cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f0b2f083/5
title: Source code for composite disequilibrium

description: This compressed directory contains the source code for estimating Burrow's composite linkage and Hardy-Weinberg disequilibrium, as described in the publication. Please contact the Zach Gompert (zgompert@uwyo.edu) to inquire about updates to the software, usage, and whether a manual or example files exist.
DOI: 10.5061/dryad.336n3gt0/1
title: oak_defense_archive

description: A species-level data frame describing oak leaf traits (standardized as z-scores), latitude (as decimal degrees), and climatic associations (using Worldclim codes e.g. "BIO14"). The 56 oak species are referred to by specific epithet.  Trait data was collected from trees in a common garden at the UC Davis Shields Oaks Grove.
DOI: 10.5061/dryad.6b678210/3
title: forested_landscape_30pts

description: coordinates of the 30 random points for the forested landscape, in North America Lambert Conformal Conic projection
DOI: 10.5061/dryad.6b678210/4
title: settled_landscape_30pts

description: coordinates of the 30 points for the settled landscape, in North America Lambert Conformal Conic projection
DOI: 10.5061/dryad.f1q20jr4/1
title: dppdiv_1.0b.tar
DOI: 10.5061/dryad.f1q20jr4/2
title: turtles
DOI: 10.5061/dryad.f1q20jr4/3
title: simulated_data_files.tar
DOI: 10.5061/dryad.fc30r431/3
title: Table_3_Li_2008

description: This file contains all of the input and output files for table 3 in the paper. Including Li et al's alignment file, and partitioning files for all of the different schemes in table 3 of the paper. It also contains the mac-compiled version of RaxML that I used for the analysis, although any version of raxML should work.
DOI: 10.5061/dryad.fc30r431/4
title: Table_1_and_2_datasets

description: There are 10 subfolders, each of which contains a dataset and a partitionfinder.cfg file. The datasets are described in table 1 of the paper, and the results are in table 2. The files in the folders should reproduce all of the results in table 2. All analyses are were run with PartitionFinder v0.9. To download this particular version (which is guaranteed to work with these files, while later versions might not be) follow this link: . Later versions of PartitionFinder are available here: .
DOI: 10.5061/dryad.20fc5v4j/1
title: Chaetodon trifasciatus X C. lunulatus genotypes

description: Genepop format input file utilised for population genetic analyses and DAPC. The file includes genotypes of both parental species and their hybrids from all locations investigated.
DOI: 10.5061/dryad.7180nf60/1
title: SSR_genotypes_Hortaletal_MolEcol2012
DOI: 10.5061/dryad.b064t9c5/1
title: StruggleTest

description: Struggle test scores collected in the field. See ReadMe for more information.
DOI: 10.5061/dryad.b064t9c5/2
title: OpenField+MIS

description: Raw scores from analysis of open field and mirror-image stimulation trials using JWatcher. See ReadMe for more information.
DOI: 10.5061/dryad.b064t9c5/3
title: pedigree

description: Pedigree. See ReadMe for more information.
DOI: 10.5061/dryad.b064t9c5/4
title: ReadMe

description: ReadMe for data.
DOI: 10.5061/dryad.pk8997k0/1
title: Dryad_RawData_AFinger

description: Microsatellite and GPS data of adult and seedling individuals.
DOI: 10.5061/dryad.v5t5t5d5/1
title: data for upload_0121
DOI: 10.5061/dryad.2q3n104v/1
title: JOH sequence data

description: All the sequence data that was used in this study
DOI: 10.5061/dryad.2q3n104v/2
title: SupplementaryTable1 Dec 14 references

description: All accession numbers for the sequences used in this study.
DOI: 10.5061/dryad.3486n266/2
title: Kinetics_CHIKV
DOI: 10.5061/dryad.3486n266/3
title: Relative_density_bacteria_Ae. albopictus_ALPROV
DOI: 10.5061/dryad.3486n266/4
title: Relative_Intensity_Probes discriminating infected from noninfected
DOI: 10.5061/dryad.6vn7t861/1
title: GCalabria_JEB2463-HSP70induction
DOI: 10.5061/dryad.m2271pf1/1
title: rfseq_protocol

