cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rf7g5/34
title: Breinholt_et_al_degen12_DS3

description: Dataset 3 (acrossLEP_AHE+ALLtrans ). Nexus file consists of both AHE and the transcriptomic data of Kawahara and Breinholt 2015. The file contains codon position 1 & 2 for 2948 loci and 76 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5/35
title: Breinholt_et_al_aminoacid_DS2

description: Nexus file containing amino acid data for 557 loci and 75 taxa. See taxa_list.txt for species names of each taxon, this is an amino acid nexus file with a CHARSET that defines each loci. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5/36
title: Breinholt_et_al_degen12_DS2

description: Dataset 2 (acrossLEP_AHE+PARTtrans). Nexus file containing codon position 1 & 2 for 557 loci and 75 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5/37
title: Breinholt_et_al_degen12_DS1

description: Dataset 1 (acrossLEP_AHE). Nexus file containing codon position 1 & 2 for 557 loci and 23 taxa. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene that starts with codon position 1. Synonymous signal was removed using degen v1.4 Perl script (http://www.phylotools.com), and the third codon has been removed. Loci names correspond to Loci numbers in the Lep1 enrichment kit included in this DRAYD package. For further information see Breinholt et al. (2017) and Breinholt_et_al_Supplementary_File_1_S1-S11.xlsx in this Dryad package for more details.
DOI: 10.5061/dryad.rf7g5/38
title: README

description: README File containing list of files and script contained in this dryad package
DOI: 10.5061/dryad.sm379/1
title: CONTROL_OUTPUTFILES

description: R-Processed output files for Control simulations
DOI: 10.5061/dryad.sm379/2
title: RAND0.5_OUTPUTFILES

description: R-processed output files for random extinction, intensity = 0.5
DOI: 10.5061/dryad.sm379/3
title: RAND0.75_OUTPUTFILES

description: R-processed output files for random extinction, intensity = 0.75
DOI: 10.5061/dryad.sm379/4
title: RAND0.9_OUTPUTFILES

description: R-processed output files for random extinction, intensity = 0.9
DOI: 10.5061/dryad.sm379/5
title: SOD0.5_OUTPUTFILES

description: R-processed output files for SOD extinction, intensity = 0.5
DOI: 10.5061/dryad.sm379/6
title: SOD0.75_OUTPUTFILES

description: R-processed output files for SOD extinction, intensity = 0.75
DOI: 10.5061/dryad.sq2g4/1
title: First milking data

description: FPLC absorbance time-series output for the initial (before treatments, t=0) venom extraction. Each of the four treatments are presented on separate sheets. Each column is a different scorpion, values are absorbance at 280nm. The leftmost column specifies the volume eluted in mL (beginning at 5mL due to an initial 5 mL to prime the equipment).
DOI: 10.5061/dryad.sq2g4/2
title: Second milking data

description: FPLC absorbance time-series output for the second (after completion of treatments, t=1) venom extraction. Each of the four treatments are presented on separate sheets. Each column is a different scorpion, values are absorbance at 280nm. The leftmost column specifies the volume eluted in mL (beginning at 5mL due to an initial 5 mL to prime the equipment).
DOI: 10.5061/dryad.sq2g4/3
title: Third milking data

description: FPLC absorbance time-series output for the third (3 weeks after the second venom extraction, t=2) venom extraction. Each of the four treatments are presented on separate sheets. Each column is a different scorpion, values are absorbance at 280nm. The leftmost column specifies the volume eluted in mL (beginning at 5mL due to an initial 5 mL to prime the equipment).
DOI: 10.5061/dryad.sq2g4/4
title: xCELLigence output for vertebrate cell assays

description: Raw xCELLigence output measuring changes to cell index in response to each venom fraction and the whole venom mixture (20 µL). Cell response is a combination measure of changes in media conductivity or cell contact/toxicity, which varies as the cells deform in response to exposure to a chemical sample. The maximum drop value in 2 hours after venom addition was deemed the predator cell response. Each fraction was replicated with 3 cell wells.
DOI: 10.5061/dryad.sq2g4/5
title: Cricket bioassay results

