cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1f240/6
title: data for analysis of four fitness parameters in year 1, Cost of reproduction

description: data for analysis of four fitness parameters in year 1, data collected in the field during a long-term population monitoring project, data set compiled from original data which are stored in Excel files, description of variables (column headings) can be found in the ReadMe file
DOI: 10.5061/dryad.3v321/1
title: Kropackova-et-al-data

description: Data on fetal and placental weights in F1 crosses and backcrosses. X chromosome genotypes of backcross individuals.
DOI: 10.5061/dryad.j167m/1
title: MISPI_dataset

description: The dataset contains general information about the construction of the dwelling, source of cooking fuel, light etc., eating habits within the household (HH), HH  expenditure, HH assets, and respondent general views about various aspects of inclusion of persons with disabilities.
DOI: 10.5061/dryad.js408/1
title: GWAS results for immune defense when data from both diets pooled

description: Columns are: SNP position, factor, denominator DF, numerator DF, F, P, Chromosome
DOI: 10.5061/dryad.js408/2
title: GWAS for interaction between diet and SNP for immune response

description: Columns are: SNP, factor, denominator DF, numerator DF, F, P, chromosome
DOI: 10.5061/dryad.js408/3
title: GWAS for immune response on high glucose diet

description: Columns are: SNP, factor, denominator DF, numerator DF, F, P, chromosome
DOI: 10.5061/dryad.js408/4
title: GWAS for immune response on low glucose diet

description: Columns are: SNP, factor, denominator DF, numerator DF, F, P, chromosome
DOI: 10.5061/dryad.534f0.2
title: Data from: Fisher's geometric model with a moving optimum
DOI: 10.5061/dryad.657cc/2
title: Appendix 1

description: Excel file containing all data on ichthyosaur completeness, environmental parameters, references, and model outputs.
DOI: 10.5061/dryad.657cc/3
title: Supplement

description: Supplementary information, including additional tables, figures, data, and R codes.
DOI: 10.5061/dryad.fh472/1
title: All_DNA_sequences_assembly

description: Final DNA sequences assembly for testing the monophyly, delineate species and reconstruct Bayesian phylogeographic spatial diffusion models
DOI: 10.5061/dryad.fh472/4
title: ReadMeFile

description: ReadMeFile
DOI: 10.5061/dryad.js408/5
title: Line means for all phenotypes from study

description: Columns are self-explanatory with all values for nutritional indices being mg/fly, bacterial load is natural log load per fly, weight is in mg.  Data from linear models as described in manuscript.
DOI: 10.5061/dryad.n1d61/1
title: appendix1

description: List of Paleobiology Database collections used in this study, including collection number, age, paleolatitude, paleolongitude, sedimentary environment, country, state, tectonic plate, lithification state, lithology, reference number, and collection size.
DOI: 10.5061/dryad.n1d61/2
title: Estimates of theta for all data sets in this study

description: Columns include data set number, number of specimens, number of species, theta, geologic age, lithification state, lithology, and sedimentary environment.
DOI: 10.5061/dryad.v105s/1
title: Microsattellite genotypes for L.fluviatilis and L. planeri
DOI: 10.5061/dryad.v105s/2
title: Alignment of mtDNA sequences (ATPase subunit 6&8)

description: Alignment of mtDNA sequences (ATPase subunit 6&8) including 16 haplotypes form both Lampetra planeri and Lampetra fluviatilis
DOI: 10.5061/dryad.534f0.1
title: Data from: Fisher's geometric model with a moving optimum
DOI: 10.5061/dryad.534f0.2/1.2
title: SimulateMovingOptimum

description: C++ code used for "adaptive-walk" simulations of the multidimensional moving-optimum model. In these simulations, the population is assumed to be monomorphic at all times, and new mutations are  immediately lost or fixed. As a result, adaptation proceeds as a series of discrete "steps". Adaptive-walk simulations are much faster than individual-based simulations, and are more closely related to the analytical results in the paper. Similar assumptions have been used in other models of the genetics of adaptation (Gillespie, Orr...), and have been justified by the so-called strong-selection-weak-mutation assumption.
DOI: 10.5061/dryad.534f0.2/2.2
title: MovingOptimum_IndBased

