cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6rs23/7
title: GLM_Data

description: Generalized linear model data input for DNA concentration analysis.
DOI: 10.5061/dryad.70ng4/1
title: ASReml-R analysis

description: Data, inverse A-matrix, and R code to conduct the analysis using ASReml in R.
DOI: 10.5061/dryad.70ng4/2
title: WOMBAT analysis

description: Data, inverse A-matrix, and code to run the quantitative genetic analyses using the WOMBAT software. Also, code is included to conduct the Monte Carlo simulations to obtain model parameter sampling distributions.
DOI: 10.5061/dryad.70ng4/3
title: Simulation code from Supporting Information
DOI: 10.5061/dryad.76735/1
title: Clutch Size Data

description: Dataset for clutch size analyses
DOI: 10.5061/dryad.76735/2
title: Egg Mass Data

description: Dataset for egg mass analyses
DOI: 10.5061/dryad.7st12/3
title: Data for Fig 5A - B73 x Ky21 marker data

description: This Excel file contains molecular marker data for B73 x Ky21 recombinant inbred lines.  Marker data were downloaded from www.panzea.org. The same marker data, in a format for use with the WinQTL genetic mapping program, are included in the file "WinQTL data for Fig 5A - QTL mapping of aphid progeny on B73xKY21 RILs,
DOI: 10.5061/dryad.9gn07/10
title: 1371AJM0007

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/11
title: 1371AJM0008

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/12
title: 1371AJM0009

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/13
title: 1371AJM0010

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/14
title: 1533AJM0004_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/15
title: 1533AJM0005_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/16
title: 1533AJM0006_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/17
title: 1533AJM0007_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/9
title: 1371AJM0006

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.b971k/1
title: Reference genome modified with SNVs in starter

description: Drosophila melenogaster reference genome release 5 modified based on the SNVs detected in isogenized 2nd and 3rd chromosomes FRT40A and FRT80B, used as starters in the EMS screening. Fasta format.
DOI: 10.5061/dryad.b971k/2
title: Mapped NGS reads of starter FRT40A

description: Mapped NGS reads obtained form isogenized starter chromosome carrying FRT40A, used in the EMS screening. This BAM file includes only reads on chromosome 2L.
DOI: 10.5061/dryad.bh19d/1
title: RossetalMasterDatasetVMEsOriginal

description: Raw presence absence data for the modelled species (habitats)
DOI: 10.5061/dryad.cs3t8/1
title: PLoS biology Figure 1 data

description: Prevalence of reporting of randomisation, blinded assessment of outcome, sample size calculation and conflict of interest in 146 publications describing in vivo research identified through random sampling from PubMed;
DOI: 10.5061/dryad.cs3t8/2
title: PLoS biology Figure 3 data

description: Reporting of randomisation, blinded assessment of outcome, sample size calculations and conflict of interest reporting and journal impact factor  for 2671 publications describing the efficacy of interventions in animal models of eight different diseases identified in the context of systematic reviews,
DOI: 10.5061/dryad.cs3t8/3
title: PLoS biology Figure 5 data

description: Reporting of randomisation, blinded assessment of outcome, sample size calculation and of inclusion or exclusion criteria in 1173 publications describing in vivo research published from 5 leading UK institutions (labelled A through E).
DOI: 10.5061/dryad.h0246/1
title: Phylogeny of the 100 mammalian species

description: Phylogeny in NEXUS format of the 100 mammalian species used in the study.
DOI: 10.5061/dryad.h0246/2
title: Data of the 100 mammalian species

description: Data on sperm number (in millions), sperm length (um), combined testes mass (g) and male and female body mass (g) of all 100 mammalian species used in this study.
DOI: 10.5061/dryad.h0246/3
title: size.number.references

description: References of the data sources.
DOI: 10.5061/dryad.m186r.1
title: Data from: Parallel evolution of local adaptation and reproductive isolation in the face of gene flow
DOI: 10.5061/dryad.m186r.2/4.2
title: Mitochondrial sequences

description: MtDNA sequences in fasta format
DOI: 10.5061/dryad.m186r.2/5.2
title: ThioPer-2_Final-NoIndel_Intron
DOI: 10.5061/dryad.m186r.2/6.2
title: ElFac_Final-NoIndel_Intron
DOI: 10.5061/dryad.m186r.2/7.2
title: Cal-1_Final-NoIndel_Intron
DOI: 10.5061/dryad.mk649/1
title: AtwaterEtAl2015EcographyData

