cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fs375/1
title: Carr & Lima dove flight data

description: Data for all hypothermic mourning doves subjected to flight tests and included in our analyses.  The variable "Dep #" corresponds to the duration of the food-deprivation period (1 - 3 days).  The variable "Flight #" represents the number of the flight test during each deprivation night, listed in sequential order within Dep #.  "Tb drop" denotes the drop in body temperature compared to normal daytime body temperature for each bird.  Lastly, "Flight (1/0)" codes for a bird's ability to fly during each flight test (1 = fly-capable; 0 = no flight).
DOI: 10.5061/dryad.gk23s/1
title: WRIGHT ET AL. MasterData_P16_2009
DOI: 10.5061/dryad.hm690/1
title: Risk

description: Includes the prevalence of each foraging mode as a function of several independent variables including spatial position and food availability.
DOI: 10.5061/dryad.kt062/11
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/12
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/13
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/14
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/15
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.kt062/16
title: SNP data for Raleigh/Winters genotypes

description: SNP calls for the Raleigh and the Winters genotypes mentioned in the paper. They are in the vcf format, and were generated using the GATK software.
DOI: 10.5061/dryad.mg0v4/1
title: Firmat etal 2014 Walk the line DataDryad

description: The folder contains: [1] the raw data as used in the analysis (site abbreviations follow Table 1), [2] The posterior distribution of (co)variance matrices estimated at the two levels (within and among populations) using the MCMCglmm approach. [3] Data for the Cososmys primus lineage from Lich’s paper (1990, Paleobiology) reanalyzed in figure 4 (sample means).
DOI: 10.5061/dryad.n40hc/1
title: Supplemental Dataset 1. Classification of TAIR9 other RNAs
DOI: 10.5061/dryad.n40hc/2
title: Supplemental Dataset 2. Classification of the TUs identifed by ESTs
DOI: 10.5061/dryad.n40hc/3
title: Supplemental Dataset 3. Classification of the TUs previously reported by Matsui.A et.al 2008
DOI: 10.5061/dryad.n40hc/4
title: Supplemental Dataset 4. Classification of the TUs previously reported by Okamoto.M et.al 2010
DOI: 10.5061/dryad.n40hc/5
title: Supplemental Dataset 5. Tiling array datasets we used for analysis
DOI: 10.5061/dryad.n40hc/6
title: Supplemental Dataset 6. Classification of the TUs identifed by RepTAS
DOI: 10.5061/dryad.q2610/1
title: Bicknell et al - Inter-colony movement of pre-breeding seabirds - Supplementary Data

description: Raw stable isotope values of Leach's storm-petrel blood samples and calanus copepod CPR samples. Mixing model parameters for the original and sensitivity models with results of models comparison.Random sampling process and calculations.
DOI: 10.5061/dryad.rb75g/1
title: Microsatellite Dataset

description: Microsatellite information for three different populations, O. histrionica, pHYB (putative hybrid) and O. lehmanni. Data for seven microsatellite markers, two columns per locus, one column per allele. Column names are locus markers as named by the authors of the primers. References are listed at the bottom of the list. Missing values= 0.
DOI: 10.5061/dryad.s8c2c/7
title: OTU tables

description: The OTU tables produced from MOTHUR
DOI: 10.5061/dryad.s8c2c/8
title: MOTHUR input files

description: MOTHUR input files for DNA and RNA sequences analysis
DOI: 10.5061/dryad.t80fp/1
title: BIOMASS

description: Measured biomass from experimental plots.
DOI: 10.5061/dryad.t80fp/2
title: planted

description: Successfully planted species in each plot
DOI: 10.5061/dryad.t80fp/3
title: Spp_codes

description: Species names
DOI: 10.5061/dryad.t80fp/4
title: EXP1_MLtree_codes

description: Phylogenetic tree
DOI: 10.5061/dryad.t80fp/5
title: anal_dat

description: data for analysis, including diversity metrics
DOI: 10.5061/dryad.tb50m/5
title: blue cardinalid ND2 data set used in *BEAST analyses

description: Nexus file with subset of ND2 sequences used in *BEAST analyses. See ReadMe file to match sample names with species and voucher specimens.
DOI: 10.5061/dryad.1k4gq/5
title: QTL analysis scripts for North Carolina data

