cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7d3v4/16
title: Pheidole wilsoni major worker (CASENT0184311)

description: Original scan files (dicom format) of Pheidole wilsoni major worker CASENT0184311
DOI: 10.5061/dryad.7d3v4/8
title: Pheidole knowlesi minor worker (CASENT0184016)

description: Original scan files (dicom format) of Pheidole knowlesi minor worker CASENT0184016
DOI: 10.5061/dryad.7d3v4/9
title: Pheidole knowlesi queen (CASENT0184086)

description: Original scan files (dicom format) of Pheidole knowlesi queen CASENT0184086
DOI: 10.5061/dryad.bg2s4/1
title: Data and Analysis Scripts for Ecological Trap Paper

description: Data and Analysis Scripts for Ecological Trap Paper.  Including R projs to ensure clear documentation of analyses.
DOI: 10.5061/dryad.bg684/1
title: Microsatellite genotype data for Allocasuarina humilis

description: Genotype data for 27 Allocasuarina humilis populations assayed for 8 microsatellite markers
DOI: 10.5061/dryad.bg684/2
title: Nexus file for Allocasuarina humilis cpDNA haplotype data

description: Dataset consists of 25 cpDNA haplotypes sampled from 27 populations of Allocasuarina humilis. Haplotypes were based on analysis of rpl32-trnL, trnQ-rps16 and trnG sequences. Haplotype names are consistent with those used in the Journal of Biogeography publication.
DOI: 10.5061/dryad.c1657/1
title: RhabdomysPumilio_Mark-Recapture

description: Partial data from 9 years of a monthly mark-recapture study of African striped mice (Rhabdomys pumilio) from the Succulent Karoo in South Africa (females with estimable age only).

Monthly mean values of three environmental factors: temperature, plant cover and mouse population density. 

More detailed information can be found in the ReadMe file.
DOI: 10.5061/dryad.d4m77/5
title: Churchill and Beluga Chick Growth Data 2009-2011

description: This file contains the data which can be used to calculate the growth rates of Hudsonian godwit, Limosa haemastica, chicks hatched at Beluga River, Alaska and Churchill, Manitoba from 2009-2011. The first column denotes the site at which the chick was hatched (BR = Beluga River, CH = Churchill); the second column the year in which they were hatched; the third column the date on which they were hatched; the fourth the date of the capture; the fifth their individually unique flag code, which can be linked to the chick data file; the sixth their mass (g) at the time of capture; the seventh their USGS or CWS band number; and the last column whether or not they were hatched from a renest (0 = first nest, 1 = renest).
DOI: 10.5061/dryad.df86m/1
title: ReadMe file for data files associated with the manuscript “Sperm morphology, ATP concentration and swimming velocity: unexpected relationships in a passerine bird”

description: This readme file describes the data files accompanying the above publication.
DOI: 10.5061/dryad.df86m/2
title: Experimental males summary data

description: This data file contains all the data collected from each experimental male. Data include semen characteristics (e.g. 		sperm measurements) and morphological data (e.g. body weight).
DOI: 10.5061/dryad.df86m/3
title: Microplate sample repeatability

description: This is the data file containing the data from experimental males used to test the repeatability of ATP content across triplicate wells. Descriptions of variables are included in the R code file “Sperm morphology, swimming velocity and ATP content.r”.
DOI: 10.5061/dryad.df86m/4
title: R script for analyses

description: This file provides the code for the analyses carried out in the manuscript.
DOI: 10.5061/dryad.f2n6f/2
title: Inputs/Outputs of each Surface Calculation run in VASP

description: For the convenience of the readers, we have included the relevant inputs of each surface calculation run using the Vienna Ab intio Simulation Package (VASP). The relevant outputs generated from these calculations have also been included in this file.
DOI: 10.5061/dryad.f6mb0/1
title: Random mating simulations

description: These R commands will perform simulations of the Chino, NC, and NY populations without selection. Commands are also given for plotting the simulation results, reproducing the figures in the manuscript.
DOI: 10.5061/dryad.f6mb0/2
title: Selection simulations with fitness assigned at the genotype level

description: This python script simulates a population with random  mating and selection. Fitness values are randomly assigned to each genotype. The script can be run in parallel on multiple processors, assigned on the command line. The script appends new simulation results to existing simulations that have the same jobID.
DOI: 10.5061/dryad.f6mb0/3
title: Simulations with selection coefficients assigned to alleles

