cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6gr7t/13
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu.parsed.filtered

description: Parsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/14
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_hits

description: Gene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/15
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_unique_hits

description: Gene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/7
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filtered

description: Parsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores. &gt;=80.
DOI: 10.5061/dryad.6gr7t/8
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits

description: Gene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/9
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits

description: Gene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.85q50/10
title: Supplementary Figure 2

description: Effective prior distributions (red) and posterior distributions (blue and green) for two separate MCMC runs for six nodes of interest to this study (Fig. 1). The rows correspond to the seven different fossil calibration schemes detailed in Table 1. The y-axis scales are identical within, but not across, columns.
DOI: 10.5061/dryad.85q50/6
title: Cladogram (analysis #5)

description: Cladogram used for MCMCtree analysis #5 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85q50/7
title: Cladogram (analysis #6)

description: Cladogram used for MCMCtree analysis #6 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85q50/8
title: Cladogram (analysis #7)

description: Cladogram used for MCMCtree analysis #7 (see Table 1 in the main text). Fossil alibrations, formatted for MCMCtree, are embedded as node labels.
DOI: 10.5061/dryad.85q50/9
title: Supplementary Figure 1

description: Specified prior probability distributions for fossil calibrations used in this study (Table 1). Vertical red lines mark minimum ages, based on fossil evidence outlined in the Materials and Methods section.
DOI: 10.5061/dryad.89735cr0/1
title: Hoban_EvolApps_microsat_Data_For_Dryad

description: The genotypes for trees used in this study for all analyses, after clones, etc. have been removed. The data are referred to in the publication as "1515 unique genotypes for analysis: 79 J. ailantifolia reference, 7 hybrid 231 reference, 66 J. cinerea reference, and 1363 naturally occurring trees." The names of the populations are as in table one, or similar abbreviation. File format is Convert, tab delimited. All 12 microsatellite loci. Missing data with a '?'. Details about collections are in the manuscript.
DOI: 10.5061/dryad.8jd18/1
title: ContigSNP_annotated_Md (613 seq)

description: 613 concensus sequences annotated with SNPs variants from Mesodesma donacium transcriptome.
DOI: 10.5061/dryad.8jd18/2
title: Raw data of 454 transcriptome pyrosequencing from M. donacium

description: FASTA file with 180,159 ESTs.
DOI: 10.5061/dryad.8jd18/3
title: Multi BLAST (613 sequences)_MmSNP

description: BLAST results for the 613 sequences with SNP annotations
DOI: 10.5061/dryad.8jd18/4
title: GOAnalysis MmSNPs

description: GO analysis from contigs annotated with SNP variants.
DOI: 10.5061/dryad.8k0d8/1
title: Achroia_phenotypes_females

description: Phenotypes measured in Achroia grisella females. Data used for the QTL analysis.
DOI: 10.5061/dryad.8k0d8/2
title: Achroia_phenotypes_males

description: Phenotypes measured in Achroia grisella males. Data used for the QTL analysis.
DOI: 10.5061/dryad.8k0d8/3
title: Achroia_genotypes_females

description: Genotypes of Achroia grisella females. 0 / 1 = absence / presence of AFLP markers. Data used for the QTL analysis.
DOI: 10.5061/dryad.8k0d8/4
title: Achroia_genotypes_males

description: Genotypes of Achroia grisella males. 0 / 1 = absence / presence of AFLP markers. Data used for the QTL analysis.
DOI: 10.5061/dryad.8q34c/1
title: Costus microsatellite data

description: Genotypes scored at 15 microsatellite loci. Missing data are indicated by -9. Open Document Spreadsheet format
DOI: 10.5061/dryad.bv4k7/1
title: HITChip microarray data

description: The file contains phylogenetic microarray signal intensities for 1037 species and uncultured phylotypes, and for 130  genus-like group (≥ 90% sequence similarity in the 16S rRNA gene). More information about the phylogenetic design of the HITChip can be found at http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2009.01900.x/full
The data are extracted with using min/max normalisation and log-transformed (not subjected to between-study normalization; for details see the publication).
DOI: 10.5061/dryad.cp4tc417/1
title: Mm. appendicocostales projection angle

description: Angle at which the Mm. appendicocostales projects from the uncinate processes in four extant bird species (Alca torda, Branta leucopsis, Falco tinnunculus and Alectoris rufa).
DOI: 10.5061/dryad.cp4tc417/2
title: SMF Av 418

