cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0065k4k/1
title: Parasites and genotype data for "Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish"

description: This sheet contains sampling site, selfing lineage (according to INstructure), parasite counts, scaled parasite loads, homozygosity by locus, inbreeding status (selfed or outcrossed according to q-value) for all mangrove killifish (Kryptolebias hermaphroditus) sampled in Berbel-Filho et al. (2019).
DOI: 10.5061/dryad.3g5f4m0/1
title: Crayfish genotypes 2014

description: This file contains the genotypes of crayfish sampled in 2014 in a Genepop format.
DOI: 10.5061/dryad.3g5f4m0/2
title: Coordinates crayfish populations 2014

description: This file contains the names and geographic coordinates of crayfish populations sampled in 2014.
DOI: 10.5061/dryad.3g5f4m0/3
title: Crayfish genotypes 2016

description: This file contains the genotypes of crayfish sampled in 2016, in Genepop format.
DOI: 10.5061/dryad.3g5f4m0/4
title: Coordinates crayfish populations 2016

description: This file contains the names, geographic coordinates and category of crayfish populations sampled in 2016.
DOI: 10.5061/dryad.3g5f4m0/5
title: Landscape map

description: This file is a map of the study area in raster format, with NA = terrestrial habitat; 1 = ponds; 2 = marsh; 3 = watercourse.
DOI: 10.5061/dryad.3g5f4m0/6
title: Fluctuating asymmetry

description: This file contains the morphological data used to detect fluctuating asymmetry in crayfish populations. Columns 1 to 3 describe the individual label, population and category. Columns 4 to 11 are morphological measurements of each segment (antennae, merus 1, merus 3, merus 4), for each side (L = left and R = right). Columns 12 to 15 are the difference between left and right measurements for each trait. Columns 16 to 19 are this difference corrected for size-dependence. Columns 20 to 37 are the genotypes of each individual. Column 38 is multilocus heterozygosity.
DOI: 10.5061/dryad.6h6s350/2
title: Martillichthys NHMUK P61563

description: The mimics file containing the scan data for Martillichthys renwickae (NHM P61563), and segmented structures used for the fossil description and analysis.
DOI: 10.5061/dryad.6h6s350/3
title: Martillichthys TIF stack

description: The TIF stack produced by the Martillichthys renwickae (NHM P61563) scan.
DOI: 10.5061/dryad.6h6s350/5
title: README

description: Details of the specimen scanned, and the scanning parameters used for the description of Martillichthys renwickae.
DOI: 10.5061/dryad.7d4t0g6/1
title: Forest and agricultural bird communities in the Himalayas

description: This dataset describes the species encountered on six transects each in agricultural and forest habits in the Himalayas. For each habitat (agriculture or forest), three transects were in the western Himalayas and three in the eastern Himalayas. The column headings represent: (1) region: whether western or eastern Himalayas; (2) habitat: whether agriculture or forest; (c) transect: the identity of the transect (which is the sampling unit); (d) rep: the replicate sample of each transect; (e and f): date and time of each observation; (g and h): the genus and species of each bird recorded; and (i) the group size of each bird record.
DOI: 10.5061/dryad.7nm4970/1
title: Miller_et_al_Germination

description: Germination data for seeds buried in soils conditioned by conspecific and heterospecific plant species
DOI: 10.5061/dryad.7nm4970/2
title: Miller_et_al_FungalCommunities

description: Matrix of fungal taxa by sample found in soils conditioned by seven different plant species.
DOI: 10.5061/dryad.90qg722/10
title: J.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/11
title: Ka.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/12
title: KaSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/13
title: Ko.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/14
title: KoSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/7
title: HkSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/8
title: HL.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/9
title: HLSorted

description: 16s rRNA
DOI: 10.5061/dryad.c0t1892/5
title: R code for figure 1b, 3, S2 and S3

description: R code used to generate figure 1b, 3, S2 and S3. It uses the files: papers.csv, pert.csv and fig_hist_metricsfreq.csv which were extracted from the data base "merged_db_final.json".
DOI: 10.5061/dryad.c0t1892/6
title: fig_hist_metricsfreq csv file

description: Data file extracted from the data base containing the names of all the metrics (first column) and the number of times each of these metrics was used in the papers from the data base. This file is called by the code Plot_fig_1b-3-S2-S3.R and is used to generate fig 1b.
DOI: 10.5061/dryad.c0t1892/7
title: papers csv file

description: Data file extracted from the data base containing all the elements (presented in guidelines_literature-analysis.docx ) that have been recorded for each paper of the data base. This is called by the code Plot_fig_1b-3-S2-S3.R and is used to generate fig. S2 and S3
DOI: 10.5061/dryad.c0t1892/8
title: pert csv file

