cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1f4nj20/1
title: phylo_sumatra

description: The phylogeny used in the paper in newick format.
DOI: 10.5061/dryad.1f4nj20/2
title: metrics_sumatra

description: The community data used in the paper in csv format.
DOI: 10.5061/dryad.1h5717p/1
title: Main dataset

description: Main dataset including data for the whole season and all sites - see the read me file.
DOI: 10.5061/dryad.1h5717p/2
title: Co-flower dataset

description: Dataset including only data for sites where the phacelia and clover both flowered - see the read me file.
DOI: 10.5061/dryad.32b87rn/4
title: SpatialModel

description: Code for model simulations and data to calculate mean number of cells in multicellular clusters.
DOI: 10.5061/dryad.38889/1
title: Alignment - section Fumigati; concatenated data from benA, CaM, act and RPB2 loci, 76 taxa

description: Combined dataset of benA, CaM, act and RPB2 sequences for 76 taxa belonging to section Fumigati. Aspergillus clavatus NRRL 1 (sect. Clavati) represents an outgroup. BenA: positions 1-534; CaM: positions 535-1231; act: positions 1232-1662; RPB2: positions 1663-2661.
DOI: 10.5061/dryad.38889/2
title: Phylogeny of Aspergillus sect. Fumigati inferred from combined data: benA, CaM, act and RPB2

description: Phylogenetic relationships of the section Fumigati members inferred from Bayesian analysis of the combined, 4-gene data set of β-tubulin (benA), calmodulin (CaM), actin (act) and RNA polymerase II second largest subunit (RPB2) genes. Bayesian posterior probability (PP) and Maximum likelihood bootstrap support (BS) are appended to nodes; only PP ≥ 95% and BS ≥ 70% and are shown; lower supports are indicated with a hyphen, whereas asterisks indicate full support (1.00 PP or 100% BS); ex-type strains are designated by a superscript T; species names in quotes are considered synonyms. The tree is rooted with Aspergillus clavatus NRRL 1. The reproductive mode of each species is designated by icons before the species name (see legend).
DOI: 10.5061/dryad.38889/3
title: Combined alignment: benA, CaM, act and RPB2 loci; Aspergillus viridinutans complex

description: Combined dataset of benA, CaM, act and RPB2 sequences for 110 taxa belongmembers of Aspergillus viridinutans complex. Aspergillus lentulus NRRL 35552 represents an outgroup. BenA: positions 1-475; CaM: positions 476-1172; act: positions 1173-1516; RPB2: positions 1517-2483.
DOI: 10.5061/dryad.38889/4
title: Phylogeny of Aspergillus viridinutans species complex phylogeny inferred from combined data: BenA, CaM, act, RPB2

description: Phylogenetic relationships of the section Aspergillus viridinutans species complex members inferred from Bayesian analysis of the combined, 4-gene data set of β-tubulin (benA), calmodulin (CaM), actin (act) and RNA polymerase II second largest subunit (RPB2) genes. Bayesian posterior probability (PP) and Maximum likelihood bootstrap support (BS) are appended to nodes; only PP ≥ 90% and BS ≥ 70% and are shown; lower supports are indicated with a hyphen, whereas asterisks indicate full support (1.00 PP or 100% BS); ex-type strains are designated by a superscript T; species names in quotes are considered synonyms. The tree is rooted with Aspergillus lentulus NRRL 35552. The geographic origin, and reproductive mode with MAT idiomorph (if known) is designated by icons before the isolate number while substrate of origin is designated by icons after isolate number (see legend).
DOI: 10.5061/dryad.38889/5
title: Alignment - Aspergillus viridinutans complex, A. felis clade: concatenated data of act, benA, CaM, mcm7, RPB2 and tsr1

