cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k5s20/2
title: S2 Table Standards  for Marine water ecosystem

description: S2 Table.: Australian and international standards and guidelines for marine water ecosystem.
DOI: 10.5061/dryad.kd1d4/10
title: CHELSA_prec_10_land
DOI: 10.5061/dryad.kd1d4/11
title: CHELSA_prec_11_land
DOI: 10.5061/dryad.kd1d4/12
title: CHELSA_prec_12_land
DOI: 10.5061/dryad.kd1d4/13
title: CHELSA_temp10_1_land
DOI: 10.5061/dryad.kd1d4/6
title: CHELSA_prec_6_land
DOI: 10.5061/dryad.kd1d4/7
title: CHELSA_prec_7_land
DOI: 10.5061/dryad.kd1d4/8
title: CHELSA_prec_8_land
DOI: 10.5061/dryad.m248h/1
title: Phenotype data to estimate divergence in mean

description: Ten phenotypic traits with ecotype and population identifiers.
DOI: 10.5061/dryad.m248h/2
title: Phenotype data to estimate genetic variance

description: Ten phenotypic traits with ecotype, population (block), sire and dam identifiers.
DOI: 10.5061/dryad.mb622/1
title: ReynaBurggren_MetaData

description: Data associated with Reyna and Burggren, 2017. Altered Embryonic Development in Northern Bobwhite Quail (Colinus virginianus) Induced By Pre-incubation Oscillatory Thermal Stresses Mimicking Global Warming Predictions
DOI: 10.5061/dryad.n9077/1
title: Illumina MiSeq data ITS2 Vascular plants

description: Contains 12 fastq files corresponding to R1 and R2 data from 6 Illumina MiSeq 250 bp PE sequencing libraries. 130 soil samples from Denmark were amplified with tagged primers (S2F and ITS4) and build into TruSeq PCR free libraries. Each sample was amplified in triplicates. Fastq files R1A and R1B contain reads from the first replicates, R2A and R2B from the second, etc. Data were produced as part of the Biowide (Biodiversity in width and depth), carryied out in Denmark from 2014-2018) supported by the Villum foundation. The vascular plant data included here was used in the validation of the LULU algorithm for post-clustering curation of OTU tables for reliable biodiversity metrics, as described in the publication. Tagging scheme and other information needed to demultiplex and analyse the data are accessible on the GitHub repository accompanying the publication/r-package.
DOI: 10.5061/dryad.p9v3q/1
title: KhanEtal_AmNat_AllDataFiles

description: Raw data for all figures in the manuscript
DOI: 10.5061/dryad.q88sm/1
title: data_for_Supplementary_Material_antisocialpunishment

description: This file includes the data for Aleta Pleasant & Pat Barclay's "Why hate the good guy? Antisocial punishment of high cooperators is higher when people compete to be chosen". The Excel file includes one worksheet describing the variables, and another worksheet with the actual data. Please note that the data include both individual data and averages for each group of 4. In other words, every fifth row or sixth row is not an individual, but a group total. This is clearly labeled in column B ("group") as either a 0 (individual data) or a 1 (group average). When analyzing the data, you must either exclude the rows for individual data (to analyze group averages) or exclude the rows for group data (to analyze individual data); otherwise you will double count. The data also include participants in the Markets Condition who did not play a public goods game but were "Observers" (i.e., Trustors in a Trust Game)... these are identified as 1's in column G (Observer), and they provided no data on contributions or punishment because they did not play the public goods game.
DOI: 10.5061/dryad.q88sm/2
title: Supplementary Material for Pleasant & Barclay antisocial punishment: instructions, questionnaires, supplementary analysis

description: This Supplementary Online Material for Aleta Pleasant and Pat Barclay's article in Psychological Science "Why hate the good guy? Antisocial punishment of high cooperators is higher when people compete to be chosen". This file includes instructions to participants, comprehension questions, post-experimental questionnaires, and a supplementary analysis that categorizes punishers into people who did not punish, did moralistic punishment only, did antisocial punishment only, or did both moralistic and antisocial punishment.
DOI: 10.5061/dryad.qc7n5/1
title: Thailand_AlphaScreen_data

description: AlphaScreen measurements of antibody response in longitudinal cohort from Thailand.
DOI: 10.5061/dryad.qc7n5/2
title: Brazil_AlphaScreen_data

description: AlphaScreen measurements of antibody response in longitudinal cohort from Brazil.
DOI: 10.5061/dryad.rd912/1
title: LTDS - Ambrosia PDXPP data archive

