cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4rq51/1
title: SNPs in accession 1408

description: SNPs in accession 1408 identified by whole-genome resequencing
DOI: 10.5061/dryad.4rq51/2
title: Differences between accession 1408 and reference accession MTE in final mapping interval

description: Variants were called with SHORE v0.8 and pindel v0.2.4s. The FLC gene model is highlighted in bold and red.
DOI: 10.5061/dryad.528td/7
title: Fern images from Waikato Herbarium

description: Zipped folder with images of ferns from Waikato Herbarium. Folder also includes ReadMe file and image key.
DOI: 10.5061/dryad.77hn0/2
title: Heredity Dryad eggs laid data submission

description: These data were used in the analysis investigating the relationship between female size and the number of eggs laid by females.
DOI: 10.5061/dryad.8066v/2
title: Simulated data - deleterious recessive alleles - A populations
DOI: 10.5061/dryad.8066v/3
title: Simulated data - deleterious recessive alleles - D populations
DOI: 10.5061/dryad.8066v/4
title: Simulated data - balancing selection - A populations
DOI: 10.5061/dryad.8j1hb/2
title: PredictedBreeding_DRYAD

description: The data in this file were generated from an R script that estimated the mortality of D. ebraccatus eggs that would have been laid between 1972-2010. The script used the experimental data in TerrAqEggs_DRYAD.csv to create functions of aquatic and terrestrial egg mortality based on the rain falling on eggs during the 48 h post-oviposition (figures 1D-F of the ms). Combining these functions, specific to each pond used in the study, egg mortality was estimated for each rainstorm 5mm or greater between 1972-2010 (data available from the Smithsonian Tropical Research Institute, as described above).
DOI: 10.5061/dryad.9c568/9
title: flu H1 MCMCtree control file
DOI: 10.5061/dryad.b1068/1
title: Lecanora_ITS_mtSSU_combi

description: Alignment
DOI: 10.5061/dryad.b8d08/1
title: Murphy et al Final Data Set

description: Males raised in laboratory, environmental chamber. SL = standard length (mm); Diet= diet mother was reared on, LQ = low quality, HQ = high quality; Mating block is the ID of the group of males (all courters) mated to mother; SM = Sexual maturity, Social = social context during development (treatment = seeing an adult male; control = no other fish); sizes (SL) of males at different ages (14, 70) GR1 = growth rate before social context treatment; GR2 = growth rate after social context treatment
DOI: 10.5061/dryad.c316t/1
title: Dryad 1 - Emergence dates and haplotypes

description: Contains eclosion dates of all D. muliebre wasps in the study, alongside scored haplotypes (numbered 1-5 and corresponding with sequences on GenBank).
DOI: 10.5061/dryad.d1013/2
title: Oxytricha trifallax macronuclear IDBA assembly

description: Contigs in gzipped fasta format.
DOI: 10.5061/dryad.d1013/3
title: Oxytricha trifallax macronuclear ABySS assembly
DOI: 10.5061/dryad.dc56n/11
title: Pairwise effective resistance between Puccinellia maritima population (TIDE model)

description: Matrix of pairwise effective resistance (TIDE model) between Puccinellia maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.dc56n/12
title: Pairwise effective resistance between Puccinellia maritima population (SEDCELLS model)

description: Matrix of pairwise effective resistance (SEDCELLS model) between Puccinellia maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.dc56n/13
title: Pairwise effective resistance between Puccinellia maritima population (TIDE_SEDCELLS model)

description: Matrix of pairwise effective resistance (TIDE_SEDCELLS model) between Puccinellia maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.dc56n/14
title: Triglochin maritima population assignment to DAPC regions (K=4)

description: Triglochin maritima input file for the implementation of the AMOVA
DOI: 10.5061/dryad.dc56n/15
title: Triglochin maritima population assignment to DAPC regions (K=5)

description: Triglochin maritima input file for the implementation of the AMOVA
DOI: 10.5061/dryad.dc56n/16
title: Triglochin maritima population assignment to DAPC regions (K=6)

description: Triglochin maritima input file for the implementation of the AMOVA
DOI: 10.5061/dryad.dc56n/17
title: Triglochin maritima AMOVA script

description: R script permitting to compute AMOVA for Triglochin maritima
DOI: 10.5061/dryad.dc56n/18
title: Triglochin maritima samples assignment to population of origin

description: Triglochin maritima input file for the implementation of the AMOVA
DOI: 10.5061/dryad.dc56n/19
title: Triglochin maritima DAPC script

description: R script permitting to compute DAPC for Triglochin maritima
DOI: 10.5061/dryad.f058c/17
title: Pop14