description: Combined dataset of act, benA, CaM, mcm7, RPB2 and tsr1 sequences for 33 taxa belonging to Aspergillus viridinutans complex - A. felis clade only. act: positions 1-329; benA: positions 330-803; CaM: positions 804-1484; mcm7: positions 1485-2107; RPB2: positions 2108-3074; tsr1: positions 3075-3835.
DOI: 10.5061/dryad.5g76b10/1
title: Confirmed_Breeding_Pairs_Genotypes

description: File contains genotypes for DAB1 and DAB2 MHC alleles, for all established breeding pairs identified between 2010-2015. Female allele IDs are listed in columns FDAB1.1 : FDAB2.2; males in MDAB1.1 : MDAB2.2.
DOI: 10.5061/dryad.5g76b10/3
title: DAB1_Amino_Acid_Matrix

description: Number of amino acid substitutions between Ocle-DAB1 MHC allele pairings.
DOI: 10.5061/dryad.5g76b10/4
title: DAB2_Amino_Acid_Matrix

description: Number of amino acid substitutions between Ocle-DAB2 allele pairings.
DOI: 10.5061/dryad.5g76b10/5
title: Adult_morphometric_data

description: Year, mass, tarsus length, wing chord, for adults used in morphometrics*genotype analyses
DOI: 10.5061/dryad.5tg4sv6/2
title: Caterpillar parasitism & plant defenseive proteins
DOI: 10.5061/dryad.5tg4sv6/3
title: Caterpillar saliva & plant defense responses
DOI: 10.5061/dryad.5tg4sv6/4
title: GOX enzyme activity time course
DOI: 10.5061/dryad.5tg4sv6/5
title: GOX gene expression time course
DOI: 10.5061/dryad.5vp4vs3/1
title: Selection on seed size experiment in the wild

description: Data from a natural selection experiment where we manipulated water avaliability and conspecific denisty to investigate the effects of the environment on selection on seed size. We used naturally germinated plants and we related relative fitness to standardized seed diameter to test slope differences between treatments.
DOI: 10.5061/dryad.641hb/10
title: Figure 5C
DOI: 10.5061/dryad.641hb/11
title: Figure 2G
DOI: 10.5061/dryad.641hb/12
title: Figure 2H
DOI: 10.5061/dryad.641hb/13
title: Figure 3B
DOI: 10.5061/dryad.641hb/14
title: Figure 3B
DOI: 10.5061/dryad.641hb/15
title: Figure 3C
DOI: 10.5061/dryad.641hb/7
title: FIgure 1G
DOI: 10.5061/dryad.641hb/8
title: Figure 1H
DOI: 10.5061/dryad.641hb/9
title: Figure 2I
DOI: 10.5061/dryad.683br42/1
title: Supplementary Data 1 - R output of occurrences used in final analysis

description: R output of specimen occurrences used in the final analysis. This includes occurrences from the middle Permian remaining after pruning of specimens with unacceptably high uncertainty surrounding their stratigraphic provenance. It also includes occurrence data for the late Permian Tropidostoma AZ.
DOI: 10.5061/dryad.683br42/2
title: Supplementary Table 1 - Input data for analysis

description: Supplementary Table 1. Excel sheet with occurrence data used in this study. Sheet 1 shows occurrences in the Eodicynodon, Tapinocephalus and Pristerognathus assemblage zones. Sheet 2 shows occurrences in the Tropidostoma Assemblage Zone. Explanation of data collection is in the Materials and Methods.
DOI: 10.5061/dryad.82jv0/1
title: Supplementary file 1 (PDF format)

description: All data extracted from publications based on confirmatory studies
DOI: 10.5061/dryad.82jv0/2
title: Supplementary file 1 (CSV format)

description: All data extracted from publications based on confirmatory studies
DOI: 10.5061/dryad.bg06fn2/1
title: BornToRun_DATA

description: White-tailed deer FIDs, alert distances, and angle of approach from encounters with a human approacher.
DOI: 10.5061/dryad.bg06fn2/2
title: BornToRun_CODE