description: This .zip file contains the data used for this paper, along with a ReadMe file describing each data set.
DOI: 10.5061/dryad.pd256/1
title: Contest behaviours and striking dataset

description: Data on which contests escalated to striking, how many strikes each contest included, how many strikes were not on the telson, and the first behaviour of each contest.
DOI: 10.5061/dryad.pr065/1
title: Environmental, Genotype and GESTE input files
DOI: 10.5061/dryad.q2h4s/13
title: Figure S2
DOI: 10.5061/dryad.q2h4s/14
title: Figure S3
DOI: 10.5061/dryad.q2h4s/15
title: Movie S1
DOI: 10.5061/dryad.qs552/1
title: Band encounter data from hunter recovered mallards (MALL), northern pintails (NOPI), American green-winged teal (AGWT), and Canada geese (CAGO) between 2004 and 2013 in North America.

description: Included fields are the band number (BAND), species (SPEC), banding date (BMONTH, BDAY, BYEAR), recovery date (RMONTH, RDAY, RYEAR), banding location reported at the node level (BNODELAT, BNODELONG), and recovery location reported at the node level (RNODELAT, RNODELONG). For information on requesting the full band and encounter data, please go to https://www.pwrc.usgs.gov/BBL/homepage/datarequest.cfm.
DOI: 10.5061/dryad.qt30h/1
title: Schefferville Mines: Gagnon mine and surrounding vegetation flora

description: Site by species matrix of species found on and around the Gagnon mine in Schefferville, Quebec, Canada. This data was collected in the field. Please see the associated ReadMe file for more information.
DOI: 10.5061/dryad.qt30h/2
title: Schefferville Mines: Retty mine and surrounding vegetation flora

description: Site by species matrix of species found on and around the Retty mine in Schefferville, Quebec, Canada. This data was collected in the field. Please see the associated ReadMe file for more information.
DOI: 10.5061/dryad.qt30h/3
title: Schefferville Mines: Timmins mine and surrounding vegetation flora

description: Site by species matrix of species found on and around the Timmins mine in Schefferville, Quebec, Canada. This data was collected in the field. Please see the associated ReadMe file for more information.
DOI: 10.5061/dryad.sg5s0/1
title: DS-ZACKANIM intrasp divergence and distance to NN raw data

description: Raw data on the intraspecific divergence and distance to nearest neighbour for the dataset DS-ZACKANIM (dx.doi.org/10.5883/DS-ZACKANIM) and the DNA barcode region CO1
DOI: 10.5061/dryad.sg5s0/2
title: DS-ZACKPLAN ITS2 intrasp divergence and distance to NN raw data

description: Raw data on intraspecific divergence and distance to nearest neighbour for the dataset DS-ZACKPLAN (dx.doi.org/10.5883/DS-ZACKPLAN) and the DNA barcode region ITS2
DOI: 10.5061/dryad.sg5s0/3
title: DS-ZACKPLAN rbcLa intrasp divergence and distance to NN raw data

description: Raw data on intraspecific divergence and distance to nearest neighbour for the dataset DS-ZACKPLAN (dx.doi.org/10.5883/DS-ZACKPLAN) and the DNA barcode region rbcLa
DOI: 10.5061/dryad.t57k5/1
title: Pygmy rabbit reproduction data

description: Demographic and genetic data used to evaluate pygmy rabbit reproduction in field breeding enclosures in central Washington, USA during 2012-2014 as part of the recovery for the endangered Columbia Basin pygmy rabbit.
DOI: 10.5061/dryad.tk4b5/1
title: Rendon_et_al_Proc_Roy_Soc_B_Agonistic_Adrenal

description: Data from Rendon et al. Proc Roy Soc B Manuscript - Agonistic Adrenal. Data include reproductive physiology, aggressive behavior, non-aggressive behavior, and adrenocorticosteroid hormone levels.
DOI: 10.5061/dryad.14762/1
title: annasairdata

description: trial information, wing morphology, body mass, load lifting performance, and flight maneuvering performance of Anna's hummingbirds
DOI: 10.5061/dryad.31q7p/1
title: Interactome of E2f1 and E2f3 in Rb family deficient liver cancer

