cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s30t4/1
title: Phylogenetic analyses

description: fasta, nexus, and xml files used for phylogenetic analyses.
DOI: 10.5061/dryad.s30t4/2
title: SNP matrices used for PCA STRUCTURE TREEMIX

description: plink and structure data formats with various filtering criteria.
DOI: 10.5061/dryad.s30t4/3
title: dadi files for demographic analysis

description: fasta and plink files used for dadi analysis of divergence time.
DOI: 10.5061/dryad.sh391/1
title: Mate choice and genetic divergence data

description: Worksheets with microsatellite and MHC genotypes used for calculations of genetic divergence, and offspring assignment data from mate choice experiment.
DOI: 10.5061/dryad.vb766/6
title: Com_ndhFrpl32_NexusAlignment

description: This nexus file is an alignment containing all sequences for the ndfH-rpl32 chloroplast spacer used in this study.
DOI: 10.5061/dryad.01c7s/1
title: PPM-Algeria-microsat-9loci-25pops-arp

description: microsatellite dataset in Arlequin format of 25 pine processionary moth populations sampled in Algeria
DOI: 10.5061/dryad.01c7s/2
title: PPM-Algeria-microsat-9loci-25pops-genepop

description: microsatellite dataset in Genepop format of 25 pine processionary moth populations sampled in Algeria
DOI: 10.5061/dryad.0bg04/1
title: CLRV_R1

description: CLRV-aligned reads R1
DOI: 10.5061/dryad.0bg04/2
title: CLRV_R2

description: CLRV-aligned reads R2
DOI: 10.5061/dryad.0bg04/3
title: PVSA_R1

description: PVSA-aligned reads R1
DOI: 10.5061/dryad.26v53/1
title: Mather Sharman Participant Data

description: This file contains the data values for individual participants which were analysed in the reported ANOVA tests. It also contains additional data relating to a control condition without adaptation.
DOI: 10.5061/dryad.271dk/1
title: DBGC: A Database of Human Gastric Cancer

description: Our work collected the data from transcriptome, proteome, mutation, biomarker and drug-sensitive genes. Totally comes out 9 files:1，transcriptome.txt -- transcriptome related to gastric cancer, that contains the type of experiment, platform, sample, volume, result and the linkage of those.2，up_genes.txt -- up-regulated gene list come from transcriptome which based on experiment3，down_genes.txt -- up-regulated gene list come from transcriptome which based on experiment4，proteome.txt -- proteome related to gastric cancer, that contains the type of experiment, sample, technology and result etc.5，up_proteins.txt -- up-regulated genes list come from proteome6，down_proteins.txt -- down-regulated genes list come from proteome7，mutation.txt -- mutation related to gastric cancer, that mainly include mutation type, postion etc.8，biomarker.txt -- biomarker related to gastric cancer including types, stages as well sensitivity, specifity ect.9，pharmacogenomics.txt -- include gastric cancer gene and drug detail as well as resistance mechanism etc
DOI: 10.5061/dryad.32md8/3
title: Cunning_PLoSONE_Dryad_Archive

description: This archive file contains all data and scripts necessary to reproduce the analyses and figures presented in this manuscript.
DOI: 10.5061/dryad.3mr26/1
title: all5_672loci_nex

description: Nexus alignments of 672 loci containing transcriptomic sequence data from Trogulus, Ortholasma, Hesperonemastoma, Acuclavella, and Sabacon.
DOI: 10.5061/dryad.3mr26/2
title: 672lociCharacterizations_all5Dyspnoi

description: An .xls file characterizing aspects of the 672 loci used in phylogenetic analyses, including: evolutionary rates and branch lengths, AT and AT3 content, bootstrap distributions, subsampled loci, hidden support analyses, and concordance factors.
DOI: 10.5061/dryad.3mr26/3
title: all5_672loci_concatRAxML

description: Alignment and partitions file for the concatenated RAxML analysis of 672 loci
DOI: 10.5061/dryad.3mr26/4
title: all5_672loci_PhyML-trees

description: 672 gene trees generated via PhyML
DOI: 10.5061/dryad.49p7f/1
title: Bionomic database for the dominant vectors of malaria in Africa