description: Data file extracted from the data base containing information about all the perturbations studied in the papers of the data base. It is called by the code Plot_fig_1b-3-S2-S3.R and is used to generate fig. 3 and S3.
DOI: 10.5061/dryad.d3q3220/1
title: Supplementary materials

description: Supplementary figures S1-S7
DOI: 10.5061/dryad.d3q3220/2
title: gila_ub.vcf.tar.gz

description: VCF file for running admixture. Analyses were completed using an open source pipeline by Steve Mussman, available at https://github.com/stevemussmann/admixturePipeline, which completes per-locus filtering (e.g. by coverage, minor allele freuency) internally using command-line options.
DOI: 10.5061/dryad.d3q3220/3
title: gila_ub_snps.tar

description: Data files containing an all-SNP alignment (in pyRAD .snps format), unlinked SNPs (=1 sampled per locus) in phylip format, and a filtered unlinked SNP alignment in phylip format. A filtered dataset of unlinked SNPs were used to run STRUCTURE and DAPC. See Methods for more details.
DOI: 10.5061/dryad.d3q3220/4
title: gila_ub.loci.tar.gz

description: Full-locus alignments for all retained loci assembled by pyRAD, in pyRAD's .loci format
DOI: 10.5061/dryad.d3q3220/5
title: gila_ub.str.tar.gz

description: STRUCTURE formatted unlinked SNPs
DOI: 10.5061/dryad.d3q3220/6
title: gila_ub_introgress.tar.gz

description: Gzipped tar archive containing input files and R code for running genomic cline analyses
DOI: 10.5061/dryad.f45gh6s.2
title: Data from: The evolutionary origin of associative learning
DOI: 10.5061/dryad.m15cn37/1
title: The data file consists of microsatellite allele lengths for 11 high informative microsatellites loci described in the paper

description: A data set based on 11 high informative microsatellites loci genotypes from nine populations was used to estimate the population genetic parameters. The first column is the data file of each individuals organized in rows, whereas the abbreviation name of the goat populations in the second column. The subsequent columns correspond to microsatellite data (two columns per locus). The markers in color were excluded from further analysis. Missing data are coded by zero. Abbreviations for the names of the goat populations as follows: Jabal Akhdar (JKH), Batinah (BTN), Dhofar (DHR), Ash Sharqiyah (SHR), Musandam (MSN), Somalia (SOM), Iran (IRN), Pakistan (PAK) and India (IND).
DOI: 10.5061/dryad.s75p458/1
title: data
DOI: 10.17632/cgfhfz34fr.1
title: SNP genotype data for PRD x TMK RIL rice population

description: SNP genotype and grain physical and textural data for 310 PRD x TMK recombinant-inbred lines
DOI: 10.17632/f8hf24hfg9.1
title: Data for: Incidence of Podosphaera clandestina on sweet cherries (Prunus avium) and the influence of postharvest handling practices on the survival of conidia on harvested fruit

description: The file contains data from all the experiments used and listed in the manuscript. The qPCR analysis, calculations and standards are also listed in the file, in different tabs.
DOI: 10.17632/m5nkkftgtb.2
title: Data for: On the asphericity of the figures of Pluto and Charon

description: Functions Oblate(q, beta) and Stokes(q, beta) deduce numerical values of $\alpha$ and $I_2$ for given $q$ and $\beta$. In the body of each function the numeric type of data 'long double' is used to calculate the coefficients $p_k, s_k$, which provides a more accurate decimal representation of rational numbers compared to the type 'double'. Both functions are defined in the PlutoCharon.cpp library file. More detailed description of the operation of these functions can be found in the file PlutoCharon.h.
DOI: 10.17632/r6p6x4pthd.1
title: Data for: IPsec for High Speed Network Links: Performance Analysis and Enhancements
DOI: 10.17632/xg4kc5vrhv.1
title: Data for: Glacial fluctuations over the last 3,500 years reconstructed from a lake sediment record in the northern Tibetan Plateau

description: The values under different C numbers are exhibited by peak area.
DOI: 10.17632/xs62sjxsrt.1
title: Data for: Survival Estimation through the Cumulative Hazard with Monotone Natural Cubic Splines Using Convex Optimization-the HCNS approach

description: This files contains all codes, data as well as descriptions of its use accompanied with reproducible examples.
DOI: 10.17632/yzbwhmcycr.1
title: Data for: Origin of the Xiaohekou skarn copper deposit and related granitoids in the Zha-Shan ore cluster area, South Qinling, China

