cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qj367/3
title: Rate-heterogeneity prevalence and patterns

description: Functions that determine the patterns and prevalence of trait rate-heterogeneity across trees, using as input scaled trees obtained after fitting variable-rates models to the phylogeny & associated tip trait data.
DOI: 10.5061/dryad.qt104/1
title: Host plant choice in Melinaea: female preference & larval performance

description: Data for both female preference and larval performance of different species of Melinaea on two different host plants (Juanulloa parasitica & Trianaea speciosa), including the number of eggs laid in choice and no choice experiments, survival, duration of larval development and pupal weight.
DOI: 10.5061/dryad.qv56d/1
title: Population data

description: File contains information of the geographic location, elevation, climate, and genetic variability for eleven populations of Pyrenean Morales grasshopper (Chorthippus saulcyi moralesi).
DOI: 10.5061/dryad.qv56d/2
title: Individual data

description: File contains information on morphology (femur length, forewing length, forewing length relative to femur length, in centimetres), forewing shape variation (Relative Warps) and genotypic data (16 microsatellite loci) for 202 Pyrenean Morales grasshoppers (Chorthippus saulcyi moralesi)
DOI: 10.5061/dryad.v0cf2/1
title: Multiple aligned OTU sequences associated with midgut microbiota of Anopheles mosquitoes sampled from Ghana

description: Data file included the following information: Operational Taxonomic Unit (OTU) name;Bacterial taxon assigned to OTU;Mosquito species associated with the OTU;Status of collection site from with the mosquito samples were collected;Season during which mosquito samples were collected.
DOI: 10.5061/dryad.vf5fk/10
title: Table S10 (Excel): Adaptively differentiated genes between Atlantic and Mediterranean samples.

description: Genes that were adaptively differentiated between Atlantic and Mediterranean samples, and enriched in biological processes (Tab. S10a) or molecular functions (Tab. S10b). Tab. S10c represents those genes that were not represented in enriched GO-terms. Each row represents one gene with its mapped sequence ID (mRNAID, column A), gene ID (ZosmaID, column B, based on the Zostera marina genome annotation v2.1, GenBank Accession: LFYR00000000), the source (column C) of annotation (inference from homology or top BLAST hit), and the name of the gene (column D). For Tab. S10a and Tab. S10b, the GO-term that each gene represents is represented in column E, and the description for this GO-term in column F.
DOI: 10.5061/dryad.vf5fk/11
title: Table S11 (Excel): Adaptively differentiated genes between Northern and Southern samples.

description: Genes that were adaptively differentiated between Northern and Southern samples, and enriched in biological processes (Tab. S11a) or molecular functions (Tab. S11b). Tab. S11c represents those genes that were not represented in enriched GO-terms. Each row represents one gene with its mapped sequence ID (mRNAID, column A), gene ID(ZosmaID, column B, based on the Zostera marina genome annotation v2.1, GenBank Accession: LFYR00000000), the source (column C) of annotation (inference from homology or top BLAST hit), and the name of the gene (column D). For Tab. S11a and Tab. S11b, the GO-term that each gene represents is represented in column E, and the description for this GO-term in column F.
DOI: 10.5061/dryad.vf5fk/12
title: Dataset S1 (vcf file): Biallelic neutral SNPs

description: Set of 139,321 biallelic neutral SNPs with genotypes (GT), allelic depths (AD), read depth (DP), genotype quality (GQ), and Phred-scaled likelihood for genotypes (PL) listed for each sample.
DOI: 10.5061/dryad.vf5fk/5
title: Table S5 (Excel): Targeted GO-terms.

description: GO-terms covered by the umbrella terms 'Heatstress' (Tab. S5a), 'Metabolism' (Tab. S5b), 'Oxidative-reductive' (Tab. S5c), 'Ribosomal' (Tab. S5d), 'Cellwall' (Tab. S5e), and 'Photosynthesis' (Tab. S5f) with ontologies (C: Cellular Process, F: Molecular Function, P: Biological Process) and descriptions.
DOI: 10.5061/dryad.vf5fk/6
title: Table S6 (Excel): Differential expression.

