cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.26p87/1
title: dataset for Klemme & Karvonen 2016

description: Complete dataset for study by Klemme & Karvonen, including fish morphometric data, results from repeated personality tests and from repeated avoidance learning tests as well as parasite numbers acquired before the behavioural tests, during the behavioural tests and during a resistance test.
DOI: 10.5061/dryad.3kf74/1
title: Chironomus_dryweight_raw

description: Dry weight data for deployed Chironomus tepperi
DOI: 10.5061/dryad.3kf74/2
title: cyst_metab_LC data

description: Concentrations of amine containing metabolites involved in the cysteine metabolism of Chironomus tepperi deployed in microcosms. Detected by LCMS
DOI: 10.5061/dryad.3kf74/3
title: other_LC_metab_data

description: Concentrations of amine containing metabolites not involved in the cysteine metabolism of Chironomus tepperi deployed in microcosms. Detected by LCMS
DOI: 10.5061/dryad.3kf74/4
title: Gene expression data

description: Gene expression data of the cysteine metabolism of Chironomus tepperi deployed in microcosms
DOI: 10.5061/dryad.3kf74/5
title: Microcosm abundance data

description: Species and abundance from copper spiked microcosms
DOI: 10.5061/dryad.3kf74/6
title: Physa_raw_data

description: Survival and reproduction data of Physella acuta exposed in copper spiked microcosms
DOI: 10.5061/dryad.3kf74/7
title: Potamopyrgus data

description: Survival and reproduction data of Potamopyrgus antipodarum exposed in copper spiked microcosms
DOI: 10.5061/dryad.5gv12/1
title: Microsatellite genotypes of canyon live oak

description: Collecting localities of all individuals sampled and genotypes at 13 microsatellite loci. Asterisk (*): population excluded from analysis due to insufficient sample size; dagger (†): individual excluded from analysis due to incomplete data (&lt; 10 successfully genotyped microsatellite loci).
DOI: 10.5061/dryad.5gv12/2
title: Occurrence records of canyon live oak

description: Latitude and longitude of occurrence records used to construct ecological niche models. Citations for database sources and methods for filtering occurrence records prior to use are described in the Supplementary Methods.
DOI: 10.5061/dryad.80dc6/1
title: Data record 1

description: Data sheet containing the sex ratio at birth of 104 litters.
DOI: 10.5061/dryad.80dc6/2
title: Data record 2

description: Data sheet containing the details of 95 mother-litter groups who were followed up to their 7th month of age.
DOI: 10.5061/dryad.8v234/1
title: Pseudomonasdensitydata
DOI: 10.5061/dryad.8v234/2
title: Totalbacterialdensitydata
DOI: 10.5061/dryad.8v234/3
title: Phagedensitydata
DOI: 10.5061/dryad.8v234/4
title: Fitnessdata
DOI: 10.5061/dryad.91g52/1
title: RosinPoulsen_SeedFateGabon

description: Seed fate experimental data, collected as described in the paper's Methods section.
DOI: 10.5061/dryad.92h5d/1
title: Tensor data

description: MATLAB data structure containing all analyzed data.
DOI: 10.5061/dryad.cd546/86
title: Mitochondrial tree, upper 50% of taxa in terms of coverage
DOI: 10.5061/dryad.cd546/87
title: RAxML nuclear partition file, by gene
DOI: 10.5061/dryad.cd546/88
title: RAxML nuclear partition file, by splice site
DOI: 10.5061/dryad.cd546/89
title: RAxML chloroplast partition file, coding vs. non-coding
DOI: 10.5061/dryad.cd546/90
title: RAxML chloroplast partition file, Sanger loci, by gene
DOI: 10.5061/dryad.cd546/91
title: RAxML mitochondrial partition file, coding vs. non-coding
DOI: 10.5061/dryad.cd546/92
title: ASTRAL tree
DOI: 10.5061/dryad.cd546/93
title: SVDquartets tree
DOI: 10.5061/dryad.cg35k/2
title: Drosophila_PRG_double_FISH_data

