cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s0c34/4
title: Alignment_JEV full genome

description: Aligned nucleotide sequences of the complete genome of JEV/Bo/Aichi/1/2010 and other JEV isolates (aligned by using MEGA5).
DOI: 10.5061/dryad.s3060/10
title: DNA sequence alignments of P. likiangensis Pch
DOI: 10.5061/dryad.s3060/11
title: DNA sequence alignments of P. likiangensis Sb16
DOI: 10.5061/dryad.s3060/12
title: DNA sequence alignments of P. likiangensis Sb29
DOI: 10.5061/dryad.s3060/13
title: DNA sequence alignments of P. likiangensis Sb62
DOI: 10.5061/dryad.s3060/14
title: DNA sequence alignments of P. likiangensis Sel1364
DOI: 10.5061/dryad.s3060/15
title: DNA sequence alignments of P. likiangensis Sel1390
DOI: 10.5061/dryad.s3060/16
title: DNA sequence alignments of P. likiangensis Xy1420
DOI: 10.5061/dryad.s3060/8
title: DNA sequence alignments of P. likiangensis Moo2
DOI: 10.5061/dryad.s3060/9
title: DNA sequence alignments of P. likiangensis Moo7d1
DOI: 10.5061/dryad.sb669/10
title: Supplemental Data Set 10. P-proteins with their p-15-mers and their most significant motifs (from Table 2).
DOI: 10.5061/dryad.sb669/11
title: Supplemental Figure 1A. Hierarchical clustering (average linkage method) of all 364 non-redundant pS motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
DOI: 10.5061/dryad.sb669/12
title: Supplemental Figure 1B. Hierarchical clustering (average linkage method) of all 26 non-redundant pT motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
DOI: 10.5061/dryad.sb669/13
title: Supplemental Figure 2. Kinase recognition motifs for different kinase families in Arabidopsis.
DOI: 10.5061/dryad.sb669/9
title: Supplemental Data Set 9. Motifs for pS, pT and pY found by motif-x and MMFPh for sets A and B and subcellular sets at all occurrence thresholds
DOI: 10.5061/dryad.t8g16/8
title: blastAnalysis30

description: Python script used to process results of matching non-redundant sequencing reads to their database match. Called for by "AmpSeqpipeline30.sh"
DOI: 10.5061/dryad.1db54/1
title: Parental immune priming and offspring immunocompetence and reproductive investment

description: First tab: the effect of maternal and paternal immune challenge on offspring immunity (lytic and PO activity) and reproductive investment. Second tab: the effect of maternal and paternal immune challenge on the likelihood of the paternal generation successfully mating
DOI: 10.5061/dryad.41r51/1
title: Ecosystem Service Indicator Measurements

description: Zip files contains comma-delimited data files of ecosystem service indicator measurements for data collected in the field for 2010 and 2011, for both above- and belowground ecosystem service indicators. An associated readme file describes each file and the column headings.
DOI: 10.5061/dryad.41r51/2
title: R Scripts

description: R Scripts for data analysis. Includes a file for the generalized additive mixed model analysis (JAE_GAMMAnalysis_20140131), a file to create the associated generalized additive mixed model figures (JAE_GAMMPlots_20140201), the Spearman rank correlation analysis between ecosystem service indicators (JAE_Corr_20140203), and the multifunctionality analysis (JAE_Star_20140205). Files can be used in RStudio, opened in a text editor, or opened directly in R and use the associated data files also archived in DRYAD. These scripts were run in R version 3.0.2 for the Journal of Applied Ecology paper.
DOI: 10.5061/dryad.52c2h/4
title: Aplexa marmorata microsatellite genotypes (GenAlEx)

description: Aplexa marmorata microsatellite genotypes asGenAlEx format. For more information on sampling locations see the corresponding habitat characteristics data file.
DOI: 10.5061/dryad.52c2h/5
title: Aplexa marmorata microsatellite genotypes (Genepop)