description: This is a protocol for enzymatically guided genomic reduction and highly multiplexed Illumina library preparation.
DOI: 10.5061/dryad.m2271pf1/2
title: c_code_bass

description: C code for bayesian association mapping
DOI: 10.5061/dryad.m2271pf1/3
title: P_contorta_assembly.bam

description: Assembly in BAM format. This assembly was created by using an artificial reference created through a denovo assembly. This artificial reference was then used a template onto which we assembled the remaining Illumina reads.
DOI: 10.5061/dryad.m2271pf1/4
title: pine_ref

description: This artificial reference consists of contig consensus sequences created with a de novo assembly of a subset of reads, joined by stretches of 30 Ns. This was then used in a template guided assembly, where all Illumina reads were assembled onto the reference.
DOI: 10.5061/dryad.42413173/1
title: all052411

description: Main GENEPOP data file with all 31 loci included. Population and locus names follow the manuscript.
DOI: 10.5061/dryad.42413173/2
title: allinRpts

description: GENEPOP data file for 27 loci with alleles recoded into repeat units. Population and locus names follow the manuscript.
DOI: 10.5061/dryad.6vn7t861/2
title: GCalabria_JEB2463-KnockdownTemperature
DOI: 10.5061/dryad.d6q7q72g/1
title: Apis vs  Native 20 yr interval mar 2010
DOI: 10.5061/dryad.d6q7q72g/2
title: DRONE DATA
DOI: 10.5061/dryad.d6q7q72g/3
title: WING MORPHOLOGY DATA HIGH VAR
DOI: 10.5061/dryad.d6q7q72g/4
title: AHB Sample Sizes by Article
DOI: 10.5061/dryad.d6q7q72g/5
title: DEF DATA for PUB ANALYSIS
DOI: 10.5061/dryad.d6q7q72g/6
title: HYGENE FROZEN BROOD ASSAY
DOI: 10.25678/00020v
title: Data for: Linking transformations of organic carbon to post-treatment performance in a biological water recycling system

description: Ozone, electrolysis and granular activated carbon (GAC) were examined as potential post-treatments to follow a household-scale biologically activated membrane bioreactor (BAMBi), treating a wash water containing trace urine and feces contamination. Each post-treatment was evaluated for abilities and reaction preferences to remove or transform dissolved organic carbon (DOC), chemical structures that contribute color, and assimilable organic carbon (AOC), which can support bacterial regrowth. Batch treatment with each technology demonstrated an ability to remove ≥95% DOC. Ozone demonstrated a reaction selectivity through increased reaction rates with larger compounds and color-contributing compounds. Electrolysis and GAC demonstrated generally less-selective reactivity. Adding post-treatments to full-scale systems reduced DOC (55-91%), AOC (34-62%), and color (75-98%), without significant reaction selectivity. These reductions in DOC and AOC were not linked to reduction of bacterial concentrations in treated water. Reductions in bacterial concentrations were observed with ozone and electrolysis, but this is credited to oxidation chemicals produced in these systems and not the removal or transformations of organic materials.
DOI: 10.5061/dryad.3ck64027/2
title: Kivelä et al. 2012_JEB_data

description: data file
DOI: 10.5061/dryad.7384037h/1
title: data for dryad

description: The attending spreadsheet contains data from all 3 levels of diversity and 2 group sizes. Data were collected by JBS, ETA, JG, MH, and NM. The “diversity” column refers to the level of wildtype genetic diversity in the group (L= low, M= medium, H= high). “Number of tester survivors” and “number of wildtype survivors” are the number of tester and wildtype individuals, respectively, who eclosed from that group. Groups in which either the number of wildtype or tester survivors was 0 were excluded from the analysis. “Date” is the date the vial was created. “Genotype combination” describes the complement of wildtype genotypes present in the group; information about specific genotype combinations is available in the Supplemental Information to the paper. “Group size” is the number of first-instar larvae originally added to the vial (72 for small groups, 144 for large groups).
DOI: 10.5061/dryad.7p1r30q5/1
title: FF-VI_348_study_Dryad-DATA
DOI: 10.5061/dryad.ct00428d/1
title: Healy et al Incidence of Schizophrenia - table
DOI: 10.5061/dryad.ct00428d/2
title: Healy et al Incidence of Schizophrenia - workbook

