cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.43548/6
title: R source file

description: Modified version of geiger's sim.char function that allows a vector of root values and modified µ.
DOI: 10.5061/dryad.4cg3j/1
title: Sora.Kron.Husband_Factors.influcing.unreduced.gametes

description: CSV data file of all plants used in analysis. Codes are included in data file
DOI: 10.5061/dryad.65k4n/10
title: Table S4 Summary of reads and assembly of the gut transcriptomes in H. melpomene.

description: “host” and “non” represent the samples from individuals reared with host and non host plant, respectively. The number after the sample name means replicates.
DOI: 10.5061/dryad.65k4n/11
title: Table S5 Annotations and expression signals of 326 DEGs in larval gut after host plant shift.

description: The protein sequences of all the genes were used as queries to Blastp search against nr database in NCBI (http://www.ncbi.nlm.nih.gov/). Transporter Classification DataBase (TCDB) was searched for the best hits of transporter genes (Saier et al. 2009). Peritrophin and genes related to nutrient digestion were classified by search against PFAM database (http://pfam.xfam.org/).
DOI: 10.5061/dryad.65k4n/12
title: Table S6 GO enrichment ananlysis of the differentially expressed genes.
DOI: 10.5061/dryad.65k4n/13
title: Table S7 Orthologous divergence of detoxification genes among Heliconius butterflies.
DOI: 10.5061/dryad.65k4n/14
title: Table S8 Differentially expressed genes detected by DESeq2 package
DOI: 10.5061/dryad.65k4n/9
title: Table S3 Sequences of detoxifying genes were used for PAML analysis.
DOI: 10.5061/dryad.86n40/10
title: Correlation matrices of schizophrenia patients constructed from wavelet coherence between time series
DOI: 10.5061/dryad.86n40/11
title: README
DOI: 10.5061/dryad.86n40/3
title: Correlation matrices of healthy controls constructed from correlation coefficients between MODWT wavelet coefficients
DOI: 10.5061/dryad.86n40/4
title: Correlation matrices of schizophrenia patients constructed from correlation coefficients between MODWT wavelet coefficients
DOI: 10.5061/dryad.86n40/5
title: Correlation matrices of healthy controls constructed from correlation coefficients between MODWT wavelet details
DOI: 10.5061/dryad.86n40/6
title: Correlation matrices of schizophrenia patients constructed from correlation coefficients between MODWT wavelet details
DOI: 10.5061/dryad.86n40/7
title: Correlation matrices of healthy controls constructed from partial correlation coefficients between MODWT wavelet coefficients
DOI: 10.5061/dryad.86n40/8
title: Correlation matrices of schizophrenia patients constructed from partial correlation coefficients between MODWT wavelet coefficients
DOI: 10.5061/dryad.86n40/9
title: Correlation matrices of healthy controls constructed from wavelet coherence between time series
DOI: 10.5061/dryad.8br54/1
title: Male barn swallow phenotypic & reproductive data

description: Data file with maximum tail streamer length, right wing length, and tetrahedral color measures for 4 ventral patches for male barn swallows from the Czech Republic, Romania, Turkey, and Israel. Clutch initiation date is provided for all populations but Romania. There are two years of data for the potential contact zone in Turkey. Color patch codes: T=throat, R=breast, B=belly, and V=vent. Also included are rotated factors summarizing phenotypic characters which were used in analyzing divergence in phenotypes and selection pressures: [BodyBrightness], [ThroatBrightness], [Saturation], and [StreamerLength]. Age is denoted for individuals we could confidently assign to a first-year or older age-class (i.e. which we had banded as a hatchling or which was an unbanded breeder at a site where we had banded all adults the previous year.)
DOI: 10.5061/dryad.97s4d/2
title: Raw data of the psychological experiment.

description: Participants' impressions elicited by the sound stimuli of 12 dental drills in idling and drilling conditions.
DOI: 10.5061/dryad.97s4d/4
title: Raw data of the physical metrics.