description: Compilation of bionomics data for the dominant vectors of malaria in Africa from published and unpublished sources reporting data collected from 1985-2013.
DOI: 10.5061/dryad.49p7f/2
title: Bionomic database for the dominant vectors of malaria in the Americas

description: Compilation of bionomics data for the dominant vectors of malaria in the Americas from published sources reporting data collected from 1985-2014.
DOI: 10.5061/dryad.49p7f/3
title: Bionomic database for the dominant vectors of malaria in the Asia-Pacific

description: Compilation of bionomics data for the dominant vectors of malaria in the Asia-Pacific from published sources reporting data collected from 1985-2014.
DOI: 10.5061/dryad.4f92n/1
title: SubA_Sleep1
DOI: 10.5061/dryad.4f92n/2
title: SubA_Sleep2_part1
DOI: 10.5061/dryad.4f92n/3
title: SubA_Sleep2_part2
DOI: 10.5061/dryad.4f92n/4
title: SubA_Wake1_part1
DOI: 10.5061/dryad.4f92n/5
title: SubA_Wake1_part2
DOI: 10.5061/dryad.4f92n/6
title: SubA_Wake2_part1
DOI: 10.5061/dryad.4f92n/7
title: SubA_Wake2_part2
DOI: 10.5061/dryad.4nb46/1
title: Population environmental, sociobiological and spatial parameters

description: This file contains data used for building Presence/absence models. Details of the analyses are provided in the main text under Presence/absence models in the Data Analysis section. Excel table with 4 sheets: i) Somport data; ii) Candanchú data; iii) Formigal data; iv) pooled data for the three populations.
DOI: 10.5061/dryad.4nb46/2
title: Population accuracy measures

description: This file contains population accuracy measures derived from model transferability among model evaluation types. Details of the analyses are provided in the main text under Model Evaluation and Transferability of distribution models across populations in the Data Analysis section. Excel table with 5 sheets: i) sensitivity values; ii) specificity values; iii) correct classification rate (CCR); iv) area under the ROC curve (AUC); v) prevalence.
DOI: 10.5061/dryad.7vf87/1
title: Experimental chambers

description: This file contains the temperature data for the experimental chambers used in the study. The column headings are all very self explanatory. Temperature is degrees C
DOI: 10.5061/dryad.7vf87/2
title: Incubation length

description: This file contains the data regarding the incubation duration of clutches in the experimental treatment. Column headings are self-explanatory. The locations given in 'Colony' are all found in the Gap Hills area, as described in the paper.
DOI: 10.5061/dryad.80jh7.1
title: Data from: Epigenetic divergence as a potential first step in darter speciation
DOI: 10.5061/dryad.80jh7.2/4.2
title: Final Potomac Matrices

description: Methylation susceptible (MS) and unmethylated (UM) matrices from six sampling locations in the Potomac River.
DOI: 10.5061/dryad.8hk5t/1
title: Silver fir growth (BAI) in the Pyrenees

description: The Excel file contains two sheets: 1) silver fir basal area increment from 1960 to 2000 in different populations across the Pyrenees; 2) silver fir growth (mean BAI), growth trend (BAI trend), Resistance index (Rt), Recovery index (Rc) and Resilience index (Rs) in different populations across the Pyrenees. In addition, we provide several explanatory variables describing topographic and stand characteristics that were used to explain the variation in the above mentioned variables.
DOI: 10.5061/dryad.8jb83/1
title: Genome coverage of the mm10 mouse reference genome of four closely related species

description: Genome coverage of the mm10 mouse reference genome. Computed from genomic alignments of Apodemus uralensis, Mus mattheyi, Mus spicilegus, and Mus spretus. The first six fields correspond to the genomic location and the following four to each of the species mentioned here, in the same order. Features were generated with bedtools, converted into SAF format, and extracted from BAM alignments using the featureCounts suite.
DOI: 10.5061/dryad.8jb83/2
title: Transcriptome coverage of the mm10 mouse reference genome across 200bp windows in ten closely related taxa and three tissues.

