cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jr6r5/5
title: Aquatic Voucher PART 2 (AV) Metagenome (Illumina reads)

description: Illumina reads after quality control with Trimmomatic and Printseq (data generation and protocols described in the manuscript). Reads in fasta format.# this archive was split in 2 files with the unix command$ gzip -c my_large_file | split -b 1024MiB - myfile_split.gz_# to uncompress, use$ cat myfile_split.gz_* | gunzip -c &gt; my_large_file# to uncompress in windows (ensure file parts are in correct order)$ copy /b file_aa + file_ab + file_ac + file_ad filetogether
DOI: 10.5061/dryad.mk870/1
title: QC files of all samples

description: QC files of all samples
DOI: 10.5061/dryad.mk870/2
title: Raw_variations

description: Raw variations of all samples including the tissue and plasma
DOI: 10.5061/dryad.n0k69/1
title: Experiment 1 Data Set

description: Data for the first experiment
DOI: 10.5061/dryad.n0k69/2
title: Experiment 2 Data Set

description: Data for the second experiment
DOI: 10.5061/dryad.n0k69/3
title: Read Me

description: Description of the variables reported in the data sets
DOI: 10.5061/dryad.n14ph/1
title: Raw data for cubozoan statolith morphometrics

description: These are the raw data for Length: Width measurements and Normalised Elliptical Fourier coefficients resulting from analyses conducted for "Statolith morphometrics can discriminate among taxa of cubozoan jellyfishes". Morphometric analyses were conducted on statolith silhouettes in R using scripts detailed in the manuscript.
DOI: 10.5061/dryad.ng8pf/1
title: FraserFSCSalmonFisheries_CatchData_1983_2012

description: This is a dataset of food, social, and ceremonial (FSC) fisheries weekly catch numbers of salmon on the Fraser River, BC, Canada from 1983 to 2012. FSC fisheries are indigenous fisheries that are jointly managed by Fisheries and Oceans Canada and indigenous groups. Data are available online (http://www.pac.dfo-mpo.gc.ca/fm-gp/fraser/archives-a-eng.html#First_Nations) and through request. Fisheries are managed by region. Column headers are: downstream_point (downstream point of each fishery management region), species (species of salmon caught), year, day (day number of year, represents beginning of week where fish were caught), weeklycatch (number of fish caught in that week), tributary (1 if the fishery was on a tributary, 0 if the fishery was on the mainstem of the Fraser), hells (0 if the fishery was downstream of Hell's Gate, 1 if the fishery was upstream of Hell's Gate), richness (population richness that the fishery had access to, see Nesbitt & Moore for more details), km (distance the downstream point of the fishery is from the ocean, along the river network), ind.mass (average mass of an individual fish of that species, in kg), lat_ds_point (latitude of downstream point of fishery), long_ds_point (longitude of downstream point of fishery).
DOI: 10.5061/dryad.q1sq0/1
title: data_bird_density_2
DOI: 10.5061/dryad.q1sq0/2
title: script_density
DOI: 10.5061/dryad.s5k6k/1
title: genotype data

description: Hyposoter horticola DNA microsatellite genotype data
DOI: 10.5061/dryad.s5k6k/2
title: habitat patches geographic coordinates

description: habitat patches geographic coordinates
DOI: 10.5061/dryad.v1r28/1
title: Suppl.Doc.J.Paleo.Steadman.MacFadden

description: Supplemental File. Archival photo of the Gaillard Cut, Panama Canal, with annotations by Dr. John Turner concerning the fossil site (UF VP Locality YPA 002) where UF 281480 was collected. Image provided courtesy of J. Turner.
DOI: 10.5061/dryad.340p0/1
title: Hahn_JEcol_seedling_DATA

description: Data from the seed addition experiment. All data were collected in the field by the authors.
DOI: 10.5061/dryad.3780c/1
title: Coord_msat_alleles

