cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr318/3
title: Eastern Coyote Raw Data

description: This file contains raw Illumina sequence data for the Eastern Coyotes (Canis latrans var.). Please check the metadata to confirm and cross-reference sample IDs.
DOI: 10.5061/dryad.pr318/4
title: Great Lakes Boreal Wolf Raw Data

description: This file contains raw Illumina sequence data for the Great Lakes Boeal Wolves (Canis lupus var). Please check the metadata to confirm and cross-reference sample IDs.
DOI: 10.5061/dryad.pr318/5
title: Grey Wolf Raw Data

description: This file contains raw Illumina sequence data for the Grey Wolves (Canis lupus) and Dog (Canis lupus familiaris). Please check the metadata to confirm and cross-reference sample IDs.
DOI: 10.5061/dryad.rf7g5.1
title: Data from: Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics
DOI: 10.5061/dryad.rf7g5.1/38.1
title: README

description: README File containing list of files and script contained in this dryad package
DOI: 10.5061/dryad.rf7g5.1/5.1
title: Breinholt_et_al_Supplementary_Figure_S1

description: Supplementary Figure S1 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.1/6.1
title: Breinholt_et_al_Supplementary_Figure_S2

description: Supplementary Figure S2 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.1/7.1
title: Breinholt_et_al_Supplementary_Figure_S3

description: Supplementary Figure S3 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.1/8.1
title: Breinholt_et_al_Supplementary_Figure_S4

description: Supplementary Figure S4 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.1/9.1
title: Breinholt_et_al_Supplementary_Figure_S5

description: Supplementary Figure S5 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.2/31.2
title: Breinholt_et_al_DS6

description: Dataset 6 (shallow_flanks). Nexus file containing 749 loci and 35 taxa. The Extract_probe_region.py script was used on Dataset 4 to isolate data coming from the flanking regions region. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. 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.rf7g5.2/32.2
title: Breinholt_et_al_DS5

description: Dataset 5 (shallow_probe). Nexus file containing 749 loci and 48 taxa. The Extract_probe_region.py script was used on Dataset 4 to isolate data coming from the probe region. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. 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.rf7g5/21
title: split

description: python script to split a single line fasta file with many loci into locus specific fasta files
DOI: 10.5061/dryad.rf7g5/22
title: alignment_DE_trim

description: python script to trim alignments by density and entropy
DOI: 10.5061/dryad.rf7g5/23
title: flank_dropper

description: python script to remove poorly aligned sequences in the flanking head and tail regions
DOI: 10.5061/dryad.rf7g5/24
title: counting_monster

description: python script to count the loci per taxa and put into a tab separated matrix
DOI: 10.5061/dryad.rf7g5/25
title: removelist

description: python script to remove list of sequences from a fasta file
DOI: 10.5061/dryad.rf7g5/26
title: getlist

description: python script to get list of sequences from a fasta file
DOI: 10.5061/dryad.rf7g5/27
title: Breinholt_et_al_acrossLep_full_assemblies_all_loci

description: Fasta formatted sequence file containing sequences that pass pipeline step 1-6 for all loci and taxa in dataset 1-3. This file can be split using the split.py to separate into fasta files of individual loci.
DOI: 10.5061/dryad.rf7g5/28
title: Breinholt_et_al_shallow_full_assemblies_all_loci

description: Fasta formatted sequence file containing sequences that pass pipeline step 1-6 for all loci and taxa in dataset 4-6. This file can be split using the split.py to separate into fasta files of individual loci.
DOI: 10.5061/dryad.rf7g5/29
title: Breinholt_et_al_allcodonpostion123_acrossLep

description: Nexus file containing codon position 1 & 2  & 3 for 557 loci and 75 taxa used to make dataset 1-3. 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. 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.s508j/1
title: Measurements of telomere length and blood parasitism in tawny owls

description: Data are collected in the field. Molecular qPCR methods used to estimate telomere length and parasite intensity from blood samples
DOI: 10.5061/dryad.sq72d.1/10.1
title: SiteEvents

description: File describes observations from site visits made to measure water chemistry, water quality, and amphibian development between 2010 and 2012.
DOI: 10.5061/dryad.sq72d.1/11.1
title: SiteLocations