description: This file is the Excel workbook containing the diagnostic data and the population data for North Wales against which the diagnostic rates have been standardized.
DOI: 10.5061/dryad.d6q7q72g/7
title: VARROA DATA JULY 4
DOI: 10.5061/dryad.d6q7q72g/8
title: Varroa groom intensity
DOI: 10.5061/dryad.mn159hq6/1
title: Data and Programs HDY-11-OR0427R

description: This folder contains many files related to the manuscript number HDY-11-OR0427R. In the Simulation folder, there are two datasets (binary and binomial) and two SAS programs used to analyze these data. In the Wheat folder, there is a dataset collected from a wheat QTL mapping experiment (Dou et al. 2009) and a SAS program that analyzes this dataset. The wheat data can also be downloaded from the original publication's journal website (Supplemental Material).
DOI: 10.5061/dryad.4m301n7m/1
title: Microsatellite data
DOI: 10.5061/dryad.4m301n7m/2
title: STRUCTURE data file
DOI: 10.5061/dryad.4m301n7m/3
title: STRUCTURE parameter file with priors
DOI: 10.5061/dryad.4m301n7m/4
title: mtDNA sequence data
DOI: 10.5061/dryad.4m301n7m/5
title: mtDNA sequences 9 colonies
DOI: 10.5061/dryad.gc2260qm/2
title: Multi-Scale Model of CRISPR-Induced Coevolutionary Dynamics

description: This code presents a flexible framework for considering the co-evolutionary dynamics of hosts and viruses which interact via a CRISPR immune mechanism. The code is written in Matlab. Instructions on how to utilize the code including an example file are found in the README file.
DOI: 10.5061/dryad.h90j32v2/1
title: MixedModelData
DOI: 10.25678/00021w
title: Aquasim model for: Biofilm Modelling (Chapter 17)

description: Aquasim model for Biofilm Modelling chapter (Chapter 17 by Eberhard Morgenroth)
DOI: 10.25678/00022x
title: Sumo model file for: Biofilm Modelling chapter

description: SUMO model for Biofilm Modelling chapter in IWA Biological Wastewater Treatment: 2nd edition.
DOI: 10.5061/dryad.4m301n7m/10
title: IMa2 mtDNA input file
DOI: 10.5061/dryad.4m301n7m/6
title: LAMARC Atlantic sample file
DOI: 10.5061/dryad.4m301n7m/7
title: LAMARC Pacific sample file
DOI: 10.5061/dryad.4m301n7m/8
title: LAMARC Atlantic infile
DOI: 10.5061/dryad.4m301n7m/9
title: LAMARC Pacific infile
DOI: 10.5061/dryad.5vp21b10/1
title: appendix
DOI: 10.5061/dryad.5vp21b10/2
title: ENm001

description: Sequence of the ENm001 region of the ENCODE Pilot Project (position 115,810,521 to position 117,687,946 on chromosome 7) from the hg19 version of the human genome, together with aligned sequences from nine other primate species (Chimpanzee, Gorilla, Orang-utan, Macaque, Baboon, Marmoset, Tarsier, Gray mouse lemur, Galago) as available from the Galaxy web tool (http://galaxy.psu.edu/).
DOI: 10.5061/dryad.5vp21b10/3
title: ENm001_AR

description: Portion of ENm001 made from "Ancestral" repeated elements, according to the RepeatMasker annotations on the human sequence from the UCSC Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) Pieces of the alignment corresponding to simple repeats, low complexity regions, members of the Alu family, and RNA elements that diverged less than 25% and L1 elements that diverged less than 20% from the reference RepBase sequence, were  removed.
DOI: 10.5061/dryad.sh7rm2pt/1
title: DRYAD FILES

description: This is a zipped folder of all of the data files and scripts to run the statistical analyses associated with the manuscript.
DOI: 10.5061/dryad.1rk18128/1
title: WelchMicrosHeredity

description: This file contains data for 15 microsatellite loci genotyped in modern Hawaiian petrel (Pterodroma sandwichensis) samples from the islands of Hawaii, Maui, Lanai, and Kauai in the Hawaiian Islands, USA. The file is in the three digit Genepop format. See the ReadMe file for additional details.
DOI: 10.5061/dryad.4sb063bn/1
title: Galligan et al__Panmixia__data

