cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sb175.2/1.2
title: Data4Dryad

description: CSV file with 1 header line, 26 columns, and 9830 rows of data. Data collated from literature reviews (sources cited in the main text or in column 23). Version 2 of this data set corrects a scaling issue in the original column 18 (that is, ca. 2% of the originally reported values for BREEDING.RANGE.AREA were reported in m2 rather than km2). V2 also provides recomputed values for the composite variables derived from principal components analysis (cols. 19-22). PLEASE NOTE THAT: (i) All original values can still be accessed through v1; and (ii) this minor correction does not affect qualitatively the findings reported in our MEC paper. ABBREVIATIONS and UNITS: DISSECTED.BY.MOUNTAINS = True if breeding range is divided into two or more isolated regions by a mountain chain; LAT.RANGE = Latitudinal range; ENV.SHIELDING = Environmental shielding (1 = migratory bird or hibernating mammal); GLACIATION: 1= 20% or more of current breeding range overlap with areas glaciated in the last 21,000 years; ISLAND.DWELLING: 1 = 20% or more of the breeding range occurs on islands; HABITAT.HETEROGENEITY: number of biomes covering at least 5% of the breeding range; BODY.SIZE: Adult body size in grams; PRECIP = Precipitation (in mm); TEMP = Temperature (in degrees Celsius); NPP = Net Primary Productivity (in log10[ g carbon per yr ] ); BREEDING.RANGE.AREA = Area of the breeding distribution (in km2); ENV.HARSHNESS = Environmental harshness (Raw values for PC1); GEOGRAPHIC.COVERAGE = Raw values for PC2; RAINFALL.UNPREDICTABILITY = Raw values for PC3; RESIDUAL.BODY.SIZE = Raw Values for PC4; N.MOST.LAT = Northernmost latitude in the breeding range; S.MOST.LAT = Southernmost latitude in the breeding range; CENTROID = centroid latitude for the breeding range.
DOI: 10.5061/dryad.pv85m/1
title: Data: Original Images

description: This contains two data sets (MGH - Training and BIDMC - Evaluation).
DOI: 10.5061/dryad.pv85m/2
title: Data: Segmented Images

description: This contains nuclei segmented images.
DOI: 10.5061/dryad.pv85m/3
title: Data: Original and Segmented Images

description: This contains both original and segmented images.
DOI: 10.5061/dryad.pv85m/4
title: Fig: Analysis Figures

description: This contains analysis figures that describes the framework performance on data sets.
DOI: 10.5061/dryad.pv85m/5
title: Code: Texture Features Computation

description: This is C++ code that computes intensity and texture features of each segmented nuclei. This code requires ITK 4 or above version and Boost library to compile and run. It also requires a library of color transformation into different color spaces which you can find at this link (https://github.com/midas-journal/midas-journal-780.git).
DOI: 10.5061/dryad.pv85m/6
title: Code: Nuclei Segmentation & Morphological Features

description: This contains a Fiji (ImageJ) Macro that segment nuclei and compute morphological Features.
DOI: 10.5061/dryad.pv85m/7
title: File: Selected Features List

description: This file contains a list of selected features.
DOI: 10.5061/dryad.vn2sh/1
title: Relative percentage of species LDV (lichen diversity value) per sampling site

description: Relative percentage of species LDV (lichen diversity value) collected along an aridity gradient in SW Europe (Iberian Península). Columns are species, sows are sampling sites. Species can be decoded in the ReadMe file.
DOI: 10.5061/dryad.4fn4g.2
title: Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
DOI: 10.5061/dryad.4fn4g.2/1.2
title: shell script to exectue commands for STC genotyping
DOI: 10.5061/dryad.4fn4g.2/2.2
title: R script for performing STC genotyping
DOI: 10.5061/dryad.4fn4g.2/3.2
title: perl script for demultiplexing raw read data
DOI: 10.5061/dryad.4fn4g.2/4.2
title: Chimeras functions
DOI: 10.5061/dryad.4fn4g.2/5.2
title: R script to create 'barcodes' file for de-multiplexing

description: NOTE: This file is part of the original version of this data package. It is superfluous to the new version.
DOI: 10.5061/dryad.4fn4g.2/6.2
title: R script to create "sequences" file for de-multiplexing
DOI: 10.5061/dryad.pv85m/10
title: Code: Analysis in R

description: This code used computed features as input and generate analysis figures as output that described the framework performance.
DOI: 10.5061/dryad.pv85m/8
title: File: Computed Features with Class Label