description: File contains data for each sample with the locality (name of locality), coordinates (WGS84) and microsatellite genotypes for all individuals
DOI: 10.5061/dryad.3780c/2
title: Mantel_Matrix

description: Matrix of individual pairwise geographic distance (kilometers; below diagonal) and genetic distances (above diaginal; Nei´s DA; Nei et al. 1983).
DOI: 10.5061/dryad.3rk33/1
title: SBP-box genes in Brassica napus genome
DOI: 10.5061/dryad.3rk33/2
title: SBP-box protein Brassica napus, rice and Arabidopsis
DOI: 10.5061/dryad.3rk33/3
title: SBP-box proteins in Brassica napus, rice and Arabidopsis
DOI: 10.5061/dryad.43508/1
title: qtc_database to share
DOI: 10.5061/dryad.457br/6
title: Zipped library of Supplementary files 1-12

description: A zipped collection of all manuscript supplementary files in their native format (ie. not *.pdf)
DOI: 10.5061/dryad.4v5r8/1
title: Barn Swallow free-flight trajectories

description: Zip archive containing the trajectory kinematics and wind conditions for Barn Swallows engaged in foraging near the Oregon Institute of Marine Biology station in Coos Bay, Oregon.
DOI: 10.5061/dryad.604b8.2
title: Data from: Sequence capture versus restriction site associated DNA sequencing for shallow systematics
DOI: 10.5061/dryad.604b8.2/1.2
title: UCE and Exon Alignments from 40 Neotropical Birds

description: Alignments of 2,416 loci from 40 species of Neotropical birds. For each species at each alignment, a single sample was selected from a population-level dataset.
DOI: 10.5061/dryad.604b8.2/2.2
title: Supplemental Methods, Figures, and Tables

description: Additional information on methods and results of analyses of sequence capture and RAD-Seq datasets from Xenops minutus.
DOI: 10.5061/dryad.604b8.2/3.2
title: Raw reads from sequence capture with 8 *Xenops minutus* samples

description: Illumina reads from sequence capture of 1,358 ultraconservedelement (UCE) loci in 4 *X. minutus* samples from either side of the Andes. Tissue numbers corresponding to those used in the Table S1 and barcodes are provided in the filename for each sample.
DOI: 10.5061/dryad.6p2v0/3
title: Microsatellite genotypes of Thaumeatopoea pityocampa individuals from 5 portuguese populations

description: The file is organized according to NEWHYBRID format. Individuals codes (first column) are the ones used in the paper. Complete information on the sampling is available in Table S1.
DOI: 10.5061/dryad.6s2h0/1
title: DATA_Schrama&Bardgett_JoE_Invasibility_and_soil_community_composition

description: Data behind all figures with the exception of the NMDS (fig S2)
DOI: 10.5061/dryad.6s2h0/2
title: NMDS (fig S2)
DOI: 10.5061/dryad.812mm/1
title: haplotypeSequences

description: DNA sequences of partial cytochrome oxidase I sequences used for our analyses. These include both sequences from our study and those from Petersen (2007) doi:10.1007/s00227-006-0442-x
DOI: 10.5061/dryad.812mm/2
title: totalSnpCounts

description: For each sample of individuals, number individuals with each of the four different nucleotides at sequence position 461 (SNP-461). The first section of the table is for SNP genotypes determined by TaqMan probes, the second sequence is for SNP genotypes determined by sequencing, and the third section combines numbers from both methods of genotyping.
DOI: 10.5061/dryad.812mm/3
title: totalSnpFrequencies

description: SNP-461 allele frequencies for SNP genotypes determined from TaqMan probes, sequencing, and totals for both methods combined.
DOI: 10.5061/dryad.812mm/4
title: combinedSequences

description: All partial COI sequences from this study and Petersen (2007), trimmed alignment.
DOI: 10.5061/dryad.812mm/5
title: sequenceOrganizer