description: This file contains the R scripts used for QTL analysis of the F2 data from the NC field site.  Use of the various scripts is described in comment lines within the file.  Scripts require loading the qtl package for R.
DOI: 10.5061/dryad.1k4gq/6
title: QTL analysis scripts for Norway data

description: This file contains the R scripts used for QTL analysis of the F2 data from the Norway field site.  Use of the various scripts is described in comment lines within the file.  Scripts require loading the qtl package for R.
DOI: 10.5061/dryad.1k4gq/7
title: SEM analysis scripts for North Carolina data

description: This file contains the R scripts used for structural equation model (SEM) analysis of the F2 data from the NC field site.  Use of the various scripts is described in comment lines within the file.  Scripts require loading the sem package for R, and prior generation of the R/qtl object for these data.
DOI: 10.5061/dryad.1k4gq/8
title: SEM analysis scripts for Norway data

description: This file contains the R scripts used for structural equation model (SEM) analysis of the F2 data from the Norway field site.  Use of the various scripts is described in comment lines within the file.  Scripts require loading the sem package for R, and prior generation of the R/qtl object for these data.
DOI: 10.5061/dryad.1rf75/1
title: DataSheetForDryad

description: Microsatellite data for the seven study populations. The excel file has seven sheets labeled by site corresponding to the study sites in the paper. The data is formatted as a two-column per locus format, and entered in the GENALEX template. For any questions regarding the data, please contact the corresponding author.
DOI: 10.5061/dryad.1t93v/1
title: Data & R Code from: Dietary macronutrients modulate the Fatty Acyl composition of rat liver mitochondrial cardiolipins.

description: The zip file contains all data and R code used to analyze Cardiolipin and related data. Please refer to README within the zip file for instructions on how to run the R code to produce all figures, including those found in the supplement and statistical tables in the supplement.
DOI: 10.5061/dryad.1vp3j/1
title: Community and Landscape Dynamic Simulation Code

description: This code allows the simulation of landscape habitat loss and reserve designation and resulting community dynamics, as described in the article. The code relies on R and python and includes a 'README' file.
DOI: 10.5061/dryad.24bn2/1
title: Survival

description: Abbreviations: Bird = individual identifier; LayYear = year of birth; AFR = age of first reproduction as a dominant; ELGS = early-life group size; ELYearQual = early-life year quality; ELTQ = early-life territory quality; year = year of observation; survival = survived until the next year or not
DOI: 10.5061/dryad.24bn2/2
title: Reproductive lifespan and age of first reproduction

description: Abbreviations: BirdID = individual identifier; LayYear = year of birth; AFR = age of first reproduction as a dominant; RLS = reproductive lifespan; event = whether an individual died before the end of the study period; NatalGS = natal group size; NatalYQ = natal year quality; NatalTQ = Natal territory quality
DOI: 10.5061/dryad.266h9/1
title: rawvar_rmdup.ind1

description: Raw SNP data from Index 1 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/10
title: rawvar_rmdup.ind10

description: Raw SNP data from Index 10 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/11
title: rawvar_rmdup.ind11

description: Raw SNP data from Index 11 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/12
title: rawvar_rmdup.ind12

description: Raw SNP data from Index 12 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.27n36/1
title: Hawkes et al. raw data

description: Comma separated values file of all unfiltered hawksbill turtle captures used in this study.
DOI: 10.5061/dryad.3gm8c/4
title: CHLO

description: Benthic sample from Chiers river on Mainland France that usually displays low diversity of diatom taxa.Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs.After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions.Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
DOI: 10.5061/dryad.3gm8c/5
title: COIN

description: Benthic sample from Coconi river on French tropical islands in the Indian Ocean (Mayotte) that usually displays high diversity of diatom taxa.Sample collected by scraping material from the surface of stones taken from this river following the French standard (AFNOR 2007) used in routine biomonitoring programs.After DNA extraction and amplification of three markers (SSU rDNA, rbcL and CO1), we sequenced the fragmented PCR products in one random direction a GS FLX Titanium PicoTiterPlate 454 (Roche, Basel, Switzerland) according to the manufacturer’s instructions.Reads were removed if they were too short, contained ambiguous bases, or showed low complexity when examined using PyroCleaner software version 1.0.
DOI: 10.5061/dryad.3ps4r/1
title: 1. Whole-tree dN/dS and overall substitution rates analysis