description: This archive contains 648 double channel TIFF images of wild-type Drosophila embryos that have undergone fluorescent in situ hybridisation for 32 pairwise combinations of pair-rule gene and segment-polarity gene transcripts. Most embryos are between mid-stage 5 and early stage 7. Images are 1024x1024 pixels, and were collected on a Leica SP5 confocal microscope. The unpacked archive is 5.15 GB.
DOI: 10.5061/dryad.cm08m/6
title: HDplot_simulation

description: R code to simulate data for HDplot.  This code also runs HDplot internally and produces plots showing expected distributions based on simulation parameters.  Simulation parameters include the number of singleton, duplicate, and diverged duplicate loci, the total population size, the sampled population size, average read depth per locus, statistical distribution of reads per locus to sample from and distribution of reads per allele to sample from.
DOI: 10.5061/dryad.cm08m/7
title: Chinook_sequenceReads

description: Chinook salmon dataset processed with HDplot in this manuscript.  File is in the .vcf format output by the Stacks genotyping program.
DOI: 10.5061/dryad.cm08m/8
title: Barberry_sequenceReads

description: Mountain Barberry dataset processed with HDplot in this manuscript.  File is in the .vcf format output by the Stacks genotyping program.
DOI: 10.5061/dryad.cm08m/9
title: Parrotfish_sequenceReads

description: Dusky Parrotfish dataset processed with HDplot in this manuscript.  File is in the .vcf format output by the Stacks genotyping program.
DOI: 10.5061/dryad.d7j73/1
title: Cooling data, nest temperatures and body mass for blue tit nestlings

description: Data on cooling rate, nest temperature, body mass and validation of thermal imaging measurements/cloacal measurements from field experiments on blue tit nestlings. Explanations of all variables are provided in the sheet named "Metadata".
DOI: 10.5061/dryad.fb240/1
title: source data 1

description: Effect Size/Correlation Coefficients and p-values for CFS patch-patch interactions
DOI: 10.5061/dryad.fg65j/1
title: Data from: Clinical and metabolic characteristics among Mexican children with different types of diabetes mellitus

description: Characteristics of patients from study: Clinical and metabolic characteristics among Mexican children with different types of diabetes mellitus
DOI: 10.5061/dryad.fp505/1
title: Data supporting the paper

description: Data1 is a dataframe with 7 variables: 1) id = female identity, 2) RS = annual reproductive success of females aged 7 years and over (0 = failed, 1 = success), 3) year, 4) ROSutero =  rain on-snow events experienced in utero (0 = high, 1 = low), 5) alo = age at last observation, 6) ROScurrent = rain-on-snow experienced in current year, 7) age.                                                                                 Data2 is a dataframe with 7 variables: 1) id = female identity, 2) RS = annual reproductive success of females aged 2-6 years (0 = failed, 1 = success), 3) year, 4) ROSutero =  rain on-snow events experienced in utero (0 = high, 1 = low), 5) alo = age at last observation  between 2 and 6 years, 6) ROScurrent = rain-on-snow experienced in current year, 7) age .Data3 is a dataframe with 5 variables: 1) id = female identity, 2) year, 3) preg = annual pregnancy probability of females aged 2-6 years, 4) ROSutero = rain on-snow events experienced in utero (0 = high, 1 = low), 5) BM = body mass.All continuous variables have been centered and divided by two standard deviations.
DOI: 10.5061/dryad.gf246/1
title: 46vsTD_fastq

description: Raw FASTQ files for COI marker PCR-amplified using either the published touchdown (TD) or a single annealing temperature (46) thermal cycling protocol.
DOI: 10.5061/dryad.gf246/2
title: Cop16S_fastq

description: Raw FASTQ files for Storm Bay zooplankton assemblages amplified with the Cop16S marker.
DOI: 10.5061/dryad.gf246/3
title: Uni18S_fastq