description: This file contains all computed features including Morphological, intensity and textural features with class label.
DOI: 10.5061/dryad.pv85m/9
title: File: Breast Cancer Cases (UDH & DCIS)

description: This file contains a list of all cases with clinical data that used for class labelling.
DOI: 10.5061/dryad.4fn4g.2/10.2
title: FASTA file of all unique amplicon sequences found in reads.fna

description: Contains all the unique amplicon sequences (no primers) along with numeric identifiers. This file is created from the output of readFNA.pl and make_sequences.R. It can be used as input for stc.R. Please see the README.txt file for more information.
DOI: 10.5061/dryad.4fn4g.2/11.2
title: table of samples and barcode IDs used in for genotyping

description: Contains rows designating the sample ID numbers and forward and reverse barcode ID numbers used for each sample genotyped in the paper. See barcode_sequences.csv for barcode nucleotide sequences. This file can be used as input for stc.R. Please see README.txt for more information and meta data.
DOI: 10.5061/dryad.4fn4g.2/7.2
title: functions for stc.R
DOI: 10.5061/dryad.4fn4g.2/8.2
title: FASTA format file of raw sequence reads used to generate dataset described in the paper

description: This file contains the raw-read data from the 454 sequencing run used to produce the results in the paper. It can be used as input for readFNA.pl. Please see README.txt for more information.
DOI: 10.5061/dryad.4fn4g.2/9.2
title: empty fasta format file for de-multiplexing

description: Needed for de-multiplexing using readFNA.pl.
DOI: 10.5061/dryad.4fn4g.1
title: Data from: Stepwise Threshold Clustering: a new method for genotyping MHC loci using next-generation sequencing technology
DOI: 10.5061/dryad.4fn4g.2/12.2
title: table of nucleotide sequences used as barcodes

description: Contains the sequences of all barcodes used to genotype samples described in the paper. Numeric ID numbers correspond to the ID numbers in samples_barcodes.csv. Can be used as input to the 'make_barcodes.R" script to create a list of barcode sequences for de-multiplexing. Please see README.txt for more information.
DOI: 10.5061/dryad.4fn4g.2/13.2
title: table of processed reads from 454 sequencing run

description: Contains the output of running the readFNA.pl script on the included reads.fna input file. Output includes barcode IDs, seuqence IDs and indicates to which sample each read was assigned. Please see the README.txt file for meta-data and more information.
DOI: 10.5061/dryad.4fn4g.2/14.2
title: post-genotyping data set used for analyses

description: Contains the output of stc.R after processing the samples described in the paper. Data includes the number of alleles for each sample and the presence/absence of each unique sequence within each sample. Please see the README.txt file for more information and meta-data
DOI: 10.5061/dryad.4fn4g.2/15.2
title: README file for STC genotyping
DOI: 10.5061/dryad.dp4qg/1
title: Average life-time reproductive success of simulated male crickets

description: Average life-time reproductive success of simulated male crickets as a function of tendency for satellite behavior across variation in risk of parasitism if calling, under variation in population density, sex ratio, mortality rate, female phonotaxis, and female propensity to mate.
DOI: 10.5061/dryad.q2h13/1
title: Saline treated control NMR data
DOI: 10.5061/dryad.q2h13/2
title: AMP-treated NMR data
DOI: 10.5061/dryad.p2501/1
title: Gobiomorus dormitor divergence between prey regimes

description: Data associated with Gobiomorus dormitor populations inhabiting blue holes in the presence and absence of fish prey. Demographic and habitat data was collected using underwater survey techniques. Diet data was collected using gastric lavage and stomach dissections. Morphology data was taken from standardized photographs of live individuals and feeding/kinematics and performance data was calculated from video-taped lab trials. See “Predicting ecological and phenotypic differentiation in the wild: a case of piscivorous fish in a fishless environment, Martin, Ryan, McGee, Matthew, Langerhans, Brian” for a detailed description of the methods.
DOI: 10.5061/dryad.qd018/1
title: Microsatellite_Genotypes_Saddlebacks
DOI: 10.5061/dryad.qd018/2
title: Microsatellite_Genotypes_robins
DOI: 10.5061/dryad.qd018/3
title: MHC_Genotypes_robins_North Island
DOI: 10.5061/dryad.qd018/4
title: MHC_Genotypes_robins_South Island
DOI: 10.5061/dryad.qd018/5
title: MHC_Genotypes_saddlebacks_North Island
DOI: 10.5061/dryad.qd018/6
title: MHC_Genotypes_saddlebacks_South Island
DOI: 10.5061/dryad.qd018/7
title: Rscript_univariate models