description: Photograph of C. sanctus SMF Av 418 used to calculate mechanical advantage of the uncinate processes for movements of the ribs.
DOI: 10.5061/dryad.cp4tc417/3
title: SMF Av 421

description: Photograph of C. sanctus SMF Av 421 used to calculate mechanical advantage of the uncinate processes for movements of the ribs.
DOI: 10.5061/dryad.cp4tc417/4
title: SMF Av 419

description: Photograph of C. sanctus SMF Av 419 used to calculate mechanical advantage of the uncinate processes for movements of the ribs.
DOI: 10.5061/dryad.f3b66/1
title: Hensel and Sargent Botany data

description: The file contains two worksheets. One sheet contains phenology, fruit type, growth form, forest strata layer, floral colour, and reproductive schedule data for 465 temperate deciduous forest species. The second sheet contains a legend explaining the coding of the character states of the traits. The data was collected from the The New Britton and Brown Illustrated Flora of the Northeastern United States and Adjacent Canada (Gleason 1952) and was used to investigate correlated evolution between flowering phenology and a suite of ecological, reproductive, and vegetative traits.
DOI: 10.5061/dryad.fc517819/1
title: Male age and female preferences in bulb mite
DOI: 10.5061/dryad.hj4t4/1
title: Life-history data and genotypes of a population of banded mongooses in Western Uganda

description: Life-history data on a population of banded mongooses including the sex, group of birth (social group) and year of birth for each individual (one individual per row), followed by the 14-locus genotype of each individual. Genotypes are given in two columns per locus, one representing each allele. Genotype columns are labelled with the name of the locus followed by 'a' or 'b', representing the first and second alleles. Zeros indicate cases where genotyping failed.
DOI: 10.5061/dryad.hk46g/1
title: growth curve and carrying capacity

description: Date set contains the data for growth curve and carrying capacity data for 5 strain identitis at 5 temperatures in 3 replicates
DOI: 10.5061/dryad.jv387/1
title: Datafile

description: Datafile. See Readme file for further description.
DOI: 10.5061/dryad.k6qb1/1
title: Genotype dataset

description: Microsatellite genotyping including population location.
DOI: 10.5061/dryad.k7r52/1
title: Hayward et al_Elephant senescence_JEB dryad data

description: Contains two dataframes in an Excel spreadsheet. The first of these gives age-specific fecundity and survival for all female elephants aged &gt;5 years. All abbreviations are as described in the main text. These contain data allowing analysis of reproduction across life as well as survival and reproduction in later life as a function of age and early-life fecundity and the association between early-life fecundity and lifetime breeding success. The second dataframe contains data on calf survival, which may be used for the analysis of age-specific calf survival in later life in relation to early-life fecundity.
DOI: 10.5061/dryad.kh43b/1
title: Morphological measurements of stamnate flowers and pith cells

description: Measurements of lengths of staminal columns and pith cells of Dalechampia bernieri and D. parvifolia. Measurements made on FAA-preserved material that were thin-sectioned, using a compound microscope in the lab.
DOI: 10.5061/dryad.m33cb/1
title: Rhododendron pseudochrysanthum cmplex_26loci

description: Microsatellite data format: microsatellite analalyzer. RTG: Rhododendron rubropunctatum population Tsaigongkeng; RTK: R. rubropunctatum population Tsankuanliao; PTH: R. pseudochrysanthum population Tashueshan; PHH: R. pseudochrysanthum population Hohuanshan; PLL: R. pseudochrysanthum population Lulinshan; MAL: R. morii population Alishan; MTH: R. morii population Tashueshan; MHH: R. morii population Hohuanshan; HNH: R. hyperythrum population Nanhutashan
DOI: 10.5061/dryad.mj0rs0dt/1
title: Ansonia submitted dataset
DOI: 10.5061/dryad.q0fh6734/1
title: Alignment_rbclmatk

description: DNA sequences from plant leaf materials collected in the Diabrelets area. Additional sequences (72) was sourced from GenBank.
DOI: 10.5061/dryad.r6ng71d4/2
title: Predel_SystBiol_supplMat2
DOI: 10.5061/dryad.r8f04fk2/1
title: CorSIM_v0.3

description: Zipped archive of the CorSiM package described in this paper.
DOI: 10.5061/dryad.rk5fp6n9/1
title: DataSetForPublication

description: The data reflect the performance of 5 MA lines and the founder in multiple environments. The 5 MA lines were fully sequenced. The file is an Excel file.
DOI: 10.5061/dryad.s1b07/1
title: Carpinteria Microsatellite Data