description: File provides locations of all sites sampled for amphibians or water quality on the Kenai Peninsula, AK between 2000 and 2012.
DOI: 10.5061/dryad.sq72d.1/12.1
title: Temperature Data

description: Contains temperature data from deep and shallow loggers programmed to record hourly during the summer months. When loggers were out of water or data were otherwise suspect, data were deleted. Please see TemperatureAnomalies.csv file for issues with loggers and their resolution when dates are missing from the Temperature.csv file.
DOI: 10.5061/dryad.sq72d.1/13.1
title: WaterQuality

description: This table describes water quality information collected with a YSI sonde and by field observers during each site visit. See “Methods.txt” file for more information on field data collection methodology.
DOI: 10.5061/dryad.sq72d.1/14.1
title: WetlandDepthVolume

description: The WetlandDepthVolume.csv data set includes wetland depth and area data that were collected for 36 sites between 2010 and 2012 to follow up on the published study.
DOI: 10.5061/dryad.sq72d.1/16.1
title: ANC_WQ_STUDY_2009

description: This file contains information on a study from 2009, which was a follow-up to the published study and a pre-cursor to data shared in this submission. The study title was: Storm Water Runoff: What effects do best management practices (BMPs) and storm events have on water quality in wetlands in the Anchorage Bowl? More information about the study is included in the readme file.
DOI: 10.5061/dryad.sq72d.1/17.1
title: AnchorageRawSedWaterResultsMethodsQC

description: This file includes information about laboratory methods and quality control information for the Anchorage water quality study data included in this submission.
DOI: 10.5061/dryad.sq72d.1/18.1
title: AnchorageSampleLog

description: This file contains Information about the sites sampled for the Anchorage Water Quality Pilot Study and provides a join field to the “SiteLocations.csv” file, which provides the latitude and longitude for each site included in this data submission.
DOI: 10.5061/dryad.sq72d.1/9.1
title: RoadsInfo

description: This file contains the measured distance from each wetland to the nearest road and whether the road was paved or gravel.
DOI: 10.5061/dryad.013d5/1
title: Brent et al. Survival_FamilySize

description: Data Frame, 9 columns: A = Animal ID, B = year, C= survival outcome, D = age at time X, E = age at time X+1, F = number of adult female relatives (r &gt; 0.063) at timeX, G = number of adult female reltiaves (r &gt; 0.125) at timeX, H = number of adult female reltiaves (r &gt; 0.25) at timeX, I = number of adult female reltiaves (r = 0.5) at timeX.
DOI: 10.5061/dryad.013d5/2
title: Brent et al. Survival_GroupSize

description: Data frame for survival relative to group size, 11 columns: A = animal ID, B = year, C = group size, including all animals, D = group size, adult females only, E = survival outcome, F = age at time X, G = age at time X+1, H = number of adult female reltiaves (r &gt; 0.063) at timeX, I = number of adult female reltiaves (r &gt; 0.125) at timeX, J = number of adult female reltiaves (r &gt; 0.25) at timeX, K = number of adult female reltiaves (r =0.5 ) at timeX,
DOI: 10.5061/dryad.013d5/3
title: Brent et al. Survival_MatrilinealRank

description: Dataframe for survival relative to matrilineal rank, 10 columns: A = animal ID, B = year, C = survival status, D = age at time X, E = age at time X+1, F = matrilineal rank (L = low rank, H = high rank), G = number of adult female reltiaves (r &gt; 0.063) at timeX, H = number of adult female reltiaves (r &gt; 0.125) at timeX, I = number of adult female reltiaves (r &gt; 0.25) at timeX, J = number of adult female reltiaves (r =0.5) at timeX,
DOI: 10.5061/dryad.107h6/1
title: Supplementary Figures, Tables, and text

description: Supporting figures, data and analyses for Darroch and Saupe (2017).
DOI: 10.5061/dryad.1pm3r/1
title: SNP genotyping data from the Yemeni and Eritreans

