic and functional guild assignments for all fungal OTUs
DOI: 10.5061/dryad.bm2qp7n/6
title: rbcl_barcode_library_qiime

description: rbcLa barcode reference library used to match root tip samples to plant species.
DOI: 10.5061/dryad.bm2qp7n/7
title: rbcLa_root_library

description: rbcLa amplicon sequences (Sanger) from each root sample
DOI: 10.5061/dryad.bn0655b/1
title: Data_Tielemanetal_auk2019

description: Data used for all analysis of Tieleman et al, Auk, 2019
DOI: 10.5061/dryad.fg8kq66/5
title: visit-data

description: Data on conditions during site visits when bird detections were made that might influence detection probability.
DOI: 10.5061/dryad.fg8kq66/6
title: readme

description: A description of data columns in all other files.
DOI: 10.5061/dryad.gd702q0/2
title: Flight trial data files

description: This zip folder contains all flight trial data files. There is a separate file for each flight trial. Each file has the necessary information to uniquely identify each bee, which can then be matched with the data overview spreadsheet. Each file also contains the raw data for the number of circuits flown by each bee and the interval time for each circuit. The velocity flown for each circuit has also been calculated and added.
DOI: 10.5061/dryad.gf4f363/16
title: 13863_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/17
title: 13907_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/18
title: 13910_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/19
title: 13999_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/20
title: 14005_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/21
title: 14134_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/22
title: 14744_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/23
title: 14771_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/24
title: 14851_data

description: Preprocessed MEG datasets and anatomical data
DOI: 10.5061/dryad.gf4f363/25
title: README
DOI: 10.5061/dryad.kb2f352/1
title: Data_cod_flounder

description: Adult cod, juvenile cod and flounder CPUE data (in grams). The datasets contain also the associated bottom temperature, salinity and oxygen concentration of each haul as well as the latitude and longitude in decimal degrees.
DOI: 10.5061/dryad.m42t6tm/1
title: Fig. S1 petro

description: Additional parallel and crossed polarizers photomicrographs
DOI: 10.5061/dryad.m42t6tm/2
title: Fig. S2 CL

description: Additional cathodoluminescence photomicrographs
DOI: 10.5061/dryad.m42t6tm/3
title: Fig. S3 XRD

description: X Ray Powder Diffraction (XRPD) analyses
DOI: 10.5061/dryad.m42t6tm/4
title: Fig. S4 SEM

description: Additional SEM photomicrographs
DOI: 10.5061/dryad.m463f7k/1
title: SNPs called from the RNA-Seq data of RILs

description: SNPs called from the RNA-Seq data of RILs and their two parents, S. lycopersicum breeding line NC EBR-1 and S. pimpinellifolium accession LA2093. The file is in vcf format.
DOI: 10.5061/dryad.m463f7k/2
title: Tomato non-reference genome sequences

description: Non-reference genome sequences of tomato pan-genome
DOI: 10.5061/dryad.m463f7k/3
title: gene models in non-reference genome

description: gene models annotated in the non-reference sequences of the tomato pan-genome, in gff3 format
DOI: 10.5061/dryad.qp313np/1
title: Monkey EEG data for Dryad
DOI: 10.5061/dryad.rm8bk77.2
title: Data from: New small-bodied ornithopods (Dinosauria, Neornithischia) from the Early Cretaceous Wonthaggi Formation (Strzelecki Group) of the Australian-Antarctic rift system, with revision of Qantassaurus intrepidus Rich and Vickers-Rich, 1999
DOI: 10.5061/dryad.rs39059.2
title: Data from: Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area
DOI: 10.5061/dryad.s11f216/10
title: ML phylogeny inferred under mixture model PMSF

description: Contains the tree with bootstrap support values in Newick format. Obtained using IQ-TREE v1.6.6 using matrix 'echinoids70_noarba.fa'.
DOI: 10.5061/dryad.s11f216/11
title: Bayesian phylogeny inferred under CAT-Poisson

description: Contains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'.
DOI: 10.5061/dryad.s11f216/12
title: Bayesian phylogeny inferred under CAT-GTR

description: Contains the consensus tree with posterior probabilities in Newick format. Obtained using PhyloBayes-MPI v. 1.8.1 using matrix 'echinoids70_noarba.fa'. WARNING: this analysis was run for only 3,000 cycles and did not converge.