cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.04fj885/8
title: Brassicaceae ITS Bayesian majority-rule consensus tree

description: Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for Brassicaceae and the ITS dataset.
DOI: 10.5061/dryad.04fj885/9
title: Brassicaceae ITS Maximum likelihood tree

description: Maximum likelihood tree for Brassicaceae generated with RAxML using the ITS dataset.
DOI: 10.5061/dryad.0v9n6j4/1
title: Size and Physiology Data

description: Size and physiology data for all plants across the course of the experiment.
DOI: 10.5061/dryad.0v9n6j4/2
title: Total Reproduction Data

description: Total number of inflorescences for all plants in the experiment.
DOI: 10.5061/dryad.0v9n6j4/3
title: Seed Data

description: Inflorescence weight, seed number, seed weight, and germination data.
DOI: 10.5061/dryad.14k55m8/1
title: Original data

description: BORIS software was used to extract the occurrence and duration of aggressive behaviors in Experiment 2: one-to-two encounters.
DOI: 10.5061/dryad.18qv7ks/1
title: Data used for all analyses

description: This single-sheet excel file contains the raw data extracted from the CO2, O2 and temperature datafiles.
DOI: 10.5061/dryad.43c323g/1
title: species.list

description: List of plant species identified in the experiment.
DOI: 10.5061/dryad.43c323g/2
title: percent.cover.alldates

description: Percent cover of plant species greater than 5% for all time points in the experiment.
DOI: 10.5061/dryad.43c323g/3
title: percent.cover.summers

description: Percent cover of all plant species identified for summer dates in the experiment.
DOI: 10.5061/dryad.43c323g/4
title: plot.treatment.identifier

description: List of treatments applied to plots.
DOI: 10.5061/dryad.43c323g/5
title: soil.moisture

description: Soil volumetric water content measured in four locations in each plot.
DOI: 10.5061/dryad.43c323g/6
title: README

description: This file provides an explanation of the datasets in this folder.
DOI: 10.5061/dryad.51rk4v4/1
title: orthologous groups of genes in the H. melpomene and the H. erato transcriptomes

description: OrthoFinder was used to identify orthologous groups of genes in
the H. melpomene and the H. erato transcriptomes (options: -t
48 -a 6). 1-1 orthologous gene sequences were selected for use in subsequent analysis (Supporting Information Table S2)
DOI: 10.5061/dryad.66jt1.1
title: Data from: Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers)
DOI: 10.5061/dryad.66jt1.1/2.1
title: Genotype GBS files for 15 parental (allopatric) and 175 individuals from the Sapsucker transects

description: Genotype GBS files for 15 parental (allopatric) birds (5 S. varius, 5 S. ruber, 5 S. nuchalis) and 175 individuals from the Sapsucker transects of all three species in .fa format
DOI: 10.5061/dryad.66jt1.2
title: Data from: Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers)
DOI: 10.5061/dryad.66jt1.2/1.2
title: Illumina RAD GBS sequence of Sphyrapicus Sapsuckers

description: Illumina RAD sequences of 176 Sphyrapicus Sapsuckers from
Western Canada.
DOI: 10.5061/dryad.66jt1.2/2.2
title: Summary data - illumina RAD GBS sequences of Sphyrapicus Sapsuckers

description: Summary of the GBS sequences of the 176 individuals of
Sphyrapicus Sapsuckers from Western Canada.
DOI: 10.5061/dryad.683870h/1
title: R Code for simulations

description: R Code for simulations described in Danchin et al.
DOI: 10.5061/dryad.683870h/2
title: CulturalFlies_Danchin et al

description: Data of the experiments described in Danchin et al.
DOI: 10.5061/dryad.78sb41t/1
title: data_ECOG-04125.R1

description: Original data and summary statistics for Table 1 and Figure 1
DOI: 10.5061/dryad.83jm680/1
title: Raw Data_Bhattacharyya and Ishtiaq 2018