description: R script with package MCMCglmm for the univariate-response Bayesian mixed-effects meta-analysis (BMM) models described in Table 2.
DOI: 10.5061/dryad.0p468/1
title: Catton et al Fig 1 data June 8 2013

description: This data file was used to generate Figure 1 in Catton et al. (2015). It contains the results for the presence or absence of M. crucifer herbivory scars on Cynoglossum officinale and Hackelia micrantha plants target common or target rare sites (where applicable) in years 0, 1, and 2 following a point release of 300 M. crucifer on each site on 4 June 2009.
DOI: 10.5061/dryad.0p468/2
title: Catton et al Fig 2 data June 10 2013

description: This data file was used to generate Figure 2 in Catton et al. (2015). It contains the results of dissectionsfor M. crucifer eggs and larvae in Cynoglossum officinale and Hackelia micrantha plants on M. crucifer release sites where both plant species were present.
DOI: 10.5061/dryad.0p468/3
title: Catton et al Fig 3 data June 17 2013

description: This data file was used to generate Figure 3 in Catton et al. (2015). It contains the results of dissection for M. crucifer eggs and larvae in Hackelia micrantha plants relative to the level of C. officinale herbivory on each site, expressed as the back-transformed mean ln(number of eggs per C. officinale plant +1) on M. crucifer release sites where both plant plant species were present.
DOI: 10.5061/dryad.0p468/4
title: Catton et al Fig 4 data June 4 2014

description: This data file was used to generate Figure 4 in Catton et al. (2015). It contains the results of dissection for M. crucifer eggs and larvae in Cynoglossum officinale and Hackelia micrantha plants on release sites in years where M. crucifer was known to be present.
DOI: 10.5061/dryad.0p468/5
title: Experimental Release Site dissections after 2 years Dec 7 2014

description: This data file was used to test for M. crucifer population establishment on experimental target common and target rare release sites after 2 years. It displays Cynoglossum officinale and Hackelia micrantha plants sampled and dissected in search of M. crucifer eggs and larvae. Plants were kept refrigerated between harvest and dissection, and whole plants were dissected.
DOI: 10.5061/dryad.5cb17/1
title: Ct values from qPCR

description: The file contains raw Ct values from qPCR for all genes assayed in the study.  Data are organized by the three main experiments performed in the study, and can be used to reconstruct all gene expression analyses and figures in the paper.
DOI: 10.5061/dryad.024bn/1
title: Conifer needle phloem geometry

description: This data contains the measurements for phloem geometry (number of sieve tubes, sieve tube area as function of distance from the tip) for 3-6 needles of four conifer species (Abies nordmanniana, Pinus cembra, Pinus palustris, Picea omerika)
DOI: 10.5061/dryad.4t806/1
title: mtDNA and microsatellite_data

description: A zip file containing two data files plus a third text file containing descriptions of the data files. See file "File annotations.txt" included int the archive for more information.
DOI: 10.5061/dryad.5cb17/2
title: Survivorship after heat stress during hspb1 suppression

description: This file contains the proportion of copepods surviving each day for 5 days post heat stress.
DOI: 10.5061/dryad.5jt5j/1
title: BEAST XML file for model 1

description: This BEAST XML file specifies model 1 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/2
title: BEAST XML file for model 2

description: This BEAST XML file specifies model 2 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/3
title: BEAST XML file for model 3

description: This BEAST XML file specifies model 3 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/4
title: BEAST XML file for model 4

description: This BEAST XML file specifies model 4 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.s4dv0/1
title: Protozoan infection prevalence data from migratory and non-migratory monarchs

description: These data show the number of infected (and total) monarchs found per site when citizen scientists or the authors tested monarch butterflies for the protozoan parasite Ophryocystis elektroscirrha (OE). We were interested in differences in infection prevalence for migratory vs. sedentary (non-migratory) monarchs. Sites were located in one of several source populations: the monarchs' summer-breeding range (migratory monarchs), Mexico overwintering areas (migratory monarchs), winter-breeding areas (non-migratory monarchs), or at coastal overwintering areas. One line of data shows results from one site for one year of the study (year 1 = 2011-2012 and year 2= 2012-2013). For each site and year, geographic coordinates, observer initials, city, state, number of total samples, and number of infected samples are listed. We calculated prevalence for sites with 8 or more total samples per year. Prevalence is the proportion of total samples that were heavily infected with OE. Prevalence was arc-sine-square-root-transformed. Each site was also assigned to a sub-region, as detailed in the Electronic Supplementary Material.
DOI: 10.5061/dryad.s4dv0/2
title: Virulence for parasite isolates collected from migratory vs. non-migratory monarchs