description: Caption: Results of invertebrate toxicity assays, evaluating toxin activity using the righting response of immature crickets to each venom fraction. 3 µL of one of the 14 chemical fractions was injected ventrally into the pronotum of an immature cricket, which was then rolled onto its back every 10 seconds 18 times for a total of 3 minutes. A compromised righting response was recorded when a cricket was unable to right itself within 60 seconds of being rolled onto its dorsal side. Each fraction was replicated with 10 crickets.
DOI: 10.5061/dryad.sq72d.1/15.1
title: Kenai_Roads_AmphibianAbnormalities_ClimateChange_Proposal

description: A follow up study to the published study was conducted. This document is the proposal under which the data collection for this submission was funded. Unfortunately the data were not analyzed due to federal budget cuts, but we wanted to share the data and the proposed analyses with the public.
DOI: 10.5061/dryad.sq72d.1/19.1
title: AnchorageSedimentMetals

description: The “AnchorageSedimentMetals.csv” file provides metals concentrations in sediment for the Anchorage 2009 study. These are  metals data analyzed by ICP/MS and are sediment digest samples, and are comparable to the sediment samples from the Kenai data set, based on the methods used. Further information regarding quality control, and analytical lab methodology can be found in the file: “AnchorageRawSedWaterResultsMethodsQC.pdf”, included with this data submission.
DOI: 10.5061/dryad.sq72d.1/20.1
title: AnchorageWaterMetals

description: The “AnchorageWaterMetals.csv” file provides metals concentrations in sediment for the Anchorage 2009 study. These are metals data analyzed by ICP/MS and are unfiltered water samples, and are comparable to the samples labeled as sample type, “total” from the Kenai data set, based on the methods used.
DOI: 10.5061/dryad.sq72d.1/21.1
title: BDFilterResults

description: BDFilterResults.csv data set includes information on 222 water filters that were analyzed for Bd (Batrachochytrium dendrobatidis), a chytrid fungus that can cause chytridiomycosis in amphibians. Samaples were analyzed by the U.S. Geological Survey using methods similar to those described in Kirshtein et al., 2007.
DOI: 10.5061/dryad.sq72d.1/22.1
title: WaterQualityBDFilters

description: “WaterQualityBDFilters.csv” – This table describes water quality information collected with a YSI sonde concurrent with sampling for Batrachochytrium dendrobaditis in water. See “Methods.txt” file for more information on field data collection methodology.
DOI: 10.5061/dryad.sq72d.1/23.1
title: Site Selection

description: This is a text file documenting the site selection procedures for the project. This information is also included with figures and tables in the "DataSummaryReport.pdf" document.
DOI: 10.5061/dryad.sq72d.1/24.1
title: Field methods

description: Text contained in this document is repeated with maps and other figures in the “DataSummaryReport.pdf” file included with this data submission. This file describes field methods in a .txt format to ensure readability in multiple computer formats.
DOI: 10.5061/dryad.sq72d.1/25.1
title: ListOfFiles

description: Contains a brief description of all files included in this data submission.
DOI: 10.5061/dryad.sq72d.1/26.1
title: Project Data Summary Report

description: This report provides background on the project, a full summary of site selection and field methods (with maps and figures), and a summary of the information contained in each data file included with this submission.
DOI: 10.5061/dryad.sv601/1
title: electronic supplementary material
DOI: 10.5061/dryad.t10p2/1
title: RSOS-170750data
DOI: 10.5061/dryad.ts47s/1
title: Supplementary Figures and Videos of ROM 75860, Zuul crurivastator