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 14. Individuals that belong to population-pool 14 are listed in Table 1.
DOI: 10.5061/dryad.f68f0/1
title: Data to Figure 1

description: Fig. 1A: Chromosome numbers reported in selected holokinetic genera. Fig. 1B: Chromosome size divergence in monocentric and holocentric plant genera.
DOI: 10.5061/dryad.fb280/1
title: Poecilia_ATPn90_Dryad

description: ATPase8/6 gene data set obtained from species of the Poecilia sphenops species complex and closely related species and sister genus Limia (n=90). Full information of species and sampling localities, and additionally sequenced genes is indicated in the attached README file (Table 1 form the original manuscript).
DOI: 10.5061/dryad.gv4n5/1
title: moth_list

description: a list of moth (Macrolepidoptera) from Germany used in extinction cascade analysis
DOI: 10.5061/dryad.h988s/1
title: The high quality Illumina short read dataset used for the illustration in Figure 1

description: The high quality Illumina short read data was generated on Illumina HiSeq2000 platform with 100bp read length for a fungal genomic sequencing experiment. The first 7bp of each read is barcode sequence and has been removed.
DOI: 10.5061/dryad.h988s/2
title: Commands used for all QC tool evaluations
DOI: 10.5061/dryad.h988s/3
title: Simulated Illumina short read datasets used for the evaluation of adapter trimming tools

description: All data are 100bp paired-end Illumina reads simulated from the human genome (hg19.fa.masked) using pIRS which can simulate reads with realistic sequencing error profile and GC-bias. For paired-end reads simulation, pIRS selects randomly select insert sizes from a normal distribution with preset mean and standard deviation values. To simulate adapter contamination, the pIRS was modified so that when selected insert sizes are shorter than the preset read length (100bp in this study), adapter sequences will be concatenated at ends of genomic sequences before subsequent simulation of sequencing errors. Multiple simulations were performed with mean values of insert size ranging from 80 to 130 in order to approximate high to low levels of adapter contamination (the mean value used for each simulation was included in the file name of simulated dataset). All simulations were done with standard deviation of 10bp and 0.1x coverage.
DOI: 10.5061/dryad.h988s/4
title: Illumina short read dataset used for the illustration in Figure 3

description: The Illumina short read dataset was generated for a fungal genomic sequencing experiment and likely contains cross contamination from other samples prepared in the same experiment.
DOI: 10.5061/dryad.j248q/1
title: STRUCTURE - Belize Felids - Wultsch et al. 2014

description: STRUCTURE file for the manuscript "Noninvasive Individual and Species Identification of Jaguars (Panthera onca), Pumas (Puma concolor) and Ocelots (Leopardus pardalis) in Belize, Central America using Cross-Species Microsatellites and Fecal DNA". The file includes microsatellite genotype data for the three target species detected in Belize for this study.
DOI: 10.5061/dryad.j248q/2
title: Cytb_BZ_Felids

description: Alignment of cytochrome b (H15149, Kocher et al. 1989; Farrell-R, Farrell et al. 2000) sequence data in nexus format. Sample ID is tied to selected specimen (fecal DNA samples) of three Neotropical felids (jaguar, Panthera onca; puma, Puma concolor; ocelot, Leopardus pardalis) collected in Belize, Central America.
DOI: 10.5061/dryad.j248q/3
title: 12S_BZ_Felids

description: Alignment of 12S (L1085, H1259, Kitano et al. 2007) sequence data in nexus format. Sample ID is tied to selected specimen (fecal DNA samples) of three Neotropical felids (jaguar, Panthera onca; puma, Puma concolor; ocelot, Leopardus pardalis) collected in Belize, Central America.
DOI: 10.5061/dryad.j248q/4
title: 16S_BZ_Felids

