cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f058c/9
title: Pop6

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 6. Individuals that belong to population-pool 6 are listed in Table 1.
DOI: 10.5061/dryad.g216n/5
title: Microsatellite genotypes and mtDNA haplotypes

description: Genepop-like format; 000000 - missing data (may inbclude null homozygotes); 999999 - confirmed null homozygotes; for individuals with sequenced mtDNA haplotype and GenBank Accession are given
DOI: 10.5061/dryad.g89m0/2
title: female body size

description: Body length (in mm) of adult female Tigriopus californicus from lines selected for increased thermal tolerance and for lines held as unselected controls. Second column is population name (see sampling locations file). Third column is selection status: S = selected line U = unselected line. N= 6 individuals per line, 3-4 selected and unselected lines per population
DOI: 10.5061/dryad.g89m0/3
title: male body size

description: # Body length (in mm) of adult male Tigriopus californicus from lines selected for increased thermal tolerance and for lines held as unselected controls. # first column is population name (see sampling locations file). # second column is selection status: S = selected line U = unselected line # N= 6 individuals per line, 3-4 selected and unselected lines per population
DOI: 10.5061/dryad.j04r6/1
title: Functional morphology of 75 species of Cichlinae

description: Table includes mean values for functional morphology and body size from 75 species of Neotropical cichlids from both South and Central America and including all tribes of Cichlinae.
DOI: 10.5061/dryad.j57c0/10
title: 5_mtlsu_Simmap_27seqs

description: Dataset collapsed to haplotypes per geographic region to be used for Stochastic mapping
DOI: 10.5061/dryad.j57c0/8
title: 5_ITS_Simmap_60seqs

description: Dataset collapsed to haplotypes per geographic region to be used for Stochastic mapping
DOI: 10.5061/dryad.j57c0/9
title: 5_GPD_Simmap_47seqs

description: Dataset collapsed to haplotypes per geographic region to be used for Stochastic mapping
DOI: 10.5061/dryad.j5g7m/2
title: NPF_brainstains

description: This zip file contains the z-stack confocal microscopy image data from Drosophila melanogaster brains stained with anti-NPF antibody.
DOI: 10.5061/dryad.jm453/12
title: caecilian_DECJ_M0_unconstrained_v1

description: Output for DECj model from caecilian subtree analysis.
DOI: 10.5061/dryad.jm453/13
title: salamander_ecoregions

description: Salamander ecoregion data for 6-area BioGeoBEARS run. Code given below.
DOI: 10.5061/dryad.jm453/14
title: salamander_ecoregions

description: R Code for BioGeoBEARS analysis of salamander subtree with 6 areas. Data produced are given below.
DOI: 10.5061/dryad.jm453/15
title: amph_shl_dates_salamanders

description: Salamander subtree from NNI-optimized, SHL-supported ML tree. Used for 6-area salamander analysis in BioGeoBEARS.
DOI: 10.5061/dryad.jm453/16
title: salamander_DEC_M0_unconstrained_v1

description: R data object produced by R code given above, from 6-area salamander-subtree analysis in BioGeoBEARS. Load to view ancestral area estimates.
DOI: 10.5061/dryad.jm453/17
title: salamander_DECJ_M0_unconstrained_v1

description: R data object from DECj analysis of 6-area salamander subtree in BioGeoBEARS. Load for ancestral-area estimates.
DOI: 10.5061/dryad.jm453/18
title: frog_ecoregions_reduced

description: Ecoregion data for 2875-taxon subtree analysis of frogs (Appendix S3).
DOI: 10.5061/dryad.jm453/19
title: frog_ecoregions_reduced

description: R Code for frog subtree analysis using BioGeoBEARS (Appendix S3).
DOI: 10.5061/dryad.jm453/20
title: amph_shl_dates_frogs

description: 2875-taxon subtree for frogs (Appendix S3).
DOI: 10.5061/dryad.n56t9/1
title: Code for DNA barcoding Gaps

description: A custom Python script ‘getSixValue.py’ for calculating intra- and interspecific Kimura 2-parameter (K2P) distances of the congeneric species of the ITS1 and ITS2 regions in different taxonomic groups
DOI: 10.5061/dryad.n7080/3
title: Development time assay and Nf1 genotyping results (Figure3_data)

