cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dc195/3
title: Competition dataframe

description: This file contains the progeny counts used to analyze the competitive fertilizations experiments.
DOI: 10.5061/dryad.h58n0/1
title: Callinectes spp. settlement in 2010 and 2011 at various sites in the Gulf of Mexico

description: This data file has 3 fields. "Site" is the site from which the sample was collected. "Date" is the date of collection (note that there were 2-4 replicates at a site each day). "Callinectes_Meg_N" is the number of Callinectes spp. megalopae caught on that replicate collector. All megalopae samples were collected using a standard collection method as described in the associated manuscript. Exact coordinates (Long/Lat in decimal degrees) of the sites were: APALACHICOLA -84.980706, 29.726056, RIGOLETS -89.793158, 30.064297, DAUPHIN -88.077806, 30.251275, GALVESTON -94.817131, 29.312742, GRAND ISLE -89.962331, 29.262911, OCEAN SPRINGS -88.800297, 30.39155, PENSACOLA -87.159075, 30.337825 and RIGOLETS -89.634422, 30.152858. All seven sites were sampled in 2010 and in 2011 only GALVESTON, GRAND ISLE, DAUPHIN, and PENSACOLA were sampled.
DOI: 10.5061/dryad.h58n0/2
title: Callinectes sp. megalopae dry weights

description: This data includes the mean dry weights of Callinectes sp. megalopae fixed in ethanol as described in the associciated manuscript. The dataset includes four fields. First is "Year", either 2010 or 2011. The second is "Site", one of 7 sites (see notes on Settlement file for site coordinates). The third field is the biweekly weight period. Period A starts on May 16th, B on May 30th, C on June 13th and so on until October 31st for a total of 12 biweekly periods each year. The "WPU_mg" field is the individual dry weight in milligrams measured for that time period.
DOI: 10.5061/dryad.k543p/1
title: Rcode

description: This folder contains four Rcode files necessary to reproduce our analyses. map.qtls.gemma.PCs.R is the master code that requires functions from other.code.R, run.gemma.R, and analyses.PCs.R.
DOI: 10.5061/dryad.k543p/2
title: Eigenvectors_PCA

description: This folder contains two files with the eigenvectors of the PCA done with skull shape and mandible shape data. These files can be used to project new shape data into our PCA.
DOI: 10.5061/dryad.k543p/3
title: Phenotype file

description: This file contains skull and mandible shape principal component (PC) scores for each mouse. PC scores were normalized to mean 0 and std of 1. Mandible PC scores were calculated from the regression residuals of shape ~ BMD. Skull and mandible centroid size (CS) data is also included.
DOI: 10.5061/dryad.k543p/4
title: Genotype data

description: This files contains genotype (SNP) data for each mouse.
DOI: 10.5061/dryad.nn77p/1
title: Online data browser

description: This package contains supplementary material for the paper "How mechanisms ofhabitat preference evolve and promote divergence with gene flow" in Journal ofEvolutionary Biology. An interactive version of this material can also be foundat http://xavier.thibert-plante.com/habitatPref .Download this package habPrefSupp.tar.bz2 into a directory of your choice. Wewill call this directory .Unload the package using for example:tar -xjf habPrefSupp.tar.bz2 (UNIX)http://www.7-zip.org/download.html (MS Windows)Using your favorite web browser "open file":/DIR.bernerThibert-Plante/index.htmland you can start browsing the supplementary material.
DOI: 10.5061/dryad.p412k/1
title: Maternal effect Moricandia

description: Raw data for the experiments pool together
DOI: 10.5061/dryad.q675s/1
title: Gynogenetic_haploids_genotypes

description: Genotype data for the haploid progeny
DOI: 10.5061/dryad.rk345/1
title: Spatial_DataSet
DOI: 10.5061/dryad.rk345/2
title: Temporal_DataSet
DOI: 10.5061/dryad.rk345/3
title: crosstalks
DOI: 10.5061/dryad.rk345/4
title: diopters
DOI: 10.5061/dryad.sr3g0/3
title: Body_mass_cadmium_diet

description: Female and male body mass measured in cadmium diet. Each separate file is the data for one replicate population after excluding the outliers. “Dam” column shows the female ID (full-sib family ID). “Sire” column shows the male ID (half-sib family ID). “Female_Mass” column shows the average female mass per full-sib family. “Male_Mass” shows the average male mass per full-sib family.
DOI: 10.5061/dryad.sr3g0/4
title: Body_mass_salt_diet