description: Raw FASTQ files for Storm Bay zooplankton assemblages amplified with the Uni18S marker.
DOI: 10.5061/dryad.gf246/4
title: LerayCOI_fastq

description: Raw FASTQ files for Storm Bay zooplankton assemblages amplified with the Uni18S marker.
DOI: 10.5061/dryad.gf246/5
title: OTU_tables

description: OTU tables for Storm Bay zooplankton assemblages amplified using three metabarcoding markers (mitochondrial COI, 16S, and nuclear 18S), and the comparison of the COI marker using two different thermal cycling protocols.
DOI: 10.5061/dryad.hj5m4/1
title: Mathur_Schmidt_rawdata

description: This is all of the phenotypic information and data analyzed in the paper.
DOI: 10.5061/dryad.hv6gf/1
title: Agent-Based Model data

description: Simulation data for figures in the article.
DOI: 10.5061/dryad.mb0sh/1
title: Epiphyte community data from East Anglian productive orchards

description: The file contains presence and absence data for epiphytic bryophytes surveyed from five productive East Anglian orchards between 2005-2009
DOI: 10.5061/dryad.n21f4/9
title: Sample and sequence data information for Sicyopterus stimpsoni

description: Excel file including sample data information for the 818 cytochrome-b sequences (612bp) of Sicyopterus stimpsoni from Hawaii analyzed in Alda et al. Sample ID, Year of collection, Watershed, Islands, Hawaiian Division of Aquatic Resources (DAR) Code, Sequence name.
DOI: 10.5061/dryad.ng3bv/1
title: chal_empirical_data

description: Empirical SNP dataset for Carex chalciolepis. These data were used to create summary statistics in arlsumstat for comparison with modeled data in the ABC procedure. They also informed the sampling of the modeled data across the landscape (so that the modeled data had the same pattern of missing data as the empirical data). This file can be viewed and manipulated in a text editor or Excel. It was generated by converting a vcf output file from the populations program in Stacks using PGDSpider.
DOI: 10.5061/dryad.ng3bv/2
title: nova_empirical_data

description: Empirical SNP dataset for Carex nova. These data were used to create summary statistics in arlsumstat for comparison with modeled data in the ABC procedure. They also informed the sampling of the modeled data across the landscape (so that the modeled data had the same pattern of missing data as the empirical data). This file can be viewed and manipulated in a text editor or Excel. It was generated by converting a vcf output file from the populations program in Stacks using PGDSpider.
DOI: 10.5061/dryad.ng3bv/3
title: changeArpAfterSim

description: This python script is integrated into the modeling simulations (see 'chalciolepis_ABCsampler_input_file'). After each coalescent simulation in Splatch, this script changes the resulting modeled dataset to have the same pattern of missing data as the empirical data. A companion file is needed for the script to work properly (see 'chal_missing_example'). The script can be viewed and modified in a text editor and was created by myself and members of the Knowles lab.
DOI: 10.5061/dryad.ng3bv/4
title: chal_missing_example

description: This is an example file that describes the pattern of missing data in an empirical dataset ('chal_empirical_data'). The file is utilized by the changeArpAfterSim.py script (see script in this data archive) to create modeled datasets with the same pattern of missing data as the empirical datasets. The file can be viewed in a text editor.
DOI: 10.5061/dryad.ng3bv/5
title: create_mask

description: This is an R script that creates a text file describing the pattern of missing data in an empirical dataset (see example mask file 'chal_missing_example' created from 'chal_empirical_data'). The resulting mask file is used by the changeArpAfterSim script to change modeled datasets into modeled datasets with the same pattern of missing data as the empirical data. This script was generated by and modified by myself and members of the Knowles lab.
DOI: 10.5061/dryad.ng3bv/6
title: chalciolepis_parameters_example