description: Supplementary Figure 1: ROM 75860 skull in right lateral view.
Supplementary Figure 2: ROM 75860 skull in left lateral view.
Supplementary Figure 3: ROM 75860 skull in anterior  view.
Supplementary Figure 4: ROM 75860 skull in posterior view.
Supplementary Figure 5: ROM 75860 skull in dorsal view.
Supplementary Figure 6: ROM 75860 skull in ventral view.
Supplementary Figure 7: ROM 75860 left lower jaw in lateral view.
Supplementary Figure 8: ROM 75860 left lower jaw in medial view.
Supplementary Figure 9: ROM 75860 left lower jaw in dorsal view.
Supplementary Figure 10: ROM 75860 left lower jaw in ventral view.
Supplementary Figure 11: ROM 75860 right lower jaw in lateral view.
Supplementary Figure 12: ROM 75860 right lower jaw in medial view.
Supplementary Figure 13: ROM 75860 right lower jaw in dorsal view.
Supplementary Figure 14: ROM 75860 right lower jaw in ventral view.
Supplementary Figure 15: ROM 75860 right lower jaw in anterior view.
Supplementary Figure 16: ROM 75860 right lower jaw in posterior view.
Supplementary Figure 17: ROM 75860 tail in dorsal view.
Supplementary Figure 18: ROM 75860 tail in dorsal view.
Supplementary Video: Photogrammetric reconstruction of the skull and jaws of ROM 75860.
DOI: 10.5061/dryad.013d5/4
title: Brent et al. Behaviour vs Age

description: Dataframe for social behaviours relative to age, 9 columns: A = animal ID, B = year, C = age in year, D = number of adult female relatives (r &gt; 0.063), E = dominance rank in year (L = low ranking, H = high ranking), F = z-score for rate of grooming received from others, G = z-score for rate of grooming given to others, H = z-score for rate of aggression received from others, I = z-score for rate of aggression given to others.
DOI: 10.5061/dryad.157c8/1
title: Koprivnikar & Urichuk Biol Letter 2017 Dryad data

description: Larval amphibian activity with/without predator cue exposure and parasite risk
DOI: 10.5061/dryad.1rd15/1
title: Lucas et al 2017 Data

description: Excel file of insects recorded during study
DOI: 10.5061/dryad.2h3f2.2
title: Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens
DOI: 10.5061/dryad.2h3f2.2/1.2
title: Coordinates of Hosts
DOI: 10.5061/dryad.2h3f2.2/14.2
title: Dataset of records of ticks, hosts, and pathogens (with climate and coordinates) in Western Palearctic

description: This file contains a description of the data package contents for Estrada-Peña and de la Fuente (2016) "Species interactions in occurrence data for a community of tick-transmitted pathogens"
DOI: 10.5061/dryad.2h3f2.2/5.2
title: Coordinates of ticks with hosts records
DOI: 10.5061/dryad.2h3f2.2/8.2
title: Environmental variables
DOI: 10.5061/dryad.2ng4k/1
title: competitive fitness data

description: Excel workbook with four worksheets.  Sheet 1, "malefitness" contains male fitness data; sheet two, "malefit_readme" contains descriptions of column headings.  Sheet 3, "hermfitness" contains hermaphrodite fitness data; sheet 4, "hermfit_readme" contains descriptions of column headings.
DOI: 10.5061/dryad.2sv68/1
title: 2017-06-30 Raw data for Lan-Hui Li et al.

description: The raw data of "A synthetic cationic antimicrobial peptide inhibits inflammatory response and the NLRP3 inflammasome by neutralizing LPS and ATP".
DOI: 10.5061/dryad.395sm/1
title: Appendix S1 Benthic foraminiferal counts and taphonomic traits

description: This appendix includes all raw data from the article: 1) raw counts of benthic foraminifera (63-125 microns and &gt;125 microns); and 2) raw counts of taphonomic traits (63-125 microns and &gt;125 microns)
DOI: 10.5061/dryad.4735b/1
title: Dryad_AmNat_Fowler_Williams

description: Life-history and physiology data
DOI: 10.5061/dryad.4m3r4/1
title: Acristatellus_alignment