description: C++ code used for individual-based simulations of the multidimensional moving-optimum model. These simulations implement all model assumptions (i.e., they represent the "full" model). In particular, they keep track of the action of selection, recombination and mutation on multilocus genotypes in a finite population. Individual-based simulations are, thus, realistic (but also more time-consuming) than "adaptive-walk simulations" (see SimulateMovingOptimum.cpp).
DOI: 10.5061/dryad.534f0.2/3.2
title: IndividualBased_SimulationData

description: Simulation data from the individual-based simulation procedure described in the 'Model and Methods' section (paragraph 'Individual-based simulations'). Corresponding simulation program: MovingOptimum_IndBased.cpp. ReadMe files are contained within the .zip archive.
DOI: 10.5061/dryad.534f0.2/4.2
title: MonteCarlo_SimulationData

description: Simulation data from the Monte-Carlo simulation procedure described in the 'Model and Methods' section (paragraph 'The adaptive-walk approximation'). Corresponding simulation program: SimulateMovingOptimum.cpp. ReadMe files are contained within the .zip archive.
DOI: 10.5061/dryad.534f0.2/5.2
title: Mathematica_SimulationData

description: Simulation data from the analytical results (using Mathematica) as described in the 'Supporting Information 4'. ReadMe files are contained within the .zip archive.
DOI: 10.5061/dryad.5m2q0/1
title: Main data

description: This data file contains all variables used for the analyses reported in our article published in PLOS One. It is a CSV file that contains 48 variables for 2994 subjects. Data originate from from the 2010 wave of the SIRS cohort, a representative socio-epidemiological survey of the French-speaking adult (≥18) population conducted since 2005 in the Paris metropolitan area (population 6.5 million). Further description of the data is available in the ReadMe file.
DOI: 10.5061/dryad.5nd50/1
title: Goolsby_EW_SystBiol_2015

description: Zip file containing 5 R scripts for performing function-valued ancestral curve reconstruction, and all simulations conducted in the Syst Biol paper. Also included is a README file explaining use of each R script.
DOI: 10.5061/dryad.665np/1
title: Genotypes of individuals analysed

description: Allelic profile for each of the 699 individuals analysed for 10 microsatellites. The format follows the three digits coding used by the program Genepop, with #000000 indicating missing data.
DOI: 10.5061/dryad.665np/2
title: Geographical coordinates of the sites sampled

description: Location and sample size of each site. Most of the sites in England are private properties.
DOI: 10.5061/dryad.665np/3
title: Unique mitochondrial haplotypes

description: FASTA file containing the sequences of unique mitochondrial DNA
DOI: 10.5061/dryad.7ss03.1
title: Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype
DOI: 10.5061/dryad.7ss03.2
title: Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype
DOI: 10.5061/dryad.7ss03.2/1.2
title: all data files and directory structure for processing

description: This zip file contains all raw data in the "input" directory, and the fieldvsgh_final/README.md contains instructions on how to obtain and run R scripts to process the data.  Once the scripts are obtained, a README.md file provides further information.
DOI: 10.5061/dryad.c5n08/1
title: X-ray diffraction data

description: X-ray diffraction data for wild type and mutant Y99L.The coordinates have been deposited in the Research Collaboration for Structural Bioinformatics (RCSB) Protein Data Bank with the following accession codes: 3TN3 for wild-type GkaP, and 3TN5 for Y99L.
DOI: 10.5061/dryad.c5n08/2
title: Primary data

description: Primary data(table1, table2 and table3 in the maintext were extracted from these data, it also contains screening data for tyr99 saturation mutagenesis)
DOI: 10.5061/dryad.5jc73/1
title: Fig2A_cpDNA_Platycodoneae

