cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4n28n/1
title: Helianthus chloroplast

description: This file contains the aligned 96789bp chloroplast sequences from 103 accessions across 37 diploid Helianthus species/subspecies and the outgroup Phoebanthus tenuifolius.
DOI: 10.5061/dryad.4n28n/2
title: Chloroplast_tree

description: The cholorplast tree in newick format containing 103 accessions.
DOI: 10.5061/dryad.4n28n/3
title: Helianthus_Species_branchlengths

description: This is the file that contains the branch lengths as estimated with RAxML and using the MP-EST topology for the diploid Helianthus species.
DOI: 10.5061/dryad.4n28n/4
title: Helianthus_population_branchlengths

description: This file contains the population level tree with branch lengths estimated by RAxML with the fixed MP-EST topology for the diploid Helianthus species.
DOI: 10.5061/dryad.4n28n/5
title: MPEST_Speciestree

description: The MP-EST species tree in newick format for 103 accessions estimated from 170 genes.
DOI: 10.5061/dryad.4n28n/6
title: MPEST_population

description: The MP-EST population level tree estimated using 170 genes across 103 accessions.
DOI: 10.5061/dryad.5ms6t/1
title: Bruder et al_2015_FE_rawdata

description: Rawdata used in the publication: litter mass remaining, decomposition rates, litter toughness, fungal biomass, shredder biomass, fine sediment cover (see variable description on first sheet).
DOI: 10.5061/dryad.66t00/1
title: WL_file basic data

description: basic data file of investigated patients
DOI: 10.5061/dryad.8br20/1
title: Mating Types of Strains

description: This file contains the mating type information for all the Neurospora crassa strains used to test the SPREAD algorithm. The column labelled "FGSC" lists the Fungal Genetics Stock Center strain IDs and the column labelled "mat" lists the mating type. "AA" = mating type "A", "a" = mating type "a".
DOI: 10.5061/dryad.8br20/2
title: All pairwise matings with genetic and geographic distance data

description: This CSV contains all 576 possible pairwise matings between the 24 mat-a and 24 mat-A Neurospora crassa strains used to test the SPREAD algorithm. FGSC1 and FGSC2 are the strain IDs of the pair, GeneticDistance is the genetic distance between the pair (number of different SNPs between parents) and GeographicDistance is km between strain isolation locales.
DOI: 10.5061/dryad.8br20/3
title: Simulated spore production data for all pairwise matings

description: This CSV contains the simulated spore production data used to compute the population GLMM. Subsets of this data-set were used to calculate sample GLMMs. Please see readme file for information on column names.
DOI: 10.5061/dryad.8br20/4
title: Figure2 R Script

description: R script to produce figure 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.
DOI: 10.5061/dryad.8br20/5
title: Figure3 Table2 R script

description: R script to produce figure 3 and table 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.
DOI: 10.5061/dryad.8br20/6
title: Figure4 R Script

description: R script to produce figure 4 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.
DOI: 10.5061/dryad.8br20/7
title: Table1 R Script

description: R script to produce Table 2 from data in the SPREAD_Rdata.zip file. To run script, working directory should be the directory containing the unzipped data files.
DOI: 10.5061/dryad.92pd3/2
title: patient_table

description: Table providing patient-level concordance information.
DOI: 10.5061/dryad.92pd3/3
title: Lanman_2015

description: This file is a zipped folder containing the variants tables for each of the 165 matched tumor and liquid biopsy samples.
DOI: 10.5061/dryad.b2hc1/2
title: Reads from HEK293-GFP-PBmut mapped to hg19+pb-ef1-neo

description: Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-GFP-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.
DOI: 10.5061/dryad.b2hc1/3
title: Reads from HEK293-PGBD5-PBwt mapped to hg19+pb-ef1-neo

description: Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBwt, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.
DOI: 10.5061/dryad.b2hc1/4
title: Reads from HEK293-PGBD5-PBmut mapped to hg19+pb-ef1-neo

description: Reads obtained from sequencing FLEA PCR products to amplify transposon reporter insertions in sample HEK293-PGBD5-PBmut, filtered, quality trimmed and mapped to a hybrid genome consisting of hg19 and the reporter plasmid sequence. Reads were mapped with bwa-mem using default parameters.
DOI: 10.5061/dryad.b2hc1/5
title: Summary table of DNA transposon integration loci