description: see publication
DOI: 10.5061/dryad.rd912/2
title: LTDS - Ambrosia plots, Removal records archive

description: see publication
DOI: 10.5061/dryad.rd912/3
title: LTDS - Ambrosia size data archive

description: see publication
DOI: 10.5061/dryad.rd912/4
title: LTDS - KEY for plots and treatments

description: see publication
DOI: 10.5061/dryad.rd912/5
title: LTDS - Larrea PDXPP data archive

description: see publication
DOI: 10.5061/dryad.s04ng/1
title: critical thermal maximum

description: CTmax of three redband trout populations and a hybrid.  Heating rate of water was 0.3°C min−1 to 22°C and 0.1°C min−1 thereafter until CTMAX was reached.
DOI: 10.5061/dryad.s04ng/2
title: maximum heart rate

description: Maximum heart rate of three redband trout populations and a hybrid. Maximum heart rate was stimulated by an intraperitoneal injection of atropine sulfate and isoproterenol. Heating rate of water was 1 C every 6 minutes.
DOI: 10.5061/dryad.s04ng/3
title: metabolic rate and aerobic scope

description: Standard and maximum metabolic rate of three redband trout populations and a hybrid at 12°C, 15°C, 18°C, 21°C and 24°C. Maximum metabolic rate was achieved by exercise. Aerobic scope was calculated as the difference between standard and maximum rate.
DOI: 10.5061/dryad.s04ng/4
title: RAD TAG catelog

description: RAD Tag sequence (75 bp ) and  SNP position of the 5903 genetic markers.
DOI: 10.5061/dryad.sp5ff.1
title: Data from: Contrasting ecological roles of non-native ungulates in a novel ecosystem
DOI: 10.5061/dryad.sp5ff.2/8.2
title: Supplementary script for ungulate and forest abundance regressions

description: Script to exclude highest extreme values of ungulate abundance and to replicate analyses and figures showing regression of forest abundances and ungulate scat counts.
DOI: 10.5061/dryad.tq0qc/3
title: data_cites

description: Altmetric and citation data for 878 articles from 10 ornithological journals and 15 non-specialist journals (2014). 'jif' is 2015 journal impact factor, 'score' is Altmetric Attention Score.
DOI: 10.5061/dryad.tq0qc/4
title: script v2

description: Reproducible R code for manipulating, analysing and plotting the data.
DOI: 10.5061/dryad.v0k4h/10
title: Lepidoptera-UCE-1.3K-v1 Bait Design

description: A target enrichment probe set designed from 1,381 UCE loci identified among Lepidoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.5061/dryad.v0k4h/4
title: Coleoptera-UCE-1.1K-v1 Bait Design

description: A target enrichment probe set designed from 1,172 UCE loci identified among Coleoptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.5061/dryad.v0k4h/5
title: Diptera Bait Design and Testing Files

description: The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Diptera.  The *-design-steps.md file is a description of the design steps followed for the group.  The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group.  The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing.  The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file.  The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file.  The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
DOI: 10.5061/dryad.v0k4h/6
title: Diptera-UCE-2.7K-v1 Bait Design

description: A target enrichment probe set designed from 2,711 UCE loci identified among Diptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.5061/dryad.v0k4h/7
title: Hemiptera Bait Design and Testing Files

description: The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Hemiptera.  The *-design-steps.md file is a description of the design steps followed for the group.  The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group.  The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing.  The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file.  The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file.  The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
DOI: 10.5061/dryad.v0k4h/8
title: Hemiptera-UCE-2.7K-v1 Bait Design

description: A target enrichment probe set designed from 2,731 UCE loci identified among Hemiptera. This is a ZIP archive of a FASTA file that is ready for submission of the probe set for synthesis.
DOI: 10.5061/dryad.v0k4h/9
title: Lepidoptera Bait Design and Testing Files

description: The ZIP archive contains the files used to identify, design, and test probes targeting conserved loci in Lepidoptera.  The *-design-steps.md file is a description of the design steps followed for the group.  The "BAM" directory contains mappings of real/simulated reads to the base genome sequence for the group.  The "BED" directory contains BAM files converted to BED, as well as intermediate BED files created during BED processing.  The "BED" directory also contains the database of putatively conserved loci in the exemplar+base genome taxa, and the temporary probe design file.  The "*-probes" directory contains the database of temporary probe mappings to exemplar taxa, several intermediate files, and the principal probe design file.  The "in-silico-test" directory contains all data from in-silico testing of the principal probe design file.
DOI: 10.5061/dryad.vv469/93
title: README file

description: A description of what all the other files contain.
DOI: 10.17632/37d3gnm4nh.1
title: Data for: Floodplain habitat is disproportionately important for bats in a large river basin.