description: This dataset includes SNP genotyping data from 90 Yemeni (divided into three populations) and three Eritreans.
Genotyping data have been provided in binary Plink format (.bed, .bim, .fam) for all 607,938 autosomal SNPs, which we exported from Affymetrix Genotyping Console.
Affymetrix and dbSNP identifications for all 607,938 SNPs included as well as for the 585,413 SNPs analyzed in our study have also been provided.
All samples were genotyped on the Affymetrix Human Origins array with support from NSF BCS-1258965 to Connie J. Mulligan and Deven N. Vyas. 
Yemeni samples were collected in Yemen in 2007 with support from NSF BCS-0518530 to Connie J. Mulligan. The Eritrean samples were collected from international students at the University of Florida.
Yemeni_metadata.xlsx includes sex, first language, and population and governate identifications for all 90 Yemeni.
DOI: 10.5061/dryad.222j0/1
title: Estimates of Land Area for Sugarcane Expansion in Brazil

description: This is a zipped shapefile with data on land area for 557 microregions of Brazil
DOI: 10.5061/dryad.222j0/2
title: Sugarcane yield and production projection in Brazil

description: zipped file contains four different shapefiles. One is for sugarcane yield projection under historical and future projection of climate in Brazil. Remaining three shapefiles correspond to production or delivery of biomass at the mill under the three different land use scenarios.
DOI: 10.5061/dryad.222j0/3
title: Analyses in R

description: This folder provides codes, inputs, and output data and output Figures which were generated during this study.
DOI: 10.5061/dryad.25f7g/3
title: Supplementary File S7

description: Summary of jModelTest output for all loci.
DOI: 10.5061/dryad.25f7g/6
title: Raw_data_alignments_trees_CNEEs_Syst_Biol
DOI: 10.5061/dryad.2vh5c/1
title: Rogalski et al ProcB Raw data 042117

description: Sediment heavy metal concentrations, eutrophication indices (including sediment pigments and carbon to nitrogen ratio), and densities of daphniid zooplankton diapausing eggs for time periods spanning the mid to late 1800s-2011 in four lakes. These lakes are found in Connecticut, USA.
DOI: 10.5061/dryad.3n15h/1
title: Whole Achilles Tendon Longitudinal Elongation and Strain for the Contralateral and Tendinopathic Sides
DOI: 10.5061/dryad.3n15h/2
title: Proximal Achilles Tendon Longitudinal Elongation and Strain for the Contralateral and Tendinopathic Sides
DOI: 10.5061/dryad.3n15h/3
title: Free Achilles Tendon Longitudinal Elongation and Strain for the Contralateral and Tendinopathic Sides
DOI: 10.5061/dryad.3n15h/4
title: Free Achilles Tendon Cross Sectional Area Deformation and Strain for the Contralateral and Tendinopathic Sides
DOI: 10.5061/dryad.3n15h/5
title: Free Achilles Tendon Volume Deformation and Strain for the Contralateral and Tendinopathic Sides
DOI: 10.5061/dryad.4b6rv/1
title: Occurrence of food items found in Didelphis aurita and Metachirus nudicaudatus fecal samples

description: The study was conducted in an Atlantic Rainforest area, in the Serra do Mar State Park (23°20’S and 44°50’W), southeast of Brazil (São Paulo State coast), at altitudes between 43 and 89m asl (Eisenlohr et al. 2013). A trapping session of four consecutive nights was conducted monthly from October 2013 to November 2014. In order to capture the animals, we used one hundred Tomahawk traps (45 x 16 x 16 cm) on the ground, baited with banana, peanut butter, and bacon. The traps were 20 m apart from each other, forming a 3.4 ha grid (280m x 120m). Individuals captured were marked in each ear with one 1g monel ear tag (National Band and Tag Co.®), weighted, and identified by sex and age (Tyndale-Biscoe and MacKenzie 1976). Samples of scats were collected from adults only. Scats were collected from the bottom of the trap where the animal spent the night. The traps were placed on a platform of hardboard in order to isolate the scats from litter. Feces samples were dissolved in water and then filtered through a 1mm mesh screen sieve under running tap water. Then the material retained on the sieve was dried at ambient temperature. This undigested material was analyzed with a stereoscope and the taxonomic classification of the prey items found was done by specialists. After one year of trapping sessions (48 nights of trapping, 4800 trap-nights) we recorded 35 individuals (i.e., adults and juveniles) of *Didelphis aurita* and 19 individuals of *Metachirus nudicaudatus*. In order to avoid differences in the diet samplings of individuals, only adult feces were taken. Thirty-eight fecal samples were collected from 18 adults of *D. aurita*, and 32 fecal samples were collected from 15 adults of *M. nudicaudatus*. Their diet items are described in Table 01.
DOI: 10.5061/dryad.75mt7/1
title: family3