description: Endogenous E2f1 and E2f3 were pulled-down from Rb family deficient liver cancer derived cell lines (in parallel, an anti HA pull-down was performed as a negative control). The resulting fractions were loaded on a polyacrylamide gel and different bands were excised to be run on a Mass Spectrometer. The experiment was performed independently three times and the associated file is one of the three replicates.
DOI: 10.5061/dryad.3447g/1
title: Sanger sequencing

description: Sanger sequencing  for Assay sensitivity
DOI: 10.5061/dryad.3447g/2
title: PGM sequencing

description: PGM sequencing for assay sensitivity
DOI: 10.5061/dryad.3f2t2/1
title: Main vcf file with allele frequency estimates

description: vcf including SNPs on all chromosomes, and allele frequency estimates. See README file for more information.
DOI: 10.5061/dryad.3f2t2/2
title: chr1_1.all.filter
DOI: 10.5061/dryad.3f2t2/3
title: chr1_2.all.filter
DOI: 10.5061/dryad.3f2t2/4
title: chr2.all.filter
DOI: 10.5061/dryad.3f2t2/5
title: chr3.all.filter
DOI: 10.5061/dryad.3f2t2/6
title: chr4.all.filter
DOI: 10.5061/dryad.3f2t2/7
title: chr5.all.filter
DOI: 10.5061/dryad.3pc7c/1
title: Alricetal_micros_genotyping

description: Microsatellite genotyping for populations of Daphnia longispina species complex in Lakes Geneva, Bourget and Annecy
DOI: 10.5061/dryad.3pc7c/2
title: Alricetal_mtDNA_haplotypes

description: Mitochondrial haplotypes for populations of Daphnia longispina species complex in Lakes Genena, Bourget and Annecy.
DOI: 10.5061/dryad.4p24g/1
title: Accessions, alignments, and trees
DOI: 10.5061/dryad.4s61t/1
title: Raw Data: DNA methylation, behavior and rainfall

description: (1) Whole Region DNA Methyl: DNA methylation of the coding and regulatory region for 11 birds.  (2) Regulatory region DNA Methyl: DNA methylation in the regulatory region for 96 birds, including behavior and rainfall data.  (3) Recapture DNA Methyl: DNA methylation in a portion of the regulatory region for 12 birds recaptured after initial sampling.
DOI: 10.5061/dryad.5md80/1
title: B1_Replicate Early Ontogeny_Oct 1

description: Digitized images documenting colony morphology for replicate films. Scale bar = 1mm. Blue open circle corresponds to size and location of fed polyp. Red open circles correspond to size and locations of unfed stolons.
DOI: 10.5061/dryad.5md80/10
title: A5 Late ontogeny_12 June_Long_pt 1

description: Late ontogeny colony_12 June 2014_Long First image at 16 minutes post-feeding, subsequent images at 10 sec intervals. Exposure = 5 sec. The short exposure was used to quantify the luminosity of the fed polyp. Scale: 5.97 µm/pixel.  To meet upload specs, tiff files from this study have been divided into 2 folders- this is part 1.
DOI: 10.5061/dryad.5md80/2
title: B2_Replicate Mid-Ontogeny_2 Jul

description: Digitized images documenting colony morphology for replicate films. Scale bar = 1mm. Blue open circle corresponds to size and location of fed polyp. Red open circles correspond to size and locations of unfed stolons.
DOI: 10.5061/dryad.5md80/3
title: B3 Replicate_Late Ontogeny_March 19

description: Digitized images documenting colony morphology for replicate films. Scale bar = 1mm. Blue open circle corresponds to size and location of fed polyp. Red open circles correspond to size and locations of unfed stolons.
DOI: 10.5061/dryad.5md80/4
title: B4_Replicate_Medusae-bearing Colony_8 July

description: Digitized images documenting colony morphology for replicate films. Scale bar = 1mm. Blue open circle corresponds to size and location of fed polyp. Red open circles correspond to size and locations of unfed stolons.
DOI: 10.5061/dryad.5md80/5
title: B5_Replicate Stolon Growth_20 Jun

description: Digitized images documenting colony morphology for replicate films. Scale bar = 1mm. Blue open circle corresponds to size and location of fed polyp. Red open circles correspond to size and locations of unfed stolons.
DOI: 10.5061/dryad.5md80/6
title: A1 Early ontogeny_15 Oct_Short