description: These data show results of an experiment to compare the virulence of Ophryocystis elektroscirrha (OE) parasites from migratory vs. non-migratory monarch butterflies. In the laboratory, monarch larvae (2nd instars) were inoculated with 10 parasite spores from one of 57 parasite isolates (indicated by parasite ID) and then reared to adulthood. The source population of each wild-collected parasite isolate is listed. Details on parasite origins are available in the Electronic Supplementary Material. Experimental monarchs originated from one of five monarch lineages (or families), which were randomly assigned to treatments. We inoculated 10 larvae for each isolate and also reared 80 additional control larvae which were not inoculated. Larvae were given fresh, uncontaminated milkweed following inoculation. Key dates, including date of inoculation, monarch pupation, monarch eclosion and monarch death are listed. When monarchs were in the pupa stage, we weighed each pupa (pupal weight in grams) and also noted signs of OE disease (dark patches on the pupa), ranking the pupal infection on a scale from 0 to 5. A pupal score of 0 indicates no dark patches due to OE on the pupa, a score of 1 indicates minimal patching, 2 indicates about 25% of the pupa shows dark patches, 3 indicates about 50%, 4 indicates about 75%, and 5 indicates about 100% of the pupa showing darkening due to OE spores under the cuticle. We pupal-scored each monarch starting on day 6 of pupation and repeated this daily until eclosion. Monarchs with a maximum pupal score of 0 or 1 were tested for the parasite after eclosion using the tape method described in the manuscript -- in order to verify absence of infection. All monarchs were classified as either uninfected or infected (infected = having a pupal score of 2 or higher, or an adult infection tape-score of 4 or higher). All adult monarchs were kept at 12C and day of death was noted. Adult longevity (days until death) was calculated and used as a proxy of parasite virulence (shorter adult longevity indicates higher parasite virulence). After death, we quantified the parasite load on each infected monarch's abdomen, as described in the manuscript. Parasite load was log-transformed. Monarch sex is also indicated.
DOI: 10.5061/dryad.5jt5j/10
title: BEAST XML file for model 10

description: This BEAST XML file specifies model 10 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/11
title: BEAST XML file for model 11

description: This BEAST XML file specifies model 11 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/12
title: BEAST XML file for model 12

description: This BEAST XML file specifies model 12 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/5
title: BEAST XML file for model 5

description: This BEAST XML file specifies model 5 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/6
title: BEAST XML file for model 6

description: This BEAST XML file specifies model 6 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/7
title: BEAST XML file for model 7

description: This BEAST XML file specifies model 7 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/8
title: BEAST XML file for model 8

description: This BEAST XML file specifies model 8 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.5jt5j/9
title: BEAST XML file for model 9

description: This BEAST XML file specifies model 9 for Bayesian species tree inference (see Supplementary Table 4)
DOI: 10.5061/dryad.33fv8/1
title: Etienne et al. Data_Evolution_14.0446.R2

description: This data file contains the raw data from the survivorship assays that are used in the LT50 assays for the mutation accumulation (MA) lines.
DOI: 10.5061/dryad.5jt5j/13
title: Set of 100 species trees

description: This tree set contains 100 species trees randomly sampled from the posterior distribution of the BEAST analysis based on model 12
DOI: 10.5061/dryad.5jt5j/14
title: Set of 1000 species trees

description: This tree set contains 1000 species trees randomly sampled from the posterior distribution of the BEAST analysis based on model 12
DOI: 10.5061/dryad.qc3s0/1
title: Cicurina Nuclear Alignments

description: DNA sequence alignments of phased nuclear data
DOI: 10.5061/dryad.qc3s0/2
title: Cic_COI_Dryad

description: Cicurina mitochondrial (COI) alignment
DOI: 10.5061/dryad.qc3s0/3
title: RAxML and BEAST tre files

description: tre files from RAxML and BEAST analyses, both nuclear & mitochondrial
DOI: 10.5061/dryad.qc3s0/4
title: Morphology Images

description: original JPG files for male/female genital morphologies
DOI: 10.5061/dryad.78k38/1
title: Walrus ms data