description: NEXUS and tre files with the analysis settings used in MrBayes inferred from the concatenated chloroplast dataset (psbJ-petA, trnL-trnF, petB-petD) for the Platycodoneae
DOI: 10.5061/dryad.63k6q/1
title: Expt1_Data

description: Matlab .mat file containing data from Experiment 1.
DOI: 10.5061/dryad.63k6q/2
title: Expt2_Data

description: Matlab .mat file containing data from Experiment 2.
DOI: 10.5061/dryad.63k6q/3
title: Expt3_Data

description: Matlab .mat file containing data from Experiment 3.
DOI: 10.5061/dryad.bh980/1
title: Hermit crab startle response haemocyanin  spermatophore data

description: Data on startle response durations (x8) with: Crab weight (WT); mean spermatophore length (SPERM); haemocyanin concentration (HC) and population (POP). Data stored in wide format, must be re-shaped into long format for analysis with JAGS.
DOI: 10.5061/dryad.h13vg/1
title: Avian Life History Trait Dataset

description: Core dataset upon which the study was based. Details of contents described in the ReadMe file.
DOI: 10.5061/dryad.h13vg/2
title: ALHTTreesFile

description: File containing 500 phylogenetic trees for the taxa included in tests of phylogenetic signal in responses of clutch size to elevational differences as described in the README file associated with the main data file.
DOI: 10.5061/dryad.n2649/1
title: Wing data

description: Wing length, wing width, patch length and patch width, separated for fore- and hindwings and for alive and predated individuals.
DOI: 10.5061/dryad.n2649/2
title: Landmarks

description: Landmark coordinates for the studied wings in .tps format. There are four files, corresponding to fore- and hindwings and alive and predated individuals.
DOI: 10.5061/dryad.4gv50/1
title: Sequence alignments used for divergence analysis

description: Contains 2649 phylip alignment files used to calculate divergence in PAML. Each phylip file contains cDNA sequence of the six species plus zebra finch outgroup. Orthogroups were aligned with PRANK v121218 using the orthologous Taeniopygia guttata cDNA (taeGut3.2.4.75) as an outgroup and specifying the following guidetree; (((A. cygnoides, A. platyrhynchos), (N. meleagris, (P. cristatus, (M. gallopavo, P. colchicus)))), T. guttata). APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus, TGU= Taeniopygia guttata.
DOI: 10.5061/dryad.4gv50/2
title: Polymorphism data for each of the six Galloanserae species

description: Contains a vcf file for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Polymorphism data was obtained by first mapping RNA-seq reads to orthogroups using the two pass alignment method of the STAR aligner with default parameters (Dobin et al. 2013). SNPs were called using varscan v2.3.6 (Koboldt et al. 2009; Koboldt et al. 2012) and Samtools (Li et al. 2009) following the recommendations of Quinn et al 2013 (Quinn et al. 2013).
DOI: 10.5061/dryad.4gv50/3
title: Sequences of Trinity contigs for each of the six Galloanserae species

description: Contains a fasta file of Trinity assembly contig sequences for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus.The left gonad and spleen were dissected separately from five males and five females of each species. The exceptions were P. colchicus, where six male gonad and spleen samples were collected, and M. gallopavo, where four male and two female spleens were collected. Samples were homogenzied and stored in RNAlater until preparation. We used the Animal Tissue RNA Kit (Qiagen) to extract RNA, and the samples were prepared and barcoded at The Wellcome Trust Centre for Human Genetics, University of Oxford using Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit with an insert size of 280bp. RNA was sequenced on an Illumina HiSeq 2000. The data was quality assessed using FastQC v0.10.1 (www.bioinformatics.babraham.ac.uk/projects/fastqc) and filtered using Trimmomatic v0.22 (Lohse et al. 2012). Specifically, we removed reads containing adaptor sequences and trimmed reads if the sliding window average Phred score over four bases was &lt;15 or if the leading/trailing bases had a Phred score &lt;4. Reads were removed post filtering if either read pair was &lt;25 bases in length. We constructed de novo transcriptome assemblies for each species using Trinity with default parameters (Grabherr et al. 2011).
DOI: 10.5061/dryad.4gv50/4
title: RPKM data for each of the six Galloanserae species