description: Development time assay produced two phenotypic classes (Fast and Slow). Flies were genotyped for both the 45-bp INDEL and the A/G SNP (locus L17277) of the Nf1 gene. These results were used for development time-Nf1 haplotype association analysis, as well as for linkage disequilibrium calculation.
DOI: 10.5061/dryad.ng93k/1
title: Ackerman2012_dryad_submission(sockeye)
DOI: 10.5061/dryad.nn3j4/1
title: Data, R code, manual

description: See README.txt
DOI: 10.5061/dryad.q96d7/10
title: fitContinousMCMC

description: An R script containing source code for functions related to fitContinuousMCMC. These are beta versions of the code that were used to conduct analyses in the manuscript. More user-friendly code with expanded options (different priors, for example) is available in a temporary package from http://www.webpages.uidaho.edu/~lukeh/software/index.html or from Graham Slater at gslater@ucla.edu
DOI: 10.5061/dryad.q96d7/7
title: fossils as tips swapping

description: This script is identical to the fossils as tips addition script, except that here proportions of extant taxa are replaced with fossil taxa to test the signal contributed by fossils relative to extant taxa. See the description for the aforementioned script for further details/ warnings.
DOI: 10.5061/dryad.q96d7/9
title: fossils as nodes fossil record

description: This R script performs simulation tests using MCMC using a simulated fossil record to derive informative node priors for a comparative dataset. Results are those in Appendix 1.
DOI: 10.5061/dryad.qb251/3
title: S1. Nucleotide alignments of 310 nuclear genes in PHYLIP format.
DOI: 10.5061/dryad.qv6hr4mq/2
title: Richards-Zawacki et al. - FROG MSAT GENOTYPES

description: Microsatellite genotypes, sex, age class, and dorsal color phenotype information for all frogs in the study. Missing genotypes are denoted as 000. Input files for GenePop 4.1, ARLEQUIN 3.0, CERVUS 3.0, COLONY 2.0 and MASTERBAYES 2.47 were derived from the data in this Excel file.
DOI: 10.5061/dryad.rt31g/1
title: 14002 Huntley and Scarponi Supplementary Information

description: Supplementary Tables 1-3.
DOI: 10.5061/dryad.s1092/1
title: Virgin.sim

description: Data on sperm transfer and storage after first mating for D. simulans. Variables: Treat – treatment, transfer or storage; Male – transgenic line by sperm label, GFP or RFP; Cop – copulation duration in minutes; Bursa – number of sperm in the bursa; Prox – number of sperm in the proximal half of the seminal receptacle (SR); Dist – number of sperm in the distal half of the SR; Caps – number of sperm in the paired spermathecal caps combined; Ducts – number of sperm in the paired spermathecal ducts combined
DOI: 10.5061/dryad.s1092/4
title: Remate.maur

description: Sperm numbers in space and time after second mating for D. mauritiana. Variables: MinASM – time after the start of mating at which female was frozen; FirstM – transgenic line of first male by sperm label, GFP or RFP. Second male is automatically the reciprocal label; Remate – day after first mating (day 0) on which female remated; Cop1 – duration in minutes of the first copulation; Cop2 – duration in minutes of the second copulation; PriorProg – number of progeny produced by female before remating; Bursa1 – number of first-male sperm in the bursa; Bursa2 – number of second-male sperm in the bursa; Prox1 – number of first-male sperm in the proximal half of the SR; Prox2 – number of second-male sperm in the proximal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist2 – number of second-male sperm in the distal half of the SR; Caps1 – number of first-male sperm in the two spermathecal caps combined; Caps2 – number of second-male sperm in the two spermathecal caps combined; Ducts1 – number of first-male sperm in the two spermathecal ducts combined; Ducts2 – number of second-male sperm in the two spermathecal ducts combined
DOI: 10.5061/dryad.s1092/5
title: Remate.mel

description: Sperm numbers in space and time after second mating for D. melanogaster. Variables: Block - different experimental blocks, A and B; MinASM – time after the start of mating at which female was frozen; FirstM – transgenic line of first male by sperm label, GFP or RFP. Second male is automatically the reciprocal label; Remate – day after first mating (day 0) on which female remated; Cop2 – duration in minutes of the second copulation; Bursa1 – number of first-male sperm in the bursa; Bursa2 – number of second-male sperm in the bursa; Prox1 – number of first-male sperm in the proximal half of the SR; Prox2 – number of second-male sperm in the proximal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist2 – number of second-male sperm in the distal half of the SR; Caps1 – number of first-male sperm in the two spermathecal caps combined; Caps2 – number of second-male sperm in the two spermathecal caps combined; Ducts1 – number of first-male sperm in the two spermathecal ducts combined; Ducts2 – number of second-male sperm in the two spermathecal ducts combined
DOI: 10.5061/dryad.s1092/7
title: Ejection.maur