description: Genes differentially expressed between Atlantic and Mediterranean samples under control (Tab. S6a) , stress (Tab. S6b), and recovery conditions (Tab. S6c); and genes differentially exprelssed between Northern and Southern samples under control (Tab. S6d), stress(Tab. S6e) and recovery conditions (Tab. S6f). Each row represents one gene with: ZosmaID (gene ID based on the Zostera marina genome annotation v2.1, GenBank Accession: LFYR00000000); mRNAID, the mapped sequence ID; Source, the source of annotation (inference from homology or top BLAST hit); Description, the gene description; baseMean, the mean of normalized counts for allsamples; log2FoldChange, the log2 fold difference in normalized expression between Atlantic and Mediterranean (Tab. S6a-c) or between Northern and Southern samples (Tab. S6d-f, values &gt; 1 indicate higher expression in Mediterranean/Southern samples); lfcSE, the standard error of the log2 fold difference; stat, the Wald test statistic for differential expression; pvalue, the p-value; padj, the p-valueadjusted by the Benjamini-Hochberg method to control for false discovery rate; sdcol, the standard deviation of expression counts that were normalized by size factors for all samples; followed the regularized log-transformed expression values of all samples that were included in the test.
DOI: 10.5061/dryad.vf5fk/7
title: Table S7 (Excel): Genes responding to heat stress.

description: Genes that responded to acute heat stress (time points 2 and 3) are represented for samples from all four populations in Tab. S7a, for Doverodde samples Tab. S7c, for Gabicce Mare samples in Tab. S7d, and for Waquoit samples in Tab. S7e.  Genes that responded to heat in the recovery phase (time points 5, 7, and 9) are represented for all samples in Tab. S7b, for Doverodde samples Tab. S7f, for Gabicce Mare samples in Tab. S7g, for Great Bay samples in Tab. S7h, and for Waquoit samples in Tab. S7i.  ZosmaID (column A): the gene ID based on theZostera marina genome annotation v2.1 (GenBank Accession: LFYR00000000); mRNAID (column B): the mapped sequence ID; Source (column C): the source of annotation (inferencefrom homology or top BLAST hit); Description (column D): the gene description; baseMean (column E): the mean of normalized counts for all samples; log2FoldChange (column F): the log2 fold change innormalized expression between all control samples and all stressed samples; lfcSE (column G): the standard error of the log2 fold change; stat (column H): the Wald test statistic for differential expression;pvalue (column I): the p-value; padj (column J): the p-value adjusted by the Benjamini-Hochberg method to control for false discovery rate; sdcol(column K), the standard deviation of expression counts that werenormalized by size factors for all samples. The following columns represent regularized log-transformed expression values of all libraries that were included in the test.
DOI: 10.5061/dryad.vf5fk/8
title: Table S8 (Excel): Enriched functions and processes under acute heat-stress and in the recovery.

description: GO-terms that were significantly enriched in genes that were upregulated under acute heat stress (Tab. S8a for molecular functions MF, Tab. S8e for biological processes BP) or downregulated under acute heat stress (Tab. S8b for MF, Tab. S8f for BP) and in genes that were upregulated under recovery (Tab. S8c for MF, Tab. S8g for BP) or downregulated under recovery from heat stress (Tab. S8d for MF, Tab. S8h for BP). Each row represents one function with: the GO-term ID; the GO-term description, the number of annotated genes within this GO-term; the number of significantly upregulated genes within this GO-term; the expected number of upregulated genes; the p-value based on Fisher's exact test for enrichment.
DOI: 10.5061/dryad.vf5fk/9
title: Table S9 (Excel): Heat-responsive genes respresenting enriched functions and processes.