description: Spreadsheet listing human genome and transposon coordinate positions of transposon integrations, integration type (ITR transposition vs non-ITR transposition), and DNA sequences surrounding the genomic integration sites.
DOI: 10.5061/dryad.b2hc1/6
title: Transposon reporter plasmid sequence: pb-ef1-neo

description: Plasmid sequence of NEO reporter flanked by PiggyBac ITRs. Reads from FLEA PCR were mapped to a hybrid genome consisting of this sequence and the hg19 human genome reference.
DOI: 10.5061/dryad.bf206/1
title: Atlantic salmon mortality data

description: The Excel sheet contains mortality data of Atlantic salmon during epidemics of three disease-causing agents.
DOI: 10.5061/dryad.c402q/1
title: Specimen BF2 surface STL used in CFD

description: Oreochromis niloticus specimen BF2 (Royal Museum for Central Africa), female, mass = 63 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/2
title: Specimen BF5 surface STL used in CFD

description: Oreochromis niloticus specimen BF5 (Royal Museum for Central Africa), male, mass = 100 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/3
title: Specimen BF6 surface STL used in CFD

description: Oreochromis niloticus specimen BF6 (Royal Museum for Central Africa), male, mass = 103 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/4
title: Specimen BF8 surface STL used in CFD

description: Oreochromis niloticus specimen BF8 (Royal Museum for Central Africa), male, mass = 125 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/5
title: Specimen BF10 surface STL used in CFD

description: Oreochromis niloticus specimen BF10 (Royal Museum for Central Africa), female, mass = 63 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/6
title: Specimen BF11 surface STL used in CFD

description: Oreochromis niloticus specimen BF11 (Royal Museum for Central Africa), female, mass = 54 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c9s55/1
title: Teichroeb Vervet Heuristics

description: Vervet paths taken through six baited sites while alone and while in competition.
DOI: 10.5061/dryad.g00v5/1
title: Tigriopus sex ratio phenotype and genotype data

description: Data from intercross design F2 females.  Initially started with 2 lines (male-biased and female-biased selection lines) in each of 2 populations (San Diego, California, USA (SD) and Agiuliar, Bamfield, BC, Canada (AG)). Each row represents an individual F2 female and gives her phenotype (number of brood, number of males, females in brood) and her genotype at 46 SNP loci. See ReadMe.txt for more information.
DOI: 10.5061/dryad.g00v5/2
title: QTL raw data
DOI: 10.5061/dryad.hm2jf/10
title: de-novo draft assemblies

description: This is a gzip/tar compressed data archive containing the draft contig de-novo assemblies generated in this study.
DOI: 10.5061/dryad.hm2jf/11
title: Whole-genome SNP phylogeny (restricted dataset), related to Figure 3

description: RAxML phylogenetic tree obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.
DOI: 10.5061/dryad.hm2jf/12
title: Whole-genome SNP phylogeny (restricted dataset), related to Figure S3

description: RAxML phylogenetic tree in newick format, obtained from the whole-genome SNP alignment of the restricted dataset and with S. paradoxus as outgroup, related to Figure 3.
DOI: 10.5061/dryad.hm2jf/13
title: Multilocus tree including the Chinese strains, related to Figure S4

description: Neighbor-Joining tree in newick format, inferred from a concatenated alignment of 13 loci and including Chinese strains, related to Figure S4
DOI: 10.5061/dryad.hm2jf/14
title: Raw data of microsatelite genotypes used in figure S1

description: This table contains 3 columns indicating the strain name, the locus name and the allele values (size bins). When only one allele was found the value has been doubled as the stain is assessed to be diploid. For some strains additional values can be observed (ie Bread strains). For such cases, additional lines are added to described all values found at this loci.
DOI: 10.5061/dryad.hm2jf/8
title: Raw results from compute (libsequence analysis package), related to Table S2

description: This is a gzip/tar compressed data archive containing the results of compute from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) and non-CDS in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS and the nucleotide positions are used to identify non-CDS.
DOI: 10.5061/dryad.hm2jf/9
title: Raw results from polydNdS (libsequence analysis package), related to Table S2