description: This perl script runs simulations of populations with natural selection. Recursions are used to simulate a population with non-overlapping generations. Selection coefficients are randomly assigned to the III^M and Y^M chromosomes in males and females, and to the Md-tra^D allele in females. From these selection coefficients, genotype fitness values are calculated assuming additive interactions of the selection coefficients within and between loci.
DOI: 10.5061/dryad.f6mb0/4
title: Expected time to fixation

description: These R commands estimate the expected time to fixation of sex determining variants due to genetic drift, and also plot graphs to reproduce those published in the manuscript.
DOI: 10.5061/dryad.f6mb0/5
title: Initial genotype frequencies for simulations and analyses

description: These archive contains files needed to run simulations and analyses. Each file has genotype frequencies that are needed for some of the scripts in this Dryad submission.
DOI: 10.5061/dryad.f6mb0/7
title: Md-tra females vs Multi-M males

description: This table contains the frequency of multi-M males and Md-tra^D females from previously published results and data published in this paper.
DOI: 10.5061/dryad.h5vb2/1
title: Data for Dryad

description: This file contains two worksheet. One describes in detail all material collected during prey remains collections from on or below Verreaux's eagles nests in the Cederberg and the Sandveld. The second worksheet summaries all diet, breeding and landcover data used in the published analysis. Both worksheets include comments in column headers for further descriptions.
DOI: 10.5061/dryad.hj722/2
title: DryadDatabaseAccessionFinal

description: Contains sample data and genetic data, including identifiers, museum accession Nos (where applicable), location, date, mtDNA haplotype names (identifiable in Genbank), alleles at 13 microsatellite loci
DOI: 10.5061/dryad.j34hk/10
title: Fir seedlings height growth on CWD
DOI: 10.5061/dryad.j34hk/11
title: Spruce seedlings height growth on CWD
DOI: 10.5061/dryad.j34hk/7
title: Fir seedlings survival on CWD
DOI: 10.5061/dryad.j34hk/8
title: Spruce seedlings survival on CWD
DOI: 10.5061/dryad.j34hk/9
title: Beech seedlings height growth on CWD
DOI: 10.5061/dryad.k2f04/1
title: PhyML tree of the ABLIM family.

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the ABLIM family. ABLIM is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML implementation in the Seaview 4.5.3 program.
DOI: 10.5061/dryad.kp6n4/1
title: Run1

description: Compressed file containing: 1) Forward sequence file 2) Reverse sequence file 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associated.
DOI: 10.5061/dryad.kp6n4/2
title: Run2

description: Compressed file containing: 1) Forward sequence file 2) Reverse sequence file 3) File with experiment name, sample name and the tags, the forward primer and the reverse primer sequence associated.
DOI: 10.5061/dryad.n62p4/1
title: Nexus file of DNA sequence alignments for mtDNA control region without nine positions with signs of homoplasy
DOI: 10.5061/dryad.n62p4/2
title: Nexus file of DNA sequence alignments for ATPase 6 and 8
DOI: 10.5061/dryad.n62p4/3
title: Nexus file of DNA sequence alignments for phased alleles of the intron 5 of the TGFB2
DOI: 10.5061/dryad.vn52f/1
title: canidae_traceLogs_ALL_v2

description: Trace plots of key variables for all 60 analyses.
DOI: 10.5061/dryad.vn52f/2
title: canidae_treeLogs_ALL_v2

description: Plots of the MCC trees for all 60 analyses.
DOI: 10.5061/dryad.vn52f/3
title: expert_vs_estimated_node_ages

description: Linear regressions showing the correlation between the expert tree and estimated node ages, for nodes shared between the expert tree and estimated trees. Caveats for these regressions are discussed in Supplemental Text.
DOI: 10.5061/dryad.vn52f/4
title: Canidae_expert

description: The "expert" tree, derived from digitization of the phylogenies of Canidae published in the monographs of Wang and Tedford, using TreeRogue.
DOI: 10.5061/dryad.0c42k/1
title: Dataset for finalized Arctic Grayling MS_Cutting et al. 2016