description: alignment for mtDNA ND2 locus
DOI: 10.5061/dryad.4m3r4/2
title: FigS1

description: expanded version of Fig. S1
DOI: 10.5061/dryad.4m3r4/3
title: FigS1_Treefile

description: Treefile (.nex) for Figure S1
DOI: 10.5061/dryad.4ps2t/1
title: Lin_etal_2017_praetermissus_Appendix1
DOI: 10.5061/dryad.4ps2t/2
title: Lin_etal_2017_praetermissus_Appendix2
DOI: 10.5061/dryad.4ps2t/3
title: Lin_etal_2017_praetermissus_Appendix3
DOI: 10.5061/dryad.4ps2t/4
title: Lin_etal_2017_praetermissus_FigS1
DOI: 10.5061/dryad.6s48n/1
title: RSOS Paper

description: Compressed archive of all the Figures in the paper, the measurement data used to generate them and the beam path data files used in the experiments.
DOI: 10.5061/dryad.72mr1/1
title: Kingsolver&Buckley.PRSb.Supplement_13June2017

description: Description of the set of models used in the studies and simulations, and climatic data for each study site during the time period of the simulations (1960-2010).
DOI: 10.5061/dryad.75mt7/3
title: family1

description: Quality filtered 100 base pair reads sequenced with RADseq (SbfI digest).
DOI: 10.5061/dryad.7nd95/1
title: reef_carbon_sequestration_publication 20170425

description: all raw data and calculations
DOI: 10.5061/dryad.ct8j4/1
title: Swan microsatellite data with coordinates

description: Complete Microsatellite Dataset used in the publication with geographic coordinates and sex assignment of individuals
DOI: 10.5061/dryad.ct8j4/2
title: BlackSwansDryad
DOI: 10.5061/dryad.g4q06/1
title: data_dryad_doi: 10.1111/ecog.03220

description: Changes in efective number of species as well as changes in species abundance in the seed availabiltiy seed rain transition. Changes in diversity in the seed rain seedling transition.
DOI: 10.5061/dryad.gr6q0/1
title: Arctops Data Matrix

description: Character data (in NEXUS format) used in the phylogenetic analysis.
DOI: 10.5061/dryad.k6j12/8
title: Supplemental Fig 2

description: Delta K analysis for D. destructiva population
DOI: 10.5061/dryad.k6j12/9
title: Supplemental Fig 3

description: Dendrogram of Discula destructiva isolates
DOI: 10.5061/dryad.m9s45/1
title: A metacognitive illusion in monkeys - Data
DOI: 10.5061/dryad.mj3cd/1
title: data_teotonioetal.2006

description: the excel files contains the data from Teotonio et al. 2006 Evolution, regarding male proportions, population performance, etc. in separate sheets.  Details on the methods can be found in the original MS. Please contact teotonio@biologie.ens.fr if you have questions about experimental design or data coding
DOI: 10.5061/dryad.pf684/1
title: Organic substances with TLV and physicochemical properties

description: The file in the supplementary data is a table that lists the organic chemical substances that were studied as well as their Cramer classes, CASRN, occupational exposure limits (i.e. 8-h TLV-TWA), LogP, and vapor pressure.
DOI: 10.5061/dryad.pp127/1
title: dosimeters_raw_2012

description: Neonicotinoid deposition data from fields sown in 2012
DOI: 10.5061/dryad.pp127/2
title: dosimeters_raw_2013

description: Neonicotinoid deposition data from fields sown in 2013
DOI: 10.5061/dryad.pp127/3
title: drift_data_Relative_to_wind

description: Neonicotinoid deposition data, relative to prevailing wind direction at time of sowing
DOI: 10.5061/dryad.pr4d0/1
title: All ITS

description: nuclear DNA (nuclear marker internal transcribed spacer 1)
DOI: 10.5061/dryad.pr4d0/2
title: All MT