description: R script for goodness of fit and likelihood ratio analyses on one and two risk factor models of prey escape behavior. See README for more information.
DOI: 10.5061/dryad.cj262df/4
title: Miller_et_al_Alignments

description: Folder containing the alignments used for analyses. DN12_rDNA_ML.fas was used in IQ-TREE for the DNA1&2 ML analysis (code used is included at top of file). DN12_rDNA_MrBayes.nex was used in the DNA1&2+rDNA MrBayes analysis (code is at bottom of file). AA_for_ML.phy and rDNA_for_ML.phy were used in IQ-TREE for the AA+rDNA ML analysis (code is contained in the AA_rDNA_ML.nex file). AA_rDNA_Bayes.nex was used in the AA+rDNA MrBayes analysis (code included at the bottom).
DOI: 10.5061/dryad.cj262df/5
title: Miller_et_al_Loci

description: Folder contains alignments of each loci used in the study.
DOI: 10.5061/dryad.cj262df/6
title: Miller_et_al_ST1-ST2

description: Supplementary tables for Miller_et_al 2017 that include genbank accessions.
DOI: 10.5061/dryad.cj262df/7
title: Miller_et_al_SF1

description: Supplementary figures. Bayesian and Maximum Likelihood trees for AA+rDNA and DNA1&2+rDNA datasets.
DOI: 10.5061/dryad.cj262df/8
title: ML_Bayes_Con

description: Trees in newick format, in the following order: AA+rDNA Bayesian, AA+rDNA ML, DNA1&2+rDNA Bayesian, DNA1&2+rDNA ML, Constraint.
DOI: 10.5061/dryad.cv74242.2
title: Data from: Conservation of sex-linked markers among conspecific populations of a viviparous skink, Niveoscincus ocellatus, exhibiting genetic and temperature-dependent sex determination
DOI: 10.5061/dryad.cv74242.2/1.2
title: Readme_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242.2/2.2
title: SNPs_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242.2/3.2
title: PA_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242.2/4.2
title: FASTA_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.g6r7943/1
title: voucher_table

description: A tab-delimited text file of the individuals sampled for the phylogenetic analyses with voucher information and GenBank accession numbers.
DOI: 10.5061/dryad.g6r7943/2
title: alignment_trimmed.nex

description: Trimmed alignment used in analyses in nexus format.  Order of regions is ITS (bases 1-664), followed by trnK-matK (bases 665-3418), followed by rbcL (bases 3419-4799).
DOI: 10.5061/dryad.g6r7943/3
title: alignment_untrimmed.nex

description: Untrimmed original alignment in nexus format.  Order of regions is ITS (1-664), followed by trnK-matK (bases 665-3668), followed by rbcL (bases 3669-5518).
DOI: 10.5061/dryad.g6r7943/4
title: Fig_S1.pdf

description: Fig. S1. Best tree from the RAxML analysis of the combined trnK-matK and rbcL core Caryophyllales dataset showing branch lengths. Branch labels show bootstrap values from 1000 bootstrap rep¬licates. When more than one accession per species was included, the localities after the names correspond to those in Appendix 1. SAfr refers to South Africa.
DOI: 10.5061/dryad.g6r7943/5
title: Fig_S2.pdf

description: Fig. S2. Best tree from the RAxML analysis of the ITS Kewa dataset showing branch lengths. Branch labels show bootstrap values from 1000 bootstrap rep¬licates. When more than one accession per species was included, the localities after the names correspond to those in Appendix 1. SAfr refers to South Africa.
DOI: 10.5061/dryad.g6r7943/6
title: Fig_S3.pdf

description: Fig. S3. Best tree from the RAxML analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset showing branch lengths. Branch labels show bootstrap values from 1000 bootstrap rep¬licates. When more than one accession per species was included, the localities after the names correspond to those in Appendix 1. SAfr refers to South Africa.
DOI: 10.5061/dryad.hg5473q/1
title: Data and Code