description: Transcriptome coverage of the mm10 mouse reference genome. Computed from transcriptome alignments of three populations of Mus musculus domesticus (AH from Iran, CB from Germany, MC from France), two populations of Mus musculus musculus (KH from Kazakhstan, WI from Austria), Mus musculus castaneus (TA), Mus spicilegus (SC), Mus spretus (SP), Mus mattheyi (MA) and Apodemus uralensis (AP). The first six fields correspond to the genomic location and the following each of the transcriptomes of the species mentioned here. Brain samples (pbrain), liver samples (pliver) and testis samples (ptestis), correspond to sequencing done at approximately one third of an Illumina HiSeq 2000 lane per taxon, while additional brain samples (xbrain) were done in a whole illumina HiSeq 2000 lane per taxon. Features were generated with bedtools, converted into SAF format, and extracted from BAM alignments using the featureCounts suite.
DOI: 10.5061/dryad.8jb83/3
title: rarefaction.200b.windows

description: Transcriptome coverage of the mm10 mouse reference genome. Computed from transcriptome alignments of three populations of Mus musculus domesticus (AH from Iran, CB from Germany, MC from France), two populations of Mus musculus musculus (KH from Kazakhstan, WI from Austria), Mus musculus castaneus (TA), Mus spicilegus (SC), Mus spretus (SP), Mus mattheyi (MA) and Apodemus uralensis (AP). This is a summary over three tissues (brain, liver, testis) for each of the taxa, resampled to obtain coverage rarefaction estimates by taxon and by fraction of data sequenced. Number in columns indicates the percentage, with total representing the maximum available sampling for each taxon. Each of the rows on this file corresponds to the rows of the transcriptome file, present together in this submission, and must be analyzed together to obtain genomic position information. Features were generated with bedtools, converted into SAF format, and extracted from BAM alignments using the featureCounts suite.
DOI: 10.5061/dryad.9f1p2/10
title: 24BUASsdcdeltaC2myc8

description: Raw image for Figure 3
DOI: 10.5061/dryad.9f1p2/11
title: 24BUASsdcdeltaCytomyc14

description: Raw image for Figure 3
DOI: 10.5061/dryad.9f1p2/12
title: sdcdeltaecto

description: Raw image for Figure 3
DOI: 10.5061/dryad.9f1p2/13
title: sdctmswap

description: Raw image for Figure 3
DOI: 10.5061/dryad.9f1p2/14
title: 24bflsdcpbs3

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/15
title: 24Bsdcdeltac1pbs13

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/16
title: 24Bsdcdeltac2pbs11

description: Raw image for Figure 4
DOI: 10.5061/dryad.9f1p2/8
title: 24BUASFLsdcmyc1

description: Raw image for Figure 3
DOI: 10.5061/dryad.9f1p2/9
title: 24BUASsdcdeltaC1myc6

description: Raw image for Figure 3
DOI: 10.5061/dryad.bc94c/1
title: Dryad data

description: Excel-file containing data on Morphology, Life history, Development times and Population Productivity. For data on sex-specific lifetime reproductive success, see Berger et al. 2014 (Evolution).
DOI: 10.5061/dryad.fp17j/1
title: Appendix2_CE

description: Character and Character State Descriptions for Phylogenetic Analysis
DOI: 10.5061/dryad.fp17j/2
title: Appendix3_CE

description: Formatted Data File Used in the Phylogenetic Analysis
DOI: 10.5061/dryad.g3122/1
title: Markers and Important markers

description: Genpop files (in a slightly modified format used for the random forest and contaminants work) of all markers for both eel species, in addition to the identification and statistics of important markers, the similarity matrix obtained from these important markers and the PCoAs produced from these similarity matrix.
DOI: 10.5061/dryad.g3122/10
title: Important_marker_annotation.tar

description: Annotation results for the important markers.
DOI: 10.5061/dryad.g3122/2
title: bayescan
DOI: 10.5061/dryad.g3122/3
title: Pollutants

description: Individual contamination of 24 organic and 10 metal pollutants for both species.
DOI: 10.5061/dryad.g3122/4
title: Database link.tar

description: A csv that links each individual with their BioSample Accession in SRA
DOI: 10.5061/dryad.g3122/5
title: A.anguilla_genotypes.tar