description: The excel table contains all the data used in the manuscript by Cutting et al. (2016) titled, "Seasonal Change in Trophic Niche of Adfluvial Arctic Grayling (Thymallus arcticus) and Coexisting Fishes in a High-elevation Lake System". Data are separated by individual spread sheets names. Individuals sheets can be used to reproduce all figures and analyses.
DOI: 10.5061/dryad.11rn5/1
title: Figure 1

description: Phylogenetic trees of SaV and NoV(GI, GII) based on dependent RNA polymerase●: diarrhea cases over five years;       ○: controls over five years;▲: diarrhea cases under five years;     △: controls under five years; The contents in brackets is that the number of same genotypeThe molecular analysis of SaV and NoV (GI, GII) among diarrhea cases and healthy controls in this study, NoV GII was the major pathogen and GII.4 was the most predominant strain detected in diarrhea patients, novel GII.17 variant was emergence in diarrhea cases.
DOI: 10.5061/dryad.11rn5/2
title: Phylogenetic trees of SaV and NoV(GI, GII)

description: The representative gene sequences
DOI: 10.5061/dryad.15m0d/1
title: newalldata_corrected
DOI: 10.5061/dryad.326r8/47
title: Assembled scaffolds for Polymixia japonica
DOI: 10.5061/dryad.326r8/48
title: Assembled unitigs for Polymixia japonica
DOI: 10.5061/dryad.326r8/49
title: Assembled scaffolds for Percopsis transmontana
DOI: 10.5061/dryad.326r8/50
title: Assembled unitigs for Percopsis transmontana
DOI: 10.5061/dryad.326r8/51
title: Assembled scaffolds for Typhlichthys subterraneus
DOI: 10.5061/dryad.326r8/52
title: Assembled unitigs for Typhlichthys subterraneus
DOI: 10.5061/dryad.326r8/53
title: Assembled scaffolds for Zeus faber
DOI: 10.5061/dryad.326r8/54
title: Assembled unitigs for Zeus faber
DOI: 10.5061/dryad.326r8/55
title: Assembled scaffolds for Cyttopsis roseus
DOI: 10.5061/dryad.37hb7/1
title: PlosOne_capteur_cleaned

description: Cleaned database of included patients, with the time-intensity curve parameters obtained by the bolus tracking of computed tomography angiography (CTA) in pulmonary embolism and ventricular ratios
DOI: 10.5061/dryad.7d3v4/17
title: Pheidole wilsoni minor worker (CASENT0184378)

description: Original scan files (dicom format) of Pheidole wilsoni minor worker CASENT0184378
DOI: 10.5061/dryad.7d3v4/18
title: Pheidole wilsoni queen (CASENT0184003)

description: Original scan files (dicom format) of Pheidole wilsoni queen CASENT0184003
DOI: 10.5061/dryad.b3f33/1
title: Steel Creek survey - Heteroptera

description: This dataset includes records for Heteroptera collected near Steel Creek campground along the Buffalo Nation River in Newton County, Arkansas.  The dataset uses DarwinCore standard column headings, which are explained in the ReadMe file.
DOI: 10.5061/dryad.dm437.2
title: Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken
DOI: 10.5061/dryad.dm437.2/1.2
title: Read Me file for the immune response data file

description: Describes variables and models used to test the relationship between immune assays and genetic variation
DOI: 10.5061/dryad.dm437.2/10.2
title: MHC_II_counts_per_indiv

description: Summary of the alleles and reads for each individual at MHC class II
DOI: 10.5061/dryad.dm437.2/2.2
title: APC_immune_response_for_Dryad

description: Immune response and genetic data for 144 birds. For an explanation see  "Read Me File for immune response data file"
DOI: 10.5061/dryad.dm437.2/3.2
title: R code for APC survival analyses

description: R scripts to analyze survival of prairie-chickens (Table 2 in manuscript)
DOI: 10.5061/dryad.dm437.2/4.2
title: APCcoxme input (n=116)

description: Input data file for analysis of survival (using the R scripts in the file "R code for APC survival analyses.txt")
DOI: 10.5061/dryad.dm437.2/6.2
title: Johnson_2787X

description: FASTA file of reads from first 454 pyrosequencing run
DOI: 10.5061/dryad.dm437.2/7.2
title: Johnson_2821X