description: mitochondrial DNA (COI, COII and CytB)
DOI: 10.5061/dryad.pr4d0/3
title: BI TREE export
DOI: 10.5061/dryad.pr4d0/4
title: ITS haplotypes10
DOI: 10.5061/dryad.r0q02/1
title: pseudo-reference genomes for species included in study

description: pseudo-reference genomes for the 44 species included in this study and one outgroup; each file is annotated with respect to our targets
DOI: 10.5061/dryad.r0q02/2
title: VCF for Colobosaura modesta

description: variant data for Colobosaura modesta, including variant and invariant sites; filtered for coverage &gt;=10x and quality &gt;=20 and phased using read-backed phasing
DOI: 10.5061/dryad.r8251/1
title: Milk Composition Phenotype Data

description: Milk composition records were measured as part of standard herd testing procedures. Abbreviations used: id = animal identification, sire = sire animal identification, pgsire = parternal sire animal identification, pmgsire = partern	fr = friesian, je = jersey, hol = holestein, FxJ = freisian x jersey, FxH = freisian x holestein, JxH = jersey x holestein, fat = fat yield, fat_pct = fat percentage, milk = milk yield, prot = protein, prot_pct = protein percentage, ydlwt = liveweight
DOI: 10.5061/dryad.r8251/2
title: Gene Expression Data

description: Gene expression data for genes at the chromosome 14 liveweight locus from lactating mammary tissue biopsies. RNAseq read counts have been normalised using variance-stabilisation transformation. Abbreviations used: id = animal identification, sire = sire animal identification, pgsire = parternal sire animal identification, pmgsire = partern	fr = friesian, je = jersey, hol = holestein, FxJ = freisian x jersey, FxH = freisian x holestein, JxH = jersey x holestein,
DOI: 10.5061/dryad.rf7g5.1/18.1
title: extract_probe_region

description: python script to split alignment into head, probe, and tail regions based on the beginning and end of a reference sequence in the alignment
DOI: 10.5061/dryad.rf7g5.1/19.1
title: s_hit_checker

description: python script to process the output of BLAST to find sequences that fit the single hit critera
DOI: 10.5061/dryad.rf7g5.1/20.1
title: ortholog_filter

description: python script to process the output of BLAST to find if the location of the best hit on the genome is the same location as the probe target from that genome.
DOI: 10.5061/dryad.rf7g5.1/21.1
title: split

description: python script to split a single line fasta file with many loci into locus specific fasta files
DOI: 10.5061/dryad.rf7g5.1/22.1
title: alignment_DE_trim

description: python script to trim alignments by density and entropy
DOI: 10.5061/dryad.rf7g5.1/23.1
title: flank_dropper

description: python script to remove poorly aligned sequences in the flanking head and tail regions
DOI: 10.5061/dryad.rf7g5.1/24.1
title: counting_monster

description: python script to count the loci per taxa and put into a tab separated matrix
DOI: 10.5061/dryad.rf7g5.1/25.1
title: removelist

description: python script to remove list of sequences from a fasta file
DOI: 10.5061/dryad.rf7g5/15
title: JAVA_SourceCode

description: Compressed directory holding A.R.L (alemmon@evotutor.org) java source code
	This directory contains readme and instructions for use and to compile the java code for IdentifySpacedKmers7, QuickScan5, and ShallowMapper4. It also contain the Lep1_ProbeDesign directory used with the java programs to design the Lep1 probe set
	(IdentifySpacedKmers7, IdentifySpacedKmers7_readme.txt, Lep1_ProbeDesign, LepRefFiles.txt, QuickScan5_readme.txt, QuickScan5.java, ShallowMapper4_readme.txt, ShallowMapper4.java)
	ShallowMapper4: java script by A.R.L used to identify intron boundaries in genes for five reference taxa by mapping raw genomic reads to the corresponding transcriptomic sequences 
	QuickScan5: java script by A.R.L used to scan the additional 23 transcriptomes and ESTs by generating reference kmers using the 5-species alignments and using those kmers to map contig sequences from the transcriptomes to the candidate locus set
DOI: 10.5061/dryad.rf7g5/16
title: remove_duplicates