description: Alignment of 16S (L2513, H2714, Kitano et al. 2007) sequence data in nexus format. Sample ID is tied to selected specimen (fecal DNA samples) of three Neotropical felids (jaguar, Panthera onca; puma, Puma concolor; ocelot, Leopardus pardalis) collected in Belize, Central America.
DOI: 10.5061/dryad.j248q/5
title: 16Scp_BZ_Felids

description: Alignment of 16Scp (16Scp-F, 16Scp-F, Kitano et al. 2007) sequence data in nexus format. Sample ID is tied to selected specimen (fecal DNA samples) of three Neotropical felids (jaguar, Panthera onca; puma, Puma concolor; ocelot, Leopardus pardalis) collected in Belize, Central America.
DOI: 10.5061/dryad.j248q/6
title: ATP6_BZ_Felids

description: Alignment of adenosine triphosphate-6 (ATP6-DF3, ATP6-DR2, Chaves et al. 2012) sequence data in nexus format. Sample ID is tied to selected specimen (fecal DNA samples) of three Neotropical felids (jaguar, Panthera onca; puma, Puma concolor; ocelot, Leopardus pardalis) collected in Belize, Central America.
DOI: 10.5061/dryad.j7581/2
title: readme: instructions for using code and simulation data here
DOI: 10.5061/dryad.j9769/1
title: DNA sequence alignments

description: Alignment of the phased data
DOI: 10.5061/dryad.pf013/1
title: Joop et al. 2014_JEB

description: Including raw data on quinone seection, PPO activity, quinone flux, number offspring, bacterial inhibition and survival in the presence and absence of microsporidia and/or quinones, using the red flour beetle, Tribolium castaneum.
DOI: 10.5061/dryad.qc537/3
title: Lau and Lennon PNAS plant data
DOI: 10.5061/dryad.rd47d/1
title: AlleleSizeLamprologuslemairii

description: genotype data underlying the paternity analysisin Lamprologus lemairii
DOI: 10.5061/dryad.t114v/1
title: Oreobates_sequences

description: Compressed zip file containing the alignments of DNA sequences used in the study in NEXUS format
DOI: 10.5061/dryad.t114v/2
title: Oreobates_distances_16S

description: File containing the aligned sequences of 16S gene in NEXUS format
DOI: 10.5061/dryad.tj1k5/1
title: Data for Dryad

description: Excel spreadsheet of all genotypes for 12 microsatellite loci (in fragment sizes)for Phyllodactylus tuberculosus. Loci were obtained both by molecular cloning and by 454 sequencing.
DOI: 10.5061/dryad.0674n/11
title: S. paradoxus CE distance matrix

description: Cavalli-Sforza and Edwards rDNA-based distance matrix for 26 S. paradoxus strains plus S. cerevisiae strain S288c
DOI: 10.5061/dryad.0674n/12
title: Updated S cerevisiae CE distance matrix

description: Cavalli-Sforza and Edwards rDNA-based distance matrix for 34 S. cerevisiae strains plus S. paradoxus strain Q32.3
DOI: 10.5061/dryad.0674n/13
title: Updated S. paradoxus NJ tree

description: Neighbor-Joining phylogenetic tree derived from the S. paradoxus CE distance matrix
DOI: 10.5061/dryad.0674n/14
title: Updated S. cerevisiae NJ tree

description: Neighbor-Joining phylogenetic tree derived from the S. cerevisiae CE distance matrix
DOI: 10.5061/dryad.1012q/1
title: Kin selection data

description: Raw data weight by hatch and minigeneration and method of selection
DOI: 10.5061/dryad.17bn1/2
title: ASU_Acar_v2.1.gtf - The gtf annotation file.
DOI: 10.5061/dryad.1cd80/2
title: SupportingPop_baru_characteristics

description: Characteristics of Dipteryx alata populations sampled for genetic structure analysis
DOI: 10.5061/dryad.1h0b7/1
title: Sea beet flowering  phenology JEB 2014