description: This is a gzip/tar compressed data archive containing the results of polydNdS from the libsequence analysis package (http://molpopgen.org/) (Thornton 2003), related to Table S2. The archive contains results for coding sequences (CDS) in the Mediterranean oak population (MO) and the wine population (wine), with one file per locus. The SGD systematic name is used to identify CDS.
DOI: 10.5061/dryad.j91v7.1
title: Data from: No enhancement of 24-hour visuomotor skill retention by post-practice caffeine administration
DOI: 10.5061/dryad.j91v7.2/12.2
title: Hussain&Cole2015 All Raw Data

description: This .zip folder includes all raw data (i.e., force values) for each subject tested. The force values are in column 3 of each file.
DOI: 10.5061/dryad.k7c64/10
title: Multiply imputed data set 9
DOI: 10.5061/dryad.k7c64/12
title: Transitions between alternative reproductive tactics in female striped mice
DOI: 10.5061/dryad.k7c64/13
title: Comparing solitary breeders and returners with communal breeders
DOI: 10.5061/dryad.k7c64/14
title: Striped mouse breeding synchrony
DOI: 10.5061/dryad.kc1q1/1
title: SNP raw data

description: Excel file containing all SNP raw data for 113 individuals
DOI: 10.5061/dryad.nj957/1
title: fronhofer_2015_ELE_dryad_data

description: Data for Fronhofer, Klecka, Melian & Altermatt (2015): Condition-dependent movement and dispersal in experimental metacommunities, Ecology Letters.Data files:1) dispersal_data.txt: This file contains the dispersal data recored as manual counts at the end of the experiment. "treatment" refers to the experimental community composition. "density" is reported in individuals/ml. patch: "S" (starting conditions, i.e., at the beginning of the experiment), "P1" (start/origin patch), "P2" (target patch)2) movement_data.txt: contains the individual-level movement and morphology data from the video analysis. The file contains information on: velocity ("velocity_metric") measured in mm/s, turning angle distribution width ("sd_turning") measured as the standard devidation, the net distance travelled ("euclidean_metric") measured in mm, as well as morphological parameters, specifically the length along the major axis in µm and the aspect ratio (major/minor).3) growthCurves_data.txt: Sample-level density data from video analysis for determining r0 and K of all three species (see Fig. S1). "time" is reported in hours and captures the time since the beginning of the growth experiment.4) communityDynamics_data_interactionCoefficients.txt: Sample-level data from video analysis of all 2-species communities used to determine interaction coefficients (see Fig. S3).
DOI: 10.5061/dryad.s31sp/1
title: Dataset

description: Values of colour and pattern analyses for all the species used in the study
DOI: 10.5061/dryad.sj548/3
title: NeighborNet graph based on Nei genetic distance

description: NeighborNet graph based on Nei genetic distance of 37 bovine populations. Breeds belonging to one of the three types :African, European and Zebu, were grouped together. Sets of parallel edges (reticulations) on the NeighborNet graph observed between populations indicate past hybridization events.
DOI: 10.5061/dryad.sj548/4
title: Maximum likelihood tree with no migration events

description: Maximum likelihood tree inferred from a subset of 13 cattle populations when no migration edges were fit. Nelore breed (NEL) was set as a rooting outgroup. The scale bar shows 10 times the average standard error of the estimated entries in the sample covariance matrix.
DOI: 10.5061/dryad.sj548/5
title: Maximum likelihood tree with eight migration events

description: Maximum likelihood phylogenetic network inferred from a subset of 13 populations. Migration events (modeled as arrows) were added sequentially up to eight migrations. Migration arrows are colored according to their weight. The scale bar shows 10 times the average standard error of the estimated entries in the sample covariance matrix.
DOI: 10.5061/dryad.sr3g0/1
title: Survival_cadmium_diet

description: Egg to adult survival measured in cadmium diet. Each separate file is the data for one replicate population. Each male crossed with ~4 females to produce a half-sib family. “Dam” column shows the female ID (full-sib family ID). “Sire” column shows the male ID (half-sib family ID). “Egg” shows the number of eggs produced per female. “Adult” shows the number of adult emerged from those eggs.
DOI: 10.5061/dryad.sr3g0/2
title: Survival_salt_diet