description: python script to identify and remove sequences for each taxon that had more than one sequence per locus
DOI: 10.5061/dryad.rf7g5/39
title: contamination_filter

description: python script to process blast results of blasting sequences from each loci against themselves using usearch to identify contamination
DOI: 10.5061/dryad.rf7g5/40
title: IBA_trans

description: python script to assemble AHE data loci by loci for using a fastq file from transcriptome data
DOI: 10.5061/dryad.rf7g5/41
title: Breinholt_et_al_RAW_DATA.tar.gz

description: compressed file containing the raw Illumina (2X100) AHE data
DOI: 10.5061/dryad.rr6rt/1
title: Capture_histories_Mark_fromat_2008_2014

description: Text file containing capture histories, which is the raw data used in all capture-mark-recapture analyses of Capensibufo rosei in this paper, and are in the format used by program Mark (White and Burnham 1999). Each '1'/'0' represents a positive (captured) or negative (not captured) history respectively, for a particular year from 2008 to 2014; the number thereafter represents n individuals with that particular capture history.
DOI: 10.5061/dryad.rr6rt/2
title: Model_covariates

description: These data are all the model covariates needed to run all capture-mark-recapture models in this paper. Although the variable titles are mostly self-explanatory, refer to the paper Methods for a more detailed description of each covariate.
DOI: 10.5061/dryad.rs449/1
title: Fig. S1: Crown angiosperm age trace

description: Figure S1: Traces of the age of the crown angiosperm node across replicate analyses (burnin phase only) for Beaulieu et al. (2015) (top) and Magallo ́n et al. (2015) (bottom) data sets. Top: prior (lognormal priors), orange (n = 2); posterior (lognormal priors), blue (n = 3); prior (exponential priors), red (n = 2); posterior (exponential priors), green (n = 3). Bottom: prior (no angiosperm constraint), orange (n = 4); posterior (no angiosperm constraint), blue (n = 4); prior (all constraints), green (n = 4); posterior (all constraints), red (n = 3; note that this is mostly obscured by the green prior trace). All analyses were initialized with the age of crown angiosperms set at ∼140 Ma.
DOI: 10.5061/dryad.sc682/1
title: Host metadata

description: Table contains information on the host specimens of the Laboulbeniales included in the study.
DOI: 10.5061/dryad.sm379/10
title: SOR0.9_OUTPUTFILES

description: R-processed data files for SOR extinction, intensity=0.9
DOI: 10.5061/dryad.sm379/11
title: R_Scripts_for_Dryad_1

description: Collection of R Scripts for processing MeSA output files
DOI: 10.5061/dryad.sm379/12
title: R_files_for_Dryad_2

description: More R scripts for processing MeSA output files
DOI: 10.5061/dryad.sm379/13
title: Excel_files_for_Dryad

description: Excel files containing data used for main text figures
DOI: 10.5061/dryad.sm379/14
title: MESA_X5.tar

description: Source code for version of MeSA
DOI: 10.5061/dryad.sm379/15
title: MESASCRIPTS

description: Input scripts for MeSA simulation runs
DOI: 10.5061/dryad.sm379/7
title: SOD0.9_OUTPUTFILES

description: R-processed output files for SOD extinction, intensity = 0.9
DOI: 10.5061/dryad.sm379/8
title: SOR0.5_OUTPUTFILES

description: R-processed output files for SOR extinction, intensity = 0.5
DOI: 10.5061/dryad.sm379/9
title: SOR0.75_OUTPUTFILES

description: R-processed output files for SOR extinction, intensity=0.75
DOI: 10.5061/dryad.sq72d.1/27.1
title: 2010 Kenai Chemistry Analysis Pilot Year Summary

description: This document describes the results of preliminary analyses conducted after the 2010 pilot year of the study. These results were used to determine the sampling design for 36 sites in 2011 and 2012.