description: The file contains microsatellite raw data used in the study.
DOI: 10.5061/dryad.98rf2f1/1
title: Gff-16microsats-251-genepop

description: Gff microsatellite data in GenePop format. Data from 251 individuals (that were also included in the ddRAD dataset in the manuscript) from 16 microsatellites loci (A03b, B05, C7b, CAG29, GpCAG133, D05, D101, Gmm8, GpB20b, GpC10, Pgp28, GmL03, GmmA06, GmmH09, GmmL11, GmD15) with varying repeat motifs (of lengths 2, 2, 3, 3, 3, 3, 3, 4, 3, 3, 2, 2, 2, 2, 2, and 2 bp) and varying repeat lengths (80, 110, 80, 60, 70, 40, 60, 40, 60, 65, 70, 100, 90, 95, 125, and 80).
DOI: 10.5061/dryad.9bq5n41/10
title: Calculate_Ancestral_States

description: R script to calculate morphological ancestral states (CHRIS COONEY - 2017)
DOI: 10.5061/dryad.gr36743/1
title: Alignments

description: Alignments of nuclear and mitochondrial sequences for ground-dove Columbicola.
DOI: 10.5061/dryad.gr36743/2
title: Cophylogenetic link comparisons

description: Table of statistics from cophylogenetic analyses of ground-dove wing and body lice.
DOI: 10.5061/dryad.gr36743/3
title: Distances

description: Distances of nuclear and mitochondrial sequences between wing and body lice from Metriopelia melanoptera and Metriopelia ceciliae.
DOI: 10.5061/dryad.gr36743/4
title: SNPs

description: VCF files containing SNPs for ground-dove Columbicola and Physconelloides. Includes SNPs for Columbicola passerinae, C. passerinae 1, C. passerinae 2, Physconelloides eurysema, and P. eurysema 3.
DOI: 10.5061/dryad.gr36743/5
title: Trees

description: Tree files for ground-dove Columbicola. Includes gene trees, tree from the concatenated alignment, coalescent tree, mitochondrial tree, and mitochondrial BEAST tree.
DOI: 10.5061/dryad.kg593qs/3
title: Temperature Data

description: Dataset containing temperature observations. Please note that small time increments are missing due to inclement weather.
DOI: 10.5061/dryad.kg593qs/4
title: Read Me

description: This file explains all of the variables in each of the datasets that accompany: Gordon SCC, Meadley-Dunphy SA, Prior KM, Frederickson ME, 2018ms. Asynchrony between ant seed dispersal activity and fruit dehiscence of myrmecochorous plants.
DOI: 10.5061/dryad.kn3p693/1
title: Savriama_Gerber_2018_Sc_Rep_Data

description: Raw coordinates for landmark data used in this study.
DOI: 10.5061/dryad.kn3p693/2
title: Savriama_Gerber_2018_Sc_Rep_Lantern3D

description: CT-Scan of the Aristotle’s lantern of the ‘regular’ sea urchin Paracentrotus lividus that is being displayed in the figures of this study. This model can be opened in software such as Meshlab and is ready for 3D printing.
DOI: 10.5061/dryad.pn371m9/1
title: Data_Schmdit et al. JAB01946

description: Summary data for chipmunk annual aggregation, local cluster indices, and cluster indices at the 9-trap neighborhoods surrounding veery and ovenbird nests
DOI: 10.5061/dryad.qv871g8/1
title: R function to add fossils to a tree
DOI: 10.5061/dryad.qv871g8/2
title: Amniotes tree (15423 taxa)
DOI: 10.5061/dryad.rj083bv/1
title: Hawaii_regimes

description: Hawaii_regimes.csv is a comma-separated file containing data used to define reef regimes for the Hawaii Islands. The file includes metadata for 1027 replicates, 10 reef community metrics used to define regimes in a cluster analysis, and the resulting reef regime. Reef community metrics are averages of individual replicates grouped based on spatial proximity. Details of the analysis can be found in the accompanying publication. Parties interested in using this data for other purposes are asked to contact Mary Donovan (donovan.maryk@gmail.com).
DOI: 10.5061/dryad.s8n5674/10
title: C642