description: Equivalent continuous A-weighted sound pressure levels (LAeq) and sharpness in relation to drilling conditions of dental drills.
DOI: 10.5061/dryad.9bv73/1
title: Fig1

description: Fig 1. Construction of an OsMDHAR-expressing yeast vector and the stress response of OsMDHAR-expressing yeast to hydrogen peroxide. (A) Schematic diagram of the p426GPD::OsMDHAR construct. The OsMDHAR gene (approximately 1.5 kbp) was subcloned to generate the p426GPD::OsMDHAR construct with OsMDHAR under the control of the constitutive GPD promoter. Semi-quantitative RT-PCR (B), immunoblotting (C), and an enzymatic assay (D) were performed to examine whether OsMDHAR is expressed in this yeast strain. PDA1 and tubulin (Tub) were used as housekeeping controls for RT-PCR and western blotting, respectively. The molecular size of the PCR product and molecular weight of the detected band were approximately 494 bp and 47 kDa, respectively. Stress tolerance to hydrogen peroxide was evaluated by cell survival, growth kinetics, and spotting assays. (E) To monitor cell viability, yeast cells precultured in YPD medium were inoculated into fresh YPD medium and exposed to different concentrations of H2O2 for 16 h at 28°C. Then, the optical density at 600 nm (OD600) was measured. Circles, cells transformed with p426GPD-OsMDHAR (TC cells); squares, wild-type (WT) cells transformed with an empty vector. (F) For the growth kinetics assay, precultured yeast cells were inoculated into YPD medium containing 5 mM H2O2, and the OD600 was measured at 2-h intervals for 36 h. A streaking assay was also performed, in which mid-log phase yeast cells (OD600 ≈ 2.0) were streaked onto YPD agar plates supplemented with 5 mM H2O2. WT (squares) and TC (circles) cells in the absence of 5 mM H2O2; WT (upward triangles) and TC (diamonds) cells in the presence of 5 mM H2O2. (G) Mid-log phase yeast cells were exposed to 20 mM H2O2 for 1 h with shaking, and serially diluted with YPD medium. A 5-µL aliquot of each dilution was spotted onto YPD agar plates.
DOI: 10.5061/dryad.9bv73/2
title: Fig2

description: Fig 2. Analyses of cell rescue proteins, redox state, and protein oxidation under oxidative conditions. (A) Expression changes in antioxidant and metabolic enzymes in mid-log phase yeast cells exposed to 20 mM H2O2 for 1 h with shaking. Tubulin (Tub) was used as a loading control. (B) Hydroperoxide levels in TC cells in the absence (red bar) and presence (green bar) of 20 mM H2O2 were assessed using FOX reagent and were calculated relative to that in WT cells grown under normal conditions, which was set to 100%. (C) Mid-log phase yeast were exposed to 20 mM H2O2 for 1 h at 28°C with shaking. Redox state was analyzed by measuring DCFHDA oxidation as an indicator of cytosolic ROS. (D) Sensitivity of mutants (sod1Δ, tsa1Δ, por1Δ, and por2Δ) to oxidative stress. Yeast cells (OD600 ≈ 1.0) were exposed to 10 mM H2O2 for 1 h at 28°C with shaking, serially diluted with YPD medium, spotted onto YPD agar plates, and incubated for 2–3 days. (E) Expression changes in molecular chaperones in mid-log phase yeast cells exposed to 20 mM H2O2 for 1 h with shaking. Tubulin (Tub) was used as a loading control. (F) Protein carbonylation in yeast cells exposed to 20 mM H2O2 for 1 h was calculated relative to that in WT cells under normal conditions, which was set to 100%. Red bar, normal conditions; green bar, H2O2 treatment; WT, yeast cells with an empty vector; TC, OsMDHAR-expressing yeast cells; N, normal conditions; S, H2O2 treatment.
DOI: 10.5061/dryad.9bv73/3
title: Fig3