description: Table ES1 Major (wt.%) and trace element (ppm) analyses of the ore-related granitoids in the Xiaohekou ore district. Table ES2 LA−ICP−MS zircon U−Pb data of the ore-related granitoids. Table ES3 LA−ICP−MS analytical results of zircon rare earth and trace elements (ppm) and oxygen fugacity parameters. Table ES4 Zircon Hf isotopic compositions of the ore-related granitoids.
DOI: 10.5061/dryad.0065k4k/2
title: MSAFLP data for "Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish"

description: MSAFLP raw data for 381 loci found for 115 individuals analysed in Berbel-Filho et al (2019) to be used as input into the msap R. package. From the transformed MSL (methylation susceptible loci) dataset, we calculated the methylation percentages to be used in the linear models.
DOI: 10.5061/dryad.1nn0206/1
title: ND2 and cytb sequences of Sulawesi adrianichthyids

description: Mitochondrial ND2 and cytb sequences of Sulawesi adrianichthyids
DOI: 10.5061/dryad.2v4h7bv/1
title: Appendix 1 Tutorial

description: Tutorial presenting the regPhylo R package with a short example
DOI: 10.5061/dryad.2v4h7bv/2
title: Appendix 2 Tutorial

description: In-depth tutorial presenting the regPhylo R package for the case study
DOI: 10.5061/dryad.2v4h7bv/3
title: Data for Appendix 1

description: All data related to the example described in the tutorial from the Appendix 1
DOI: 10.5061/dryad.2v4h7bv/4
title: Data for Appendix 2

description: All data related to the case study of New Zealand marine ray-finned fishes described in the tutorial from the Appendix 2.
DOI: 10.5061/dryad.7nm4970/3
title: Miller_et_al_FeedbackDistance

description: Data relating distance (in multivariate space) of fungal communities in soils conditioned by different plant species to the magnitude of plant soil feedback observed
DOI: 10.5061/dryad.843814d/1
title: The effect of lime addtion on microbial siderophore production in polluted soil communities

description: The first data sheet in this Excel file contains a brief description of the study locations as well as data quantifying the effect of lime addition on changes in soil pH measured over a time frame of 12 weeks. The second data sheet provides information about the availability of 16 heavy metals in limed and control soil microbial communities. The third data sheet provides information about siderophore production (measured using liquid CAS assays) of 24 clones per unique community and across three different selection regimes (natural, lime and control soil communities
DOI: 10.5061/dryad.864pt1f/1
title: Data from: Aphids influence soil fungal communities in conventional agricultural systems

description: This file contains data from a field experiment where aphid presence was manipulated and plant and soil fungal parameters were measured. The file contains the treatment for each replicate, measurements on plant biomass and nutrition, as well as measurements of arbuscular mycorrhizal structures, and the identity and relative abundance of soil fungal taxa.
DOI: 10.5061/dryad.90qg722/15
title: LL.raw
DOI: 10.5061/dryad.90qg722/16
title: LS.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/17
title: LSSorted
DOI: 10.5061/dryad.90qg722/18
title: MH.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/19
title: Mi.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/20
title: MiSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/21
title: Mm.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/22
title: Mu.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/23
title: MuSorted

description: 16s rRNA
DOI: 10.5061/dryad.d3q3220/7
title: gila_newhyb.tar.gz

description: Outputs and datafiles for running newhybrids and associated power analyses in the hybriddetective R package
DOI: 10.5061/dryad.d3q3220/8
title: gila_ub_sra_metadata

description: Sample metadata for linking between NCBI SRA accession names (raw data) and sample names in datasets used for analyses
DOI: 10.5061/dryad.d84hg87/1
title: Data for Dryad

description: File contains estimates of abundance and three indices of age (mean age, and median age of adults and the proportion of adults in the population that were considered senescent) structure for each of the four study populations.
DOI: 10.5061/dryad.f45gh6s.2/1.2
title: Avida configuration instructions

description: This zip file contains a MS Word document with instructions on how to configure Avida to replicate the experiments from the paper. It also contains a folder "Analyze_file_for_lineage_extraction" with a sample Avida 'analyze file' used to extract the lineage of the final predominant organism from a given population.
DOI: 10.5061/dryad.f45gh6s.2/2.2
title: Raw data from Experiment 1

description: This zip file contains the Avida raw data output for Experiment 1. The data is divided in four folders according to the experimental environment (treatment): Nutrient Cued, One Fixed Turn, Random Start, and Two Fixed Turns. Each of these folders contains a sub-folder "Experiment_configuration_files" with the files necessary to configure Avida to recreate the particular experiment. Finally, each environment folder contains another 50 sub-folders, with the data from each replicate.
DOI: 10.5061/dryad.f45gh6s.2/3.2
title: Raw data from Experiment 2 (part 1 of 4)