description: Perl script to organize sequences in combinedSequences.pl. Finds all unique haplotypes, names them h1, h2, h3... and writes fasta file of all unique haplotypes, writes file with number of occurrences of each haplotype, writes file of counts of each haplotype in each sample, writes input file for the software Arlequin, writes input file for the software IMa2
DOI: 10.5061/dryad.812mm/6
title: combineSnps

description: Reads counts of SNPs alleles (A, T, C, or G) from one file with counts in samples for TaqMan genotyping and another file with counts in samples from sequence-based genotyping and combines them. Output SNP counts and SNP frequencies by location and an input file in Genepop format. Allows samples to be pooled into named aggregate collections
DOI: 10.5061/dryad.812mm/7
title: sequencesToSnps

description: Reads sequences in fasta file, outputs SNP counts
DOI: 10.5061/dryad.b06f9/1
title: Master file_with Bivalvia and Gastropoda
DOI: 10.5061/dryad.d2680/5
title: Data2

description: This file contains 13 columns (variables) x 160 rows (excluding the first row, which contains the header with the variable names). The data were used to create: (1) a boxplot with DBH (diameter at breast height) inside bark versus categories of early growth (Fig. 2a in Bigler 2016); (2) a boxplot with lifespan versus categories of early growth (Fig. 2b in Bigler 2016); (3) pairwise scatter plots between lifespan, early growth, DBH inside bark and topographical variables (S1 Fig. in Bigler 2016); and (4) a scatter plot between early growth and lifespan (S3 Fig. in Bigler 2016). The data were further used to estimate linear mixed-effects models for predicting lifespan of mountain pines (Tables 1 and 2 in Bigler 2016).
DOI: 10.5061/dryad.d2680/6
title: Data3

description: This file contains 5 columns (variables) x 24546 rows (excluding the first row, which contains the header with the variable names). The data were used to plot establishment and mortality dates classified by early growth and colored by lifespan (Figure 3 in Bigler 2016) and to plot plot-specific variability of early growth (S2 Fig.). The year of establishment was estimated as the formation year of the first tree ring (corrected for missed rings between pith and first tree ring on the core). The year of mortality was estimated by the formation year of the last tree ring on the core. Due to the occurrence of partial cambial mortality, the year of mortality was only approximated (see Bigler & Rigling 2013).
DOI: 10.5061/dryad.d52n0/1
title: Evaluation of the bladder stimulation technique in infants (Data)

description: This data set contains all data that are statistically readable. No abbreviation. No additional user guidance is needed
DOI: 10.5061/dryad.f89h2/1
title: Food provisioning and brooding behaviors of orange-crowned warblers

description: Measures of parental provisioning and brooding effort by the sexes of orange-crowned warblers breeding in Fairbanks, Alaska (Oreothlypis celata celata; AK) and on Santa Catalina Island, California (O. c. sordida; CA) in the early (day 3 after hatching) and late (day 6 in Alaska; day 7 in California) nestling stages: (1) per-trip food loads scored as one if the volume of food load was equal to the beak size (see Methods), (2) hourly feeding trips, (3) hourly food delivery rate (the number of feeding trips × food load / hr), (4) proportional female brooding time (brooding min / videotaped min), and (5) ambient temperature (degrees Celsius).
DOI: 10.5061/dryad.g1228/1
title: Steyn et al. Data file
DOI: 10.5061/dryad.h0h4s/1
title: Supplementary Information

description: Supplementary tables and figures
DOI: 10.5061/dryad.h0h4s/2
title: Drosophila datasets

description: Datasests D1-D5 from the Drosophila analysis
DOI: 10.5061/dryad.hr0qt/1
title: Reduced reference genome and bismark output files

description: Reduced representation genome sequences built concatenating RADseq loci in Heliosperma and Dactylorhiza. Bismark output files for the three experiment described in the paper.
DOI: 10.5061/dryad.kh654/1
title: Fully-crossed Model Output