description: Timing and number of sperm ejected after mating for D. mauritiana. Variables: Block – different experimental blocks, A and B; FirstM – transgenic line of first male by sperm label, GFP or RFP. Second male is automatically the reciprocal label; Mates – number of times each female mated; Remate – day after first mating (day 0) on which female remated; Cop1 – duration in minutes of the first copulation; Cop2 – duration in minutes of the second copulation; EjTime1 –Ejection time after first mating, in minutes after the start of the mating; EjTime2 – Ejection time after second mating, in minutes after the start of mating; PriorProg – number of progeny produced by female before remating; Eject1 – number of first-male sperm in ejection after first mating; EjMale1 – number of first-male sperm in ejection after second mating; EjMale2 – number of second-male sperm in ejection after second mating; Bursa1 – number of first-male sperm in the bursa; Bursa2 – number of second-male sperm in the bursa; Prox1 – number of first-male sperm in the proximal half of the SR; Prox2 – number of second-male sperm in the proximal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist2 – number of second-male sperm in the distal half of the SR; Caps1 – number of first-male sperm in the two spermathecal caps combined; Caps2 – number of second-male sperm in the two spermathecal caps combined; Ducts1 – number of first-male sperm in the two spermathecal ducts combined; Ducts2 – number of second-male sperm in the two spermathecal ducts combined
DOI: 10.5061/dryad.s1092/8
title: Velocity.sim

description: Sperm velocity and sperm numbers in the SR for D. simulans. Variables: Fem – identity assigned to individual female; Movie – name of movie file from which data were collected; Treat – treatment; A = virgin mating, B = remating, C = no remate; Region – region of the female reproductive tract, bursa or SR; Male – first- or second-male sperm; Velmps – instantaneous linear velocity in microns per second, averaged for each sperm and for all sperm recorded in a movie; N – number of sperm tracked per movie; SR1 – number of first-male sperm in the SR; SR2 – number of second-male sperm in the SR
DOI: 10.5061/dryad.s4h2j/1
title: Phuongetal_BJLS_Squirrel_species_delimitation

description: The following file contains: (1) microsatellite genotyping calls (2) mitochondrial and nuclear sequence data alignments (3) morphological data and (4) environmental data
DOI: 10.5061/dryad.vp634306/10
title: chromosome 8

description: Concatenated alignment of single-nucleotide variants from chromosome 8 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
DOI: 10.5061/dryad.vp634306/20
title: Figure S03

description: Genomic location of sliding windows with strong (≥ 0.95) posterior support for the four topological rearrangements most commonly given strong support by individual sliding windows. Filled circles indicate the weighted conflict score for the consensus tree estimated from a given sliding window of 500 consecutive sites; red circles indicate windows whose consensus topology strongly supports the given rearrangement.
DOI: 10.5061/dryad.vp634306/6
title: chromosome 4

description: Concatenated alignment of single-nucleotide variants from chromosome 4 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
DOI: 10.5061/dryad.vp634306/7
title: chromosome 5

description: Concatenated alignment of single-nucleotide variants from chromosome 5 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
DOI: 10.5061/dryad.vp634306/8
title: chromosome 6

description: Concatenated alignment of single-nucleotide variants from chromosome 6 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
DOI: 10.5061/dryad.vp634306/9
title: chromosome 7

description: Concatenated alignment of single-nucleotide variants from chromosome 7 in 29 taxa of genus Medicago (Fabaceae), collected by whole-genome resequencing and alignment to the M. truncatula reference genome.
DOI: 10.5061/dryad.07s25/1
title: Ecological_variables

description: Ecological data measured for each A. thaliana stands sampled for this study. Refer to material and method section for acquisition methods and Figure S2 for variable description.
DOI: 10.5061/dryad.08np6/2
title: Comparative Prey Capture

description: The prey capture success (0=failure, 1=success), collective mass gain, and mass of each prey item, for each of three size classes of prey item (small, medium, large)
DOI: 10.5061/dryad.10rk4/2
title: data crossinfection experiment Antagonistic coevolution accelerates the evolution of reproductive isolation in Tribolium castaneum
DOI: 10.5061/dryad.1v0tb/2
title: Result from alternative partitioning of data

description: Raw output R script testing for host associated differentiation, partitioned with either microsatellite data only, or AFLP data only.
DOI: 10.5061/dryad.5p0c3/1
title: Raw reads