description: Contains the four data files, two R scripts, and subfolder needed to replicate the analyses and figures in "Body size shifts influence effects of increasing temperatures on ectotherm metabolism". To do so, run first data_cleaning_MTEecto.R and then data_analysis_MTEecto_expanded.R using R version 3.4.1.
DOI: 10.5061/dryad.j0rh697/1
title: Fuiman_Egg_Boon_2009-2016_fatty_acid_values

description: Each line of data in this comma-delimited file represents a sample of eggs collect from the Aransas Ship Channel. The file reports collection information and the amounts of individual fatty acids (expressed as a percentage of total fatty acids) plus sums and ratios of those variables.
DOI: 10.5061/dryad.j0rh697/2
title: Fuiman_Marine_Animal_fatty_acid_values

description: Each line of data in this comma-delimited file represents a sample of a marine animal collected from the vicinity of Port Aransas. The file reports information about the sample and the amounts of individual fatty acids (expressed as a percentage of total fatty acids) plus sums and ratios of those variables for the whole animal.
DOI: 10.5061/dryad.j0rh697/3
title: Fuiman_Time_Series_Data_2007-2016

description: Each line of data in this comma-delimited file represents one month in a time series that begins January 2007 and ends December 2016. Some data are original (egg principal component scores); other data came from published data sets identified in the publication.
DOI: 10.5061/dryad.kr4031f/2
title: CTmin

description: Minimum critical limit data used in analyses
DOI: 10.5061/dryad.kr4031f/3
title: Tolerance Breadth

description: Colony mean thermal tolerance breadths
DOI: 10.5061/dryad.ms38c8k/1
title: Dryad archive data_1_metadata
DOI: 10.5061/dryad.r4mk47p/2
title: DCA scores
DOI: 10.5061/dryad.rm2n41j/1
title: Dereplicated sequences

description: This fasta file contains all different sequences found in the experiments, except sequences that occurred only once in the dataset.
    The sequences have been generated by the Illumina technology (HiSeq 2500 sequencing platform, with paired-end sequencing, 2 x 125 bp)
DOI: 10.5061/dryad.rm2n41j/2
title: dungbeetle_intermediate_results

description: This file presents filtered data after the OBITools analysis and removing the contaminants, but before the manual inspection. It contains the number of occurrences of each molecular taxonomic units (MOTUs) in the different samples and controls, as well as different columns related to the taxonomic identification of the sequences.
    The sequences have been generated by the Illumina technology (HiSeq 2500 sequencing platform, with paired-end sequencing, 2 x 125 bp)
DOI: 10.5061/dryad.rm2n41j/3
title: dungbeetle_final_table

description: This file presents the final presence/absence table of the different mammalian species identified in the different dung beetle fecal samples.
DOI: 10.5061/dryad.02f33n6/1
title: Appendix S1

description: A collection of 3D models used in this study. It contains a 3D model of complete specimen BRSUG 29950-13 how it was positioned in the matrix, and individual elements. Individual elements are in some cases presented both in their original and retrodeformed state, where the description was based off retrodeformed versions. For methods used to create models see Zaher et al. (2018).
DOI: 10.5061/dryad.0b58t3v/2
title: Clinical Correlation between Erectile Function and Ejaculatory Function in the Czech Male Population

description: When using this data, please cite the original publication. SAV is a file extension used for the saved date of SPSS (Statistical Package for the Social Sciences). SAV files contain binary data which can only be used on the platform that created the file. If migrating the file to another platform, it would have to be converted into the appropriate format. Please note that the variables education and relationship status have been removed from the original dataset in order to protect participant identity.
DOI: 10.5061/dryad.2pb356h/1
title: Similarity Matrix files