description: Female and male body mass measured in salt diet. Each separate file is the data for one replicate population after excluding the outliers. “Dam” column shows the female ID (full-sib family ID). “Sire” column shows the male ID (half-sib family ID). “Female_Mass” column shows the average female mass per full-sib family. “Male_Mass” shows the average male mass per full-sib family.
DOI: 10.5061/dryad.sr3g0/5
title: code1 MCMCglmmAnalysisVsire

description: R code for estimating the posterior distribution of Vsire for each replicate population using MCMCglmm
DOI: 10.5061/dryad.sr3g0/6
title: code2 LikelihoodMCMCglmmVsireTest

description: R code for comparing Vsire from two regimes using maximum likelihood approach
DOI: 10.5061/dryad.0nv00/1
title: 370_sequence amoA tree

description: Bayesian amoA phylogenetic tree derived from 454 sequencing
DOI: 10.5061/dryad.0nv00/2
title: Nucleotide alignment for the 370-sequence amoA tree

description: Nucleotide alignment (codon positions 1 and 2) for the 370-sequence amoA tree
DOI: 10.5061/dryad.11385/1
title: Pollination and seed dispersal data

description: This CSV file contains all the original field data collected. Please refer to the ReadMe file for an explanation of the column headers.
DOI: 10.5061/dryad.20bm4/1
title: FE-Ueno A. et al., Database

description: This file contains the data that was used in the analyses.
DOI: 10.5061/dryad.26qd7/1
title: Raw data for behaviour and chemical signature

description: Data are provided for male choice on models, male choice on virgin females, female hybrid success as well as wing and genital chemical signature from both sexes. Each set of data ison a separate sheet of the excel file with all relevant information. Please refer to the methods and Table S1 if needed
DOI: 10.5061/dryad.3g23m/1
title: inter-species alignments

description: Alignments used in inter-species analyses
DOI: 10.5061/dryad.3g23m/2
title: inter-species trees

description: Trees used in inter-species analyses
DOI: 10.5061/dryad.3g23m/3
title: gammaMap_input_files

description: Input files used for the population genetics-phylogenetics analysis
DOI: 10.5061/dryad.3n6n6/4
title: Traits of Costus arabicus white and pink flowers

description: Data regarding morphology, nectar traits, pollen deposition and colour in relation to the bee and hummingbird vision of Costus arabicus flowers
DOI: 10.5061/dryad.3n6n6/5
title: Bee and hummingbird discrimination between Costus arabicus flowers

description: Each data refers to the discrimination between a par of white and pink flower colour morphs to the bee and hummingbird vision. Data for petals, labellum and nectar guides.
DOI: 10.5061/dryad.58q00/1
title: Example workflow for parameter estimation

description: This archive contains a sample workflow for deriving the parameter sets to generate the plots in "Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity."
DOI: 10.5061/dryad.58q00/2
title: R Code for Plots in "Immunity and epidemiology: integrating theory and data for pertussis"

description: This archive contains all of the required code to generate the figures and tables in the paper "Immunity and epidemiology: integrating theory and data for pertussis."
DOI: 10.5061/dryad.8vv63.1
title: Data from: Testing convergence versus history: convergence dominates phenotypic evolution for over 150 million years in frogs
DOI: 10.5061/dryad.91nd2/1
title: Root biomass alone

description: This is the root biomass data recorded in patches and background soil for each species grown alone. Methodological details are given in the manuscript.
DOI: 10.5061/dryad.91nd2/2
title: Root biomass with neighbours

description: This is the root biomass data recorded in patches and background soil for all four species combined when grown with neighbours. It was not possible to seperate the biomass of each species individually. Methodological details are given in the manuscript.
DOI: 10.5061/dryad.91nd2/3
title: Root Presence with neighbours

description: This is the root presence/absence data recorded in patches and background soil for each of the four species when grown with neighbours. Molecular techniques were used to identify the presence of each species individually. Methodological details are given in the manuscript.
DOI: 10.5061/dryad.92c60/1
title: Asparagus officinalis transcriptome assembly

description: Raw garden asparagus transcriptome assembly for Harkess et al. (2015). Transcripts were digitally normalized to 30X and assembled in Trinity (r2012-10-05). All raw RNA-seq reads can be found in NCBI BioProject 259909.
DOI: 10.5061/dryad.bt72k/1
title: Raw data_Christin et al_PLoS One