description: These three tables contain all data used to do analyses and make tables and figures associated with: Blakey RV, Kingsford RT, Law, BS & Stoklosa J (in press) Floodplain habitat is disproportionately important for bats in a large river basin. Biological Conservation in press. Columns are labelled to match variables used in the publication. bat.master was used to make Tables 1,2 and Figs 3,4 as well as Appendix S2, S4. insect.master was used to make Table 3 and Appendix S5 bat.insect.master was used to make Appendix S6 For any questions, email the corresponding author at rachelvblakey@gmail.com
DOI: 10.17632/37d3gnm4nh.2
title: Data for: Floodplain habitat is disproportionately important for bats in a large river basin.

description: These three tables contain all data used to do analyses and make tables and figures associated with: Blakey RV, Kingsford RT, Law, BS & Stoklosa J (in press) Floodplain habitat is disproportionately important for bats in a large river basin. Biological Conservation in press. Columns are labelled to match variables used in the publication. bat.master was used to make Tables 1,2 and Figs 3,4 as well as Appendix S2, S4. insect.master was used to make Table 3 and Appendix S5 bat.insect.master was used to make Appendix S6 For any questions, email the corresponding author at rachelvblakey@gmail.com
DOI: 10.17632/8p2sh847m7.1
title: Data for: Pharmacokinetic Studies of a Three-Component Complex that Repurposes the Front Line Antibiotic Isoniazid against Mycobacterium tuberculosis

description: Data report providing experimental details
DOI: 10.17632/sds9ngvvjw.1
title: Data for: A hybrid search-tree discriminant technique for multivariate wear particles classification
DOI: 10.17632/sds9ngvvjw.2
title: Data for: A hybrid search-tree discriminant technique for multivariate wear particles classification
DOI: 10.5061/dryad.14c73/1
title: Mycorrhizal trait data and niche characteristics for vascular plants in the Dutch flora

description: File includes updated mycorrhizal status, type and flexibility data with new additional references, and realized niche optima, widths and volumes along soil fertility, pH, moisture, salinity, light and temperature axes for the vascular plant species in the Dutch flora. Also, a legend is provided as a separate sheet in the file. More details can be found in the README file.
DOI: 10.5061/dryad.1cm80/2
title: Genotypes of reproductive trees and seeds of Miconia affinis

description: This data file has two spreadsheets, one with the genotypes for reproductive trees used in our paternity analysis for 8 microsatellite markers. We also included the geographic coordinates for each tree. The other spreadsheet has the genotypes for the seeds collected in our single pollinator visit experiment.
DOI: 10.5061/dryad.1cm80/3
title: Seed viability analysis

description: This data file has all the variables used in our seed viability model.
DOI: 10.5061/dryad.1cm80/4
title: Pollen dispersal analysis

description: This data file has all the variables that we used in our pollen dispersal model.
DOI: 10.5061/dryad.21873/1
title: FileS1_H2_EbExon2_phased

description: This file is an alignment of all sequences of the Histocompatibility 2 class II locus antigen E beta, Exon 2. Each individual is represented by its two alleles, where the phase of the two alleles
was determined by using the phasing function included in the program DNASp (Rozas, J. (2009). DNA Sequence Polymorphism Analysis using DnaSP.).
DOI: 10.5061/dryad.22tq8/1
title: Data for self-thinning analysis

description: Contains data for mean aboveground biomass per individual and  tree density for each plot.
DOI: 10.5061/dryad.2815c/1
title: morphology_dataset

description: This file contains three datasets which were used in the analysis of the manuscript: 1) data on crushing resistance, test thickness and spine length for sea urchins collected inside and outside of marine reserves in north-eastern New Zealand, 2) data on crushing resistance, test thickness and spine length for juvenile sea urchins within the 6 month mesocosm experiment and, 3) porosity data collected from individuals examined under a scanning electron microscope.
DOI: 10.5061/dryad.30h0n/1
title: Dalrymple_etal_EM2018

description: Data from Dalrymple. et al. Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration. Ecological Monographs