description: Raw RADSeq data for Alnus sampled in Alaska/adjacent Canada.
DOI: 10.5061/dryad.s8n5674/11
title: Bar Codes for C643
DOI: 10.5061/dryad.s8n5674/12
title: C643

description: Raw RADSeq data for Alnus sampled in Alaska/adjacent Canada.
DOI: 10.5061/dryad.s8n5674/7
title: Bar Codes for C511
DOI: 10.5061/dryad.s8n5674/8
title: C511

description: Raw RADSeq data for Alnus sampled in Alaska/adjacent Canada.
DOI: 10.5061/dryad.s8n5674/9
title: Bar Codes for C642
DOI: 10.5061/dryad.sk2155m/2
title: Abiotic variables Brown shrimp diet metabarcoding

description: Table including the environmental variables of 23 sites in the Netherlands, Portugal and United Kingdom measured in May-July 2016. Ordered in the following columns: (A) SiteID, (B) Country, (C) Estuary, (D) Temperature [°C], (E) Salinity, (F) pH, (H) Turbidity [NTU], (H) Oxygen [%], (I) Grain_Size [µM], (J) TOM [%]
DOI: 10.5061/dryad.sk8rb66/10
title: s10
DOI: 10.5061/dryad.sk8rb66/11
title: s11
DOI: 10.5061/dryad.sk8rb66/12
title: s12
DOI: 10.5061/dryad.sk8rb66/5
title: s05
DOI: 10.5061/dryad.sk8rb66/6
title: s06
DOI: 10.5061/dryad.sk8rb66/7
title: s07
DOI: 10.5061/dryad.sk8rb66/8
title: s08
DOI: 10.5061/dryad.sk8rb66/9
title: s09
DOI: 10.5061/dryad.sm282vt/2
title: Agent based model code

description: This is the code that defines the agent based model. See also https://github.com/csmaxwell/phage-abm
DOI: 10.5061/dryad.t7f3rc8/1
title: Primary data used in the analyses reported in the paper and its Supplementary Online Material.

description: See README file included in zip archive.
DOI: 10.5061/dryad.t7f3rc8/2
title: Molecular data used in analyses of prokaryotic community composition

description: See README file included in the zip archive.
DOI: 10.5061/dryad.tn8qs35/1
title: Simulation script 1

description: This R script will simulate two populations of microbiome samples and compare normalization methods.
DOI: 10.5061/dryad.tn8qs35/2
title: Simulation script 2

description: This R script will simulate two populations of microbiome samples and compare normalization methods via PcOAs.
DOI: 10.5061/dryad.tn8qs35/3
title: Sample.OTU.distribution

description: OTU distribution used in the paper: Methods for normalizing microbiome data: an ecological perspective
DOI: 10.5061/dryad.v07j0t0/5
title: Aphid_Expt_2

description: Data from second aphid experiment
DOI: 10.17632/3y4p9x58k6.1
title: Data for Zuliani et al

description: Subject-wise datset.
DOI: 10.17632/4j3p7r7r52.1
title: Data for: Dynamics of development of the largest cities - evidence from Poland

description: 1. Data on the number of population in the largest cities in Poland and neighboring municipalities in the years 2002-2016 2. Data on the surface of a flat per person in the largest cities in Poland and neighboring municipalities in the years 2002-2016
DOI: 10.17632/drtf68tcn8.1
title: Data for: A Multivariate Time Series Analysis of Energy Consumption, Real Output and Pollutant Emissions in a Developing Economy: New Evidence from Nepal

description: The attached file contains both the raw data and refined data used in the analysis.
DOI: 10.17632/dtwnfgky54.1
title: Data for: Are there sex differences in muscle coordination of the upper girdle during a sustained motor task?