description: The zipped folder contains two documents, the R code used to calculate the similarity matrix and produce the heatmaps, and the character-taxon matrix ("Similarity_matrix.txt") that was used for computing similarity values. The "Similarity_matrix.txt" file differs from our original character-taxon matrix in that polymorphisms were exchanged with "?", and the taxa we re-arranged to mirror our tree topology of the unordered analysis.
DOI: 10.5061/dryad.2pb356h/2
title: Appendix S1. Character_list_with_figures

description: Appendix S1 includes our character list, explanations of character modifications, optimizations for each character, character illustrations, and an extended discussion of c characters related to the cartid arterial system.
DOI: 10.5061/dryad.2pb356h/3
title: Tempelton's Tests files

description: This zipped folder contains all files used for the Templeton's test. This folder is organised in subfolders, whereas "1 - Pasimony Analysis Input files" contains the character-taxon matrix (in PAUP format), the molecular backbone constraint, and constraint files for all 20 alternative hypotheses tested. "2 - Parsimony Analysis Results" contains consensus tree files and MPT tree files for all analyses. "3- Symmetric Distance Analysis Input files" contains nexus files used to compute symmetric distances. "4 - Symmetric Distance Analysis Results" contains the symmetric distance matrices for all constraints as text-files. "5 - Tree selection for Templeton" contains the R code used to select tree-pairs for Templeton's tests. "6 - Templeton's Test Input files" contains nexus files in which selected trees to be compared are included. Files are provided for each constraint for maximum and minimum symmetric distance tree pairs. "7 - Templeton's Test Results" are PAUP log-files that include the test results.
DOI: 10.5061/dryad.31sm2/1
title: Appendix Table S1
DOI: 10.5061/dryad.31sm2/2
title: Supplementary Figures
DOI: 10.5061/dryad.31sm2/3
title: Example model code in R
DOI: 10.5061/dryad.38889/6
title: Species delimitation in Aspergillus felis clade based on six genetic loci

description: Schematic representation of results of species delimitation methods in Aspergillus felis clade based on six genetic loci. The results of multilocus method (STACEY) are compared to results of single-locus methods (mPTP, bGMYC, GMYC). The results of STACEY are shown as tree branches with different colours, while the results of single-locus methods are depicted with coloured bars highlighting congruence across methods. The displayed tree is derived from IQtree analysis based on a concatenated dataset and is used solely for the comprehensive presentation of the results from different methods. The species validation analysis results (BP&P) are appended to nodes and  shown in gray bordered boxes; the values represent posterior probabilities calculated in three scenarios having different prior distributions of parameters θ (ancestral population size) and τ0 (root age). The top value represents the results of analysis with large ancestral population sizes and deep divergence: θ ~ G (1, 10) and τ0 ~ G (1, 10), the middle value ); large ancestral populations sizes and shallow divergences among species: θ ~ G (1, 10) and τ0 ~ G (2, 2000) and the bottom value small ancestral population sizes and shallow divergences among species: θ ~ G (2, 2000) and τ0 ~ G (2, 2000).
DOI: 10.5061/dryad.4081h6b/1
title: DRYAD_data_Loeffler_and_Klotz._A_common_garden_study_of_two_species_of_shooting_star_06Apr2018

description: Data and statistics associated with figures, tables, and appendices of the associated paper of the same name and authors published in Castanea
DOI: 10.5061/dryad.5f82b32/1
title: Supplemental Data

description: Supplemental figure 1, Supplemental tables 1-5.
DOI: 10.5061/dryad.5g76b10/2
title: MHC genotypes and reproductive success

description: Ocle-DAB1 and Ocle-DAB2 MHC genotypes for all adults in sampled background population (breeders and non-breeders), with number of chicks each individual has produced.
DOI: 10.5061/dryad.5g76b10/6
title: Hatch dates