description: Allele size data for 12 microsatellites
DOI: 10.5061/dryad.6tv35cc2/1
title: Xu et al raw SNP genotyping data_Heredity

description: This file contains the raw genotyping data of the 1102 EST-derived SNPs loci with successful calls in the sample set used in this study. Column A: IDs of the plant materials; Line1: names of the SNP markers. Question marks indicate unsuccessful or ambiguous calls.
DOI: 10.5061/dryad.7b5s1s4r/1
title: QTL Results - 013012

description: Genotyping scores of the female backcross mapping population.
DOI: 10.5061/dryad.996cr8f0/1
title: dryad_geno

description: Genotype data following genotyping on the Illumina 57k SNP chip for chicken. Data is provided in a format compatible with GenABEL for R.
DOI: 10.5061/dryad.996cr8f0/2
title: dryad_pheno

description: Phenotype file for the accompanying genotype file. Present in a format compatible for use with GenABEL for R.
DOI: 10.5061/dryad.m1j968g3/1
title: Gratten_etal_Dryad
DOI: 10.5061/dryad.pb5bh7hq/1
title: CodeforDryad

description: Zip directory containing R code and simulation results associated with paper (including supplementary figures). For details on running the simulations, see readme.txt in directory.
DOI: 10.5061/dryad.14cr5345/1
title: Aubret 53172

description: Excel file contains 4 sheets. First sheet titled Adult Tiger snakes contains field data collected on Adult Tiger snakes (sex, body mass and snout-vent length). Sheet titled Mothers litters and neonates contains laboratory and museum data about reproductive output in female tiger snakes for several populations. For each female is given birth date, mean litter body mass (calculated average body mass for all neonates in a given litter), mean litter svl (calculated average snout vent length for all neonates in a given litter), and mean litter jaw (calculated average jaw length for all neonates in a given litter). Sheet titled Prey contains data collected in Museum collection for prey available at each study site. Latin names are given with body mass and maximum circumference of each prey item. Sheet titled Growth experiment contains experimental data on growth rate and food consumption in neonate Tiger snakes from several populations. Headings indicate for each mother its population of origin, neonate identification number, birth date and morphometrics at birth. Body mass and snout vent length are recorded every two months until the end of the experiment. Column titled Total growth in body mass indicates the difference in body mass between the start and the end of the experiment. The two last columns are Total food (total amount of food consumed by each neonate over the course of the experiment) and Length of experiment (total duration of the experiment). Conversion rates were calculated (column titled Increase in body mass per g of food) and daily growth rates in body mass (increase in body mass in mg per day).  Similar calculation were made for snout vent length (increase in svl per g of food; increase in svl in mm per day).
DOI: 10.5061/dryad.1s1h1530/1
title: field

description: Morphological measurements for all the field caught individuals
DOI: 10.5061/dryad.1s1h1530/2
title: experiment

description: Morphological measurements for all the experimental individuals
DOI: 10.5061/dryad.6n3d6109/1
title: BTped

description: Full blue tit pedigree. This dataset comprises 3,090 individual blue tits and a total of 4,024 breeding events between 2001 and 2008.
DOI: 10.5061/dryad.6n3d6109/2
title: GTped

description: Full great tit pedigree. Our full dataset for great tits comprises 12,724 individuals and a total of 19,395 breeding events between 1947 and 2008.
DOI: 10.5061/dryad.j8n0p7vc/1
title: fluctuationDomains

description: R package containing the software used to simulate, analyze, and visualize the data considered in this publication.
DOI: 10.5061/dryad.144v45c6/1
title: DataAmNat53179file2

description: See readme file
DOI: 10.5061/dryad.144v45c6/2
title: DataAmNat53179file1
DOI: 10.5061/dryad.23hs6/1
title: Data from Szöcs, Eduard, Ben J. Kefford, and Ralf B. Schäfer. “Is There an Interaction of the Effects of Salinity and Pesticides on the Community Structure of Macroinvertebrates?” Science of The Total Environment 437 (2012): 121 – 126.