Data for each grid cell in the study range is presented, including bird and butterfly colour (response) variables and environmental (predictor) variables. Predictor variables relate to the community diversity  and averages of the data available for the energy and resources in the environment and the habitat conditions in the grid cells. See manuscript for details on data sourcing and units on environmental variables. see Dalrymple et al 2015 Birds, butterflies and flowers in the tropics are not more colourful than those at higher latitudes. Global Ecology and Biogeography, 24(12), 1424-1432. DOI: 10.1111/geb.12368 for information on bird and butterfly color data and methodology. .csv file
DOI: 10.5061/dryad.30h0n/2
title: Dalrymple_etal_EM2018_scriptforanalyses

description: R script for application to Dalrymple_etal_EM2018.CSV data file - produces analyses and some figures. .txt file
DOI: 10.5061/dryad.56n7v/1
title: Age-0+ Steelhead Survival Input File

description: This input file was used for the among-year detection/survival probability analysis of age-0+ steelhead
DOI: 10.5061/dryad.56n7v/2
title: Age-0+ Steelhead and Coho Survival Input File (Year 2011)

description: This input file was used for the within-year detection/survival probability analysis of age-0+ steelhead and coho
DOI: 10.5061/dryad.56n7v/3
title: Mark-Recapture Spreadsheet

description: This spreadsheet was used to create the INP files used for the among-year and within-year detection/survival probability analyses. Please view README file.
DOI: 10.5061/dryad.5qk4s/3
title: other traits
DOI: 10.5061/dryad.625tn/1
title: DataS1 - Nodulation and phylogenetic data for legume genera.

description: DataS1.zip includes the following files:       
[1] File name: Nodulation_clade.csv; 
Size: 749 rows excluding header;
Format and storage mode: comma-separated values format, no compression;
Header Information: See Header_explanation.csv;
Description: Analysis-ready, searchable database of nodulation data for 749 legume genera with species diversity, subfamily associations, and phylogenetic information corresponding to family-wide trees (curated and pruned from LPWG 2013; available in pruned_tree.zip).

[2] File name: Header_explanation.csv;
Size: 6 rows excluding header;
Format and storage mode: comma-separated values format, no compression;
Header Information: NA;
Description:  Table providing description of each column contents of Nodulation_clade.csv.

[3] File name: pruned_tree.zip 
(pruned.legume.1.date.tre - pruned.legume.100.date.tre);  
Size: 100 phylogenetic trees;  
Format and storage mode: zip (.tre format within zip folder); 
Header Information: NA;
Description: The set of 100 sampled trees from the LPWG (2013) pruned down to 157 shared or “consensus” clades to achieve a distribution of backbone phylogenies representing the deep phylogenetic structure of the legumes. Our curation and pruning allows for compatibility of phylogenetic information with available nodulation data (available in Nodulation_clade.csv database).

[4] Table S1.pdf; 
Size: 1 pg;
Format and storage mode: pdf, no compression;
Header Information: Provided in file;
Description: Phylogenetic ANOVA result – difference in net diversification rates between nodulating and non-nodulating legume clades with ‘unknown’ data included as either all “nodulating’ or all ‘non-nodulating’.
DOI: 10.5061/dryad.95sh0/1
title: Graf et al Biotropica_data

description: Data on beetle (Coleoptera) assemblages on Bracket Fungi (Basidiomycota, in the orders Polyporales and Hymenochaetales) in a Brazilian Forest.
DOI: 10.5061/dryad.9gd3n/1
title: Trinotate annotation

description: The taimen transcirptome was annotated using Trinotate(https://trinotate.github.io/) according to the guidance. NR, Uniprot-Sprot and Pfam databases were used.
DOI: 10.5061/dryad.9gd3n/2
title: Interproscan annotation

description: Interproscan annotation for taimen transcriptome. 79,800 transcripts were annotated using Interproscan.
DOI: 10.5061/dryad.9gd3n/3
title: Gene Ontology annotation

description: The sequences with significant hits in the Uniprot database or Pfam database were assigned GO terms using the Trinotate package, and the GO terms were assigned using Interproscan.72,728 transcripts were assigned to 15,107 GO terms, including 10,185 biological process terms, 1,429 cellular component terms and 3,493 molecular function terms.
DOI: 10.5061/dryad.9gd3n/4
title: KEGG annotation

description: A KEGG pathway analysis was performed using GhostKOALA . A total of 51,698 transcripts were assigned to 8,052 KEGG ortholog groups
DOI: 10.5061/dryad.9gd3n/5
title: eggNOG annotation