description: Supplementary material to be published online alongside the electronic version of the article. This supplementary material provides information about the calculation of the NMI values.
DOI: 10.17632/f5dypn7vh3.1
title: Data for: Encephalomyocarditis virus 2C protein antagonizes interferon-β signaling pathway through interaction with MDA5

description: Sep 30, 2018 Dear Editors-in-Chief, Dr Gorisr Thank you so much for forwarding me the valuable reviewer’s comments. I have carefully addressed all of the issues raised by the referee as your comments. The manuscript was revised as follows (blue words): Reviewer 1 1. EMCV has four capsid proteins and eight non-structural proteins. In the study, only seven non-structural proteins were cloned into expression vectors and their inhibitions of IFN-β induction were studied. How were the other proteins? Reply: The comment is reasonable. It has been discussed in the fifth paragraph of DISSUSION 2. Luciferase assays results indicate 2C protein of EMCV affects inhibition of the type I IFN signaling pathway by MDA5 or RIG-I. However, the results of co-immunoprecipitation and confocal microscopy showed EMCV 2C only targets and interacts with MDA5. What is the possible mechanism of 2C protein inhibiting RIG-I-mediated IFN-β promoter activity? Reply: The comment is reasonable. It has been discussed at the end of the third paragraph of DISSUSION 3. Minor error, in page 9, line 368, the” (10-325)” should be deleted. Please check the full text carefully. Reply: The comment is reasonable. It has been correct. Reviewer 2 4. The introduction is an enumeration of facts, and not focused on the main studies of the paper. Sometimes is also misleading. For example, the sentence: “Nevertheless, whether EMCV regulates the innate immune response is not known.” Is incorrect, as there are described mechanisms how EMCV inhibits innate immune responses. Reply: The comment is correct. It has been addressed. 5. Most of the literature will now use the name MAVS, and not VISA. Reply: The comment is reasonable. It has been addressed. In addition, we have checked the full text carefully in grammar and spelling. The revised manuscript with modifications marked with red color is enclosed. We hope that it can be published as soon as possible. I am looking forward to hearing from you. Thanks! Sincerely, Juan Bai, PhD, Associated professor College of Veterinary Medicine Nanjing Agricultural University Nanjing 210095 P.R. China baijuan@njau.edu.cn
DOI: 10.17632/jfydkcb7hx.1
title: Data for: Electronic model «FC-FNS» of the fusion neutron source DEMO-FNS fuel cycle and modeling hydrogen isotopes flows and inventories in fueling system

description: The key task of the fuel cycle (FC) design is to create a closed system providing the conditions for fusion burning in plasma, with reduce tritium inventory in the system elements. For this purpose “FC-FNS” electronic model has been actively developing as a tool for estimating fluxes of DT fuel and T inventories in systems where tritium is used. The paper describe the conceptual fuel cycle design for the DEMO-FNS facility and results of the modeling of hydrogen isotopes flows and inventories in fuel systems for steady-state operation mode.
DOI: 10.17632/sh59zg936j.1
title: Data for: Proteolytic susceptibility of food by-product proteins: An evaluation by means of a quantitative index

description: paper plots from reaction progress and analysis
DOI: 10.17632/sn2td5j8mr.1
title: Data for: Influence of Banking Advertisement on Bank Customer Satisfaction: An Examination of Pakistani Bank Customers’Choice

description: Here, all the data of research of multiple results include, linear regression, correlation, and descriptive statistic
DOI: 10.17632/yt6py4t9ky.1
title: Data for: Biotic, geochemical and environmental changes through the early Sheinwoodian (Wenlock, Silurian) carbon isotope excursion (ESCIE), Buttington Quarry, Wales

description: Excel spread sheet of Buttington pyrite geochemistry data. Column B indicates sample heights.
DOI: 10.5061/dryad.04fj885/10
title: Brassicaceae trnL-F alignment

description: trnL-F alignment of Brassicaceae dataset.
DOI: 10.5061/dryad.04fj885/11
title: Brassicaceae trnL-F Bayesian majority-rule consensus tree