description: Fig 3. Stress response related to ascorbate (AsA)-like molecules. (A) AsA-like content in yeast cells exposed to 20 mM H2O2 for 1 h was analyzed and is shown as nmol per mg protein. The ratio shown is that of the reduced form to oxidized form. (B) ARA2 expression was evaluated by semi-quantitative RT-PCR. PDA1 was used as a control. (C) Oxidative stress response of yeast cells in the absence and presence of ARA2. Mid-log phase cells were serially diluted, and 5 µL of the diluted solutions were spotted onto YPD agar plates containing 4 mM H2O2 (upper panels). Mid-log phase cells were treated with 20 mM H2O2 for 1 h with shaking, diluted with YPD medium, and spotted onto YPD agar plates. The plates were incubated for 2–3 days and photographed. (D) Stress sensitivity of ara2Δ yeast cells, in which the erythroascorbate (EAA) biosynthesis gene was deleted. Yeast cells (A600 ≈ 1.0) were exposed to 10 mM H2O2 for 1 h at 28°C with shaking, serially diluted with YPD medium, spotted onto YPD agar plates, and incubated for 2–3 days. (E) The redox state of ara2Δ yeast cells under oxidative conditions. Yeast cells (OD600 ≈ 1.0) were exposed to 10 mM H2O2 for 1 h after DCFHDA and DHAR 123 treatment for 30 min and washed twice with phosphate-buffered saline (PBS). Probe intensity was observed by fluorescence microscopy. BY, wild-type cells without an empty vector; ara2Δ, cells with a deletion of the EAA biosynthetic gene ARA2; WT, wild-type yeast cells with an empty vector; TC, yeast cells with p426GPD::OsMDHAR; WA, ara2Δ yeast cells with an empty vector; TA, ara2Δ yeast cells with p426GPD::OsMDHAR; N, normal conditions; S, in the presence of H2O2.
DOI: 10.5061/dryad.9nv3b/10
title: Audio_Bird7
DOI: 10.5061/dryad.9nv3b/11
title: Audio_Bird8
DOI: 10.5061/dryad.9nv3b/12
title: Audio_Bird9
DOI: 10.5061/dryad.9nv3b/13
title: Audio_Bird10
DOI: 10.5061/dryad.9nv3b/14
title: Audio_Bird11
DOI: 10.5061/dryad.9nv3b/15
title: Audio_Bird12
DOI: 10.5061/dryad.9nv3b/16
title: Audio_Bird13
DOI: 10.5061/dryad.9nv3b/17
title: Audio_Bird14
DOI: 10.5061/dryad.9nv3b/18
title: Audio_Bird15
DOI: 10.5061/dryad.9nv3b/9
title: Audio_Bird6
DOI: 10.5061/dryad.cv2d5/1
title: Liefspan, size and reproduction data for all generations and silver forms

description: The file contains the raw data of the multigenerational experiment on the effect of silver ions and nanoparticles on C. elegans described in the publication. It includes data for each silver form and each generation on the lifespan in days, body size as volumetric length and reproduction in number of offspring produced by individual.
DOI: 10.5061/dryad.fj34d/1
title: Whole Brain Transcriptome for S. ocellatus

description: De novo transcriptome assembly was performed using Trinity (Haas et al. 2013) using RNA-Seq reads from male (sneaker, satellite, and nesting male) and female S. ocellatus whole brain mRNA.  Lowly-abundant transcripts with an FPKM &lt; 0.5 were filtered by RSEM, resulting in an assembly with 80,103 contigs with an N50 of 2119. To annotate the S. ocellatus transcriptome we employed Blastx (using an E-value cutoff of 1X10-10) on protein sequences for Oryzias latipes and Takifugu rubripes obtained from the Ensembl BioMart database, which resulted in the alignment of 25,856 contigs to the O. latipes genome and 25,213 contigs to the T. rubripes genome. Contigs that aligned with high confidence to more than one database were annotated based on the lowest E value and highest % identity to either reference genome, resulting in an assembly where roughly 32% of high quality contigs were successfully annotated. Contigs without annotations are labelled with contig tags generated by Trinity while annotated contigs have gene symbol following contig tags.
DOI: 10.5061/dryad.g9k62/1
title: C. funebralis multilocus SNP genotypes

description: Multilocus SNP genotypes for each of 90 Chlorostoma funebralis individuals (45 from northern California, USA and 45 from southern California) at all 2371 high quality, filtered loci (in Genepop format) obtained from ddRAD sequencing
DOI: 10.5061/dryad.gj7sn/1
title: Villa et al Allopreening Data

description: Data used for study titled "Does allopreening control avian ectoparasites?"
DOI: 10.5061/dryad.gv047/1
title: sBEAST_11genes_2mtrates