description: This zip file is 1 of 4 files containing the Avida raw data output for Experiment 2. The data from 225 out of 900 replicates is stored in individual folders. In addition, the zip file contains a folder "Experiment_configuration_files" with the files necessary to configure Avida to recreate this experiment.
DOI: 10.5061/dryad.f45gh6s.2/4.2
title: Raw data from Experiment 2 (part 2 of 4)

description: This zip file is 1 of 4 files containing the Avida raw data output for Experiment 2. The data from 225 out of 900 replicates is stored in individual folders.
DOI: 10.5061/dryad.f45gh6s.2/5.2
title: Raw data from Experiment 2 (part 3 of 4)

description: This zip file is 1 of 4 files containing the Avida raw data output for Experiment 2. The data from 225 out of 900 replicates is stored in individual folders.
DOI: 10.5061/dryad.f45gh6s.2/6.2
title: Raw data from Experiment 2 (part 4 of 4)

description: This zip file is 1 of 4 files containing the Avida raw data output for Experiment 2. The data from 225 out of 900 replicates is stored in individual folders. In addition, the zip file contains a folder "Test_Environments" with two additional environment configuration files used for evaluating an individual organism's performance.
DOI: 10.5061/dryad.f45gh6s.2/7.2
title: Raw data from the Preliminary Experiment

description: This zip file contains the Avida raw data output for the Preliminary Experiment. The data is divided in four folders according to the experimental environment (treatment): Nutrient Cued, One Fixed Turn, Random Start, and Two Fixed Turns. Under a given environment folder the data from each replicate is stored in individual sub-folders. In addition, each environment folder contains a sub-folder "Experiment_configuration_files" with the files necessary to configure Avida to recreate the particular experiment.
DOI: 10.5061/dryad.f45gh6s.2/8.2
title: Raw data from Follow Up Experiment

description: This zip file contains the Avida raw data output for the Follow Up Experiment. The data is divided in 200 folders, one for each replicate. In addition, the zip file contains a folder "Experiment_configuration_files" with the files necessary to configure Avida to recreate this experiment.
DOI: 10.5061/dryad.f45gh6s.2/9.2
title: Avida Draw - organism's path plotting tool

description: This zip file contains the software Avida Draw, written in Python and used to plot the organisms' path in the arena. It saves .EPS images of both the arena and the organism's final path.
DOI: 10.5061/dryad.pd47h4d/1
title: Rocha-Santos et al 2019 - tree recproductive traits

description: Abundance and reproductive traits of 422 tree species of Atlantic forest fragments with different percentages of forest cover at the landscape scale
DOI: 10.5061/dryad.r9m0f6r/1
title: Ng et al_2019_J Evol Biol_raw data

description: Excel spreadsheet containing the individual data of female life history traits with their protein, carbohydrate and micronutrient intakes.
DOI: 10.5061/dryad.sv90027/1
title: Growing season lengths

description: Growing season length and elevation data for each study site and year (see overall README file).
DOI: 10.5061/dryad.sv90027/2
title: Natural plant phenological phenotypes

description: Phenological measurements and identifying characteristics of naturally occurring Rhinanthus minor individuals.
DOI: 10.5061/dryad.sv90027/3
title: Transplanted phenological phenotypes

description: Phenological and site identifying characteristics for all measured transplanted individuals
DOI: 10.5061/dryad.sv90027/4
title: README
DOI: 10.17632/2k47t5rjmz.1
title: Data for: Using GPS tracking to understand the impact of management interventions on visitor densities and bird populations

description: Monitoring data of visitors of the New Forest, UK. Each track has been collected with an eTrex or eTrex Venture GPS device. Explanation of the headers can be found in Table A.3. The dataset contains 1563 tracks of which 1553 could be used for further analyses in our research.
DOI: 10.17632/3z3wg3hd5m.1
title: Data for: A Multi-Aspect Study of Commercial Coatings Under the Effect of Surface Roughness and Fouling

description: The files uploaded include following: 1. Rt50.xlsx is the roughness data collected using TQC hull roughness gauge 2. Notepad files which are the torque data measured by the rotating disk facility
DOI: 10.17632/3z3wg3hd5m.2
title: Data for: A Multi-Aspect Study of Commercial Coatings Under the Effect of Surface Roughness and Fouling