description: Contains a file of RPKM expression data for each of the six species. APL = Anas platyrhynchos, ACY = Anser cygnoides, MGA = Meleagris gallopavo, NME = Numida meleagris, PCO = Phasianus colchicus, PCR = Pavo cristatus. Gene expression was quantified using only adult gonad samples and estimated as reads per kilobase per million mappable reads (RPKM) using RSEM v1.1.21 with default parameters (Li and Dewey 2011).
DOI: 10.5061/dryad.5jc73/2
title: Fig2B_ITS_platycodoneae

description: NEXUS and tre files with the analysis settings used in MrBayes inferred from the nuclear ribosomal dataset (ITS) for Platycodoneae
DOI: 10.5061/dryad.5jc73/3
title: Fig2C_ITS_4cpdna

description: NEXUS and tre files with the analysis settings used in MrBayes inferred from the combined nuclear and chloroplast dataset (ITS, psbJ-petA, trnL-trnF, petB-petD, trnS-trnG)  for Platycodoneae
DOI: 10.5061/dryad.5jc73/4
title: Nested-dating approach analysis

description: Script (.xml) and tre files for the "Nested analyses" of all three linked datasets: Platycodoneae, C. eminii and C. canariensis
DOI: 10.5061/dryad.5jc73/5
title: Figure S1

description: Nexus and .tre files for the single-gene analyses of the Platycodoneae dataset.
DOI: 10.5061/dryad.5jc73/6
title: Figure S2

description: Nexus and .tre files for the single-gene analyses of the Canarina dataset
DOI: 10.5061/dryad.mb763/1
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters - spot 211

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/2
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 213

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/3
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 214

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.s597d/1
title: R code used in Chakarov et al. Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite

description: R code used in Chakarov et al. Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite, adaptation of source folder needed on setwd("C:/Users/Downloads")
DOI: 10.5061/dryad.s597d/2
title: Genotypes used by Chakarov et al. Apparent mother to offspring transmission

description: genotypes from loci genotyped in 126 individuals for 15 loci described in Suppl. table 1 of Chakarov et al. "Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite"
DOI: 10.5061/dryad.s597d/3
title: Dataset of Chakarov et al. vector-mediated parent-to-offspring transmission

description: Dataset on genetic distance between Leucocytozoon infections of buzzard chicks with explanatory variables - similarity of chick morphs, mother's and father's morphs (0-different, 1- same), coordinates of both hosts, geographic distance between both hosts, time difference between both hosts, identity of host broods and host mothers.
DOI: 10.5061/dryad.s597d/4
title: Lbuteonis coxIII as entered in Genbank KP640617

description: Sequence of coxIII of Leucocytozoon buteonis from common buzzards from Eastern Westphalia, Germany
DOI: 10.5061/dryad.s597d/5
title: Nestling table used by Chakarov et al apparent vector mediated parent to offspring transmission

description: Phenotypic data of nestlings used in Chakarov et al. including morphs of nestlings and parent, relative year of sampling and nest coordinates
DOI: 10.5061/dryad.s597d/6
title: Leucocytozoon buteonis microsatellites with flanking sequences

description: Leucocytozoon buteonis microsatellites with flanking sequences developed by Chakarov et al.
DOI: 10.5061/dryad.mb763/10
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1406

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/11
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1407

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/12
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1607

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/13
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1705

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/4
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 306

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/5
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 308

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/6
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 502

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/7
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1007

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/8
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1404

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/9
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1405

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/14
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1706

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/15
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 1807

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/16
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 2306

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.
DOI: 10.5061/dryad.mb763/17
title: Raw mass spec files from differentially expressed proteins of Sydney rock oysters_spot 2707

description: Tryptic peptides were analysed by reversed phase nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS) on an QExactive mass spectrometer (Thermo scientific, CA, USA).   Samples represent differentially expressed proteins from two populations of Sydney rock oyster at ambient and elevated CO2 exposure.