description: These datasets are the GPS and Argos locations of static and mobile tests conducted in the High-Arctic; experiments were replicated several times, and the files are organized in different folders according to the experiment type. All files are provided in csv format. More information is provided in the joined ReadMe file.
DOI: 10.5061/dryad.c25gd/1
title: Body_masses

description: Body masses of the experimental birds
DOI: 10.5061/dryad.c25gd/2
title: Bleeding_sessions

description: Dates of the collection of the blood samples
DOI: 10.5061/dryad.c25gd/3
title: Diet_per_ID

description: Diet (prey species) offered per individual bird
DOI: 10.5061/dryad.c25gd/4
title: Isotope_ratios

description: Stable isotope ratios in blood cells and plasma per bird per bleeding session.
DOI: 10.5061/dryad.c402q/13
title: X00_Y00_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): reference model.
DOI: 10.5061/dryad.c402q/14
title: X00_Y00_Z10_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head width +10%.
DOI: 10.5061/dryad.c402q/15
title: X00_Y00_Z20_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head width +20%.
DOI: 10.5061/dryad.c402q/16
title: X00_Y00_Z30_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head width +30%.
DOI: 10.5061/dryad.c402q/17
title: X00_Y00_Z40_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head width +40%.
DOI: 10.5061/dryad.c402q/18
title: X00_Y10_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head height +10%.
DOI: 10.5061/dryad.c402q/19
title: X00_Y20_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head height +20%.
DOI: 10.5061/dryad.c402q/20
title: X00_Y30_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head height +30%.
DOI: 10.5061/dryad.c402q/21
title: X00_Y40_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head height +40%.
DOI: 10.5061/dryad.cr020/1
title: Results Systematic review sustainability

description: For this review, 4219 items were retrieved and screened based on title and abstract, 185 studies were assessed based on full text reading and 14 studies were selected for analyses. This data file contains the endnote file with all items and the classification.
DOI: 10.5061/dryad.cv323/1
title: Microarray_raw_data.tar

description: Expression profiling analysis: Transcriptome data from four biological replicates were generated using 8x15K Customized Drosophila Genome Oligo Microarrays (Agilent). Slide image data was quantified using Agilent's Feature Extraction software.
DOI: 10.5061/dryad.cv323/2
title: diffReps_files.tar

description: Differentially changed genomic regions for histone marks were identified using the diffReps program, which uses a sliding window approach to scan the genome and find regions showing read count differences. Regions detected by diffReps were associated with genes by identifying the nearest RefSeq TSS and annotated to a genomic feature such as intergenic, intron, exon etc.
DOI: 10.5061/dryad.cv323/3
title: HOMER_peak_files.tar

description: Using HOMER with default settings, peaks for histone marks and Flag tagged Hairy protein were identified using signals from H3 ChIP and input respectively as background. Peaks called by HOMER were associated with genes by identifying the nearest RefSeq TSS and annotated to a genomic feature such as intergenic, intron, exon etc.
DOI: 10.5061/dryad.dc195/4
title: Movie S1

description: Movie file that shows courtship and copulation behavior of a Canton S male mated with a white-eyed female.
DOI: 10.5061/dryad.dc195/5
title: Movie S2

description: Movie file that shows courtship and copulation behavior of a Uas-Dcr-2; apGAL4; UAS-PoxnIR/elavGAL80 male mated with a white-eyed female.
DOI: 10.5061/dryad.f5q4f/1
title: data used to generate Figure 1

description: The zip-compressed archive contains text files used as input files to generate figure 1 in R.
DOI: 10.5061/dryad.f5q4f/2
title: sequence alignments

description: zip-compressed archive containing sequence alignments in fasta format. These sequences were used throughout the paper.
DOI: 10.5061/dryad.gt0n2/1
title: Adirondacks solid sample deuterium data

description: Deuterium isotope data for food web solid samples from the Adirondacks
DOI: 10.5061/dryad.gt0n2/2
title: Adirondacks water sample deuterium data

description: Water sample deuterium data for sites in the Adirondacks
DOI: 10.5061/dryad.gt0n2/3
title: Trinidad solid sample deuterium data

description: Solid sample isotope data from Trinidad sites
DOI: 10.5061/dryad.gt0n2/4
title: Trinidad water sample deuterium data

description: Water sample isotope data from Trinidad sites
DOI: 10.5061/dryad.hc6bv/1
title: Raw genotype data for hybridization in Begonia