description: quality filtered single-end 100 base pair reads sequenced using RADseq (SbfI digest).
DOI: 10.5061/dryad.75mt7/2
title: family2

description: Quality filtered Single end 100base pair reads sequenced using RADseq (SbfI digest).
DOI: 10.5061/dryad.cp423/5
title: Spencer & Broom GT & urban gull klepto Supplementary Material (Appendices)

description: This pdf contains the supplementary material appendices associated with the article.
DOI: 10.5061/dryad.cv791/1
title: NDVI_Values_At_GroundTruth_Points

description: This file provides NDVI values associated with forage and weedy vegetation, as derived from digitized imagery. These data are summarized in Figure 3 in the associated manuscript.
DOI: 10.5061/dryad.cv791/2
title: GroundTruthTests

description: This file contains classification values (map categories) for ground-truth point values for each classification approach x input type combination examined. Please see associated article for details.
DOI: 10.5061/dryad.cv791/3
title: Accuracy_Metrics

description: This file contains accuracy metrics for each classification approach x input type combination examined. These values are derived from ground-truth tests (see GroundTruthTests). Please see associated article for details.
DOI: 10.5061/dryad.dv415/1
title: MHC_parasite data lemurs_Kaesler et al.
DOI: 10.5061/dryad.f502p/1
title: Dataset for Wale et al. 2017 Proc R Soc B

description: Dataset used in the paper. Includes daily measurements of red blood cell densities and the weight of mouse hosts, as well as the density of each parasite strain. Information about units of measurements given in the sheet entitled 'Notes on Data'.
DOI: 10.5061/dryad.fh41b/1
title: MigrationManuscript_MorphometryDataset

description: Butterflies collected in the field were dissected and their thoracic and abdominal masses were recorded. We used the raw measurements, as well as the thorax:abdomen ratio for our analyses. This file includes details about the species collected, their sex, migratory habits, migratory diapause/reproductive status, thoracic and abdominal masses, and their individual thorax:abdomen ratios.
DOI: 10.5061/dryad.h3c18/1
title: Data behind Baron et al 2017 Impacts of thiamethoxam on bumblebee queens

description: The data file contains the raw data for all bumblebee queens that were included in the statistical analyses. The 17 columns present Bee ID (the identification number given to queens, which represents the order in which they were caught), Species (the Bombus species to which they belong), Site (whether they were caught at the Heather Gardens or Saville Gardens within the Windsor Estate), Treatment (the thiamethoxam treatment to which they were exposed), Wax (whether queens laid down wax or not), WaxTime (the day on which waxing was observed), Egg (whether they laid eggs), EggTime (the day on which eggs were laid), Survival (whether the queen survived the experiment), SurvivalTime (the day on which the queen died - given as 29 if she didn't), Average daily syrup consumption (g per day), Size (mm) (Thorax width of bee, Size (mm_) (bee volume), Syrup2 (g/mm_) (syrup consumption corrected for bee size, see paper), Z score for size (standardised and corrected size, see paper), InfectionStatus (whether queens were infected or not), Average terminal oocyte length (mm), Z score for oocyte length (excludes dead queens) (the standardised corrected oocyte length, see paper).
DOI: 10.5061/dryad.k6j12/1
title: ALL microsatellite data for the manuscript

description: Microsatellite data in base pairs in an Excel file
DOI: 10.5061/dryad.k6j12/3
title: Supplemental Tables 1 and 2

description: S1  Table Pairwise Population Differences for D. Destructiva
DOI: 10.5061/dryad.k6j12/7
title: Supplemental  Fig. 1