description: Genes that were significantly upregulated under acute heat stress and included in enriched molecular functions (Tab. S9a) or biological processes (Tab. S9e). Genes that were significantly downregulated under acute heat stress and included in enriched molecular functions (Tab. S9b) or biological processes (Tab. S9f). Genes that were significantly upregulated under recovery from heat stress and included in enriched molecular functions (Tab. S9c) or biological processes (Tab. S9g). Genes that were significantly downregulated under recovery from heat stress and included in enriched molecular functions (Tab. S9d) or biological processes (Tab. S9h). Each row shows: the GO-term ID; the GO-term description; the gene ID (based on the Zostera marina genome annotation v2.1, GenBank Accession: LFYR00000000); the mapped sequence ID (mRNAID); the name of the gene; and the source of annotation (inference from homology or top BLAST hit).
DOI: 10.17632/n2x536b2fk.1
title: TMRM staining of human skin fibroblasts

description: Confocal images of mitochondria stained with TMRM.
DOI: 10.5061/dryad.0735s/2
title: Horn&Cowley_Easypop_RunWindows

description: A text file containing the input parameters for the program EASYPOP used to generate the simulated datasets.
DOI: 10.5061/dryad.0735s/3
title: Horn&Cowley_GeneticStatistics_Simulations

description: A file containing the genetic statistics (FIS, number of alleles, levels of heterozygosity, etc.) generated from the simulated datasets. This data was used to build figure 1 in the manuscript associated with this entry, i.e. Horn and Cowley(2016).
DOI: 10.5061/dryad.0g3d5/1
title: draco_comparative data

description: Species' mean dewlap traits for males and females and sexual dimorphsims
DOI: 10.5061/dryad.2dh81/8
title: Survival[Sequential]
DOI: 10.5061/dryad.37cc5/1
title: Pest control, yield, and soil data.

description: See attached readme file.
DOI: 10.5061/dryad.3v71f/2
title: Annotations

description: Annotations associated with Tigriopus californicus transcriptome assemblies
DOI: 10.5061/dryad.3v71f/3
title: DE gene analysis in R

description: Data files and R-scripts for DE gene analysis
DOI: 10.5061/dryad.3v71f/4
title: LT50_analysis

description: Data files and R scripts for heat tolerance LT-50 analysis
DOI: 10.5061/dryad.43548/1
title: BMTrendAnalyses R script

description: Phylogenetic simulation for calculating Mean Pairwise Angle to assess directional evolution in phylogenetic comparative datasets, in R.
DOI: 10.5061/dryad.43548/2
title: R data file

description: R environment file for 1000 simulated datasets under BM, and 1000 simulated datasets under BM with a trend (µ = 3).
DOI: 10.5061/dryad.43548/3
title: Shape Data

description: Species average Procrustes residuals (202 landmarks in 3D) for 93 species of scallops.
DOI: 10.5061/dryad.43548/4
title: Phylogenetic tree

description: Phylogenetic tree (time calibrated) for 93 species of scallop.
DOI: 10.5061/dryad.4mf63/3
title: SizeAss 16-2-16

description: data of experiments and observations, updated with new and old information re standard length and gender of individuals
DOI: 10.5061/dryad.65k4n/1
title: Fig. S1 Gene ontology classification of the postman butterfly genes expressed in the gut.

description: GEG: gene expressed in the gut. GHG: gene highly expressed in the gut.
DOI: 10.5061/dryad.65k4n/2
title: Fig. S2 Scatterplot of enriched pathways for DEGs in larval gut after host plant shift.

description: The size and color of the dots represent the gene number and the range of the FDR value, respectively. Rich factor is the ratio of the differentially expressed gene number to the total gene number in a certain pathway. Four pathway databases were used in our analysis, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Reactome, BioCyc and Protein Analysis Through Evolutionary Relationships (PANTHER).
DOI: 10.5061/dryad.65k4n/3
title: Fig. S3 NJ tree and intron positions of HmelGST genes.

description: Phase 0, 1, and 2 introns are shown by black, blue, and red solid lines, respectively.
DOI: 10.5061/dryad.65k4n/4
title: Fig. S4 Distributions of H. melpomene GST and UGT genes on chromosmes.