description: Glasshouse observations
DOI: 10.5061/dryad.1hf24/3
title: Matlab Simulations (Random anisotropic migration)

description: Simulation data summarized in Table 1 of the paper. These simulations are for anisotropic migration rates that randomly vary every generation.
DOI: 10.5061/dryad.20r9k/10
title: Myotis_contigs.tar

description: Contigs assembled for little brown bat
DOI: 10.5061/dryad.23r11/1
title: Chen and Ritland supplementary data
DOI: 10.5061/dryad.27900/1
title: Green Hermit location points 2008-2012

description: Radio-telemetry location points recorded in 2008 and 2012. See README.txt for details on columns.
DOI: 10.5061/dryad.27900/2
title: Python code used to generate data to run the Step Selection Function

description: This python code allows the user to obtain the information needed to run a Step Selection Function. It generates random movements steps based on the frequency distribution of observed step lengths and turning angles, and calculates the following characteristics along those movement steps: proportion of different habitat types within user-defined buffers, habitat types at start and end points, number of gaps crossed, length of the step that takes place inside each habitat type and distance to a given feature.
DOI: 10.5061/dryad.2hr77/2
title: cells per cluster

description: # cells per cluster, from 7-227d of evolution.
DOI: 10.5061/dryad.3g57k/2
title: g2 data file

description: Data file used in analysis where term occurrence is &gt; 2.
DOI: 10.5061/dryad.3sk8p/6
title: Part 2 of the sequence data for Table2.

description: Paired end Illumina GAIIx sequence data in the format of qseq. This is the 2nd of the 2 datasets for Table 2.
DOI: 10.5061/dryad.435s1/2
title: Fraxinus angustifolia_Maxent

description: Input file used for Fraxinus angustifolia current ecological niche model in Maxent. Localities are in decimal degrees (WGS84 Coordinate System). Description, abbreviations and source of environmental variables is given in the paper in Table S2.
DOI: 10.5061/dryad.5037s/1
title: Matute_etal_JEB_ReadMe
DOI: 10.5061/dryad.50p47/1
title: Supplemental Dataset 6: All the programs written in our lab that were used for this project.
DOI: 10.5061/dryad.52565/2
title: Emberizinae.mtnuc_complete_generic_12_18_09.nex

description: Data set including only taxa with some nuclear data.
DOI: 10.5061/dryad.5bd5r/1
title: Matrices

description: Distance matrices (geographic, genetic, habitat, barriers) used in landscape genetics of Corsican blue tits.
DOI: 10.5061/dryad.6p05c/1
title: Comparative seal paper raw data for dryad
DOI: 10.5061/dryad.7c7q0/2
title: one gene per lcb

description: fasta files for the "one gene per LCB" dataset
DOI: 10.5061/dryad.7g2h4/1
title: AFLP data

description: AFLP data for Steatogenys elegans cryptic species 1 and 2 including sampling locations.
DOI: 10.5061/dryad.7h9f4/1
title: GentleSelection_CDPOP

description: 2) Gentle spatial selection gradient (‘gentle’): Here, we used a ‘gentle’ spatial selection gradient corresponding to the three river color locations. For AA, we used the relative fitness coefficients of 0.4, 0.3, and 0.2 for black, mixed, and white waters, respectively. For Aa, we implemented an opposite spatial selection gradient (relative fitness coefficients of 0.2, 0.3, and 0.4 for black, mixed, and white waters, respectively).
DOI: 10.5061/dryad.7h9f4/2
title: UniformSelection_CDPOP

description: 1) No spatial selection gradient (‘uniform’): In this scenario, the three genotypes (AA, Aa, and aa) were being selected against, but uniformly across the ‘water color’ riverscape scenario, thus having no spatial dependency and allowing us to test for type I statistical errors.
DOI: 10.5061/dryad.7m6kg/39
title: Tentacle curvature in Nectocaris pteryx from the Burgess Shale

description: Left tentacle demonstrates flexible curvature
DOI: 10.5061/dryad.9rv1h/1
title: Common Yellowthroat Female Ornamentation Data Set