description: This folder contains the input and output files used in and obtained from the program PAML (Yang 2007) for the whole-tree analysis of dN/dS ratios (program component codeml) and overall substitution rates (program component baseml). This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Note both analyses types (codeml and baseml) use the same tree and nucleotide files. Each gene folder contains 6 files: 2 control files (1 codeml, 1 baseml - “.ctl”), 1 nucleotide file (“.nuc”), 1 tree file (“.trees”), 2 output files (1 codeml, 1 baseml).
DOI: 10.5061/dryad.439vn/1
title: GenePop file

description: GenePop file for multilocus genotypes (17 microsatellite loci) obtained from Cumberlandia monodonta.
DOI: 10.5061/dryad.4cp88/1
title: rabbitmeasurements

description: Repeated left and right measurements of rabbit fetal limbs.
DOI: 10.5061/dryad.5v1r5/1
title: combined cpDNA sequences_aligned

description: an aligned sequence file of combined cpDNA sequences from 100 individual samples
DOI: 10.5061/dryad.615tj/3
title: isoscape maps for: Identifying the African wintering grounds of hybrid flycatchers using a multi–isotope (δ2H, δ13C, δ15N) assignment approach, Veen, Thor, Hjernquist, Mårten B, Van Wilgenburg, Steven L, Hobson, Keith A, Folmer, Eelke, Font, Laura, Klaassen, Marcel

description: δ2H, δ13C, δ15N isoscape maps
DOI: 10.5061/dryad.7cm6b/1
title: K formosana AFLPsurv-input-465-5

description: The data file contains 465 amplified fragment length polymorphism markers generated from 12 primers pairs for samples of Keteleeria davidiana var. formosana.
DOI: 10.5061/dryad.81884/1
title: Kapralova2013_Charr2005

description: Dataset 1 – Arctic Charr from Lake Thingvallavatn, collected in 2005. Collected in the field, phenotype and genotype of MHCIIalpha described in the lab.
DOI: 10.5061/dryad.81884/2
title: Kapralova2013_Charr2010

description: Dataset 1 – Arctic Charr from Lake Thingvallavatn, collected in 2010. Captured in the wild, phenotyped and genotyped in the laboratory.
DOI: 10.5061/dryad.bk827/7
title: 18S_26S_conc_full_profile
DOI: 10.5061/dryad.bk827/8
title: 18S_26S_conc_full_de novo
DOI: 10.5061/dryad.cg976/1
title: Complete data set

description: The file contains all variables used in the study, including forest stands removed from the study. Forest Stand Age estimated by coring is corrected to year 2000 when the species presence/absence was surveyed.
DOI: 10.5061/dryad.cg976/2
title: GIS layers

description: .shp files with broadleaved forest cover in 1850, 1920 and 2000 (RT90 2.5 V), and position of focal forest stands (SWEREF99).
DOI: 10.5061/dryad.d3f56/1
title: Absorbance measurements from Mimulus lewisii leaf extractions
DOI: 10.5061/dryad.d3f56/2
title: Absorbance measurements from Mimulus lewisii bud tissue
DOI: 10.5061/dryad.d3f56/3
title: script for leaf anthocyanin extraction analyses
DOI: 10.5061/dryad.d3f56/4
title: script for bud anthocyanin extraction analyses
DOI: 10.5061/dryad.g3375/1
title: 1 - FASTQ_IonTorrent

description: Raw Ion Torrent reads in FASTQ format
DOI: 10.5061/dryad.g3375/2
title: 2 - SAM_alignments

description: BWA alignments in SAM format
DOI: 10.5061/dryad.g3375/3
title: 3 - VCF_raw_SNP_reports

description: Raw SNP reports in VCF format
DOI: 10.5061/dryad.g3375/4
title: 4 - Filtered_SNP_report

description: Filtered SNP report used to construct consensus sequences
DOI: 10.5061/dryad.g3375/5
title: 5 - Number_reads

description: Number of reads per individual per marker
DOI: 10.5061/dryad.g3375/6
title: 6 - Genotypic_data

description: Table containing data in genotypic format
DOI: 10.5061/dryad.g3375/7
title: 7 - Allelic_variants

description: Allelic variants per marker
DOI: 10.5061/dryad.g3375/8
title: 8 - Reconstructed_sequences_FASTA

description: FASTA files of reconstructed sequences
DOI: 10.5061/dryad.gs661/1
title: Morphological measurements of Japanese quail raised at different temperatures

description: Data collected in lab. Details in ReadMe file.
DOI: 10.5061/dryad.gs661/2
title: Repeatability data for morphological measurements of Japanese quail