description: genepop file for A.anguilla individuals
DOI: 10.5061/dryad.g3122/6
title: A.rostrata_genotypes

description: Genepop file containing genotype for all A. rostrata individuals
DOI: 10.5061/dryad.gr2c7/1
title: Desventuradas_Juan_Fernandes_Fish

description: Underwater counts of fishes on transects
DOI: 10.5061/dryad.gr2c7/2
title: Desventuradas_Juan_Fernandes_mobile_inverts

description: Underwater counts of mobile invertebrates
DOI: 10.5061/dryad.gr2c7/3
title: Desventuradas_Juan_Fernandes_Sessile_Benthos

description: Underwater counts of sessile benthos
DOI: 10.5061/dryad.h30g3/3
title: env_and_time

description: data used to generate/analyse changes of SCS, heritability and evolvability over time and between environments.
DOI: 10.5061/dryad.h30g3/4
title: main_data

description: main data file.
DOI: 10.5061/dryad.m67r6/1
title: 3D ground truth models of liver tissue

description: 3D ‘ground truth’ images of idealized models of liver tissue ( 0.3 um x 0.3 um x 0.3u m per voxel)
DOI: 10.5061/dryad.m67r6/2
title: 3D simulated microscopy images of liver tissue

description: 3D simulated microscopy images of liver tissue models with 10:1, 4:1 and 2:1 signal-to-noise ratios.
DOI: 10.5061/dryad.m67r6/3
title: Scripts to generate 3D models and simulated images

description: MotionTracking scripts to generate 3D ‘ground truth’ voxelated models and simulated microscopy images of mouse liver tissue. A test example is included.
DOI: 10.5061/dryad.n3s2m/1
title: Soil water nutrient concentrations

description: Soil water samples collected in lysimeters at 60 cm depth, analyzed fornutrient concentrations: total dissolved organic carbon (NPOC, mg/L),total dissolved nitrogen (TN, mg/L), nitrate-nitrogen (NO3, mg/L), totaldissolved phosphorus (TP, ug/L), and soluble reactive phosphorus (SRP, ug/L)
DOI: 10.5061/dryad.n3s2m/2
title: Sampling site descriptions and traits

description: Information for each sampling site at tree or open turfgrass area: Tree genus/species, diameter at breast height (DBH) and total tree height; tissue chemistry (% C, N, P) for leaves, leaf litter, and roots; soil nutrients (KCl-extractable N, Brays P, and 10d net mineralization and nitrification rates)
DOI: 10.5061/dryad.nh8ph.1
title: Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing
DOI: 10.5061/dryad.nh8ph.2/11.2
title: SNIPE_all_plates_matrix_unfiltered.txt
DOI: 10.5061/dryad.np6b8/1
title: Data Carus et al

description: Data files contain data from velocity measurements in the pioneer zone of the Elbe estuary and measured plant traits of Bolboschoenus maritimus.
DOI: 10.5061/dryad.nq853/1
title: Complete table of the studies included in our review

description: In this paper we reviewed experimental studies that have tested how dispersal affects metacommunity diversity to determine why shortcomings emerge, and to provide a framework for empirical tests of theory that capture the processes structuring diversity in natural metacommunities. This table is a full list of the 50 studies of included experiments, and their corresponding methods and results.
DOI: 10.5061/dryad.q5p7g/1
title: Song-measurements_Dryad

description: file containing all song measurements. For each individual bird we recorded several song types. We obtained 22 acoustic measurements for each song type. We analysed three renditions of the same song type per bird and data presented here is averaged over these song types.
DOI: 10.5061/dryad.qj552/1
title: Matrices

description: This file contains the raw matrices analysed. For more informations on analysis them, please refer to:https://github.com/TGuillerme/Missing_living_mammals/For any queries, please email me at:guillert@tcd.ie
DOI: 10.5061/dryad.tj01t/1
title: All data associated with Cramer et al. Ecology and Evolution

description: Please see the readme file.
DOI: 10.5061/dryad.tt29d/1
title: Data from: Evaluation of Xpert® MTB/RIF assay in induced sputum and gastric lavage samples from young children with suspected tuberculosis from the MVA85A TB vaccine trial