description: This file defines the parameters and the prior ranges/distributions from which values are pulled to update the simulations at the beginning of every Splatche simulation. See the ABCSampler documentation for more information about file format and options. The file can be viewed and modified in a text editor. The file is defined in the ABCSampler input file (see 'chalciolepis_ABCsampler_input_file').
DOI: 10.5061/dryad.ng3bv/7
title: chalciolepis_ABCsampler_input_file

description: This is an example of an input file used by the ABCsampler program. It defines the values that need to be updated at every new iteration (in capital letters - taken from the parameter file 'chalciolepis_parameters_file'), as well as the programs that need to be run (and the order in which those programs are executed). This file can be viewed and modified in a text editor. See the ABCSampler documentation for detailed information about the structure and options for this file.
DOI: 10.5061/dryad.q802m/1
title: Data record 3

description: Data sheet containing the details of 148 dens.
DOI: 10.5061/dryad.q802m/2
title: Data record 4

description: Data sheet containing the details of 20 pregnant females.
DOI: 10.5061/dryad.ss7d6/1
title: ESM4_scripts

description: R and python scripts
DOI: 10.5061/dryad.t951d/12
title: scripts: converting GBS reads to genotypes

description: This text file contains scripts and notes for the steps used in converting raw Illumina GBS sequencing reads to individual genotypes (at both variant and invariant sites) across the genome. The resulting genotype files (in "012NA" format) were then used as input into R, for the rest of the analysis and production of figures.
DOI: 10.5061/dryad.18j1h.1
title: Data from: Variation of anal fin egg-spots along an environmental gradient in a haplochromine cichlid fish
DOI: 10.5061/dryad.1n542/3
title: TEM images

description: zipped archive of TEM images of nanogold-antibody labelling of FLAG-tagged PykF at different time points
DOI: 10.5061/dryad.2973n/1
title: Egg-to-adult development time

description: Eclosion timing for males and females from all evolved populations in the egg-to-adult development assay
DOI: 10.5061/dryad.2973n/2
title: Dry mass

description: Dry mass of flies from evolved populations
DOI: 10.5061/dryad.319sr/1
title: Additional file 1 Table S1

description: Additional file 1: Table S1. The 162 accessions of Daucus, and two accessionsof related genera characterized in this study, improvement status, localityinformation and new identification.
DOI: 10.5061/dryad.319sr/2
title: Additional file 2 Table S2

description: Additional file 2: Table S2. Summary of processing GBS data of Daucus.
DOI: 10.5061/dryad.319sr/3
title: Additional file 3 Figure S1

description: Additional file 3: Figure S1. Phylogenomics of Daucus from a maximum
likelihood analysis using 164 accessions and 10,814 SNPs (10% missing imputed
genotypes) obtained by GBS. Numbers above branches represent bootstrap values,
with only values higher than 70% shown. Names given to clades refer to the
geographic origin and improvement status of the accessions of D. carota
complex. Clades A and B corresponds to the two main groups of the Daucus
phylogeny.
DOI: 10.5061/dryad.319sr/4
title: Additional file 4 Figure S2

description: Additional file 4: Figure S2. Phylogenomics of Daucus from a maximum
likelihood analysis using 164 accessions and 38,920 SNPs (30% missing imputed
genotypes) obtained by GBS. Numbers above branches represent bootstrap values,
with only values higher than 70% shown. Names given to clades refer to the
geographic origin and improvement status of the accessions of D. carota
complex. Clades A and B corresponds to the two main groups of the Daucus
phylogeny.
DOI: 10.5061/dryad.319sr/5
title: Additional file 5 Figure S3

description: Additional file 5: Figure S3. Maximum likelihood reconstruction and structure
of the genetic diversity of 144 accessions of Daucus carota complex and
outgroup using 43,713 SNPs (30% missing imputed genotypes) obtained by GBS.
Each accession is represented by a horizontal bar, and each color corresponds
to a population (nine in total). Numbers above branches represent bootstrap
values, with only values higher than 70% shown. Names given to clades refer
to the geographic origin and improvement status of the accessions of D.
carota complex. The outgroup taxon is D. syrticus.
DOI: 10.5061/dryad.319sr/6
title: Additional file 6 Figure S4