description: Early ontogeny colony_15 Oct_Short First image at 22 minutes post-feeding, subsequent images at 10 sec intervals. Exposure = 1 sec. The short exposure was used to quantify the luminosity of the fed polyp. Scale: 6.74 µm/pixel.
DOI: 10.5061/dryad.5md80/7
title: A2 Early ontogeny_15 Oct_Long

description: Early ontogeny colony_15 Oct_Long First image at 22 minutes post-feeding, subsequent images at 10 sec intervals. Exposure = 4 sec. The long exposure was used to quantify the luminosity of the unfed polyps and hydrorhiza. Scale: 6.74 µm/pixel.
DOI: 10.5061/dryad.5md80/8
title: A3 Mid-ontogeny colony_22 July

description: Mid-ontogeny colony_22 Jul First image at 43 minutes post-feeding, subsequent images at 3 hour intervals. Exposure = 5 sec. Scale: 2.4 µm/pixel.
DOI: 10.5061/dryad.5md80/9
title: A4 Late ontogeny_12 June_Short

description: Late ontogeny colony_12 June 2014_Short 1.3 First image at 16 minutes post-feeding, subsequent images at 10 sec intervals. Exposure = 0.5 sec. The short exposure was used to quantify the luminosity of the fed polyp. Scale: 5.97 µm/pixel.
DOI: 10.5061/dryad.5p51r/2
title: Vachellia_matrix_Chomicki_et_al_PRSB_dryad

description: Vachellia matrix containing three plastid markers (matK, trnL-trnF, psaB-rps14)
DOI: 10.5061/dryad.5p51r/3
title: Triplaris_Ruprechtia_matrix_Chomicki_et_al_PRSB_dryad

description: Triplaris and Ruprechtia matrix with one nuclear (ITS) and four plastid markers (matK, ndhF, ndhC-trnV, rps16-trnK)
DOI: 10.5061/dryad.5p51r/4
title: Platymiscium_matrix_Chomicki_et_al_PRSB_dryad

description: Platymiscium matrix with one nuclear (ITS) and three plastid markers (matK, trnL intron, trnL-trnF spacer)
DOI: 10.5061/dryad.7dv96/1
title: Model System Data

description: Please see ReadMe file
DOI: 10.5061/dryad.7dv96/2
title: Prey_Library_Data

description: Please see ReadMe file
DOI: 10.5061/dryad.8m1v1/1
title: Plink file data for Barki Ruminants (sheep and goats)

description: The data contains SNP genotype data for Barki sheep and goats that can be used in Plink.
DOI: 10.5061/dryad.9gn07/18
title: 1533AJM0008_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.9gn07/19
title: 1533AJM0009_bwa

description: Archive of BAM files generated from exome sequencing of 16 melanoma cell lines. Exome sequences were generated using a combination of Agilent and NimbleGen captures. Variant calls as well as insertion and deletion calls were made using GATK.
DOI: 10.5061/dryad.b1v2c/1
title: Germination, survival and traits of tropical ornamentals in the field

description: These data show the germination, survival, and traits from 21 species of introduced tropical ornamental plants in Hawai'i.  Plant species were drawn from three taxonomic families and classed as invasive, casual or non-invasive.   Seeds were planted at two sites (wet or seasonally dry) in 10 blocks per site in plots with or without neighbours.  Seedlings were monitored for one year to track germination and survival.  After one year, leaf traits were measured on any remaining plants and plants were harvested to measure biomass.  Canopy cover and richness and biomass of the plant community in plots with neighbours are also included.
DOI: 10.5061/dryad.b1v2c/2
title: Germination of tropical ornamentals in germination chambers

description: These data show the results of controlled germination trials of 21 species of introduced tropical ornamental plants in Hawai'i.  Plant species were drawn from three taxonomic families and classed as invasive, casual or non-invasive.   Germination trials were conducted in two germination chambers in petri dishes of damp sand, with two dishes (specified by location on upper or lower rack) per species per chamber.  Germination trials were conducted simultaneously with experimental plantings at two field sites and germination chamber settings mimicked light and temperature regimes of the two sites.
DOI: 10.5061/dryad.b1v2c/3
title: Plant community composition in field plots with neighbours