description: Fecundity, survival, standard morphometrics (body size), plumage ornamentation, and breeding experience for female Common Yellowthroats nesting in Saratoga County, New York, USA (2005-2008).
DOI: 10.5061/dryad.d1013/4
title: Oxytricha trifallax macronuclear PCAP 2.1.8 assembly
DOI: 10.5061/dryad.d1013/5
title: Oxytricha trifallax macronuclear genome fosmids
DOI: 10.5061/dryad.d1013/6
title: Stylonychia lemnae DDE_TNP_is1595 contigs

description: Contigs in fasta format.
DOI: 10.5061/dryad.dc56n/20
title: Coastal distance between Triglochin maritima populations

description: Matrix showing coastal distance between Triglochin maritima populations
DOI: 10.5061/dryad.dc56n/21
title: Triglochin maritima microsatellite dataset

description: Individuals are in row, microsatellite alleles in columns. Microsatellite alleles are coded as present or absent (1/0) in each individuals. NA for missing data.
DOI: 10.5061/dryad.dc56n/22
title: Pairwise effective resistance between Triglochin maritima population (TIDE model)

description: Matrix of pairwise effective resistance (TIDE model) between Triglochin maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.dc56n/23
title: Pairwise effective resistance between Triglochin maritima population (SEDCELLS model)

description: Matrix of pairwise effective resistance (SEDCELLS model) between Triglochin maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.dc56n/24
title: Pairwise effective resistance between Triglochin maritima population (TIDE_SEDCELLS model)

description: Matrix of pairwise effective resistance (TIDE_SEDCELLS model) between Triglochin maritima population inferred using the software Circuitscape. This matrix is inputted in R for Mantel test.
DOI: 10.5061/dryad.fb006/1
title: Murphy et al data
DOI: 10.5061/dryad.j7581/1
title: model simulation data and Matlab code for generating paper figures
DOI: 10.5061/dryad.j7581/3
title: Matlab code for running model simulations
DOI: 10.5061/dryad.jf7sn/1
title: genotypic_data

description: Genotypic data (genepop format) of the 875 individuals sampled in the course of the study. Spatial coordinates (Lambert II), sector of origin, year of sampling and sex are provided for each individual
DOI: 10.5061/dryad.jf7sn/3
title: vole-abundance_data

description: Raw data of common vole abundance (number of caught per trap line)
DOI: 10.5061/dryad.kv733/1
title: Genotype data sets

description: Genotypes of the individuals analyzed in Sanchez-Donoso et al., Frontiers in Ecology and Evolution, 2014.
DOI: 10.5061/dryad.mn324/1
title: Leininger_Kelley

description: Inter-click and inter-CAP intervals from bouts of vocal activity from calling animals (measured using Signal Sound Analysis software) and fictive activity from isolated brains (measured using Clampfit). Click heights from isolated X. boumbaensis larynx (measured using Clampfit).
DOI: 10.5061/dryad.mq8fn/1
title: DysoxylumMalabaricumNurseryGenotypes

description: The data file contains allelic information of 297 DNA samples of Dysoxylum malabaricum on 11 microsatellite markers.
DOI: 10.5061/dryad.n435p/1
title: Struck_Platyzoa2014
DOI: 10.5061/dryad.n6sk3/1
title: Experimental data

description: The file contains all data used for statistical analysis and to produce  Figures 1-6 and Figures S2-S3 of the paper.
DOI: 10.5061/dryad.q4r60/1
title: larvaltraitsExp1_Egea-SerranoetalJan14

description: Larval morphology divergence in the lab (Experiment 1)
DOI: 10.5061/dryad.q4r60/2
title: activityrepeated_Egea-SerranoetalJan14

description: Larval activity analyses in the lab (Experiment 1, repeated measures)
DOI: 10.5061/dryad.q4r60/3
title: survivalexp2_Egea-SerranoetalJan14

description: Survival under direct predation (Experiment 2)
DOI: 10.5061/dryad.q760h/1
title: gene_counts

description: Counts of trimmed 36 bp reads that mapped uniquely to consolidated exons of genes annotated in RefSeq for 136 patients.
DOI: 10.5061/dryad.q760h/3
title: linc_KhalilGenes