description: Microsatellite data in 6-digit format, with individual ID, X and Y coordinates, and ten microsatellite markers. Missing data indicated by 000000.
DOI: 10.5061/dryad.s1b07/2
title: Goleta Microsatellite Data

description: Microsatellite data in 6-digit format, with individual ID, X and Y coordinates, and ten microsatellite markers. Missing data indicated by 000000.
DOI: 10.5061/dryad.s1b07/3
title: Mohawk Microsatellite Data

description: Microsatellite data in 6-digit format, with individual ID, X and Y coordinates, and ten microsatellite markers. Missing data indicated by 000000.
DOI: 10.5061/dryad.s1b07/4
title: R script to calculate summary statistics from microsatellite data

description: Script calculates mean number of alleles per locus, observed heterozygosity, expected heterozygosity, and Fis. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).
DOI: 10.5061/dryad.s1b07/5
title: R script to simulate one generation of inbreeding

description: Script simulates selfing, and creation of full-sibling, half-sibling, and first cousins in proportions ranging from 0 to 100%. Input files are microsatellite data only, with alleles separated into separate columns (i.e. 10 loci are presented in 20 columns, with no headers or other columns).
DOI: 10.5061/dryad.s4n76/1
title: Primary_data_Quenouille et al

description: Additional data: phenotypic and genotypic data for the QTL detection in the doubled haploid progeny. Resistance Breakdown (RB): The values indicated correspond to the average of the RB frequencies of two independent tests.For each test and each pepper line, the RB frequency was assessed by the ratio of the number of systemically infected plants over the total number of inoculated plants (30 plants per test). AUDPC : The values indicated correspond to the average of the AUDPC of three independent tests. For each test, symptoms were evaluated on the 20 plants. Virus Accumulation : The values indicated correspond to the average of virus accumulation independently evaluated on 10 individual plants per DH line. For each DH line, genotypic data are indicated in the following way : 2 corresponds to the Perennial allele, 1 corresponds to the YoloWonder allele. NA= missing data
DOI: 10.5061/dryad.td03p886/1
title: Generic level phylogenetic tree

description: Generic level phylogenetic tree for 1246 plant species. The tree was calibrated using penalized likelihood.
DOI: 10.5061/dryad.td03p886/2
title: DNA matrix

description: DNA matrix based on 7 different DNA regions for the 1246 genera
DOI: 10.5061/dryad.04562/1
title: Fig. 5. Plastidic ACCase gene partial sequence alignment

description: Partial sequence alignment (from cloned fragments) showing the three haplotype sequences of the 2088, 1781 and 2078 mutations identified in the present study, corresponding respectively to the ACCase gene copies Acc1;1, Acc1;2, and Acc1;3 in wild oat (Christoffers et al., 2002). Note that the sequence region containing the 1781, 2078 or 2088 codon was not included due to infrequent informative SNPs. Boxed regions indicate SNPs discriminating the three haplotypes (GenBank accession AF231335 for Acc1;1-1, AF231334 for Acc1;1-2, AF231336 for Acc1;2 and AF464875 for Acc1;3).
DOI: 10.5061/dryad.04562/2
title: Fig. S4( d)CAPS analysis of clones

description: Fig. S4 (d)CAPS marker analysis of ACCase mutations at (a) 1781, (b) 2078 or (c) 2088 in representative E. coli clones containing the 1122 kb ACCase cDNA insert. Each lane represents a single clone analysed by each of the three markers. Note that none of these clones contain more than one mutation (R).
DOI: 10.5061/dryad.0pn48s2t/1
title: Rundle_Fitness_data

description: See associated ReadMe text file.
DOI: 10.5061/dryad.106sd/1
title: Data for Booksmythe et al. 2012

description: Data from individual-based simulation, run in MatLab. Excel file showing population mean values at generation 5000 of sex ratio response, male trait, and female preference, given the cost of sex ratio response and cost of preference in each population.
DOI: 10.5061/dryad.2024g/1
title: Data

description: Data and R Script to repeat all calculations. Data on pesticides from field observations, toxicity data from different sources.
DOI: 10.5061/dryad.29ds0/1
title: T.truncatus COL3A1-like gene

description: Sequence alignment file (.fasta) presenting sequencing results of five T. truncatus individuals of the DNA pool for the collagen type III alpha 1-like gene (COL3A1).  There is one SNP in this fragment.  Four individuals were sampled in the Gulf of Mexico and one in the western North Atlantic.  Sequences were derived using an ABI 3130 and aligned in the program Se-Al.  All work was completed at the Southeast Fisheries Science Center (SEFSC) Marine Mammal Molecular Genetics Lab (MMMGL).
DOI: 10.5061/dryad.29ds0/2
title: T.truncatus GRP78-like gene