description: See read-me file.
DOI: 10.5061/dryad.pr3pr/1
title: Afrixalus paradorsalis annotated transcriptome

description: Whole RNA from a portion of liver sample preserved in RNA Later was extracted using the RNeasy Protect Mini Kit (Qiagen). Sequencing libraries were prepared using half reactions of the TruSeq RNA Library Preparation Kit V2 (Illumina), beginning with Poly-A selection for samples with high RIN scores (&gt; 7.0) and Ribo-Zero Magnetic Gold (Epicentre) ribosomal RNA removal for samples with low RIN scores (&lt; 7.0).  Libraries were sequenced on an Illumina HiSeq2500 with 100 bp paired-end reads. Transcriptomic data were cleaned following Singhal (2013).  Cleaned data were assembled using TRINITY (Grabherr et al. 2011) and annotated with Xenopus tropicalis (Ensembl) as a reference genome using reciprocal BLASTX (Altschul et al. 1997) and EXONERATE (Slater & Birney 2005).
DOI: 10.5061/dryad.pr3pr/2
title: Hyperolius balfouri annotated transcriptome

description: Whole RNA from a portion of liver sample preserved in RNA Later was extracted using the RNeasy Protect Mini Kit (Qiagen). Sequencing libraries were prepared using half reactions of the TruSeq RNA Library Preparation Kit V2 (Illumina), beginning with Poly-A selection for samples with high RIN scores (&gt; 7.0) and Ribo-Zero Magnetic Gold (Epicentre) ribosomal RNA removal for samples with low RIN scores (&lt; 7.0).  Libraries were sequenced on an Illumina HiSeq2500 with 100 bp paired-end reads. Transcriptomic data were cleaned following Singhal (2013).  Cleaned data were assembled using TRINITY (Grabherr et al. 2011) and annotated with Xenopus tropicalis (Ensembl) as a reference genome using reciprocal BLASTX (Altschul et al. 1997) and EXONERATE (Slater & Birney 2005).
DOI: 10.5061/dryad.pr3pr/3
title: Hyperolius riggenbachi annotated transcriptome

description: Whole RNA from a portion of liver sample preserved in RNA Later was extracted using the RNeasy Protect Mini Kit (Qiagen). Sequencing libraries were prepared using half reactions of the TruSeq RNA Library Preparation Kit V2 (Illumina), beginning with Poly-A selection for samples with high RIN scores (&gt; 7.0) and Ribo-Zero Magnetic Gold (Epicentre) ribosomal RNA removal for samples with low RIN scores (&lt; 7.0).  Libraries were sequenced on an Illumina HiSeq2500 with 100 bp paired-end reads. Transcriptomic data were cleaned following Singhal (2013).  Cleaned data were assembled using TRINITY (Grabherr et al. 2011) and annotated with Xenopus tropicalis (Ensembl) as a reference genome using reciprocal BLASTX (Altschul et al. 1997) and EXONERATE (Slater & Birney 2005).
DOI: 10.5061/dryad.pr3pr/4
title: Kassina decorata annotated transcriptome

description: Whole RNA from a portion of liver sample preserved in RNA Later was extracted using the RNeasy Protect Mini Kit (Qiagen). Sequencing libraries were prepared using half reactions of the TruSeq RNA Library Preparation Kit V2 (Illumina), beginning with Poly-A selection for samples with high RIN scores (&gt; 7.0) and Ribo-Zero Magnetic Gold (Epicentre) ribosomal RNA removal for samples with low RIN scores (&lt; 7.0).  Libraries were sequenced on an Illumina HiSeq2500 with 100 bp paired-end reads. Transcriptomic data were cleaned following Singhal (2013).  Cleaned data were assembled using TRINITY (Grabherr et al. 2011) and annotated with Xenopus tropicalis (Ensembl) as a reference genome using reciprocal BLASTX (Altschul et al. 1997) and EXONERATE (Slater & Birney 2005).
DOI: 10.5061/dryad.pr3pr/5
title: Hyperoliid Orthologous Transcript Set