description: Microsatellite genotypes in 2-column format. Missing data denoted with '-1'.
DOI: 10.5061/dryad.kd873/1
title: PLATT-PLOSONE-2015-PONE-D-15-17561R2_populationlevel_data

description: data on the estimated predation rate, density, female growth rate and ovarian weight of fish from five populations of Alticus arnoldorum from Guam
DOI: 10.5061/dryad.kd873/2
title: PLATT-PLOSONE-2015-PONE-D-15-17561R2_growth_data

description: data on the estimated age and size of female fish from five populations of Alticus arnoldorum from Guam
DOI: 10.5061/dryad.kd873/3
title: PLATT-PLOSONE-2015-PONE-D-15-17561R2_ovaryweight_data

description: data on the size, weight of ovaries and reproductive state of female fish from five populations of Alticus arnoldorum from Guam
DOI: 10.5061/dryad.m3f26/1
title: Mathematica file for Appendices 1 and 2, and Figures 2, 3, and 4

description: A Mathematica (v9.0) file containing the codes for the calculation used in appendices 1 and 2, for drawing figures 2, 3, and 4, and for numerical integration of the model.
DOI: 10.5061/dryad.nj183/1
title: Data for Esfandi_etal_2015_Flirtation reduces males fecundity but not longevity

description: This file contains all data for the paper accepted by Evolution.
DOI: 10.5061/dryad.q675s/2
title: Gynogenetic_diploids_genotypes

description: Genotype data for the diploid progeny
DOI: 10.5061/dryad.qh631/1
title: MuirheadPresgraves_Fig1_4

description: Simulation results, Figures 1 and 4
DOI: 10.5061/dryad.qh631/2
title: MuirheadPresgraves_FigA1_Lethal

description: Simulation results, Appendix figure A1 (lethal incompatibilities)
DOI: 10.5061/dryad.qh631/3
title: MuirheadPresgraves_FigA2_Asymm

description: Simulation results, Appendix figure A2 (asymmetric selection coefficients)
DOI: 10.5061/dryad.qh631/4
title: MuirheadPresgraves_FigA4_MFmig

description: Simulation results, Appendix figure A4 (male vs. female migration)
DOI: 10.5061/dryad.rk345/5
title: MatlabAnalysisCode
DOI: 10.5061/dryad.sp698/1
title: Magrach et al 2015 Dataset
DOI: 10.5061/dryad.td1g2/1
title: Ord_TJ-BEHECO-2015-0352R2_HBspeed

description: Data on the maximum speed of headbob movements for 14 adult male Anolis gundlachi
DOI: 10.5061/dryad.0nv00/3
title: 508-sequence 16S rRNA tree

description: Bayesian 508-sequence phylogenetic 16S rRNA tree derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset.
DOI: 10.5061/dryad.0nv00/4
title: 613_sequence amoA tree

description: Bayesian 613-sequence phylogenetic amoA tree derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset.
DOI: 10.5061/dryad.0nv00/5
title: Nucleotide alignment for the 508-sequence 16S rRNA tree

description: Nucleotide alignment for the 508-sequence 16S rRNA tree, derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset.
DOI: 10.5061/dryad.0nv00/6
title: Nucleotide alignment for the 613-sequence amoA tree

description: Nucleotide alignment for the 613-sequence amoA tree (codon positions 1 and 2), derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset.
DOI: 10.5061/dryad.43gt3/1
title: Supporting wing length data

description: Sheet 1 includes all raw data for each of the 2 species used in the manuscript; Year, site, sex, wing length (WL), dot of year of collection from the 1st of each year (DOY), current and previous year's snowmelt dates and current and previous year's avergage temperatures used in the analyses.
DOI: 10.5061/dryad.55p22/1
title: Rosmarinus officinalis genotypic data

description: Contains gentotypic data of 1728 individuals (96 each from 18 populations) for eleven nuclear microsatellite loci. For each individual, geographical coordinates are given in two extra columns following the individual identification code.
DOI: 10.5061/dryad.589g3/1
title: The raw data for Morella

description: These files including contig assemblies in fasta format (Morella esculenta-Contigs.fa, Morella esculenta-Contigs.fa and Morella rubra-Contigs.fa), matrix used to infer phlogenetic trees (Morella phlogeney.phy), shared SNP loci between four different populations (4Morella rubra shared.loci) and the raw RAD data
DOI: 10.5061/dryad.5gf59/1
title: Data_Yuanhu Shao et al._for_Dryad