description: Lambda phage reads processed with the 1D and 2D workflows.
DOI: 10.5061/dryad.5p0c3/2
title: Reads for snake transcriptome data

description: Reads for venom gland transcriptome of Protobothrops flavoviridis.
DOI: 10.5061/dryad.5t1b5/1
title: Pied babbler fledgling blackmail

description: Data from a series of experiments to investigate blackmail in fledgling pied babblers.
DOI: 10.5061/dryad.62hb0/1
title: or_stickleback.tar

description: The contents of or_sticleback.tar.gz relate to the study, "Thepopulation structure and recent colonization history of Oregonthreespine stickleback determined using RAD-seq" by Catchen, Julian,Bassham, Susan, Wilson, Taylor, Currey, Mark, O'Brien, Conor, Yeates,Quick, and Cresko, William.The raw data used to create these files are available from theSequence Read Archive (SRA), accession SRA070979.The Stickleback used for this study were collected from both marine andfreshwater sites along the Oregon coast, and from freshwater habitats inthe Willamette Basin and central Oregon. Extracted genomic DNA wasprocessed into RAD libraries using the restriction enzyme SbfI-HF to digestthe genome. After sequencing, reads were aligned to the sticklebackreference genome using GSnap and processed with the Stacks pipeline.File Contents-------------build_samples.sh - this file contains the commands run to clean and     demultiplex the data. This transforms the raw data files into cleaned     sample files, one per individual stickleback fish, named according to     population.build_tags.sh - this file contains the commands run to align demultiplexed     reads to the stickleback reference genome and to execute the Stacks     pipeline.batch_2.fst_summary.tsv - a summary of the Fst values for each population.batch_2.structure_1000.tsv - 1000, randomly selected loci take from the     batch_2.structure.tsv file for analysis in Structure.batch_2.structure.tsv - all variant sites in the Oregon dataset formatted     for analysis in Structure.batch_2.sumstats_summary.tsv - summaries of the summary statistics, Pi,     observed/expected heterozygosity, Fis, etc.batch_2.sumstats.tsv - summary statistics for each variable site in the     set, Pi, observed/expected heterozygosity, Fis, etc.batch_2.vcf - variant sites in the Oregon dataset formatted in VCF     (http://www.1000genomes.org/node/101).popmap - the population map file fed to the populations program. Describes     which samples belong to which populations. Here is the population key:  Crooked River        1  Cushman Slough       2  Pony Creek Reservoir 3  Paulina Lake         4  South Jetty          5  South Twin Lake      6  Winchester Creek     7  Riverbend            8  Millport Slough      9
DOI: 10.5061/dryad.7b470/9
title: Supplementary_Material_Liu_et_al

description: Table S1. List of 60 taxa sampled for the mitochondrial genomic dataset in this study.Table S2. Characteristics of 41 mitochondrial genes.Table S3. Characteristics of data matrices and statistics of the best-scoring ML trees inferred fromeach partitioning strategy.Table S4. Average GC percentage of each plant group, and difference significance test among groups.Figure S1. The average pairwise distances of the 41mitochondrial genes.Figure S2. A summary of single gene ML tree topologies.Figure S3-S19. Supplementary trees.
DOI: 10.5061/dryad.7h8n3/2
title: Frequencies of 18 genotypes of common evening primrose

description: Frequencies of 18 genotypes of common evening primrose (Oenothera biennis) in eight replicate field plots for three years after initiation of the selection experiment (estimated by microsatellite makers; 190 individuals were sampled from each plot each year).
DOI: 10.5061/dryad.80d7p/5
title: List of genes on microarray ORN-013

description: Complete list of genes on GEArray ORN-013
DOI: 10.5061/dryad.80d7p/6
title: List of genes on microarray ORN-013.2

description: Complete list of genes on GEArray ORN-013.2
DOI: 10.5061/dryad.82th6/1
title: 18S-16S rDNA clones from bioaerosol sample G4 (S4F2)

description: 18S-16S rDNA clones from a maize pollen enriched bioaerosol sample collected with a pollen trap (PMF/Sigma 2, TIEM Technique, Germany) in a coexistence field trial in the Ghent area, Belgium. Sequences obtained from sample G4. Primers used: 515f 5’-GTGCCAGCMGCCGCGGTAA-3’ (M=A-C) 1391r 5’-GACGGGCGGTGWGTRCA-3’(W=A-T; R=A-G).
DOI: 10.5061/dryad.82th6/6
title: 18S-16S rDNA clones from bioaerosol sample G6 (S6F2)

description: 18S-16S rDNA clones from a maize pollen enriched bioaerosol sample collected with a pollen trap (PMF/Sigma 2, TIEM Technique, Germany) in a coexistence field trial in the Ghent area, Belgium. Sequences obtained from sample G6. Primers used: 515f 5’-GTGCCAGCMGCCGCGGTAA-3’ (M=A-C) 1391r 5’-GACGGGCGGTGWGTRCA-3’(W=A-T; R=A-G).
DOI: 10.5061/dryad.8kk12/2
title: Proteome_t2