description: Marker set consisting of 1,265 orthologous transcripts (trimmed to 500-850 bp) from four species of hyperoliid frogs (5,060 total sequences).  We compared annotated transcripts from the four species to search for orthologs via BLAST (Altschul et al. 1990). We removed mitochondrial loci from the transcripts. We only kept transcripts with a GC between 40%-70% because extreme GC content causes a reduced capture efficiency for the targets (Bi et al. 2012).  Orthologous transcripts with a minimum length of 500 base pairs (bp) were identified across all four samples, resulting in the identification of 2,444 shared transcripts. Transcripts exceeding 850 bp were arbitrarily trimmed to this length for probe design, reflecting a trade-off decision between locus length and the total number of loci included in the experiment. The orthologous transcripts were subjected to additional filtering steps before a final gene set was chosen.  The initial filtering step applied upper and lower limits on average transcript divergence, eliminating loci with low variation (&lt; 5.0% average divergence) and exceptionally high variation (&gt; 15.0% average divergence), resulting in the removal of 266 genes.  The remaining 2,178 genes were examined for repetitive elements, short repeats, and low complexity regions, which are problematic for probe design and capture.  The four sets of transcripts per gene (totaling 8,712 sequences) were screened using the REPEATMASKER Web Server (Smit et al. 2015). This step resulted in the masking of repetitive elements or low complexity regions in 929 sequences, with 7,783 sequences passing the filters.  To be conservative, if any of the four transcripts for a gene contained masked sites, that gene was removed from the final marker set, which resulted in the removal of an additional 468 markers.  From this reduced set of 1,710 markers, 400 markers with the highest divergence were selected (average divergence ranging from 10.4% to 14.9%) followed by 860 randomly drawn markers from the remaining subset.  This marker set was supplemented with five positive controls, which consisted of nuclear sequence data generated using Sanger sequencing for five loci: POMC (624 bp), RAG-1 (777 bp), TYR (573 bp), FICD (524 bp), and KIAA2013 (540 bp).  The final marker set selected for probe design included 1,265 genes from four species and 5,060 individual sequences.
DOI: 10.5061/dryad.pr3pr/6
title: Hyperoliid MYbaits-3 custom probe set

description: The MYcroarray MYbaits-3 custom bait library (MYcroarray) design. There are 60,179 120mer baits in this file, allowing for 2x tiling (every 60 bp) of the 5,060 sequences. The kit allows 60,060 probes, therefore 119 probes were randomly dropped for final kit design.
DOI: 10.5061/dryad.pr3pr/7
title: Captured Exon Alignments

description: A fasta file of combined aligned sets of captured transcripts (exons only) for the four hyperoliid species used for transcriptome sequencing and probe design.  Only markers with all 4 species present were kept, resulting in 999 transcripts. Names of transcripts correspond to those used in annotated transcriptomes, orthologous transcript set, and probe set for cross referencing. The concatenated alignment length of flanking regions is 592,651 base pairs.
DOI: 10.5061/dryad.qg15c/1
title: Donelson et al. Evol Appl data

description: Data file containing the means and standard errors of reproductive data used in "Transgenerational plasticity of reproduction depends on on rate of warming across generations".
DOI: 10.5061/dryad.r7d8h/1
title: Nab_gene_expression_dryad

description: All expression data for transcripts in the Nacobbus aberrrans de novo assembly, indicating which are in significantly deferentially expressed super clusters (with key), and including the centred log fold change.
DOI: 10.5061/dryad.r7d8h/2
title: N.abberans_reference_transcripts

description: de novo transcriptome assembly - transcripts
DOI: 10.5061/dryad.r7d8h/3
title: N.abberans_reference_predicted_proteins

description: de novo transcriptome assembly - predicted proteins
DOI: 10.5061/dryad.r7d8h/4
title: N.abberans_reference_predicted_CDS