description: Egg to adult survival measured in salt diet. Each separate file is the data for one replicate population. Each male crossed with ~4 females to produce a half-sib family. “Dam” column shows the female ID (full-sib family ID). “Sire” column shows the male ID (half-sib family ID). “Egg” shows the number of eggs produced per female. “Adult” shows the number of adult emerged from those eggs.
DOI: 10.5061/dryad.11962/1
title: Data for testing effects on wild boar population growth

description: Data used in the European and the Austrian multi-model averages testing how wild boar population growth (lambda) is affected by climatic parameters, food availability (only for Austria), and density.
DOI: 10.5061/dryad.11962/2
title: Data on the body mass of wild boar from different regions

description: Body mass data of wild boar taken from the literature for testing the Bergmann's rule and local differences in the wild boar.
DOI: 10.5061/dryad.11962/3
title: Data on traffic accidents involving wild boar

description: Data on traffic accidents involving wild boar from Austria, Germany, and Switzerland used for testing the reliability of hunting bag data in investigating relative changes in population size.
DOI: 10.5061/dryad.1dc65/1
title: PLosONE_Morita_2015
DOI: 10.5061/dryad.2r8f9/1
title: Insect Starvation Raw Data

description: These are the raw 13C values measured in the exhaled breath of different insects at various times of fasting.
DOI: 10.5061/dryad.3n6n6/1
title: Raw reflectance of Costus arabicus flowers

description: Reflectance at 300-700nm wavelength of white and pink flowers of Costus arabicus. Reflectance of petals, labellum and nectar guides.
DOI: 10.5061/dryad.3n6n6/2
title: Flower visitation of Costus arabicus

description: Flower visitation by bees and hummingbirds on Costus arabicus flowers. Data regarding flower colour and pollinator behaviour.
DOI: 10.5061/dryad.3n6n6/3
title: Pollinator movement behaviour on Costus arabicus

description: Bees and hummingbirds movement between Costus arabicus individuals while foraging on flowers
DOI: 10.5061/dryad.4n28n/10
title: Helianthus_fasta_files

description: This is the zip folder containing the fasta files for 170 genes across 103 diploid Helianthus species. The fasta files have been aligned and trimmed with gblocks.
DOI: 10.5061/dryad.4n28n/11
title: bootstrap_genetrees

description: The zip file contains all the bootstrap gene files. There are 170 files (one for each gene) with 500 bootstrapped gene trees within each file. These were all estimated from RAxML and used in MP-EST to estimate the species tree.
DOI: 10.5061/dryad.4n28n/7
title: Accession_tree

description: MP-EST accession tree estimated from 170 genes and 103 accessions
DOI: 10.5061/dryad.4n28n/8
title: Concatenation_tree

description: Concatenation tree estimated from RAxML (106,862bp) across 103 accessions of diploid Helianthus.
DOI: 10.5061/dryad.4n28n/9
title: Helianthus_concatenated_nDNA

description: This file contains the aligned 106862bp concatenated nDNA sequences from 103 accessions across 37 diploid Helianthus species/subspecies and the outgroup Phoebanthus tenuifolius.
DOI: 10.5061/dryad.64m57/1
title: Folsomia candida morphology

description: Table with data on the external morphology of 18 characters studied on 12 differents lineages of the Collembola Folsomia candida.
DOI: 10.5061/dryad.661jb/1
title: mtDNA matrix Chiloglanis anoterus

description: Control region and CO1 sequence data
DOI: 10.5061/dryad.661jb/2
title: AFLP matrix Chiloglanis anoterus

description: configured for structure input
DOI: 10.5061/dryad.8br20/8
title: SPREAD_Rdata

description: This zip file contains 6 rdata files and one CSV file used to produce the figures. Please refer to the ReadMe for descriptions.
DOI: 10.5061/dryad.8f150/1
title: FP, NMR and HTS data

description: Fluorescence polarization, NMR chemical shift perturbations and high-throughput screening data for compounds that show binding to the HEPN domain of sacsin
DOI: 10.5061/dryad.8vv63.2
title: Data from: Testing convergence versus history: convergence dominates phenotypic evolution for over 150 million years in frogs
DOI: 10.5061/dryad.8vv63.2/1.2
title: 2nd.history.test.MoenEA