description: see README.txt
DOI: 10.5061/dryad.663b4/1
title: Myers_etal_SuppFig1

description: Supplementary Figure 1. Histogram of log(geographic range) for all reconstructed ranges of molluskan taxa during the Late Cretaceous.
DOI: 10.5061/dryad.663b4/2
title: Myers_etal_SuppTable1

description: Supplementary Table 1. Species range size (reconstructed area and latitudinal extent) and outcrop area during each geologic stage. Coding for survivors and invaders: 1 = survived or invaded in the subsequent stage, 0 = did not survive or invade in the subsequent stage. Abbreviations of geologic stages: CEN = Cenomanian, TUR = Turonian, CON = Coniacian, SAN = Santonian, CAM = Campanian, MAA = Maastrichtian.
DOI: 10.5061/dryad.663b4/3
title: Myers_etal_SuppTable2

description: Supplementary Table 2. Contingency table analysis comparing biotic sub-provinces to survivorship and invasion potential. Endemic species are those that occur in only a single BSP. BSP = biotic sub-province and EC = endemic center of Kauffman 1984.
DOI: 10.5061/dryad.663b4/4
title: Myers_etal_SuppTable3

description: Supplementary Table 3. Contingency table analysis comparing survivorship and invasion potential to benthic vs. pelagic adult lifestyle and clade membership. Endemic species are those that occur in only a single BSP.
DOI: 10.5061/dryad.85qg3/1
title: MGarcia_Data Abstraction File_BMJOpen (21-Aug-12)

description: Supplementary document: data abstraction file used to classify and score studies included in systematic review
DOI: 10.5061/dryad.9b6qj34p/1
title: Fleskes_etal_Table S1_REV

description: Table S1. Microsoft Excel file containing data used in the analysis of bird use of grain and non-grain fields treated with two types of post-harvest flooding that differed in depth and duration (Flood-type [FLD] fields were flooded with &lt;1 cm–1.5 m water for &gt;1 week; Irrigated-type [IRG] fields were flooded with &lt;1 cm–15 cm water for &lt;1 week) in the Tulare Basin of California, 19 August–6 December 2005. Surveys were grouped by time of day into early-day (&lt; 4 hours post sunrise), mid-day (&gt; 4 hours post sunrise and &gt; 4 hours before sunset) and late-day (&lt; 4 hours before sunset) periods. Counts for each survey are presented by species and for waterfowl (includes ducks and geese), other waterbirds (includes coots, shorebirds, grebes, pelicans, herons, egrets, gulls, and terns), non-waterbirds (includes passerines, raptors, and vultures) and total birds (See Table 1 for species).
DOI: 10.5061/dryad.9j67q/1
title: Soil data on landscape function analysis indices and soil physio-chemical attributes from 29 semi-arid Stipa tenacissima steppes
DOI: 10.5061/dryad.f9180/1
title: jeb_data

description: The experiment quantified the susceptibility of 15 clones of Aphis fabae to three thelytokous lines of Lysiphlebus fabarum in a fully crossed design. Each combination of aphid clone and wasp line (45 combination) was replicated six times, resulting in 270 colonies tested.
DOI: 10.5061/dryad.m6r6hc12/1
title: pmc

description: An R package containing functions to perform the method described in the package, manual for these functions, and a vignette demonstrating how the package is used to replicate the results of this study.
DOI: 10.5061/dryad.vj86fq35/1
title: selection

description: Selection on cold tolerance
DOI: 10.5061/dryad.vj86fq35/2
title: reproductive traits

description: Fecundity, egg hatching success
DOI: 10.5061/dryad.vj86fq35/3
title: developmental traits

description: larval time, pupal time, pupal mass, growth rate
DOI: 10.5061/dryad.vj86fq35/4
title: cold and heat stress

description: cold and heat tolerance after selection
DOI: 10.5061/dryad.vj86fq35/5
title: longevity and survival

description: longevity control, longevity after cold shock and survival after heat shock
DOI: 10.5061/dryad.87v741v0/1
title: Chloroplast_Peru-Galapagos

description: Arlequin data file for the chloroplast markers
DOI: 10.5061/dryad.87v741v0/2
title: Microsatellites_Peru-Galapagos