description: Linkage Disequilibrium Tests for D. destructiva
DOI: 10.5061/dryad.mb3gb/1
title: Lencer2017

description: This file contains rpkm data, DNA sequence alignment, and a RAxML tree in nexus format
DOI: 10.5061/dryad.n7832/1
title: Data for species-level analyses

description: Data includes the following variables: phylo.name=scientific names which match nomenclature used in birdtree.org; patch.loc= dorsal (d) or ventral (v); log10av.ref=log10-transformed average reflectance of dorsal or verntral plumage patches; hab.close=index of vegetation density; temp=average temperature based on the distribution of the species; log10rain=average log10-transformed annual rainfall based on the distribution of the species; lat=average latitude based on the distribution of the species; lon=average longitude based on the distribution of the species; sex=male or female.
DOI: 10.5061/dryad.n7832/2
title: Data for the assemblage-level analyses

description: Data has the following variables: cell.name=identifier for each 1 degree cell; n.species=number of species recorded in cell; av.ref.m.d= average male dorsal reflectance value for species recorded in cell; av.ref.m.v=average male ventral reflectance value for species recorded in cell;	av.ref.f.d=average female dorsal reflectance value for species recorded in cell; av.ref.f.v=average female ventral reflectance value for species recorded in cell;	Lat=latitude of centre of cell; Lon=longitude of centre of cell; n.surveys=number of surveys carried out in cell; temp=average temperature in a 50 km radius around the centre of cell; log10rain=log10-transformed average annual rainfall in a 50 km radius around the centre ; veg=average vegetation structure score in a 50 km radius around the centre of cell.
DOI: 10.5061/dryad.pr318/6
title: Western Coyote Raw Data

description: This file contains raw Illumina sequence data for the Western Coyotes (Canis latrans). Please check the metadata to confirm and cross-reference sample IDs.
DOI: 10.5061/dryad.rf7g5.1/11.1
title: Scripts_README

description: Description of the python scripts and direction how to run them.
DOI: 10.5061/dryad.rf7g5.1/12.1
title: Breinholt_et_al_LOG_COMMANDS

description: Set of commands used to run the bioinformatic pipeline to generate data for Breinholt et al. 2017
DOI: 10.5061/dryad.rf7g5.1/13.1
title: Breinholt_et_al_Supplementary_File_2_Lep1

description: Specification file for the Lep1 probe set used to order probes from Agilent Technologies (http://www.agilent.com/)
DOI: 10.5061/dryad.rf7g5.1/14.1
title: Lep1_ref

description: Compressed file containing the data for each reference for each loci in the Lep1 kit  as well as used in the IBA assembly.
DOI: 10.5061/dryad.rf7g5.1/15.1
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.rf7g5.1/17.1
title: IBA

description: python script to assemble AHE data loci by loci
DOI: 10.5061/dryad.rf7g5.1/4.1
title: Breinholt_et_al_Supplementary_File_1__S1-S11

description: Supplementary File 1: Microsoft excel document including Supplementary Table S1-S11 from Breinholt et al. (2017)
DOI: 10.5061/dryad.rf7g5.1/40.1
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.rf7g5/30
title: Breinholt_et_al_aminoacid_DS1

description: 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.rf7g5/31
title: Breinholt_et_al_DS6

description: Dataset 6 (shallow_flanks). Nexus file containing 749 loci and 35 taxa. The Extract_probe_region.py script was used on Dataset 4 to isolate data coming from the flanking regions region. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. 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.rf7g5/32
title: Breinholt_et_al_DS5

description: Dataset 5 (shallow_probe). Nexus file containing 749 loci and 48 taxa. The Extract_probe_region.py script was used on Dataset 4 to isolate data coming from the probe region. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. 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.rf7g5/33
title: Breinholt_et_al_DS4

description: Dataset 4 (shallow_probe+flanks). Nexus file containing 749 loci and 48 taxa. Alignments were trimmed with a density of 60% and entropy of 1.5 using alignment_DE_trim.py and flacking regions were processed with the flank_dropper.py to remove head or tail sequences using 2 standard deviations for both the head and tail. See taxa_list.txt for species names of each taxon, this is a nucleotide nexus file with a CHARSET that defines each gene. 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.