description: Scaffold arrangement is based on the published linkage map (Heliconius Genome Consortium 2012).
DOI: 10.5061/dryad.65k4n/5
title: Fig. S5 Duplication mechanisms and conserved motif of UGT33 family in H. melpomene.

description: MCScanX (max gaps = 50) was used to identify the segmental and tandem duplications of detoxification genes in H. melpomene. This annotated tree was predicted by the collinear and tandem relationships of the output from ‘family tree plotter of MCScanX’. The characters T and S on the nodes mean tandem and segmental duplications, respectively. All the UGT33 family members in Fig. 4 were used to create sequence logo of signature region (http://weblogo.berkeley.edu/logo.cgi).
DOI: 10.5061/dryad.65k4n/6
title: Fig. S6 Gene gain and loss of GSTs superfamily in Heliconius butterflies.

description: The species tree was derived from a phylogeny based on independent nuclear and mitochondrial DNA sequences (Beltran et al. 2007). Each class of GSTs from 10 Heliconius species were reconstructed the NJ phylogenectic tree. Gene gain and loss was estimated with the method of Nam & Nei (2005).
DOI: 10.5061/dryad.65k4n/7
title: Table S1 Primer sequences used for quantitative PCR validation.
DOI: 10.5061/dryad.65k4n/8
title: Table S2 Annotation and sequences of GST and UGT multigene families in H. melpomene and Danaus plexippus genome.
DOI: 10.5061/dryad.67876/1
title: Female preferences all treatments

description: Female preference scores for each wing patch size.
DOI: 10.5061/dryad.67876/2
title: Behaviour during experimental exposures

description: The behaviour of both females and males during the exposure treatments
DOI: 10.5061/dryad.6g735/1
title: koala microsatellite genotypes

description: Genomic sequences from one Queensland koala were obtained from 454 GS-FLX technology. Using the fragments reads from the 454 data, microsatellites repeats were identified using MSATCOMMANDER 1.0.8. Alleles were visualized and scored using GeneMapper 3.7. The number zero indicates missing genotype data.
DOI: 10.5061/dryad.6jg7g/1
title: F2 Genotype Phenotype matrix

description: This is a matrix of genotype and phenotype information in .csv file format with F2 genotype called as heterozygotes (H) and homozygotes (A = M. guttatus, B = M. laciniatus) at each SNP marker. Each row is a SNP marker and each column is an individual. Phenotypes are described in the top 6 columns. This file is formatted to be input into Rqtl.
DOI: 10.5061/dryad.6jg7g/2
title: MSG_Genotype_Parse_FerrisMS

description: A custom perl script used to call F2 genotypes in sliding windows of 75 SNPs.
DOI: 10.5061/dryad.86n40/1
title: Correlation matrices of healthy controls constructed from correlation coefficients between DWT wavelet coefficients
DOI: 10.5061/dryad.86n40/2
title: Correlation matrices of schizophrenia patients constructed from correlation coefficients between DWT wavelet coefficients
DOI: 10.5061/dryad.8852k/1
title: State Dependent Light Foraging in Mimosa Pudica

description: The data was collected in a greenhouse in Simon Fraser University, Burnaby, Canada. Descriptors of column headings: initial is the initial width of the leaflet before disturbance, closing is the width immediately after disturbance, opening is the time until the leaflet reopened to 75% of its initial width, ID2 is the individual identity of a plant, population is the seed source of the plant. Treatment codes are 1&2 = uncovered 24 hours before behavioral assay and 3&4 = covered by shade cloth 24 hours before behavioral assay.
DOI: 10.5061/dryad.8j0kf/1
title: supplementary_material_KTMISSN
DOI: 10.5061/dryad.963hr/1
title: SI_Dataset_1_Haloarcheal_opsin_seqs

description: Fasta file containing 170 haloarchaeal opsin sequences recovered by BLASTp searches of haloarchaeal genomes, after correcting for incorrectly called start sites. Sequences are marked with tags noting differences from corresponding NCBI records. Long = sequence is longer than corresponding NCBI record. ID_to = sequence perfectly matches multiple NCBI records, Not_ID = sequence is not identical to corresponding NCBI record, Cap = sequence has alternative annotation as “capsular polysaccharide biosynthesis protein”.
DOI: 10.5061/dryad.963hr/2
title: SI_Dataset_2_Haloarchaeal_opsins_tree