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 2 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.9061f/1
title: CottusAsper

description: Genepop datafile for 19 microsatellite loci genotyped for Cottus asper from seven locations in Alberta and British Columbia.
DOI: 10.5061/dryad.9js92/1
title: Sample_Larvas_Ixo_all_samples.fastq

description: FASTQ file with reads from Larvae samples
DOI: 10.5061/dryad.9js92/2
title: Sample_Glandulas_Ixo_all_samples.fastq

description: FASTQ file with the reads from Glands samples
DOI: 10.5061/dryad.9js92/3
title: IL_accepted_hits.bam.bai

description: BAI file corresponding to the BAM file of the Larvae samples Tophat accepted hits.
DOI: 10.5061/dryad.9js92/4
title: IG_accepted_hits.bam.bai

description: BAI file corresponding to the BAM file with the Glands samples Tophat accepted hits
DOI: 10.5061/dryad.9js92/5
title: IG_accepted_hits.bam

description: BAM file containing the Tophat accepted hits of the Glands samples
DOI: 10.5061/dryad.9js92/6
title: IL_accepted_hits.bam

description: BAM file containing the Tophat accepted hits of the Larvae samples
DOI: 10.5061/dryad.9js92/7
title: IG-tophat-run

description: Commands run to map the reads to the reference genome, glads sample
DOI: 10.5061/dryad.9n815/3
title: trnL sequences and taxonomic assignments Sanger
DOI: 10.5061/dryad.bc0v0/2
title: 33496_MasterCombinedAnnotationTablewHGNC.txt

description: Combined annotation information for the 33,496 coral contigs from the Acropora hyacinthus de novo assembly. Annotations are based on BLASTx matches to the ncbi nr and uniprot swissprot and TrEMBL databases.
DOI: 10.5061/dryad.d7k5r5d2/1
title: raw_competition_data

description: Raw competition colony counts and calculated fitness values for all competitions
DOI: 10.5061/dryad.f058c/12
title: Pop9

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 9. Individuals that belong to population-pool 9 are listed in Table 1.
DOI: 10.5061/dryad.f058c/13
title: Pop10

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 10. Individuals that belong to population-pool 10 are listed in Table 1.
DOI: 10.5061/dryad.f058c/14
title: Pop11

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 11. Individuals that belong to population-pool 11 are listed in Table 1.
DOI: 10.5061/dryad.f058c/15
title: Pop12

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 12. Individuals that belong to population-pool 12 are listed in Table 1.
DOI: 10.5061/dryad.f058c/18
title: Pop15

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 15. Individuals that belong to population-pool 15 are listed in Table 1.
DOI: 10.5061/dryad.f058c/19
title: Pop16

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 16. Individuals that belong to population-pool 16 are listed in Table 1.
DOI: 10.5061/dryad.f058c/22
title: Pop19

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 19. Individuals that belong to population-pool 19 are listed in Table 1.
DOI: 10.5061/dryad.g89m0/5
title: interbrood interval

description: # Mean number of days between broods for the first 3 broods of females from lines selected for increased thermal tolerance and from lines held as unselected controls. # second column is population name (see sampling locations file). # third column is selection status: S = selected line U = unselected line
DOI: 10.5061/dryad.g89m0/6
title: minimum generation time

description: # minimum generation time (in days) for females from lines selected for increased thermal tolerance and from lines held as unselected controls. # second column is population name (see sampling locations file). # third column is selection status: S = selected line U = unselected line
DOI: 10.5061/dryad.g89m0/7
title: Sampling locations

description: sampling locations and abbreviations for Tigriopus californicus
DOI: 10.5061/dryad.gd031k26/2
title: Supplemental Dataset 3
DOI: 10.5061/dryad.h30t5/1
title: tera.gut.mt.nuc.concat.ginsi

description: Nexus file used to generate phylogenetic results.