description: *BEAST v1.8.2 input file used for phylogenetic inference of Mabuyinae, using mitochondrial and nuclear DNA sequence data. Mitochondrial loci include ND2 and 16S, and nuclear loci include regions of BDNF, BRCA1, BRCA2, CMOS, EXPH5, KIF24, MC1R, MXRA5, and RAG1 protein coding genes. Includes DNA sequence data for 14 mabuyine and 2 outgroup taxa.
DOI: 10.5061/dryad.h6v7g.2/11.2
title: Matrix 2
DOI: 10.5061/dryad.h6v7g.2/9.2
title: Supplementary Table S3
DOI: 10.5061/dryad.md045/1
title: Retention forestry_plants_beetles

description: This dataset includes vascular plants recorded during field surveys (% projected foliage cover of each species, averaged from two sub-plots) and ground-active beetles collected with pitfall traps (number of specimens per species).
DOI: 10.5061/dryad.n0066/1
title: nab2008_species_data

description: Phytoplankton taxonomic data from 30 samples collected in the North Atlantic Ocean, south of Iceland, in spring 2007. Samples were preserved with acidified Lugol’s solution (approximately 2% final concentration). Phytoplankton taxa were determined to the lowest taxonomic level at which an accurate identification could be made using light microscopy and identified by Orbicon A/S, Aarhus, Denmark. Enumeration and calculation of carbon content followed the protocol used in the Danish National Water and Nature Monitoring Program. Axial dimensions of a subset of each taxon in each sample were measured and used to calculate the biovolume following standard taxon (group) specific equations. Biovolume was then converted to carbon equivalents using group specific conversions.
DOI: 10.5061/dryad.pm354/1
title: SNP genotypes

description: Genotypes from 106,492 SNP collected in 777 Atlantic Salmon. Contains a bed, bim and fam file formatted for analysis using Plinkv1.9.
DOI: 10.5061/dryad.q4h2r/2
title: BC_MCCFull_Ruhfel_clusioids

description: Full maximum clade credibility chronogram of the clusioid clade based on the analysis of a combined four-gene data set (BC placement of Paleoclusia; see text for details). Created by BEAST.
DOI: 10.5061/dryad.q4h2r/3
title: CC_MCCFull_Ruhfel_clusioids

description: Full maximum clade credibility chronogram of the clusioid clade based on the analysis of a combined four-gene data set (CC placement of Paleoclusia; see text for details). Created by BEAST.
DOI: 10.5061/dryad.rr853/1
title: Modern_archival_midden_comparison_fig1

description: Mytilus californianus data used in Fig 1 of the ms with measurements of shell dimensions, masses, age, thickness and radiocarbon data, where applicable.
DOI: 10.5061/dryad.rr853/2
title: Tatoosh_Archival_Small_Myt_californianus

description: Mytilus californianus morphological data from Tatoosh Island for modern and archival mussels. These data were used in Figs 2 and 3 of the manuscript.
DOI: 10.5061/dryad.tb5d8/1
title: expo_life-history data

description: Life-history data of breeding great tits with and without noise exposure inside their nest box
DOI: 10.5061/dryad.tk5ph/1
title: Data for maternal masses near parturition.

description: This file contains the data used for models of maternal mass near parturition and contains the following columns:  Mass (kg), momAGE.c (maternal ages in years at weighing, centered using the mean), momAGE.c.sq (the square of the previous term), momAGE.log (the log transform of maternal age in years, made by subtracting the minimum age from each animal and adding a small constant), PrevState (breeding state the previous season), NPrevPup.c (the number of previous pups for each mother, scaled by the average number of pups at each age), Season (year of measurement).
DOI: 10.5061/dryad.tk5ph/2
title: Data for pup masses near parturition, and daily gains during early and late lactation