description: The COG functional category annotation using eggNOG-mapper (Huerta-Cepas et al., 2017), 72,605 putative proteins were annotated.
DOI: 10.5061/dryad.9gd3n/6
title: Assembly transcriptome

description: The transcriptome sequences were assembled using the Trinity package. Before assembly, low-quality reads were filtered from the raw reads using Trimmomatic with the parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50. The clean reads from the two pooled libraries were merged and in silico normalized using the Trinity package with default parameters to reduce the running time and memory consumption. A parameter kmer size of 25 and a depth of at least two kmer were used for assembly with the Trinity package. The contigs resulting from Trinity were further fed to the TGI clustering Tool (version 2.1) to process alternative splicing and redundant sequences.The raw RNA-Seq reads and assembled transcripts were deposited in the European Nucleotide Archive under the project ID PRJEB19675 and accession numbers HAGJ01000001 to HAGJ01190473 for the assembled transcripts.
DOI: 10.5061/dryad.9gd3n/7
title: SNP.vcf

description: Clean reads were firstly mapped to transcripts using Bowtie2, then SNPs were called SNPs using SAMtools. Raw SNPs with a minimum depth of 4 and minimum quality of 20 were filtered out using Vcftools (Danecek et al., 2011), and SNPs clustered within 50 bp were also filtered out. SNPs were annotated using snpEFF(http://snpeff.sourceforge.net/)
DOI: 10.5061/dryad.bc498/1
title: Eremophila_mumKnown

description: microsatellite data for Eremophila glabra populations
DOI: 10.5061/dryad.bc498/2
title: AutoPoly package

description: AutoPoly R package for population assignment for autopolyploids.
DOI: 10.5061/dryad.bc498/3
title: metaPopSim_autoPoly

description: batch scripts for running and evaluating accuracy of metapopulation simulation for autopolyploid population assignment
DOI: 10.5061/dryad.bc498/4
title: powerSims

description: scripts for running metapopulation simulations
DOI: 10.5061/dryad.bc507/1
title: Appendix S1: Phylogenetic tree file, PDI

description: This file (spinal_1.pdi) of the phylogenetic tree (shown in Fig. 1) was produced in the DOS PDTREE.EXE program (Garland et al., 1999; Garland & Ives, 2000). The two-letter codes correspond to the “PDICode” column in the raw data file (Appendix S4).
DOI: 10.5061/dryad.bc507/2
title: Appendix S2: Phylogenetic tree file, DSC

description: This phylogenetic tree in DSC format (SPINAL_1_DSC_out_from_Excel.dsc), which was input to the RegressionV2.m program in Matlab for our analyses. The order of the columns and rows corresponds to the order of species in our data files (Appendices S4-6). The file was originally created in the DOS PDDIST.EXE program (Garland & Ives, 2000), from the file spinal_1.pdi (Appendix S1), with headers, then edited in Excel to verify the order and to remove headers.
DOI: 10.5061/dryad.bc507/3
title: Appendix S3: Full model comparison

description: Full tables (AppendixS3_3_Tonini.xlsx) of alternate regression models showing all possible models (including those with zero support based upon criteria described in the Methods) for all species (N = 131) in one sheet and for caenophidians only (N = 114) in the other. † Evidence Ratios greater than 10,000
DOI: 10.5061/dryad.bc507/4
title: Appendix S4: Raw data

description: Raw data used for the analysis (data_raw_JLT_8.xlsx).
DOI: 10.5061/dryad.bc507/5
title: Appendix S5: Data file for analysis of all species

description: This text file of data for all species (data_Matlab_JLT_8.txt) was input to the RegressionV2.m program in Matlab for our analyses. The order species corresponds to the order in the DSC phylogeny file (Appendix S2).
DOI: 10.5061/dryad.dd414/1
title: Perl code for finding equilibrium virulence

description: Perl code for finding equilibrium virulence of multiple species under shared costs. The number of species and the parameters of for each species is set through the arrays ab, am, b0, and m0 in lines 6-9.
DOI: 10.5061/dryad.dq28j/5
title: Aliatypus_F9F10_tartan_dryad

description: tartan protein, putative, alignment file, nexus format
DOI: 10.5061/dryad.dq28j/6
title: Aliatypus_G1G2_Sdccag1_dryad

description: Sdccag1 protein, putative, alignment file, nexus format