description: Counts of trimmed 36 bp reads that mapped uniquely to the coordinates of 2509 well-documented long-intergenic non-coding lincRNAs (Khalil et al., Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672, 2009).
DOI: 10.5061/dryad.q760h/4
title: intergenics

description: Counts of trimmed 36 bp reads that mapped uniquely to clusters in intergenic regions of the genome as described in Supplemental Methods.
DOI: 10.5061/dryad.q760h/5
title: recurrence

description: Time to recurrence or censure for 136 patients.  VSCode column contains a recurrence flag (1=recurrence, 0=no recurrence).  Years column is the time to recurrence or censuring (ie., end of observation without a recurrence).
DOI: 10.5061/dryad.q8f74/1
title: belly buttons ordination with labels
DOI: 10.5061/dryad.qm009/1
title: Piiroinen_etal_Stress_for_Invasion_Success

description: Text file, columns separated with commas. Data from the experiment to investigate separate and combined effects of insecticide stress and thermal stress history on life-history traits in the invasive Colorado potato beetle.
DOI: 10.5061/dryad.s4t7m/1
title: Plesnar_Bielak_etal_evolution_data
DOI: 10.5061/dryad.sk792/1
title: Avian point count data, image texture, and spectral unmixing fractions

description: The dataset includes the avian count data as well as image texture measures of NDVI and spectral unmixing fractions that were used in the analysis. The avian count data were collected in New Mexico, USA, between 1996 and 1998. A complete description of the methodology is available in Pidgeon et al. (1996).Pidgeon AM, Radeloff VC, Mathews NE. 2003 Landscape-scale patterns of black-throated sparrow (Amphispiza bilineata) abundance and nest success. Ecol. Appl. 13, 530 –542.
DOI: 10.5061/dryad.1c617/1
title: Zee_etal_Evolution_SwarmingData

description: This file contains the Myxococcus swarming data for the pilA-transformed and untransformed strains for all evolutionary timepoints of the E8 lineage.
DOI: 10.5061/dryad.1c617/2
title: Zee_etal_Evolution_MutationFrequencies

description: This is a table showing the presence/absence of mutations the accumulated along the E8 lineage of Myxococcus xanthus for a number of clones at each evolutionary time point.
DOI: 10.5061/dryad.1pb6t/1
title: Genotype data set of adults and offspring
DOI: 10.5061/dryad.20r9k/2
title: 8pr

description: Primers used in study (required for trimming script)
DOI: 10.5061/dryad.23g44/6
title: COI

description: alignment
DOI: 10.5061/dryad.31g77/1
title: Supplementary Figures

description: Additional figures
DOI: 10.5061/dryad.31g77/2
title: Primary references of Palebiology database occurrence data

description: List of radiolarian taxonomic references from the Paleobiology Database.
DOI: 10.5061/dryad.31g77/3
title: Radiolarian occurence data used for the analyses

description: Occurrence table of fossil radiolarians downloaded from the Paleobiology Database.
DOI: 10.5061/dryad.41r04/1
title: Kootenichela NEXUS

description: Phylogenetic data set in NEXUS file format.
DOI: 10.5061/dryad.4v0c5/3
title: Genepop_1047

description: The data from file "SNP_genotypes_1047.txt" presented in Genepop format.
DOI: 10.5061/dryad.503tf/4
title: Lacertidae vent  procrustes Sheets

description: Procrustes coordinates and CS values, with species, age/sex and habitat preference classifiers, for ventral cranium, for use in IMP series software (Sheets, 2000)
DOI: 10.5061/dryad.50p47/2
title: Supplemental Dataset 7: Insertion list for the dataset used for Figures 3 and 4, replicate a, raw.
DOI: 10.5061/dryad.50p47/3
title: Supplemental Dataset 8: Insertion list for the dataset used for Figures 3 and 4, replicate b, raw.
DOI: 10.5061/dryad.50p47/4
title: Supplemental Dataset 9: Insertion list for the dataset used for Figures 3 and 4, both replicates, filtered.