description: Sequence alignment file (.fasta) presenting sequencing results of five T. truncatus individuals of the DNA pool for the glucose-regulated protein 78kDa-like gene (GRP78).  There is one SNP in this fragment.  Four individuals were sampled in the Gulf of Mexico and one in the western North Atlantic.  Sequences were derived using an ABI 3130 and aligned in the program Se-Al.  All work was completed at the Southeast Fisheries Science Center (SEFSC) Marine Mammal Molecular Genetics Lab (MMMGL).
DOI: 10.5061/dryad.38cj7/1
title: Microsatellite genotypic data for 10 populations at 50 loci

description: GenAlEx format within a Microsoft Excel spreadsheet. Sampling localities, sample sizes, ecotype and locus information explicitly noted in the file.
DOI: 10.5061/dryad.4r8p3/1
title: README
DOI: 10.5061/dryad.4r8p3/2
title: Raw simulation results, no zero sum, tropical origin
DOI: 10.5061/dryad.4r8p3/3
title: Raw simulation results, no zero sum, temperate origin
DOI: 10.5061/dryad.4r8p3/4
title: Raw simulation results, zero sum, tropical origin, 1st of 2 files
DOI: 10.5061/dryad.4r8p3/5
title: Raw simulation results, zero sum, tropical origin, 2nd of 2 files
DOI: 10.5061/dryad.519bm/2
title: Genotypes_forGenABEL20111111.raw
DOI: 10.5061/dryad.5947m/1
title: Simulation Results

description: Raw result files from biofilm simulations used to generate Figures 4 and 5 in the main text.
DOI: 10.5061/dryad.5r09q/1
title: 1.TCA.454Reads

description: .fna file of 16S sequences generated on Roche 454jr
DOI: 10.5061/dryad.68sd84vh/1
title: Daily sampling of individual mites

description: day: day of the study (day t) | no: individual ID for each day | surv: survival to day t+1? | stage: life-history stage at day t | stage1: life-history stage at day t+1 | trns: transition to next stage at day t+1? | tsex: transition to female stage at day t+1? | dens: weighted population density at day t | size: log(body size) at day t | size1: log(body size) at day t+1 | rep: produced eggs at day t+1? | rec: number of eggs produced on day t+1 | day2: number of eggs hatched on day t+2 | day3: number of eggs hatched on day t+3 | day4: number of eggs hatched on day t+4 | day5: number of eggs hatched on day t+5 | day6: number of eggs hatched on day t+6 | day7: number of eggs hatched after day t+6 | eggsurv: proportion of eggs hatched | hrate: daily hatching rate | eggsize: average log(egg size)
DOI: 10.5061/dryad.68sd84vh/2
title: Additional experiment measuring egg-to-larva size transition

description: eggSize: log(egg size) | larvaSize: log(larva size)
DOI: 10.5061/dryad.68sd84vh/3
title: Daily population census

description: day: day of the study (day t) | e: number of eggs | l: number of larvae | p: number of protonymphs | t: number of tritonymphs | f: number of female adults | m: number of male adults | group: (c)ontrol or (s)ample group? | dens: weighted population density
DOI: 10.5061/dryad.6gr7t/16
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_all_vs_unique_hits.diff

description: Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/17
title: Car_ign_100+amino_acids_ORFs_from_1200bp+_contigs_to_Takifugu_as_aa

description: FASTA file of open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 139,329,276 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx ignobilis. Subject database (DB) was the protein list from the fully sequenced genome of Takifugu available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/18
title: Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs

description: FASTA file of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus
DOI: 10.5061/dryad.6gr7t/19
title: Car_mel_all_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed

description: Parsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI.
DOI: 10.5061/dryad.6gr7t/20
title: Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio.parsed.filtered

description: Parsed BLAST output of all potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/21
title: Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_hits

description: Gene list of all hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/22
title: Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_unique_hits

description: Gene list of only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.
DOI: 10.5061/dryad.6gr7t/23
title: Car_mel_100+amino_acids_ORFs_from_1200bp+_contigs_to_Danio_all_vs_unique_hits.diff

description: Difference file between complete gene list and only unique hit descriptors for potential open reading frames (ORFs) &gt;=100 amino acids extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. Subject database (DB) was the protein list from the fully sequenced genome of Danio available from NCBI. This file is filtered to only contain hits with bit scores &gt;=80.