description: These data were derived from an infant Tuberculosis disease vaccine trial conducted near Cape Town in South Africa, sub-Saharan Africa. We included diagnostic data that enabled us to evaluate diagnostic accuracy of Xpert MTB/RIF in induced sputum as compared to gastric lavage.
DOI: 10.5061/dryad.vp42s/1
title: RNA-seq expression count data for T. bifasciatum forebrain

description: RNA-seq expression data for three male and three female bluehead wrasse (T. bifasciatum) forebrain samples. Data is presented as a table of raw read counts per transcript (rows) in each sample (columns), processed in RSEM.
DOI: 10.5061/dryad.vp42s/2
title: RNA-seq expression count data for T. bifasciatum gonad

description: RNA-seq expression data for three male and three female bluehead wrasse (T. bifasciatum) gonad samples. Data is presented as a table of raw read counts per transcript (rows) in each sample (columns), processed in RSEM.
DOI: 10.5061/dryad.0bg04/10
title: Rumex_R2

description: Rumex-aligned reads R2
DOI: 10.5061/dryad.0bg04/11
title: TuMV_R1

description: TuMV-aligned reads R1
DOI: 10.5061/dryad.0bg04/4
title: PVSA_R2

description: PVSA-aligned reads R2
DOI: 10.5061/dryad.0bg04/5
title: PVSO_R1

description: PVSO-aligned reads R1
DOI: 10.5061/dryad.0bg04/6
title: PVSO_R2

description: PVSO-aligned read R2
DOI: 10.5061/dryad.0bg04/7
title: PVY_R1

description: PVY-aligned reads R1
DOI: 10.5061/dryad.0bg04/8
title: PVY_R2

description: PVY-aligned reads R2
DOI: 10.5061/dryad.0bg04/9
title: Rumex_R1

description: Rumex-aligned reads R1
DOI: 10.5061/dryad.1264j/1
title: data Klemme et al. coinfection 2015
DOI: 10.5061/dryad.25jp6/2
title: Vegetation data

description: All vegetation variables describing macro- and microhabitats
DOI: 10.5061/dryad.26v53/2
title: Mather Sharman Summary Data

description: This file contains derived data used for plotting graphs, and the actual graphs used in the paper. Raw data values in the accompanying file are converted in units suitable for the graphs.
DOI: 10.5061/dryad.3mr26/10
title: ep_ModelsEvolution

description: Results from models of evolution analyses used in expanded panel analyses, returned from jModelTest and PartitionFinder.
DOI: 10.5061/dryad.3mr26/5
title: all5_672loci_PhyML-BootstrapTrees

description: 100 bootstrap trees for each of 672 loci analyses in Newick format
DOI: 10.5061/dryad.3mr26/6
title: all5_672loci_MrBayes_treFiles

description: A MrBayes consensus tree and the tree files from each (2) runs for 672 loci
DOI: 10.5061/dryad.3mr26/7
title: RandomGeneSets

description: The loci used for subsampled data.  This includes 80 total subsampes, 10 each for 25, 50, 100, 200, 300, 400, 500, and 600 subsampled loci.  This includes partition files for concatenated analyses, and the resulting tree files for MP-EST, STAR, and concatenated RAxML analyses.
DOI: 10.5061/dryad.3mr26/8
title: ep_NexusAlignments

description: Alignments for 14 loci and these loci concatenated for expanded panel analyses in Nexus format.
DOI: 10.5061/dryad.3mr26/9
title: ep_RAxML_GeneTrees

description: RAxML gene trees for 14 loci used in expanded panel analyses.
DOI: 10.5061/dryad.3r85h/1
title: Mikolajewski et al. JEB
DOI: 10.5061/dryad.4f92n/10
title: SubB_Sleep2_part2
DOI: 10.5061/dryad.4f92n/11
title: SubB_Wake1
DOI: 10.5061/dryad.4f92n/12
title: SubB_Wake2_part1
DOI: 10.5061/dryad.4f92n/13
title: SubB_Wake2_part2
DOI: 10.5061/dryad.4f92n/14
title: SubC_Sleep1
DOI: 10.5061/dryad.4f92n/15
title: SubC_Sleep2_part1
DOI: 10.5061/dryad.4f92n/16
title: SubC_Sleep2_part2
DOI: 10.5061/dryad.4f92n/8
title: SubB_Sleep1
DOI: 10.5061/dryad.4f92n/9
title: SubB_Sleep2_part1
DOI: 10.5061/dryad.4vs36/1
title: Exp_I_reproduction_data