description: Arlequin data file for micorsatellite markers
DOI: 10.5061/dryad.87v741v0/3
title: IMa_Gal_2pops

description: IMA2 data file using microsatellite data
DOI: 10.5061/dryad.8m8c0/1
title: Alignments of unphased DNA sequences

description: Concatenated text files in nexus format of DNA sequences from 20 loci of 16 species of the Liolaemus darwinii group
DOI: 10.5061/dryad.8m8c0/2
title: Output files from Phase analyses

description: Concatenated output files in text format of analyses with the software Phase to phase DNA sequence data from 19 nuclear loci of 16 species of the Liolaemus darwinii group
DOI: 10.5061/dryad.8m8c0/3
title: Alignments of phased DNA sequences

description: Concatenated text files in nexus format of phased DNA sequences from 19 nuclear loci of 16 species of the Liolaemus darwinii group
DOI: 10.5061/dryad.8m8c0/4
title: Input files for BEAST analyses

description: Compressed file containing input files in xml format for estimating species trees with the software *BEAST using DNA sequence data from 20 loci of 16 species of the Liolaemus darwinii group
DOI: 10.5061/dryad.8m8c0/5
title: Simulated gene trees for Mesquite

description: Input file for Mesquite in nexus format containing 100 simulated gene trees for a species tree of 8 species and 3 sequences/species. The number of deep coalescences for each gene tree was calculated in Mesquite to group gene trees in three categories of discordance with the species tree. See more details in online Appendix 7.
DOI: 10.5061/dryad.vt6bk/10
title: 454 Transcriptome pyrosequencing (T. urticae_single)
DOI: 10.5061/dryad.vt6bk/11
title: 454 Transcriptome pyrosequencing (P. persimilis_single)
DOI: 10.5061/dryad.vt6bk/12
title: Quantitative RT-PCR
DOI: 10.5061/dryad.vt6bk/13
title: dsRNA predation experiment
DOI: 10.5061/dryad.vt6bk/6
title: Volatile analysis
DOI: 10.5061/dryad.vt6bk/7
title: predation assays
DOI: 10.5061/dryad.vt6bk/8
title: 454 Transcriptome pyrosequencing (T. urticae_contig)
DOI: 10.5061/dryad.vt6bk/9
title: 454 Transcriptome pyrosequencing (P. persimilis_contig)
DOI: 10.5061/dryad.37s6bb42/1
title: Epp_etal_metabarcodes_dryad

description: This file contains all consensus sequences retrieved from clones of environmental samples and referred to in Table S6 of the Supplementary material.
DOI: 10.5061/dryad.895jb/1
title: DRYAD_Raffertyetal
DOI: 10.5061/dryad.8m8c0/10
title: Appendix 6

description: Species trees estimated in *BEAST with variable numbers of loci using phased and unphased data.
DOI: 10.5061/dryad.8m8c0/11
title: Appendix 7

description: Simulation of 100 gene trees from a pre-specified species tree to analyze the relationship between accuracy of species-tree estimation and the distribution of gene-tree discordance.
DOI: 10.5061/dryad.8m8c0/12
title: Appendix 8

description: Phylogenetic trees estimated in previous studies of the Liolaemus darwinii group.
DOI: 10.5061/dryad.8m8c0/6
title: Appendix 2

description: Sequence alignments of unphased data for 20 loci
DOI: 10.5061/dryad.8m8c0/7
title: Appendix 3

description: Plots of regression analyses between proportion of variable sites, proportion of informative sites, clade support index, level of discordance, and precision of species trees.
DOI: 10.5061/dryad.8m8c0/8
title: Appendix 4

description: Gene trees estimated in *BEAST using the full data set. Branch lengths are in units of substitutions per site.
DOI: 10.5061/dryad.8m8c0/9
title: Appendix 5

description: Species trees estimated in *BEAST using: phased data, variable population size and tree priors, and 200 million generations. Species tree estimated with BEST using the full data set.
DOI: 10.5061/dryad.k07th/1
title: F_selysi_x_foster_egg_survival

description: Eggs were collected from field colonies and placed with rearing groups of foreign workers.  This file contains survival data for eggs that were collected by workers in each rearing group.