description: R function for the second history test (i.e. breaking down variance around optimum into variance due to history and due to random deviation). Details for use of the function are found as comments in the initial lines of the file. Executing this code will produce a table like Table 4 in the published paper.
DOI: 10.5061/dryad.8vv63.2/2.2
title: Phylogenies

description: The two phylogenies used for data analyses in this paper. See Appendix S2 for details on phylogenies.
DOI: 10.5061/dryad.8vv63.2/3.2
title: Supplementary Appendices

description: All five supplementary appendices, with supplementary figures and tables (including data from the paper).
DOI: 10.5061/dryad.8vv63.2/4.2
title: ou.optima.MoenEA

description: Table of estimated OU optima for the preferred OU model of evolution (lowest AICc). This can be used to do an example analysis with the R code for the second history test.
DOI: 10.5061/dryad.8vv63.2/5.2
title: sample.morph.data.MoenEA

description: Table of principal component data and microhabitat state for the preferred OU model of evolution (lowest AICc). This can be used to do an example analysis with the R code for the second history test.
DOI: 10.5061/dryad.9855v/1
title: meta_data

description: Meta-analysis data
DOI: 10.5061/dryad.9855v/2
title: lab_data

description: Data for the laboratory experiment
DOI: 10.5061/dryad.9855v/3
title: Field_experiment

description: Data from the field experiment
DOI: 10.5061/dryad.98c7s/1
title: ak_carots_ES2012_proofed

description: This file contains data on American kestrel carotenoid concentrations and associated information collected from kestrels in the field during the breeding seasons 2008-2012. All information was collected from adult kestrels that were in incubating eggs in nest boxes in southern Idaho.Columns are variables, and each row represents 1 bird.  Variable: "record" : unique line identifier; Variable: "ID" : individual identifier for each bird;Variable: "sex" : sex of the bird determined from plumage; Variable: "carotenoid con" : plasma carotenoid concentrations of kestrels (see Sassani et al. for methods);Variable: "Year" : year the bird was captured and sample collected;Variable: "Jcap" : Julian date of capture.  Jan 1 = 1;Variable: "Box" : Nest box identifier used to represent territory identity;Variable: "Mass" : Mass of the bird in grams (digital scale) Note: some birds are missing data on mass;Variable: "nevent" : individual identifier for the pair of birds or nest event;Variable: "Box" : Nest box identifier used to represent territory identity Variable: "Mass" : Mass of the bird in grams (digital scale) Note: some birds are missing data on mass.Variable: "nevent" : individual identifier for the pair of birds or nest event
DOI: 10.5061/dryad.bf206/2
title: I. multifiliis occurrence data

description: The Excel sheet contains data on occurrence of I. multifiliis on Atlantic salmon
DOI: 10.5061/dryad.bf206/3
title: Experimental Diplostomum exposure data

description: The Excel sheet contains data on experimental exposure of landlocked Atlantic salmon and brown trout to Diplostomum pseudospathaceum parasite
DOI: 10.5061/dryad.c402q/10
title: Specimen BF19 surface STL used in CFD

description: Oreochromis niloticus specimen BF19 (Royal Museum for Central Africa), male, mass = 95 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/11
title: Specimen BF20 surface STL used in CFD

description: Oreochromis niloticus specimen BF20 (Royal Museum for Central Africa), female, femass = 57 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/12
title: Specimen BF22 surface STL used in CFD

description: Oreochromis niloticus specimen BF22 (Royal Museum for Central Africa), male, femass = 115 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/7
title: Specimen BF13 surface STL used in CFD

description: Oreochromis niloticus specimen BF13 (Royal Museum for Central Africa), male, mass = 86 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/8
title: Specimen BF17 surface STL used in CFD

description: Oreochromis niloticus specimen BF17 (Royal Museum for Central Africa), female, mass = 48 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.c402q/9
title: Specimen BF18 surface STL used in CFD

description: Oreochromis niloticus specimen BF18 (Royal Museum for Central Africa), female, mass = 51 g, left-right assymetry removed, scaled isometrically to the same mean body volume (excluding the head)
DOI: 10.5061/dryad.dc195/1
title: Master dataframe

description: This file contains male morphological measurements and pre- and post-copulatory reproductive measurements.
DOI: 10.5061/dryad.dc195/2
title: Courtship dataframe

description: This file contains the data used to calculate Courtship Index and Wing Extension Index.