description: Collected in lab. Details in ReadMe file.
DOI: 10.5061/dryad.gs661/3
title: Thermal imaging data for Japanese quail raised at different temperatures

description: Data collected in lab. Details are in ReadMe file.
DOI: 10.5061/dryad.h702r/1
title: Micro CT scan of Nile crocodile lung (NNC9)

description: This file includes the DICOM files for the lungs of Crocodylus niloticus specimen number NNC9 (0.58kg). The lungs were excised and soaked in an iodine potassium iodide (I2KI) solution at concentrations varying from 2.25%-3.75% (following the methods of Jeffery et al., 2001; reference available in the manuscript) prior to scanning. The lungs of NNC9 were scanned in a micro CT unit at the University of Cambridge with a slice width of 0.0816 mm.
DOI: 10.5061/dryad.h702r/2
title: CT scan of Nile crocodile lungs (NNC6)

description: This file includes the DICOM files for Crocodylus niloticus specimen number NNC6 (0.8kg). The lungs of NNC6 were inflated and scanned in a medical grade CT unit at the Royal Veterinary College, London at 90 kVp and 133MA with a slice thickness of 0.75 mm The lungs were excised and soaked in an iodine potassium iodide (I2KI) solution at concentrations varying from 2.25%-3.75% (following the methods of Jeffery et al., 2001; reference available in the manuscript) prior to scanning.
DOI: 10.5061/dryad.h702r/3
title: CT scan of Nile crocodile lungs (NNC5)

description: This file includes the DICOM files for Crocodylus niloticus specimen number NNC5 (0.5kg). The lungs of NNC5 were inflated and scanned in a medical grade CT unit at the Royal Veterinary College, London at 90 kVp and 133MA with a slice thickness of 0.75 mm The lungs were excised and soaked in an iodine potassium iodide (I2KI) solution at concentrations varying from 2.25%-3.75% (following the methods of Jeffery et al., 2001; reference available in the manuscript) prior to scanning.
DOI: 10.5061/dryad.j18g0/1
title: Kinship matrix

description: Kinship matrix used as a correlation structure to describe relatedness between females in the statistical models.
DOI: 10.5061/dryad.j18g0/2
title: female_data

description: Data about all females that were raised in the lab colony: genotype, date of birth, age at contact, overall progeny number, first litter age, mean litter size, mean interbirth interval...
DOI: 10.5061/dryad.j18g0/3
title: corpora_lutea_count_data

description: Corpora lutea count for all females dissected to estimate the ovulation rate.Contains information on female identity, genotype, corpora lutea count and age of female at the time of the dissection.
DOI: 10.5061/dryad.j3mp2/1
title: Data for QTL analysis and regression analysis

description: Three spread sheets showing data for the QTL analysis and the regression analysis condunted in this paper.
DOI: 10.5061/dryad.jm4d5/1
title: Analysis1A_no max age
DOI: 10.5061/dryad.jm4d5/2
title: Analysis1B_max age 124-126
DOI: 10.5061/dryad.jm4d5/3
title: Analysis 2A_no max age
DOI: 10.5061/dryad.jm4d5/4
title: Analysis2B_max age 124-126
DOI: 10.5061/dryad.n40hc/10
title: Supplemental Dataset 10. Summary of assambled transcripts by RNA-seq
DOI: 10.5061/dryad.n40hc/11
title: Supplemental Dataset 11. Classification of the TUs identified by RNAseq
DOI: 10.5061/dryad.n40hc/12
title: Supplemental Dataset 12. Verfication of organ-preferencially expressed lincRNA by qRT-PCR
DOI: 10.5061/dryad.n40hc/13
title: Supplemental Dataset 13. Comparison of lincRNAs identifed by mutiple platforms
DOI: 10.5061/dryad.n40hc/14
title: Supplemental Dataset 14. Predicted introns of lincRNAs
DOI: 10.5061/dryad.n40hc/7
title: Supplemental Dataset 7. RCTUs identifed by RepTAS
DOI: 10.5061/dryad.n40hc/8
title: Supplemental Dataset 8. Design of ATH LincRNA v1 Array
DOI: 10.5061/dryad.n40hc/9
title: Supplemental Dataset 9. LincRNAs identified by both RepTAS and RNA-seq
DOI: 10.5061/dryad.ss548/1
title: INL_Cloud_Data