description: Nexus formatted phylogeny file for 170 haloarchaeal opsins included in this study. Best opened with FigTree v1.4.0. Corresponds to Fig 2A and SI Fig. 5.
DOI: 10.5061/dryad.963hr/3
title: SI_Dataset_3_Alignment_halo_trimmed

description: Fasta formatted alignment file for 170 haloarchaeal opsins included in this study after manual trimming. Remaining 204 positions were used for phylogenetic inference with MrBayes.
DOI: 10.5061/dryad.963hr/4
title: SI_Dataset_4_Opsin_related_genes_queries

description: Fasta formatted file containing query sequences used in BLASTp searches for brp, crtE, crtB, crtI, and crtY.
DOI: 10.5061/dryad.963hr/5
title: SI_Dataset_5_Universal_opsins_tree

description: Nexus formatted phylogeny file for 1077 Class I opsins collected from the NCBI nr and env_nr databases. Best opened with FigTree v1.4.0. Corresponds to Fig 2C and SI Fig 3.
DOI: 10.5061/dryad.963hr/6
title: SI_Dataset_6_Plasmid_sequences.fasta

description: Fasta formatted file containing sequences for expression vectors  pMTFCHIS2 and pDJLCHIS.
DOI: 10.5061/dryad.9nv3b/3
title: Audio_Bird1
DOI: 10.5061/dryad.9nv3b/4
title: Audio_Bird2
DOI: 10.5061/dryad.9nv3b/5
title: Audio_Bird3
DOI: 10.5061/dryad.9nv3b/6
title: Audio_Bird4
DOI: 10.5061/dryad.9nv3b/7
title: Audio_Bird5
DOI: 10.5061/dryad.9sf96/1
title: sequence_alignments

description: Aligned exon sequence files.
DOI: 10.5061/dryad.9sf96/2
title: phylogenetic tree

description: Phylogenetic reconstruction of four representatives of the species complex Cloeon dipterum s.l., including C. peregrinator, based on the exon sequences of the eight newly developed nuclear DNA markers (2,526 base pairs). Bayesian inference was used to reconstruct the tree based on the concatenated supermatrix alignment.
DOI: 10.5061/dryad.g7rk5/1
title: 6_population
DOI: 10.5061/dryad.h0v84.1
title: Data from: Comparing macroecological patterns across continents: evolution of climatic niche breadth in varanid lizards
DOI: 10.5061/dryad.h0v84.2
title: Data from: Comparing macroecological patterns across continents: evolution of climatic niche breadth in varanid lizards
DOI: 10.5061/dryad.h0v84.2/1.2
title: Ecography data
DOI: 10.5061/dryad.hj834/1
title: CJS_FINAL

description: This data file was used to estimate prefledging survival and growth rates of black brant goslings as a function of their Mother's PAIRSTAT in Leach and Sedinger (2016).  Each row represents a gosling.  Data fields: CH=gosling capture history; MOTHER=mother's tarsal band; BRA = brood rearing area typically used by mother (see paper); GAGE = gosling age (days) at capture; GBM = gosling mass at capture; GSEX=sex of gosling; GBD = brood rearing area where gosling was captured; PAIRSTAT (see paper): FUTCHG = Pre-switch; EXP = unfamiliar, male experienced; NON = unfamiliar, male not experienced; MALE indicates if the father was unmarked.
DOI: 10.5061/dryad.hj834/2
title: CS_FINAL

description: This file was used to estimate Clutch size, Relative nest initiation date, and brood size at hatch (GLN) as a function of the mother's PAIRSTAT in Leach and Sedinger (2016).  See paper and companion data file for descriptions of column fields.
DOI: 10.5061/dryad.ph02r/1
title: Biomass and root to shoot ratios