description: Aplexa marmorata microsatellite genotypes as genepop format. For more information on sampling locations see the corresponding habitat characteristics data file.
DOI: 10.5061/dryad.52c2h/6
title: Aplexa marmorata microsatellite genotypes (Rmes)

description: Aplexa marmorata microsatellite genotypes as Rmes format. Rmes estimates unbiased selfing rates from population genetic data, for more information or to download the Rmes sofware see :http://www.cefe.cnrs.fr/en/genetique-et-ecologie-evolutive/patrice-david.
DOI: 10.5061/dryad.52hn0/1
title: Microsatellite genotypes of Atrina pectinata

description: This files contains the microsatellite genotypes for all individuals of Atrina pectinata at 8 polymorphic microsatellite markers.
DOI: 10.5061/dryad.53j13/1
title: qPCR validation results of scallop EDGE experiments
DOI: 10.5061/dryad.58ss8/14
title: LasV-S

description: Lassa virus - structural gene
DOI: 10.5061/dryad.58ss8/15
title: YFV-NS

description: Yellow fever virus - non-structural virus
DOI: 10.5061/dryad.58ss8/16
title: JEV-NS

description: Japanese encephalitis virus - non-structural gene
DOI: 10.5061/dryad.58ss8/17
title: PRRSV-NS
DOI: 10.5061/dryad.58ss8/18
title: NoV GII.4-NS

description: Norovirus GII.4 - non-structural gene
DOI: 10.5061/dryad.58ss8/19
title: bovineCoV-S

description: Bovine coronavirus - structural gene
DOI: 10.5061/dryad.58ss8/20
title: PowV-S

description: Powassan virus - structural gene
DOI: 10.5061/dryad.59g56/1
title: Bumblebee trapping samples

description: Bumblebee (Bombus sensu stricto-group) trapping sample ID numbers, collecting dates, and trap locations from two trapping areas (S and T) in Kemiönsaari, Finland. Sequenced samples have been included in a separate alignment file except for samples with nuclear copies of mtDNA.
DOI: 10.5061/dryad.59g56/2
title: Sample information for sequenced bumblebees

description: Collection locations of sequenced bumblebee samples, castes, and the presence of nuclear copies of mtDNA (NUMTS).
DOI: 10.5061/dryad.59g56/3
title: Sequenced bumblebee samples aligned with Apis mellifera liqustica genome

description: BioEdit alignment file containing the sequenced bumblebee samples aligned with Apis mellifera liqustica genome. Samples containing nuclear copies of mtDNA or incomplete sequence data have been removed.
DOI: 10.5061/dryad.5g6312br/2
title: LineageDataSupplTablev2

description: Lineages and trait data for cichlids included in this study. Data derived from Seehausen et al 1999, Seehausen 2000 and FishBase (Froese & Pauly 2010).
DOI: 10.5061/dryad.610dd/2
title: RAD-tag data set in TSV format for northwestern Atlantic Nucella lapillus populations

description: This is the easier to visualize data output (tsv format) from the STACKs assembly described in the paper. It contains all retained "stacks" including those that contain SNPs and those that have a single consensus sequence. Note that stacks with 4 or more SNPs were not used in the analyses. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/3
title: RAD-tag depths in TSV format

description: This file contains the depths of reads in the RAD-tag assembly corresponding to the RAD-tag SNP data file. This file was used to approximate allele frequencies in limited instances. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/4
title: NucellalapillusTranscriptomeAssembly

description: Transcriptome Assembly from RNA-seq reads assembled into contigs using Trinity in fasta format. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/5
title: PCA R script for bca algorithm

description: Script used to run the bca analysis from the package adegenet (Jombart 2008). For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/6
title: IUPACwrapper

description: Converts a directory of STACKS haplotype export files (in tsv format) into phylip format in IUPAC form (thus incorporating all SNPs). Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/7
title: Calculate nucleotide diversity for each population

description: Calculates nucleotide diversity for each population from a STACKS haplotype export file. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/8
title: Extract fixed SNPs along a gradient