description: Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for Brassicaceae and the trnL-F dataset.
DOI: 10.5061/dryad.04fj885/12
title: Brassicaceae trnL-F Maximum likelihood tree

description: Maximum likelihood tree for Brassicaceae generated with RAxML using the trnL-F dataset.
DOI: 10.5061/dryad.04fj885/13
title: Halimolobeae ITS alignment

description: ITS alignment of tribe Halimolobeae dataset.
DOI: 10.5061/dryad.04fj885/14
title: Halimolobeae ITS Bayesian majority-rule consensus tree

description: Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Halimolobeae and the ITS dataset.
DOI: 10.5061/dryad.04fj885/15
title: Halimolobeae ITS Maximum likelihood tree

description: Maximum likelihood tree for tribe Halimolobeae generated with RAxML using the ITS dataset.
DOI: 10.5061/dryad.04fj885/16
title: Halimolobeae trnL-F alignment

description: trnL-F alignment of tribe Halimolobeae dataset.
DOI: 10.5061/dryad.04fj885/17
title: Halimolobeae trnL-F Bayesian majority-rule consensus tree

description: Bayesian 50% majority-rule consensus tree from 6002 trees generated by Bayesian inference with MrBayes for tribe Halimolobeae and the trnL-F dataset.
DOI: 10.5061/dryad.04fj885/18
title: Halimolobeae trnL-F Maximum likelihood tree

description: Maximum likelihood tree for tribe Halimolobeae generated with RAxML using the trnL-F dataset.
DOI: 10.5061/dryad.06cs1f9/1
title: Occurrence data

description: A table containing the occurrence data used for the endemism analysis. Contains filtered GBIF registries for 311 plant species of the Cerrado.
DOI: 10.5061/dryad.0h2br0d/1
title: pedigree

description: Pedigree of the individuals contained in the dataset. First column contain the individuals id, second is the id of the mother ("dam") and third is the id of the (reconstructed with genetic data) father ("sire").
DOI: 10.5061/dryad.0h2br0d/2
title: data

description: Phenotypic and breeding data used in the article
DOI: 10.5061/dryad.0h2br0d/3
title: BUGS model

description: Model used to estimate and analyse the optimum of laying date.
DOI: 10.5061/dryad.0h2br0d/4
title: Power analysis simulations

description: Simulations to analyse our power to estimate heritability.
DOI: 10.5061/dryad.1023m1d/2
title: Soil water retention curves in the 50-ha plot on BCI, Panama

description: BCI_retention_curves.txt holds soil water retention curves from 25 seedling census sites in the 50-ha plot on Barro Colorado Island, Panama. We constructed the curves using soil samples that we first used to measure SWP and SWC (see file BCI_SWP_SWC.txt). We used the curves to determine outliers in SWP measurements.
DOI: 10.5061/dryad.1gk3014/1
title: Diameters of human bony birth canal in different populations

description: Antero-posterior and medio-lateral diameters of the birth canal (inlet, midplane and outlet) in women from different recent and archaeological populations. The measurements were taken by Dr Lia Betti on skeletal remains using an internal caliper. The pelvic girdle was rearticulated firmly at the level of the auricular surface, and plasticine was used to fill in the pubic symphysis. Elastic bands were use to keep the bones in articulation while taking the measurements.
DOI: 10.5061/dryad.2n8055g/1
title: Jessop_data

description: provides data for estimates of daily movement, exploration and spatial mark-recapture data
DOI: 10.5061/dryad.51rk4v4/10
title: total_alignment_Z_heliconius

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/11
title: total_alignment_Z_heliconius

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/2
title: divergence_autosomes

description: Calculation of diversity and selection
statistics for 1-1
ortholog alignments between
H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/3
title: divergence_Z

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/4
title: polymorphism_autosomes

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/5
title: polymorphism_autosomes

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/6
title: results_heliconius-otherLeps

description: Overall results for calculation of diversity and selection
statistics for 1-1 ortholog alignments between
H. melpomene and H. erato & other Leps for comparison
DOI: 10.5061/dryad.51rk4v4/7
title: total_alignement_autosomes_heliconius