description: This file contains categorical descriptions of cloud cover obtained from the National Weather Service for the Idaho National Laboratory Site (INL) during each day of our study, from 6 May, 2010 to 31 October, 2012.
DOI: 10.5061/dryad.ss548/2
title: INL_Elk_Handling_Data

description: This file contains a variety of data obtained from each individual elk captured at the Idaho National Laboratory Site (INL) during our study.
DOI: 10.5061/dryad.ss548/3
title: INL_GPS_Data

description: This file contains all of the 128,854 GPS locations used in our analyses of elk at the Idaho National Laboratory Site (INL) during 2010-2012.
DOI: 10.5061/dryad.ss548/4
title: INL_Vertical_Cover_Shade

description: This file contains vegetative cover data obtained from 200 random ground-truthing locations at the Idaho National Laboratory Site (INL).
DOI: 10.5061/dryad.ss548/5
title: INL_WeatherStation_Data

description: This file contains all of the raw weather station data used to parameterize the microclimate model during our study for landscape-scale simulations at the Idaho National Laboratory Site (INL).
DOI: 10.5061/dryad.ss548/6
title: Starkey_Cloud_Data

description: This file contains the categorical descriptions of cloud cover obtained from the National Weather Service for the Starkey Experimental Forest and Range (Starkey) during each day of our study, from 14 May, 2010 to 15 November, 2012.
DOI: 10.5061/dryad.ss548/7
title: Starkey_Elk_Handling_Data

description: This file contains a variety of data obtained from individual elk captured at the Starkey Experimental Forest and Range during our study.
DOI: 10.5061/dryad.ss548/8
title: Starkey_GPS_Data

description: This file contains all of the 345,075 GPS locations used in our analyses of elk at the Starkey Experimental Forest and Range (Starkey) during 2010-2012.
DOI: 10.5061/dryad.ss548/9
title: Starkey_Vertical_Cover

description: This file contains vegetative cover data obtained from 200 random ground-truthing locations at the Starkey Experimental Forest and Range (Starkey).
DOI: 10.5061/dryad.t8f5m/1
title: Supplemental_Data.tar

description: This archive contains datasets used for the analyses in the paper and several stability analyses conducted to verify the results.  Motivations for these can be found in the supplemental material of the paper.
DOI: 10.5061/dryad.v2b8t/1
title: Tolerance to Competition Field Experiment Data
DOI: 10.5061/dryad.v2b8t/2
title: R script for Tolerance to Competition Analysis
DOI: 10.5061/dryad.v550k/1
title: Data for Didiano et al 2014 Journal of Ecology

description: Data on plant traits looking at evolution of plants following the experimental exclusion of rabbits. Traits measured on plants grown in a common garden experiment at University of Toronto. Seeds from rabbit exclosures at Silwood Park, England.
DOI: 10.5061/dryad.13v2t/1
title: RESULTS

description: Data on 4 behavioural types (exploration, dispersal, same-sex sexual behaviour, remount tendency) - H, high density; L, low density.
DOI: 10.5061/dryad.266h9/13
title: rawvar_rmdup.ind13

description: Raw SNP data from Index 13 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/14
title: rawvar_rmdup.ind14

description: Raw SNP data from Index 14 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/15
title: rawvar_rmdup.ind15

description: Raw SNP data from Index 15 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/16
title: rawvar_rmdup.ind16

description: Raw SNP data from Index 16 for Ishikawaella U.S. 2009 (ground zero) from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/17
title: rawvar_rmdup.ind17

description: Raw SNP data from Index 17 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/18
title: rawvar_rmdup.ind18

description: Raw SNP data from Index 18 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/19
title: rawvar_rmdup.ind19

description: Raw SNP data from Index 19 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/2
title: rawvar_rmdup.ind2

description: Raw SNP data from Index 2 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.266h9/20
title: rawvar_rmdup.ind20

description: Raw SNP data from Index 20 for Ishikawaella U.S. 2011 from Illumina HiSeq generated using GATK.
DOI: 10.5061/dryad.3ps4r/2
title: 2. dN/dS ratio sister-clades analysis

description: This folder contains the input and output files used in and obtained from the program PAML (Yang 2007) for the sister-clade analysis of dN/dS ratios (program component codeml). This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Each gene folder contains 4 files: 1 control file (“.ctl”), 1 nucleotide file (“.nuc”), 1 tree file (“.trees”), and 1 output file.