description: Additional file 6: Figure S4. Bayesian phylogenetic tree of 144 accessions of
Daucus carota complex and outgroup using 18,565 SNPs (10% missing imputed
genotypes) obtained by GBS. Numbers above the branches represent posterior
probabilities, with only values higher than 0.7 shown. Names given to clades
refer to the geographic origin and improvement status of the accessions of
the D. carota complex. The outgroup taxon is D. syrticus.
DOI: 10.5061/dryad.319sr/7
title: Additional file 7 Figure S5

description: Additional file 7: Figure S5. Relationships among 144 accessions of Daucus
carota complex and outgroup from an exhaustive quartet sampling inference
using 18,565 SNPs (10% missing imputed genotypes) obtained by GBS. Numbers
above the branches represent bootstrap values, with only values higher than
70% shown. Names given to clades refer to the geographic origin and
improvement status of the accessions of D. carota complex. ME & E refers to Middle East & Europe. Accessions designated by double stars are misplaced
relative to the maximum likelihood topology of Daucus carota complex using
the same number of SNPs. The outgroup taxon is D. syrticus.
DOI: 10.5061/dryad.4nc28/1
title: Phenotypic data

description: Data on mortality and fecundity
DOI: 10.5061/dryad.4nc28/2
title: SNP data files

description: Data from single nucleotide polymorphism (SNP) analysis
DOI: 10.5061/dryad.4nc28/3
title: TE data files

description: Data from transposable element (TE) insertion
DOI: 10.5061/dryad.4nc28/4
title: SV data files

description: Data from structural variant (SV) analysis
DOI: 10.5061/dryad.519qs/1
title: datasets
DOI: 10.5061/dryad.56cg8/1
title: Geosmithia sp_16_multigene dataset

description: Multigene sequence dataset of Geosmithia sp. 16 species complex (ITS+RPB2+TEF1a+TUB2)
DOI: 10.5061/dryad.56cg8/2
title: Geosmithia langdonii and sp. 26 complex, multigene

description: Multigene sequence dataset of Geosmithia langdonii and Geosmithia sp. 26 species complex (TEF1a+RPB2+TUB2)
DOI: 10.5061/dryad.56cg8/3
title: Geosmithia_pallida_complex_multigene

description: Multigene DNA sequence dataset of Geosmithia pallida species complex (TEF1a+RPB2+TUB2)
DOI: 10.5061/dryad.56cg8/4
title: ITS rDNA of Geosmithia

description: Alignment of ITS rDNA sequences of Geosmithia (excluding Geosmithia sp. 26 species complex)
DOI: 10.5061/dryad.56cg8/5
title: ITS rDNA, Geosmithia sp. 26 species complex

description: ITS rDNA alignment of Geosmithia sp. 26 species complex
DOI: 10.5061/dryad.5gv12/3
title: Custom Python scripts for iDDC models

description: Python scripts used to generate customized input files for demographic and genetic simulations (see Materials and Methods for complete details). Descriptions of each script are provided in the ReadMe file. Scripts are slightly modified from original code written by Qixin He at the University of Michigan (current address: University of Chicago), provided here with permission.
DOI: 10.5061/dryad.83fr7/1
title: Zjujuba.junzao.genome.chr.annotation

description: Zjujuba.junzao.annotation.gff3 file       Generic Feature Format Version 3 (GFF3) format of RNA products annotated on the genome.Zjujuba.junzao.pep.fa file       FASTA format of the accessioned protein products annotated on the genome assembly.Zjujuba.junzao.cds.fa file       FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly.Zj.jz.final.annotation.txt file       Tab-delimited text file reporting values for different aspects of the annotation data.
DOI: 10.5061/dryad.875n5/1
title: FASTA mtDNA alignment, 12,248 bp assembly of resequencing data from heliothine species