description: This file contains the data used for models of pup mass near parturition and contains the following columns: PartMass (kg), momAGE.c (maternal ages in years at weighing, centered using the mean), MidGain (kg/day for the first 20 days), LateGain (kg/day for days 20 to 35), Season (year of measurement), DTA (deviation from target age), Female (indicator variable for female), Btime.c (birthdate centered using the mean), Btime.c.sq (square of the previous term), momSPENO (unique identifier for mother), momAGE.c.sq (the square of the previous term), momAGE.log (the log transform of maternal age in years, made by subtracting the minimum age from each animal and adding a small constant), NPrevPup.c (the number of previous pups for each mother, scaled by the average number of pups at each age), PrevState (breeding state the previous season),  PartMass.c (parturition mass centered according to the mean).
DOI: 10.5061/dryad.v15v0/1
title: MCC_FluA_H3

description: Time-scaled phylogenetic tree of H3 influenza viruses inferred by BEAST using molecular clock model.
DOI: 10.5061/dryad.v15v0/2
title: rst

description: Output file of CODEML inferring ancestral sequences of H3 influenza viruses using codon model.
DOI: 10.5061/dryad.v15v0/3
title: mlc

description: Output file of CODEML estimating selection pressure using codon model.
DOI: 10.5061/dryad.v15v0/4
title: NAG_inHA1

description: The predicted number of N-linked glycosylation sites in the hemagglutinin proteins of H3 influenza viruses.
DOI: 10.5061/dryad.v15v0/5
title: sites

description: The sequence sites selected to display amino acid substitutions on the phylogenetic tree of H3 influenza viruses.
DOI: 10.5061/dryad.v15v0/6
title: Genotype

description: Genotype table of the H3 influenza viruses.
DOI: 10.5061/dryad.2nh23/1
title: VanWyngaardenM_etal_GeogDistMatrix

description: This file contains matrices of pairwise geographic distances (km; shortest distance and estimated ocean current-based distance) between 12 populations of the sea scallop, Placopecten magellanicus, used along with 7163 RAD-seq derived SNPs to estimate isolation-by-distance and dispersal distances among populations. Population names and geographic coordinates can be found in Table 1 of the associated publication.
DOI: 10.5061/dryad.2nh23/2
title: VanWyngaardenM_etal_RADseq_SNPs

description: This VCF file contains 7216 RAD-seq derived SNPs detected among 12 Northwest Atlantic Ocean populations of the sea scallop, Placopecten magellanicus.  The program stacks v0.9999 was used to call variants; parameters can be found in Table S1 of the associated publication.
DOI: 10.5061/dryad.2p61j/1
title: basicmodel

description: FreeBASIC codes for the main model.
DOI: 10.5061/dryad.3293r/1
title: Genome assemblies, annotations, targets, and bait sequences from Gardner et al. 2016

description: A_camansi_v1.0_scaffolds.fasta  --  Genome assembly v. 1.0 (Ray 2.3.1)A_camansi_v1.1_scaffolds.fasta  --  Genome assembly v. 1.1 (L_RNA_Scaffolder)A_camansi_v1.1_genepredictions.gff  --  Gene predictions in GFF format (Augustus)A_camansi_v1.1_genepredictions.fna  --  Predicted coding sequences (Augustus)A_camansi_v1.1_genepredictions.faa.aa  --  Predicted protein sequences (Augustus)A_camansi_v1.1_genepredictions_annotations.txt  --  Gene annotations (Trinotate)artocarpus_333genes.fasta  --  333 phylogenetic marker sequencesartocarpus_mbgenes.fasta  --  98 putativeMADS-box gene sequencesartocarpus_volgenes.fasta  --  27 putative volatile gene sequences   artocarpus_baits.fasta  --  120mer bait sequences (designed by MYcroarray)
DOI: 10.5061/dryad.3293r/2
title: HybPiper assemblies for Johnson et al. (2016)

description: Output of HybPiper for 22 Artocarpus species and six outgroups, including Ficus and Morus. BWA was used to map the reads to the targets, including 333 genes used for phylogenetics (prefix "gene"), 98 MADS-Box genes (prefix "MB") and 27 genes functionally annotated as involved in volatile compounds (prefix "Vol"). After running the main HybPiper script (reads_first.py) we also ran "intronerate.py" to extract exon sequences, "paralog_investigator.py" to extract putative paralog sequences, "depth_calculator.py" to estimate depth of coverage in recovered exon sequence, and "cleanup.py" to remove redundant files from the SPAdes contig assembly.Data from: Johnson M., E.M. Gardner, J. Shaw, Y. Liu, R. Medina, B. Goffinet, N.J.C. Zerega, and N. Wickett. HybPiper: extracting phylogenetic datasets from high-throughput sequencing reads using targeted bait capture. Applications in Plant Sciences
DOI: 10.5061/dryad.3293r/3
title: Analyses from Johnson et al. 2016

description: README for HybPiper_artocarpus_analysis.tar.gz

artocarpus_trimmed.exon.tar.gz

Trimmed coding sequence (exon) alignments for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data.