description: Identifies SNPs that vary linearly along a gradient or populations. Fixed is defined as the SNP changes from one allelic identity to another along the predefined gradient without reverting to a past identity. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.82j1g/10
title: Fig. S4
DOI: 10.5061/dryad.82j1g/11
title: Fig. S5
DOI: 10.5061/dryad.82j1g/3
title: Fig. 3
DOI: 10.5061/dryad.82j1g/4
title: Fig. 4
DOI: 10.5061/dryad.82j1g/5
title: Fig. 5
DOI: 10.5061/dryad.82j1g/6
title: Fig. S1a
DOI: 10.5061/dryad.82j1g/7
title: Fig. S1b
DOI: 10.5061/dryad.82j1g/8
title: Fig. S2
DOI: 10.5061/dryad.82j1g/9
title: Fig. S3
DOI: 10.5061/dryad.8f61v/1
title: all_MIPs

description: Phylogenetic tree of 212 MIP sequences constructed using the neighbour joining (NJ) method and the Jones-Taylor-Thornton (JTT) evolutionary model
DOI: 10.5061/dryad.8f61v/2
title: diatom_green

description: A phylogenetic tree was constructed using the neighbour joining (NJ) method and the Jones-Taylor-Thornton (JTT) evolutionary model
DOI: 10.5061/dryad.bh23t/4
title: var.flt.ind.default

description: File with SNPs called from 10 unrelated individuals from one line of laboratory colony.
DOI: 10.5061/dryad.bh23t/5
title: var.flt.pool.flat

description: File with SNPs called from one sample consisting of 10 bank vole individuals
DOI: 10.5061/dryad.bh23t/6
title: Expression_level_ind_pooled_mean

description: Expression level values for ten individual samples and one pool consisting of the same individuals; calculations of relative estimation errors
DOI: 10.5061/dryad.bh23t/7
title: genotypes_default_Q30_dp5_q30

description: Genotypes of 10 individuals for high quality SNPs. Tab delimited file
DOI: 10.5061/dryad.bh23t/8
title: Ind_reads_counts

description: File with number of reads with given variant for 10 individuals for high quality SNPs
DOI: 10.5061/dryad.bh23t/9
title: python_scripts

description: Python scripts used for VCF files filtering, Fst simulations and allele specific gene expression assesment.
DOI: 10.5061/dryad.gd031k26/20
title: Supplemental Dataset 20
DOI: 10.5061/dryad.gd031k26/21
title: Supplemental Dataset 21
DOI: 10.5061/dryad.gd031k26/22
title: Supplemental Dataset 22
DOI: 10.5061/dryad.gd031k26/23
title: Supplemental Dataset 23
DOI: 10.5061/dryad.gd031k26/24
title: Supplemental Dataset 24
DOI: 10.5061/dryad.gd031k26/25
title: Supplemental Dataset 25
DOI: 10.5061/dryad.gd031k26/26
title: Supplemental Dataset 26
DOI: 10.5061/dryad.gd031k26/27
title: Supplemental Dataset 27
DOI: 10.5061/dryad.h065g/3
title: Supplemetary Figure 3

description: Supplementary Figure 3: A comparison of the accuracy of SPR, RF and MRP supertrees as measured by the minimal SPR distance between simulated species histories and any rooting of the supertree under varying rates of random or divergence-biased simulated LGT events.
DOI: 10.5061/dryad.h065g/4
title: Supplemetary Figure 4

description: Supplementary Figure 4: One application of the cluster reduction. The subtrees on leaves 1, 2, 3, and 4 are not identical but cover the same leaf set. Thus, they can be split from the trees and solved independently. The original locations of the removed subtrees are represented by a new leaf a1 and their roots are labelled ρ1. It is preferable to cut ρ1 in any sub-MAF as we can then cut the equivalent edge above a1.
DOI: 10.5061/dryad.h065g/7
title: Bacterial_trees_and_supertrees