description: de novo transcriptome assembly - predicted CDS
DOI: 10.5061/dryad.s6217/1
title: Estimated tree using data from Fernandez et al., (2013)

description: Our estimated tree generated using data from Fernandez et al., (2013). The tree is based on the ITS DNA region (accession numbers from the supplementary material of Fernández-Mazuecos et al., (2013)) for 29 species of herbaceous plants in the genus Linaria and one outgroup, Antirrhinum graniticum. The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Fernández-Mazuecos et al., (2013). We used a GTR + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and birth-death priors. Further information and full references can be found in the supplementary material of our paper.
DOI: 10.5061/dryad.s6217/2
title: Estimated tree using data from Janz et al., (2001)

description: Our estimated tree generated using data from Janz et al., (2001). The tree is based on the mitochondrial gene (nd1) and nuclear gene (wingless) for 25 species in the butterfly tribe Nymphalini and one outgroup, Argynnis paphia. The accession numbers were taken from Nylin et al., (2001). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Janz et al., (2001). We used a HKY + Γ model of nucleotide evolution with separate partitions for each gene, a relaxed log-normal clock, and a coalescent prior. Further information and full references can be found in the supplementary material of our paper.
DOI: 10.5061/dryad.s6217/3
title: Estimated tree using data from Johnson et al., (2009)

description: Our estimated tree generated using data from Johnson et al., (2009). The tree is based on the nuclear gene (EF-1α) and mitochondrial genes (12S and COI) for 38 species in the genus Columbicola and one outgroup, Oxyliperurus chiniri. The accession numbers were taken from Johnson et al., (2007). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014), allowing the topology to vary. We used a GTR + Γ model of nucleotide evolution with separate partitions for each gene and codon position, a relaxed log-normal clock, and a birth-death prior. Further information and full references can be found in the supplementary material of our paper.
DOI: 10.5061/dryad.s6217/4
title: Estimated tree using data from Larkin et al., (2008)

description: Our estimated tree generated using data from Larkin et al., (2008). The tree is based on the mitochondrial genes (COI and COII including the intervening tRNA-leucine) and the nuclear gene (EF-1α) for 35 species of bees in the genus Andrena and one outgroup, Ancylandrena larreae. The accession numbers were taken from Larkin et al., (2006). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Larkin et al., (2008). We used a HKY + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and a yule prior. Further information and full references can be found in the supplementary material of our paper.
DOI: 10.5061/dryad.s6217/5
title: Estimated tree using data from Mendlová and Šimková (2014)

description: Our estimated tree generated using data from Mendlová and Šimková (2014). The tree is based on two partial ribosomal RNA genes (SSU and LSU) and the entire ITS1 nuclear gene region for 25 species in the genus Cichlidogyrus and 3 species in the genus Scutogyrus. The accession numbers were taken from Mendlová et al. (2012) . The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Mendlová and Šimková (2014) . We used a GTR + Γ model of nucleotide evolution, separate partitions for each gene, a relaxed log-normal clock, and birth-death priors. Further information and full references can be found in the supplementary material of our paper.
DOI: 10.5061/dryad.s6217/6
title: Estimated tree using data from Schweizer et al., (2014)

description: Our estimated tree generated using data from Schweizer et al., (2014). The tree is based on three partial nuclear genes (c-mos, RAG-1 and Zenk) and one mitochondrial gene (ND2) for 78 parrot species within the order Psittaciformes and one outgroup, Falco tinnunculus. The accession numbers were taken from the supplementary material of Schweizer et al., (2014). The tree was estimated using BEAST v2.1.3 (Bouckaert et al., 2014) on the constrained topology from Schweizer et al., (2014). We used a HKY + Γ model of nucleotide evolution with separate partitions for each gene, a relaxed log-normal clock, and a coalescent prior. Further information and full references can be found in the supplementary material of our paper.