description: Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (&gt;95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen). Nextera libraries were produced following the manufacturer’s instructions and sequence was generated as 100 bp PE reads (Illumina HiSeq 2000, Biological Resources Facility, Australian National University, Canberra, Australia, as well as at Beijing Genomics Institute, Hong Kong). Sample and sequencing data are included in the supplementary material (Table S2). Raw sequence reads obtained from whole genome sequencing were aligned to the H. armigera mitochondrial genome using BBMap v. 33.43 (http://sourceforge.net/projects/bbmap/), permitting a minimum identity of 0.6 and allowing for a minimum quality threshold equivalent to Q10 over two consecutive bases before reads were trimmed. Reads were assembled using mira v. 4 (Chevreux et al. 2004) before mitobim v. 1.7 (Hahn et al. 2013) was used to iteratively map and assemble whole mitochondrial sequences. Heterozygous bases were removed, sequences were aligned using MAFFT v. 7.017 (Katoh 2002) and sequences were trimmed using the Gblocks v. 0.91b online server (http://molevol.cmima.csic.es/castresana/Gblocks_server.html) (Talavera & Castresana 2007).
DOI: 10.5061/dryad.875n5/2
title: SNP data in plink bed format from GBS analysis of Helicoverpa armigera, H. zea and H. punctigera

description: Heliothine moths were collected between 2004 and 2014 from 16 different countries around the world across various climatic zones and altitudes (Tables S1 and S2), many of which are described in Behere et al. (2007); and Tay et al. (2013). Samples were collected as larvae from wild and crop host plants, as adult moths via light/pheromone traps, or as larvae after bioassay, and preserved in ethanol (&gt;95%) or RNAlater, or stored at -20°C prior to DNA extraction. DNA was extracted from samples using DNeasy blood and tissue kits (Qiagen), before being quantified with a Qubit 2.0.GBS library preparation and sequencing was performed by the Genomic Diversity Facility, Cornell University, NY, USA. Information regarding the samples used and sequencing output is recorded in the supplementary material (Table S1). Briefly, 50 ng of gDNA was digested using PstI, before library construction as in Elshire et al. (2011) and sequencing using an Illumina Hiseq. A negative control was included with each plate. Raw data were assessed for quality and processed using Stacks v. 1.30 (Catchen et al. 2013b). Briefly, process_radtags was used to demultiplex samples, trim to 90 bp and assess the quality of reads before being forwarded to denovo_map, which was run using default settings. The Populations module was then run, limiting the output to loci existing in at least 5% of samples from each sampling location, with at least 5x coverage. The Populations module was used to output SNP data in Plink format.
DOI: 10.5061/dryad.9fc86/1
title: BRCA1_MC_T

description: Alignment of 76 sequences from Cabrera vole tissue samples of the autossomal BRCA1 gene, exon 11.
DOI: 10.5061/dryad.9fc86/2
title: COPS7_MC_T

description: Alignment of 77 sequences from Cabrera vole tissue samples of the autossomal COPS7A gene, intron 4.
DOI: 10.5061/dryad.9fc86/3
title: CYTB_MC_TNI

description: Alignment of 284 sequences of Cabrera vole tissue samples and bones (from owl pellets) for the mitochondrial cyt-b gene.
DOI: 10.5061/dryad.9fc86/4
title: DBX5_MC_T

description: Alignment of 79 sequences of Cabrera vole tissue samples for the sex-linked (X-chromossome) DBX gene, intron 5.
DOI: 10.5061/dryad.9fc86/5
title: DBX7_MC_T

description: Alignment of 79 sequences of Cabrera vole tissue samples for the sex-linked (X-chromossome) DBX gene intron 7. There are two individuals with heterozygous indels, thus for those we provide phased sequences which are identified as "code" and "code+ii".