description: Trees and supertrees built from 244 bacterial genomes.
DOI: 10.5061/dryad.hr348/1
title: Data from: Matrix composition and patch edges influence plant-herbivore interactions in marine landscapes

description: Ecological data from seagrass meadows located in the NW Mediterranean Sea.
DOI: 10.5061/dryad.j2718/3
title: Males only B. mori alignments

description: Compressed tarball containing alignments between each B. mori gene (1st sequence) and the B. huttoni sequence (2nd sequence), the B. mandarina major allele (3rd sequence), and the B. mandarina minor allele (4th sequence). These alignments include all B. mandarina polymorphic sites detected at Q30 or above after excluding females. B. mori and B. huttoni sequence are identical to the unfiltered alignments.
DOI: 10.5061/dryad.j2718/4
title: Singletons removed B. mori alignments.

description: Compressed tarball containing alignments between each B. mori gene (1st sequence) and the B. huttoni sequence (2nd sequence), the B. mandarina major allele (3rd sequence), and the B. mandarina minor allele (4th sequence). These alignments include all B. mandarina polymorphic sites detected at Q30 or above after excluding singletons. The B. huttoni and B. mori sequences are identical to the unfiltered alignments.
DOI: 10.5061/dryad.j2718/5
title: Raw data for analysis

description: Raw data used for analysis. See readme for column descriptions.
DOI: 10.5061/dryad.j7q43/2
title: Growth Chamber Experiment Dataset from Kooyers et al. 2014

description: This is a comma delimited file which contains data from an experiment designed to examine the fitness of different cyanotypes under temperature (water) or fertilizer stress. This experiment was conducted in two growth chambers – one with a high temperature and one with a lower temperature-- and plants were watered only when 50% of plants in the low temperature growth chamber needed water. This created a drought stress for plants in the higher temperature chamber. We manipulated fertilizer treatment with plants assigned to either standard or low fertilizer treatments.  Plants in the low fertilizer treatment were fertilized half as often as plants in the standard fertilizer treatment. This dataset was used for the analyses in Kooyers et al. 2014.
DOI: 10.5061/dryad.k257g/1
title: data

description: Includes the Mathematica notebook for analysis, the C++ code for individual based simulations, and the csv files with results of simulations.
DOI: 10.5061/dryad.mm011/1
title: MLXRoots2007

description: Root length
DOI: 10.5061/dryad.mm011/2
title: MLXResources2007

description: Soil N and moisture
DOI: 10.5061/dryad.mp713/1
title: Table 1 Arctic char landmarks

description: Thirteen landmarks from 121 specimens of Arctic char from Lake Hazen, Ellesmere Island, Canada (Arbour et al. 2011, Canadian Journal of Zoology 89(1):19-30).
DOI: 10.5061/dryad.mp713/2
title: Table 2 Guianacara dacrya landmarks

description: Sixteen landmarks from 73 specimens, from the description of Guianacara dacrya (see Arbour and Lopez-Fernandez, 2011, Neotropical Ichthyology 9(1):87-96.)
DOI: 10.5061/dryad.n525j/1
title: Appendix S1

description: Appendix of measurements of specimens of Dorosuchus neoetus.
DOI: 10.5061/dryad.n525j/2
title: Appendix S2

description: Appendix of strict consensus trees from all analyses carried out.
DOI: 10.5061/dryad.n525j/3
title: Appendix S3

description: Unadjusted matrix including Dorosuchus neoetus in nexus format.
DOI: 10.5061/dryad.n525j/4
title: Appendix S4

description: Adjusted matrix including Dorosuchus neoetus in nexus format.
DOI: 10.5061/dryad.q8v3f/1
title: Visit_data

description: Row data on visits per specific target plant per plot per 15 minutes, including floral density in the plot.
DOI: 10.5061/dryad.qj840/1
title: BrandtJR_JoH_2013 Dryad