description: Raw data from a 21 day reproduction test using D.magna exposed to kaolin, and primary and secondary microplastics.
DOI: 10.5061/dryad.4vs36/2
title: Exp_II_DW_comparison

description: Dry weights of daphnids used in statistical evaluation of experiment II.
DOI: 10.5061/dryad.4vs36/3
title: Exp_III_food_consumption

description: Data from experiment III on consumption of algae in the presence of inert particles (kaolin, primary or secondary microplastics).
DOI: 10.5061/dryad.4vs36/4
title: Exp_IV_aggregates

description: Data for evaluation of MP-aggregates in the gut of D. magna from experiment IV.
DOI: 10.5061/dryad.4vs36/5
title: Exp_IV_gutevac

description: Gut evacuation data from Experiment IV.
DOI: 10.5061/dryad.609k3/1
title: Rhizophora mangle L. microsatellite genotype data and geographic and genetic distances

description: Microsatellite genotype data (tab 1) and matrices of genetic and geographic distances (tab 2) for Rhizophora mangle L. populations from the Caribbean Basin, Florida, and Northwest Africa
DOI: 10.5061/dryad.76r58/1
title: MorphLMswansArchive

description: (1) Count data of Bewick's swans at Lauwersmeer in autumns of 2005 - 2008; (2) Tuber sampling data in Lauwersmeer in autumns of 2005 - 2008; (3) Metadata water levels in Lauwersmeer and adjacent Wadden Sea in autumns of 2005 - 2008
DOI: 10.5061/dryad.76r58/2
title: Morph parameter files for basic scenarios

description: Basic scenarios (i.e., with observed water levels) to model swan usage of Lauwersmeer in autumns of 2005 - 2008
DOI: 10.5061/dryad.7s7r1/1
title: Vegetation plot data from contiguous and fragmented rainforests in the Western Ghats, India

description: Plot size: 30m X 30m. Min DBH: 3cm.
DOI: 10.5061/dryad.7v5p3/1
title: 157k_362Loci_align_9plus

description: Nexus file of 362 UCE loci from a minimum of nine individuals, with at least three informative sites. The total alignment is over 157,000 bp.
DOI: 10.5061/dryad.7v5p3/2
title: ML tree of Mitogenomes plus UCE outgroups

description: Mitochondrial tree, generated through Maximum Likelihood.
DOI: 10.5061/dryad.7v5p3/3
title: Mitogene_Tree_DCSPrior

description: Mitogenome BEAST xml file from this publication.
DOI: 10.5061/dryad.7v5p3/4
title: FcC_info

description: FasConCat data partitioning text file.
DOI: 10.5061/dryad.7v5p3/5
title: FcC_supermatrix

description: FasConCat supermatrix fasta file.
DOI: 10.5061/dryad.7v5p3/7
title: NJst_362LociSpTree

description: Species tree from NJst.
DOI: 10.5061/dryad.7vf87/3
title: location

description: This file contains the data for the descriptive component of the paper, characterising temperatures in different types of nest and locations in vegetation as described in the paper.
DOI: 10.5061/dryad.7vf87/4
title: Natural nests

description: This file contains the data that describes the variation in temperature for natural nests at Fowlers Gap with respect to environmental variables such as location, height and orientation as described in the paper
DOI: 10.5061/dryad.7vf87/5
title: Normal - Lethal

description: This data set looks at the time that the experimental nests spent at normal or lethal incubation temperatures during the experimental period (as described in the paper).
DOI: 10.5061/dryad.7vf87/6
title: Temperature Fowlers Gap

description: This file contains the data on maximum daily temperature from the Fowlers Gap automated weather station run by the Australian Bureau of Meteorology. This data is presented in Figure 1.