supercontig_trimmed_fasta.tar.gz

Trimmed supercontig sequence alignments (containing both exons and flanking "splash zone" intron sequence) for 28 taxa for 333 genes. Sequences were aligned in MAFFT and trimmed using Trimal, discarding all columns with more than 80% missing data.


artocarpus_hybpiper_genelengths.txt

Lengths of exon sequence (CDS) recovered for 458 loci for 28 taxa using the BWA method. File generated using "get_seq_lengths.py" in HybPiper, and used to generate the heatmap figure in the HybPiper manuscript (with "gene_recovery_heatmap.R")


allbaitsuppercase.fna

Nucleotide "target" file used with HybPiper. For 333 loci, there are two orthologous sequences per gene: one from the Artocarpus camansi draft genome, and one from the Morus notabalis genome. For the remaining genes, only an Artocarpus ortholog is present.


artocarpus_bwa.supercontig.supermatrix.raxml.tre

RAxML phylogeny generated from a concatenated supermatrix of supercontig sequences for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Tree generated from nucleotide data using the GTRCAT model, with one partition per gene.


artocarpus_hybseq.exon.raxml.names.tre

RAxML phylogeny generated from a concatenated supermatrix of exon sequences extracted by HybPiper for 22 Artocarpus species and six outgroups, using the 333 "phylogenetic" loci. Node labels indicate bootstrap support from 200 "fast bootstrap" replicates.

Analyses from: Johnson M., E.M. Gardner, J. Shaw, Y. Liu, R. Medina, B. Goffinet, N.J.C. Zerega, and N. Wickett. HybPiper: extracting phylogenetic datasets from high-throughput sequencing reads using targeted bait capture. Applications in Plant Sciences
DOI: 10.5061/dryad.3bc76/1
title: it_s1_10_10_29808

description: Joint SFS between P. alba and P. tremula in Italy made with dadi from Pool-seq data, 24 individuals for each species downsampled to 10 diploid individuals, 29808 SNP
DOI: 10.5061/dryad.3bc76/2
title: RAD_it_s1

description: Joint SFS for 20 P. alba and24 P. tremula in Italy  for RAD-seq data made with dadi, downsampled to 15 and 15 individuals for a total of 8876 SNPs.
DOI: 10.5061/dryad.3bc76/3
title: script_inference_anneal2_newton_mis_0

description: Script allowing to carry out demographic models comparisons using ∂a∂i on genomic data.
DOI: 10.5061/dryad.3bc76/4
title: dadi_define_models

description: Definition of the different 38 models of divergence used in our inferences with ∂a∂i.
DOI: 10.5061/dryad.6140t/1
title: Kamenos et al RSPB-2016-1159
DOI: 10.5061/dryad.6kn05/1
title: pollen collection by bee

description: Number of pollen grains collected by each bee used in the study. NA's were entered for impossible combinations due to lack of availability at a site.
DOI: 10.5061/dryad.6kn05/2
title: Inflorescence availability

description: Number of inflorescences of each plant species counted at each unique Site-date
DOI: 10.5061/dryad.6kt60/1
title: Diaz Infante et al_ITS

description: ITS_File: Psittacanthus sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA)  sequences.
DOI: 10.5061/dryad.6kt60/2
title: Diaz Infante et al_trnLF

description: trnL-F_File: Psittacanthus sequences of the trnL-F intergenic spacer region from the chloroplast genome (cpDNA).
DOI: 10.5061/dryad.6tn7c/1
title: CREST taxonomic assignments table

description: This table shows the abundance of highest-rank CREST taxonomic assignments of sequence reads for all samples.