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/8
title: total_alignement_autosomes_heliconius

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.51rk4v4/9
title: total_alignement_autosomes_heliconius

description: Calculation of diversity and selection statistics for 1-1 ortholog alignments between H. melpomene and H. erato
DOI: 10.5061/dryad.538044t/1
title: Olsson et al.Long Term effects of Superoxide

description: Telomere and reactive oxygen species data
DOI: 10.5061/dryad.75fh336/2
title: filtering_data_files

description: This directory contains files relating to filtering the data. These are divided into two subdirectories, FastQC_results and Regular_expressions_removing_adapter_pollution
FastQC_results:
This directory contains the FastQC output for each Read 1 or Read 2 raw data file for the 69 samples (including separated replicate files). The output can be viewed in a web browser.
Regular_expressions_removing_adapter_pollution:
This file contains information on the regular expressions we used to remove adapter pollution from our sequence data.
DOI: 10.5061/dryad.75fh336/3
title: stacks-based_mtdna_snp_identification_approach

description: This directory is split into two subfolders - one for KwaZulu-Natal yellowfish and one for Orange-Vaal yellowfish. The same parameters (-m 5 -M 2 -n 2 --max_locus_stacks 7 -r 0) were used between these analyses.
Files are provided for the final analysis where mitochondrial loci had been identified from the initial Stacks results and run separately on a whitelist to provide results specific to only these candidate mitochondrial loci.
For further details of the contents of this directory, please refer to the README.
DOI: 10.5061/dryad.75fh336/4
title: mitogenome_mapping_approach_result_files

description: This directory contains the NEXUS and XML files resulting from the mitogenome mapping approach. 
Consensus sequences for each of the 69 samples may be extracted from the NEXUS file, which was also used to generate the XML files, run TCS to produce haplotype networks, and run MrBayes to produce a phylogram. This NEXUS file includes the outgroup (Labeobarbus intermedius) which was removed for the MrBayes analysis. KwaZulu-Natal yellowfish and Orange-Vaal yellowfish samples were separated for the TCS analysis.
The XML files include three replicates of the run used to produce the Yule Process chronogram (Figure 6). These replicates were run to produce .log files which were assessed in Tracer. Tree output files were viewed independently using TreeAnnotator and FigTree, combined in LogCombiner and then reprocessed in TreeAnnotator and viewed in FigTree.
DOI: 10.5061/dryad.75fh336/5
title: nuclear_comparison_approach

description: This directory is split into two subfolders - one for KwaZulu-Natal yellowfish and one for Orange-Vaal yellowfish. The KwaZulu-Natal yellowfish dataset is made up of data from Read 1 fragments only, using the parameters -m 3 -M 3 -n 2 -r 0.8 --max_locus_stacks 7 --min_maf 0.03 --write_single_snp. The Orange-Vaal yellowfish dataset also uses only Read 1 fragments, and the parameters -m 3 -M 2 -n 1 -r 0.8 --max_locus_stacks 7 --min_maf 0.015 --write_single_snp.
Within each of these directories there are another two subfolders separating the nuclear runs filtering out and retaining mitochondrial SNPs (mtDNA_filtered or mtDNA_retained).
For more detailed information on the files contained in this directory, please refer to the README.
DOI: 10.5061/dryad.7d85g7b/1
title: FE SPSS complete data
DOI: 10.5061/dryad.80vd7q6/1
title: Derocles et al Data

description: Data collected from the field at Stockbridge Technology Centre, UK in 2013.
DOI: 10.5061/dryad.80vd7q6/2
title: Derocles et al Networks

description: Data collected in the field at Stockbridge Technology Centre, UK in 2013 to construct species-interaction networks.
DOI: 10.5061/dryad.80vd7q6/3
title: Derocles et al Yield

description: Yield data collected at Stockbridge Technology Centre, UK in 2013.