description: Microsatellite genotypes at nine loci for sampled river otter individuals.
DOI: 10.5061/dryad.s3060/17
title: DNA sequence alignments of P.likiangensis nad1
DOI: 10.5061/dryad.s3060/18
title: DNA sequence alignments of P.likiangensis nad5
DOI: 10.5061/dryad.s3060/19
title: DNA sequence alignments of P.likiangensis ndhKC
DOI: 10.5061/dryad.s3060/20
title: DNA sequence alignments of P.likiangensis trnLF
DOI: 10.5061/dryad.s3060/21
title: DNA sequence alignments of P.likiangensis trnSG
DOI: 10.5061/dryad.2pm60/1
title: HPV_Evaluation_english

description: PASW Statistics_18The coding instructions can be found in the README.doc file.
DOI: 10.5061/dryad.2v3p5/1
title: egg weight

description: Data on egg weight experiment.
DOI: 10.5061/dryad.2v3p5/2
title: Body Parts

description: Data on dry body part and  wing size
DOI: 10.5061/dryad.2v3p5/3
title: Oviposition-ALOLSAUP

description: Data on clutches from AL, OL, UP and SA populations
DOI: 10.5061/dryad.2v3p5/4
title: Life-HistoryTraits_ALOLSAUP

description: Data on life history traits (larval and adult) for AL,  OL,  UP and SA populations
DOI: 10.5061/dryad.35r23/1
title: Ploidal Distributions

description: In this table, we provide the chromosome count data for each genus and the observed or assumed age.
DOI: 10.5061/dryad.35r23/2
title: Parameter Estimates

description: In this table, we provide the parameter estimates under both models, and the goodness-of-fit results for the Simple Ratchet model.  The column headers follow the naming convention: model.parameter for the estimates, model.parameter.upper for the upper limit of the 95% credible interval, and model.parameter.lower for the lower limit of the 95% credible interval.
DOI: 10.5061/dryad.35r23/3
title: Summary Statistics

description: The ABC-SMC model-fitting algorithm used the following nine metrics.  The values for each metrics for the 60 genera are provided.  The ABC-SMC algorithm, in particular the box-cox correction and PLS regression, performs best on continuous metrics, which is why we did not use the number of species in each ploidal class as metrics.  Despite the reduced performance of categorical metrics, we included the highest observed ploidal level because it was highly informative for parameter inference. (1) Total genus size (2) Proportion diploids (3) Proportion tetraploids (4) Proportion species &gt; = 4n (5) Proportion species &gt; = 6n (6) Highest ploidal level observed (7) Proportion highest observed ploidal level (8) Average ploidy level (9) Variance in ploidy level.
DOI: 10.5061/dryad.41r51/3
title: Plot Locations

description: Plot locations for 2010 and 2011 in decimal latitude and longitude degrees.
DOI: 10.5061/dryad.52c2h/7
title: Habitat characteristics (Drepanotrema depressissimum sites)

description: Habitat characteristics of the 32 sites where Drepanotrema depressissimum has been sampled for genetic analysis. "Lat" and "Long" are site latitude and longitude respectively (WGS84). "Year" is the sampling year. "Si", "V", "C", "St" and "G" are the five habitat characteristics used in the study (see the Materials and methods for more details). "SR", "SR_Pulmonates" and "SR_Caenogastropods" are long-term estimations of total species richness, Pulmonate species richness, and Caenogastropod species richness respectively.
DOI: 10.5061/dryad.52c2h/8
title: Habitat characteristics (Aplexa marmorata sites)

description: Habitat characteristics of the 43 sites where Aplexa marmorata has been sampled for genetic analysis. "Lat" and "Long" are site latitude and longitude respectively (WGS84). "Year" is the sampling year. "Si", "V", "C", "St" and "G" are the five habitat characteristics used in the study (see the materials and methods for more details). "SR", "SR_Pulmonates" and "SR_Caenogastropods" are long-term estimations of total species richness, Pulmonate species richness, and Caenogastropod species richness respectively.
DOI: 10.5061/dryad.54r13/1
title: Lung Cancer Cohort Data