description: FASTA file of reads from second run of 454 pyrosequencing
DOI: 10.5061/dryad.dm437.2/8.2
title: Barcode key for raw 454 reads

description: Excel file with key to Barcodes of individuals in the 454 pyrosequencing files
DOI: 10.5061/dryad.fp0b8/1
title: Phenotype_scores

description: Values of mouth bending angle measured in each individual, and samples used to prepare the ddRAD and Poolseq library respectively
DOI: 10.5061/dryad.gd3qh/1
title: Greenhouse experiment: trait variation in response to past and present shading

description: This file contains data taken from the greenhouse experiment described in Heger (2016). Different source populations of Erodium cicutarium have been planted under three types of light filters: no shading, homogeneous shading and heterogeneous shading. Headers are explained in the second sheet (glossary).
DOI: 10.5061/dryad.jq07s/1
title: Weis PLOS ONE 2016 Data

description: These data were collected from a microcosm experiment conducted at Yale University in April 2013.  The data are presented in a Microsoft Excel format with four worksheets; one metadata worksheet and three data worksheets.  The main data worksheet includes count data across sampling dates for phytoplankton and zooplankton and the final biovolume and biomass density estimates used in the published report.  The other two data worksheets contain the raw data on individual phytoplankter and zooplankter linear measurements used to calculate average biovolume and biomass.
DOI: 10.5061/dryad.k2f04/10
title: Amino acid sequence alignment of the AFAP family

description: Amino acid sequence alignment of the AFAP family which is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program.
DOI: 10.5061/dryad.k2f04/2
title: PhyML tree of the AFAP family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the AFAP family. AFAP is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/3
title: PhyML tree of the DPYS family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the DPYS family. DPYS is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/4
title: PhyML tree of the JAKMIP family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the JAKMIP family. JAKMIP is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML implementation in the Seaview 4.5.3 program.
DOI: 10.5061/dryad.k2f04/5
title: PhyML tree of the PPP2R2 family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the PPP2R2 family. PPP2R2 is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/6
title: PhyML tree of the SH3TC family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the SH3TC family. SH3TC is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/7
title: PhyML tree of the STK32 family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the STK32 family. STK32 is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/8
title: PhyML tree of the TBC1D family

description: Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the TBC1D family. TBC1D is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).
DOI: 10.5061/dryad.k2f04/9
title: Amino acid sequence alignment of the ABLIM family

description: Amino acid sequence alignment of the ABLIM family which is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program.
DOI: 10.5061/dryad.kr3c9/1
title: Phylogenetic tree

description: Figure. 1 Phylogenetic tree of G. duodenalis based on nucleotide sequences of the tpi gene (a) and gdh gene (b). Trees were constructed using the neighbor-joining method based on genetic distance calculated by the Kimura 2-parameter model, implemented in MEGA version 5.2. Bootstrap values &gt; 50 % from 1,000 replicates is shown on nodes. Reference sequences from the major G. duodenalis sub-assemblages are written by blue color in bold. Isolates showed known and novel sequences obtained from this study are marked by rectangles (blue) and triangles (red), respectively.
DOI: 10.5061/dryad.r1n2r/1
title: zipped datafiles

description: One folder with a .mat data file for each movie
DOI: 10.5061/dryad.rd66f/1
title: Time spent at home

description: Each row corresponds to a retrospective interview (interview_id) of a study participant (part_code) who provided information about time spent at home. Information about time spent at home was summarized as the daily frequency of bouts of time spent at home (freqHome) and the average fraction of the day between 5:00 AM and 10:00 PM spent at home (durnHome). Individuals are stratified by their demographic category (category) and fever status (pathogen).
DOI: 10.5061/dryad.rd66f/2
title: Time spent at locations other than home

description: Each row corresponds to information from a retrospective interview (interview_id) of a study participant (part_code) who provided information about time spent at a location other than home. Information about time spent at each location was summarized as the daily frequency of visits to that location (absolute_frequency) and the average fraction of the day between 5:00 AM and 10:00 PM spent at that location (absolute_duration). Individuals are stratified by their demographic category (category) and fever status (pathogen). Locations are classified by their landuse designation (landuse_class).
DOI: 10.5061/dryad.s2df3.2
title: Data from: Evolutionary prediction of medicinal properties in the genus Euphorbia L.
DOI: 10.5061/dryad.s2df3.2/1.2
title: Alignment file