description: Data for "Subordinate plants sustain the complexity and stability of soil micro-foodwebs in subtropical natural forest ecosystems".
DOI: 10.5061/dryad.6324j/1
title: Influence of macroalgal contact on coral growth

description: Excel spreadsheet (.xls) of data from field-based manipulative experiment measuring monthly changes in coral (Montipora hispida) mass from December 2013 to March 2014. Corals were exposed to one of five algal treatments: 0, 2, 4, 6, or 8 fronds of the brown alga Sargassum polycystum (frond length = 15-20 cm). Numbers in column A indicate the parent colony from which a coral originated, and numbers in column B indicate the number of Sargassum fronds in contact with the coral. The percent change in coral mass was determined using the total change in mass (column G) and initial coral mass (column C).
DOI: 10.5061/dryad.68s40.2
title: Data from: Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus)
DOI: 10.5061/dryad.68s40.2/1.2
title: Nexus files for all six loci

description: DNA sequences for individuals used in all multilocus analyses.
DOI: 10.5061/dryad.68s40.2/2.2
title: Complete COI mtDNA nexus file

description: Contain mtDNA sequences for all individuals used in this study.
DOI: 10.5061/dryad.68s40.2/7.2
title: Tables S1-3

description: Supplementary tables 1-3
DOI: 10.5061/dryad.68s40.2/8.2
title: Supplemental Material

description: Supplemental material file.
DOI: 10.5061/dryad.68s40.2/9.2
title: Figures S1-10

description: Supplemental Figures 1 - 10.
DOI: 10.5061/dryad.bf771/1
title: Wolf data

description: Data used to carry out habitat selection analysis of molves
DOI: 10.5061/dryad.bf771/2
title: Moose data

description: Data used to carry out habitat selection analysis of moose
DOI: 10.5061/dryad.c402q/22
title: X10_Y00_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head length +10%.
DOI: 10.5061/dryad.c402q/23
title: X20_Y00_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head length +20%.
DOI: 10.5061/dryad.c402q/24
title: X30_Y00_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head length +30%.
DOI: 10.5061/dryad.c402q/25
title: X40_Y00_Z00_full

description: Oreochromis niloticus model for sensitivity analysis (Fig. 2 in the article): head length +40%.
DOI: 10.5061/dryad.cv323/10
title: bed_files.tar part e

description: Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
DOI: 10.5061/dryad.cv323/4
title: bedgraph_files.tar

description: ChIP-Seq experiments were visualized as custom tracks using Integrative Genomics Viewer (Broad Institute). Total uniquely mapped tags were normalized to 10 million reads to generate tracks using HOMER.
DOI: 10.5061/dryad.cv323/5
title: Machine_learning_CodeANDResults

description: To perform machine learning analysis to predict genes in the repressed and not-repressed categories, we wrote Python and Java codes to partition our dataset into 10 parts to perform feature selection and 10-fold cross validation classification utilizing the Weka machine learning software. The folder includes the codes used in this analysis and raw results that are summarized in the main text. For further description, a readme file is provided under WekaCode folder.
DOI: 10.5061/dryad.cv323/6
title: bed_files.tar.gz part a

description: Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files.tar.gz folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
DOI: 10.5061/dryad.cv323/7
title: bed_files.tar part b

description: Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
DOI: 10.5061/dryad.cv323/8
title: bed_files.tar part c

description: Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
DOI: 10.5061/dryad.cv323/9
title: bed_files.tar part d

description: Raw sequencing reads were mapped to genome as described in Materials and methods. The output bam files were converted to bed files and compressed in bed_files folder, which were broken into five pieces (part a, b, c, d and e) using split command. These files can be recombined to bed_files.tar.gz using cat command.
DOI: 10.5061/dryad.d5672/1
title: FRC Hybrid data_20150906

description: growth and stem form data at ages 5 and years from planting
DOI: 10.5061/dryad.hc6bv/2
title: Simulated genotypes for an artificial Begonia heracleifolia x B. nelumbiifolia hybrid swarm

description: Genotypic data in GenePop file format. Missing data denoted by '000'.
DOI: 10.5061/dryad.hc6bv/3
title: Simulated genotypes for an artificial Begonia heracleifolia x B. sericoneura hybrid swarm

description: Genotypic data in GenePop file format. Missing data denoted by '000'.