description: 47 clinical data elements for a cohort of 874 patients with adenocarcinoma of the lung.
DOI: 10.5061/dryad.55204/4
title: Parapharyngodon cubensis A - coxI sequence data

description: Contains 640-bp coxI sequence data for 72 Parapharyngodon cubensis A individuals, along with locality information that corresponds to GIS information in the article's online Supplementary Information.
DOI: 10.5061/dryad.55204/5
title: Parapharyngodon cubensis B - coxI sequence data

description: Contains 640-bp coxI sequence data for 106 Parapharyngodon cubensis B individuals, along with locality information that corresponds to GIS information in the article's online Supplementary Information.
DOI: 10.5061/dryad.55qb2/1
title: Processing protocol and scripts

description: A data processing protocol and all custom python scripts that were used for the analysis of the NGS data.
DOI: 10.5061/dryad.55qb2/2
title: FASTA and ALN files

description: The FASTA files of all short reads matching to at least 3 of 4 study species, and the FASTA and ALN files of all short reads matching to all 4 species. ALN files were generated using Clustal Omega.
DOI: 10.5061/dryad.58ss8/21
title: MuV-S

description: Mumps virus - structural gene
DOI: 10.5061/dryad.58ss8/22
title: MeV-NS

description: Measles virus - non-structural gene
DOI: 10.5061/dryad.58ss8/23
title: SEOV - S

description: Seoul virus - structural gene
DOI: 10.5061/dryad.58ss8/24
title: RRV-S

description: Ross River virus - structural gene
DOI: 10.5061/dryad.58ss8/25
title: RuV-S

description: Rubella virus - structural gene
DOI: 10.5061/dryad.58ss8/26
title: WEEV-S

description: Western equine encephalitis virus - structural gene
DOI: 10.5061/dryad.58ss8/27
title: VEEV-S

description: Venezuelan equine encephalitis virus - structural gene
DOI: 10.5061/dryad.58ss8/28
title: VEEV-NS

description: Venezuelan equine encephalitis virus - non-structural gene
DOI: 10.5061/dryad.58ss8/29
title: TBEV-NS

description: Tick-borne encephalitis virus - non-structural gene
DOI: 10.5061/dryad.5vd3q/1
title: BEAST_CE_haps

description: BEAST analysis file used to estimate timing of molecular divergence between major haplogroups.
DOI: 10.5061/dryad.5vd3q/2
title: Arlequin_CE_haps_by_catchment

description: The mitochondrial ND4, tRNA-Pro, and control region data of Chelodina expansa in Arlequin format.  Data are grouped by major catchments.
DOI: 10.5061/dryad.5vd3q/3
title: Network_CE_n164_variablesites_gapsexcluded

description: Mitochondrial data of Chelodina expansa in the Network format (version 4.610; Fluxus Technology Ltd), used to create the median-joining haplotype network in Figure 1.
DOI: 10.5061/dryad.610dd/10
title: Fst Bootstrap resampling statistic

description: Calculates the significance of a data subset's Fst value versus a normal distribution of bootstrap resampled data subsets of equal size. Operates on multiple cores. Take a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/11
title: Fst binomial procedure

description: Calculates Fst per population using a bionomial procedure as in Hohenlohe 2010. Accepts a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/12
title: Fst molecular diversity

description: Calculates Fst values between pairs of populations based on a molecular diversity procedure from Hudson et al. 1992. Accepts a STACKS haplotype export file as input. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.610dd/13
title: filter_read_names.fq

description: Perl script to filter raw illumina reads by name and length. Written by Stefan Kaluziak. Please contact Nathaniel Chu (nathanieldchu@gmail.com) for more information.
DOI: 10.5061/dryad.610dd/9
title: Extract SNPs fixed between two groups

description: Extracts STACKS that contain SNPs fixed between two groups, where at least a certain number of populations are represented. This script allows for missing data. Accepts a STACKS haplotype export file. Run via a bash script in python 2.7.3. For more information, please contact nathanieldchu@gmail.com
DOI: 10.5061/dryad.653k7/1
title: All data files