description: The files uploaded include following: 1. Rt50.xlsx is the roughness data collected using TQC hull roughness gauge 2. Notepad files which are the torque data measured by the rotating disk facility
DOI: 10.17632/5dtv246znd.1
title: EXTRACTION OF ELASTIN FROM TANNERY WASTES: A VALUE ADDITION TO TANNERY WASTES
DOI: 10.17632/cgfhfz34fr.2
title: SNP genotype data for PRD x TMK RIL rice population

description: SNP genotype and grain physical and textural data for 310 PRD x TMK recombinant-inbred lines
DOI: 10.17632/jc2x37dn73.1
title: Data for: Boosts to sustained attention from psychostimulants dissipate after 24 hours

description: Raw data
DOI: 10.17632/ttrxbg5f5h.1
title: Data for: Autophagy, lysosome dysfunction and mTOR inhibition in MNU-induced photoreceptor cell damage
DOI: 10.5061/dryad.1nn0206/10
title: 10_vcftosfs_joint

description: Custom scripts for transforming the SNPs data into the folded JSFS
DOI: 10.5061/dryad.1nn0206/2
title: Data for morphology

description: Raw data of morphological analyses of the three species of Poso Oryzias
DOI: 10.5061/dryad.1nn0206/3
title: 3_Egg_size_data

description: Raw data of egg size of the three species of Poso Oryzias
DOI: 10.5061/dryad.1nn0206/4
title: 4_SNP_data_Poso_Oryzias_82ind

description: SNPs data in vcf for the 82 individuals of the three species of Poso Oryzias and their outgroup O. soerotoi
DOI: 10.5061/dryad.1nn0206/5
title: 5_Popmap_for_treemix_files

description: Popmap file for the TreeMix analyses of the three species of Poso Oryzias and their outgroup O. soerotoi
DOI: 10.5061/dryad.1nn0206/6
title: 6_Pop_order_for_treemix

description: Population order file for the TreeMix analyses of the three species of Poso Oryzias and their outgroup O. soerotoi
DOI: 10.5061/dryad.1nn0206/7
title: 7_Data_for_NJ_tree

description: Concatenated sequences of RAD loci used for the NJ phylogeny among the three species of Poso Oryzias and their outgroup O. soerotoi
DOI: 10.5061/dryad.1nn0206/8
title: 8_Data_for_SNAPP

description: Input file for the SNAPP analysis of the three species of Poso species and their outgroup O. soerotoi
DOI: 10.5061/dryad.1nn0206/9
title: 9_JSFS_4sp_data

description: Folded JSFS (JSFS for minor allele) for fastcimcoal2 created using 3,188 RAD loci
DOI: 10.5061/dryad.229m0tp/1
title: Genotypic data from 6 populations of Douglas fir in Europe_data

description: The file contains genotypic data of 435 trees (old trees and natural regeneration) from six (6) populations of Douglas-fir in Europe (Austria and Germany). Samples were genotyped according to the methods described in the publication. The file contains genotypes of 13 nuclear microsatellite loci.
DOI: 10.5061/dryad.7254t7d/1
title: Impacts of bacteria and plant defenses on caterpillar performance

description: Growth data containing mixture of bacteria and different plant genotypes
DOI: 10.5061/dryad.7254t7d/2
title: Fall armyworm immune responses to bacteria and plant defenses

description: phenoloxidase, pro-phenoloxidase, and hemocyte responses of fall armyworm
DOI: 10.5061/dryad.7254t7d/3
title: Impacts of bacterial isolates and plant defenses of fall armyworm growth and mortlaity
DOI: 10.5061/dryad.90qg722/24
title: Ok.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/25
title: OkSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/26
title: R.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/27
title: RSorted

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/28
title: Rx.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/29
title: S2.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/30
title: SF.raw

description: 16s rRNA
DOI: 10.5061/dryad.90qg722/31
title: SFSorted

description: 16s rRNA
DOI: 10.5061/dryad.f45gh6s.1
title: Data from: The evolutionary origin of associative learning
DOI: 10.5061/dryad.f45gh6s.1/1.1
title: Avida configuration instructions

description: This zip file contains a MS Word document with instructions on how to configure Avida to replicate the experiments from the paper. It also contains a folder "Analyze_file_for_lineage_extraction" with a sample Avida 'analyze file' used to extract the lineage of the final predominant organism from a given population.
DOI: 10.5061/dryad.f45gh6s.1/2.1
title: Raw data from Experiment 1

description: This zip file contains the Avida raw data output for Experiment 1. The data is divided in four folders according to the experimental environment (treatment): Nutrient Cued, One Fixed Turn, Random Start, and Two Fixed Turns. Each of these folders contains a sub-folder "Experiment_configuration_files" with the files necessary to configure Avida to recreate the particular experiment. Finally, each environment folder contains another 50 sub-folders, with the data from each replicate.