description: Biomass (g) and root to shoot ratios of Centaurea solstitialis plants originating from North America and Europe
DOI: 10.5061/dryad.q4h2r/1
title: 4 gene cludioid Alignment

description: nexus alignment file with partition information
DOI: 10.5061/dryad.qg91m/7
title: Data 7 - Iterative Imputation TNT file

description: TNT file used in the analysis of the PC characters identified using Iterative Imputation
DOI: 10.5061/dryad.qg91m/8
title: Data 8 - PC character loadings

description: Top 25 most heavily loaded characters on the top three principal components
DOI: 10.5061/dryad.qg91m/9
title: Data 8

description: The top 25 most highly loaded morphometric characters for the first three principal components, identified using both methods of treating missing data. The loading is shown after the character description
DOI: 10.5061/dryad.t8v81/1
title: ElkYrRelocations

description: GPS relocations from elk collared in Southwestern Alberta from 2007 to 2013 with associated step attributes and habitat covariates. Data are from the winter seasons and files are separated by unique elk ID and year ('elk-year').
DOI: 10.5061/dryad.vd48c/1
title: Alba scaffolds

description: 162 Alba gene model super-scaffolds (i.e. gene model super-scaffolds with an Alba SNP and constructed from B. mori proteins on B. mori chromosome 15.
DOI: 10.5061/dryad.29mb7/1
title: Picea-FACE_synthesis_gas_exchange

description: Needle gas exchange rates measured on 1-year-old needles in ambient (A) and elevated (E) trees at both ambient and elevated CO2 levels (400 and 550 ppm) during five summer field campaigns (18 June, 2 July, and 19 September 2013; 23 and 26 September 2014).
DOI: 10.5061/dryad.2c2n7/1
title: Metabolic rate of Pieris napi during direct or diapause development

description: This excel file contains the full metabolic rate data of Pieris napi undergoing either direct development or diapause at low or high temperature. It contains one sheet. Samples are organized according to the chronological order they were measured. Factorial variables are coded numerically and explanations are given in the header. A quality filter shows poor measurements or groups not included in analysis. These are marked 0, while included measurements are marked 1. Please see comments for explanations of discarded measurements. Full calculations are shown in the main manuscript materials and methods section.
DOI: 10.5061/dryad.2c2n7/2
title: The whole body lipidome of Pieris napi

description: This excel file contains the whole body lipidome of Pieris napi undergoing either direct or diapause development. It has three sheets. The first contains the lipid class data, the second the lipid species data and the third the fatty acid data. All sheets are organized similarily with explanatory variables in the first four columns and each analysed pupa on its own row. See main manuscript for detailed descriptions of lipid nomenclature.
DOI: 10.5061/dryad.2c2n7/3
title: Pieris napi diapause intensity experiment and MR

description: This excel sheet contains the data for the Pieris napi diapause intensity experiment. It has one sheet, and each individual measurement has its own row. Factorial variables are coded by number and explanations are given in the column headers. The quality filter shows discarded measurements and the comments column shows motivation for discarding (even though there were very few discarded measurements). Full calculations are shown in the main manuscript materials and methods section.
DOI: 10.5061/dryad.30k4v/4
title: Supplementary_Figures
DOI: 10.5061/dryad.3118j/1
title: Data and scripts for data preparation and phenotypic analysis

description: The zip file contains the data and code files that were used in the data preparation and phenotypic analysis phases for the two rice experiments reported Al-Tamimi et al.: experiment 0254 that investigates an indica panel and experiment 0255 that investigates an aus panel.
DOI: 10.5061/dryad.3118j/2
title: Data and scripts for GWAS

description: The zip file contains the data and code files that were used in the genome wide association study (GWAS) phase for the two experiments reported by Al-Tamimi et al.: experiment 0254 that investigates an indica panel and experiment 0255 that investigates an aus panel. In addition, the combined panel (INDAUS) was subject to a GWAS.
DOI: 10.5061/dryad.43548/5
title: Group Classifier file

description: Relates species names in Shape.Data to phylogenetic tree and life habits.