description: Aligned DNA sequence from plastid marker ndhF. The matrix includes sequences (1789 base pairs) of 560 Euphorbia species retrieved from GenBank.
DOI: 10.5061/dryad.s700k/1
title: Data for study 1a-b, 2a-c, & 3a-b

description: Each dataset in the zip file is named after each study respectively.
DOI: 10.5061/dryad.tt12g/1
title: List of miR156b,c,d sequences cloned by miR-RACE

description: This file contained the three sequences of mature miR156b,c,d  cloned by miR-RACE,  these three seqeunces were same, and their size is 20 bp.
DOI: 10.5061/dryad.v26gh/2
title: Microsatellite genotype data for queens, kings, neotenics, workers, soldiers, alates and nymphs of the termite Cavitermes tuberosus

description: Microsatellite genotype data for queens, kings, neotenics, workers, soldiers, alates and nymphs. Qi (and respectively Ki) indicate that the genotype of the primary queen (respectively primary king) was inferred from nestmate individuals and the collected primary king (respectively primary queen). Qii and Kii indicate that genotypes of both primary reproductives were inferred from nestmate individuals. Inferences were obtained using the maximum likelihood method implemented in the program Colony 2.0.5. f and m indicate female and male individuals, respectively.
DOI: 10.5061/dryad.vn52f/5
title: Table_S2_TipDate_runs_v3

description: Summary of all 60 variant analyses (contains Supplemental Table S2, and some associated notes and file locations).
DOI: 10.5061/dryad.vn52f/6
title: Matzke_Wright_SuppData1

description: A zipfile of all inputs, outputs, and scripts for allanalyses. (pt 1/3)
DOI: 10.5061/dryad.vn52f/7
title: Matzke_Wright_SuppData2

description: A zipfile of all inputs, outputs, and scripts for allanalyses. (pt 2/3)
DOI: 10.5061/dryad.vn52f/8
title: Matzke_Wright_SuppData3

description: A zipfile of all inputs, outputs, and scripts for allanalyses. (pt 3/3)
DOI: 10.5061/dryad.2b2b5/1
title: Filgueiras et al 2016

description: Data pertaining to Filgueiras et al 2016 in PLOS ONE.
DOI: 10.5061/dryad.326r8/56
title: Assembled unitigs for Cyttopsis roseus
DOI: 10.5061/dryad.326r8/57
title: Assembled scaffolds for Lamprogrammus exutus
DOI: 10.5061/dryad.326r8/58
title: Assembled unitigs for Lamprogrammus exutus
DOI: 10.5061/dryad.326r8/59
title: Assembled scaffolds for Brotula barbata
DOI: 10.5061/dryad.326r8/60
title: Assembled unitigs for Brotula barbata
DOI: 10.5061/dryad.326r8/61
title: Assembled scaffolds for Carapus acus
DOI: 10.5061/dryad.326r8/62
title: Assembled unitigs for Carapus acus
DOI: 10.5061/dryad.326r8/63
title: Assembled scaffolds for Myripristis jacobus
DOI: 10.5061/dryad.326r8/64
title: Assembled unitigs for Myripristis jacobus
DOI: 10.5061/dryad.3g02j/1
title: SSR alleles at 23 loci for 280 tea accessions from 8 countries in Africa. Missing data points are denoted by a zero ("0")

description: The Excel file has 49 columns; the first three columns show the serial number, sample ID, and country of origin respectively while the rest 46 columns depict the 23 SSR loci. Missing data points are denoted by "0".
DOI: 10.5061/dryad.3k8g5/1
title: Simulated genotypes

description: Simulated genotypes based on haplotypes of 85 Caucasian individuals from the 1,000 Genome Project. Only SNPs with known positions within a 0.1M region of each of the first 5 chromosomes were used for simulations.
DOI: 10.5061/dryad.46tp6/1
title: Hutto 2016_Ecological Applications_data for Figures 2 and 3

description: Black-backed Woodpecker detection information from 7903 individual point count surveys conducted across western Montana.  File includes abundance, fire severity surrounding the point, and distance information (if a bird was detected).
DOI: 10.5061/dryad.475t2/1
title: Satler&Carstens2016