description: These data show the plant community composition of plots at two sites (wet or seasonally dry) in 10 blocks per site in plots with neighbours.  All plots were cleared of vegetation and planted with seeds of 21 species of introduced tropical ornamental plants in Hawai'i.  Subsequently, the plant community was allowed to regenerate in plots with neighbours.  In these plots, plant community was measured by visually estimating the percent cover of all species within two 1 m x 1 m quadrats (excluding experimentally planted species).  Data were collected at the end of the experiment when experimentally planted species were harvested.  Sites and blocks are the same as those recorded in Field_Seedling_Data.csv (Data 1).
DOI: 10.5061/dryad.b971k/3
title: Mapped NGS reads of 546P mutant

description: Mapped NGS reads obtained form homozygous embryos of 546P mutant. This BAM file includes only reads on chromosome 2L.
DOI: 10.5061/dryad.b971k/4
title: Variants found in 546P mutant

description: Annotated VCF file containing variants in 2L chromosome of 546P, called against reference genome 40A80B2013_8.
DOI: 10.5061/dryad.b971k/5
title: Variants unique in 546P mutants

description: Variants in 546P but not overlapped with the variants in starter FRT40A chromosome.
DOI: 10.5061/dryad.bf486/1
title: British Columbia High Elevation Bird Dataset

description: A single flat file in .csv format including all raw field-collected observation data included in the accompanying article
DOI: 10.5061/dryad.gd3dq/1
title: All.Hands.Concatenated.Data

description: This data file contains all of the plate counts for all of the fitness measurements within this paper.
DOI: 10.5061/dryad.gd3dq/3
title: Mutation.Rate.Data

description: This file contains the mutation rate data from the fluctuation tests in Table S8 in the manuscript.
DOI: 10.5061/dryad.gd3dq/4
title: All.Hands.Revised.Submission

description: This is the revised analysis script, adding a section at the end to include an additional analysis requested by a reviewer.
DOI: 10.5061/dryad.hv333/1
title: Hooded crow genome annotation v2.7A

description: Whole-genome annotation file for hooded crow (Corvus [corone] cornix) in gff format.
DOI: 10.5061/dryad.hv333/3
title: RSEM output (gene counts)

description: Contains the gene counts for each library as produced by the RSEM software. For each tissue, a separate file is provided, in which columns are libraries (with the library identifiers corresponding to those in the file containing metadata by library) and rows are genes (with gene identifiers as in the annotation file).
DOI: 10.5061/dryad.hv333/4
title: PCA input

description: A matrix with the input data (normalized gene counts) for the PCA that is presented in the paper. Columns are libraries (with the library identifiers corresponding to those in the file containing metadata by library) and rows are genes (with gene identifiers as in the annotation file).
DOI: 10.5061/dryad.hv333/6
title: Differential expression results (edgeR and ebseq output)

description: Contains files with results of the differential expression analyses conducted with edgeR and Ebseq. Separate files are present for each program for each of the comparisons that were made. Comparisons were made between carrion and hooded crow for each of the tissues: forebrain, liver, gonads, skin_bodypool (skin from torso), and skin_headpool (skin from head), and between body regions for each of the taxa: skin_CC (carrion crow skin) and skin_CX (hooded crow skin). For example, the file "ebseq_liver.txt" presents the results of carrion vs. hooded crow in liver performed with Ebseq. In each file, the columns are: gene_id (gene identifiers as in the annotation file), FDR (False Discovery Rate) and LFC (Log-Fold Change).
DOI: 10.5061/dryad.hv333/7
title: Metadata by individual

description: Metadata for each crow sampled in this study: including population of origin, GPS coordinates, dates of feather plucking, dates of sampling, times of day of sampling, weight at sampling, approximate age at sampling, and number of days of feather regrowth until sampling.
DOI: 10.5061/dryad.k5f6q/1
title: Narural nests: superb fairy-wren chatter song rate and depredation outcome

description: Superb fairy-wren chatter song rate and depredation outcome at natural nests. The data consist of chatter songs per hour per nesting phase (fertile phase, incubation, nestling) and depredation outcome (0=depredated, 1=survived) per phase for a total of 72 nests observed in South Australia.
DOI: 10.5061/dryad.k5f6q/2
title: Artificial nests: superb fairy-wren chatter song rate and predation outcome

description: Superb fairy-wren chatter song rate at artificial nests and depredation outcome. There were three treatment groups for chatter song rate: none, low (6 songs per hour), high (20 songs per hour). The study was done in South Australia.