description: Walrus GBS data in ms format
DOI: 10.5061/dryad.78k38/2
title: Walrus VCF

description: Walrus GBS data in vcf format
DOI: 10.5061/dryad.8dc26/1
title: color.pattern.data

description: Data set for color pattern divergence analyses of birds.
DOI: 10.5061/dryad.8dc26/2
title: color.pattern.R.code

description: R code for color pattern divergence analyses of birds.
DOI: 10.5061/dryad.9n741/1
title: Data_eggcontent

description: Data on carotenoids, lysozymes and ovotransferrin in eggs
DOI: 10.5061/dryad.9n741/2
title: Data_nestlings

description: Data on nestling growth, condition at fledging and immunity
DOI: 10.5061/dryad.9n741/3
title: Data_oxi

description: Data on adult oxidative damage in relation to clutch size
DOI: 10.5061/dryad.vj35n/4
title: Genome Sequence and Annotation

description: Genome sequence of the PAO1::mini-Tn7-pLAC-lux ancestral strain in FASTA format and the accompanying genome annotation file in GTF format.
DOI: 10.5061/dryad.8f409/1
title: DRYAD-SYNCERUS

description: The African buffalo microsatellite database is presented as an excel file with two sheets. The first sheet displays the allelic composition of the 14 autosomal microsatellites used within the present study, which is concentrated on southern African sampling localities. The first four lines of this first sheet refer to the title attributed to the present database sheet, the number of clusters identified with the STRUCTURE software, the number of loci studied, as well as the total number of individuals studied, respectively. The table below covers the following information for each specimen involved in the present study: species name, country of origin, sampling locality (protected area), gender, sample ID, cluster affiliation (result from the STRUCTURE analysis), followed by the allele composition for each 14 loci (diploid species).The second sheet displays the allelic composition of the 3 Y-chromosomal microsatellites used within the present study. The first three lines refer to the title attributed to the present database sheet, the number of loci studied, as well as the number of male individuals studied within the present study, respectively. The table below cover the following information for each male specimen genotyped in the present study: sample ID, alleles composition for each three Y-chromosomal microsatellites, haplotype designation for each three Y-chromosomal microsatellites, and final haplogroup determination. The haplotype designation is a number attributed to designate the combination of alleles for each of the three loci because they can appear as multicopies on the Y-chromosome. The haplogroup is thus defined as the combination of the haplotypes, written as {n UMN1113 haplotype, n UMN0304 haplotype, n INRA189 haplotype}, where n UMN1113 haplotype = 1,...,15, n UMN0304 haplotype = 1,...,9, and n INRA189 haplotype = 1,...,12. For further information, please see the main manuscript.
DOI: 10.5061/dryad.b8nf6/1
title: antioxidant and oxidative stress markers in C. elephas and C. glandium

description: This file contain measures of antioxidant defences (total antioxidant:TEAC; superoxide dismutase: SOD; and catalase: CAT activities) and oxidative damage (malondialdehyde: MDA) expressed per mg of body mass and per mg of protein.
DOI: 10.5061/dryad.6s718/1
title: Carlson_et_al_2015_GBS_Marker_Sequences

description: Genotyping-By-Sequencing Marker set sequences published in Carlson et al. 2015.
DOI: 10.5061/dryad.6s718/2
title: Carlson_et_al_2015_GBS_Marker_Genotypes

description: Genotyping-By-Sequencing Marker genotypes published in Carlson et al. 2015.
DOI: 10.5061/dryad.gp272/1
title: interaction matrices

description: The file ‘interaction matrices.zip’ is a compressed folder that contains 232 text files. Each file contains a matrix where each row (and column) represents a single individual. Cell values indicate how often the corresponding row individual groomed the column individual, or how often the column individual was the nearest neighbor of the row individual. Each file name indicates whether the corresponding matrix contains information regarding grooming or association. The first number in the file name indicates the ID of the corresponding knockout and the second number indicates the time period for each knockout. The time period before the knockout is coded as 0, the first 30-day period after the knockout is coded as 1, the second period is coded as 2 and the third period is coded as 3. All matrices of a specific knockout have identical orders of row (and column) individuals.
DOI: 10.5061/dryad.gp272/2
title: grooming and association rates

description: This file contains tables with grooming and association rates of all investigated time periods for each knockout.
DOI: 10.5061/dryad.b6gp8/1
title: bark_thickness_data

description: This file contains the full dataset of bark thickness measurements.