description: Vetted hatch dates for chicks 2011-2015, within +- 3 days.
DOI: 10.5061/dryad.5tg4sv6/10
title: Parasitoid performance
DOI: 10.5061/dryad.5tg4sv6/11
title: Plant induced defense response in different glucose oxidase (GOX) concentrations
DOI: 10.5061/dryad.5tg4sv6/6
title: McBV injection & GOX (gene expression & enzyme activity)
DOI: 10.5061/dryad.5tg4sv6/7
title: McBV injection & GOX activity
DOI: 10.5061/dryad.5tg4sv6/8
title: McBV injection & plant defense responses
DOI: 10.5061/dryad.5tg4sv6/9
title: Parasitized H. zea RGR
DOI: 10.5061/dryad.641hb/16
title: Figure 3D
DOI: 10.5061/dryad.641hb/17
title: Figure 3E
DOI: 10.5061/dryad.641hb/18
title: Figure 3F
DOI: 10.5061/dryad.641hb/19
title: Figure 4A
DOI: 10.5061/dryad.641hb/20
title: Figure 4B
DOI: 10.5061/dryad.641hb/21
title: Figure 4D
DOI: 10.5061/dryad.641hb/22
title: Figure 4E
DOI: 10.5061/dryad.641hb/23
title: Figure 5B
DOI: 10.5061/dryad.88qs138/1
title: Lockwood Dryad Submission 6-30-18

description: CSV de-identified data (3 indirect identifiers included), documentation (codebook, readme), and SAS Syntax used to produce the manuscript
DOI: 10.5061/dryad.96712kh/7
title: Sequence files for nine loci for all seperate arthropod specimens
DOI: 10.5061/dryad.96dn293/1
title: Data and R code

description: The zip archive contains the data and R code used to conduct the analyses reported in the publication. Readme files in the subdirectories contain metadata and instructions for running the code. Note that changing the directory structure will cause the R scripts to fail.
DOI: 10.5061/dryad.b4m648v/1
title: data

description: Data is saved as a tab delimited text file (data.txt). Data file has the following columns: 1) length - shell length of experimental snails (mm); 2) food_consumption - food consumption of experimental snails (g/day); 3) respiration_rate - respiration rate of experimental snails (mg/h); 4) antibacterial_activity - antibacterial activity of haemolymph of experimental snails; 5) PO_activity - phenoloxidase-like activity of haemolymph of experimental snails; 6) chemo-orientation - proportion of cercariae found in the SCW arm of the test chamber when considering those cercariae that left the central compartment; 7) attractiveness - proportion of all cercariae in the test chamber that were found in the SCW arm; 8) susceptibility - proportion of cercariae successfully infecting the snails.
DOI: 10.5061/dryad.bb3h52t/1
title: README

description: This file should be replaced by the files uploaded via FTP.
They should include two raw fastq files: "Nyssa_GBS_R1.fq.gz" and "Nyssa_GBS_R2.fq.gz"; One barcode file: "barcode2.key"; 9 parameter files for extracting different matrix via pyRAD software.
DOI: 10.5061/dryad.bb3h52t/2
title: ML_tree

description: M50 matrix for ML tree.
DOI: 10.5061/dryad.bb3h52t/3
title: parameter_setting

description: All the parameter files during RAD-seq analysis.
DOI: 10.5061/dryad.bb3h52t/4
title: Forward raw data
DOI: 10.5061/dryad.cv74242.1
title: Data from: Conservation of sex-linked markers among conspecific populations of a viviparous skink, Niveoscincus ocellatus, exhibiting genetic and temperature-dependent sex determination
DOI: 10.5061/dryad.cv74242.1/1.1
title: Readme_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242.1/2.1
title: SNPs_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242.1/3.1
title: PA_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.cv74242/4
title: FASTA_SexMarkersInSkink_Hilletal2018
DOI: 10.5061/dryad.g6r7943/10
title: Fig_S2.tre

description: Fig. S2 tree. Best tree from the RAxML analysis of the ITS Kewa dataset showing branch lengths, in nexus format. Branch labels show bootstrap values from 1000 bootstrap rep¬licates.
DOI: 10.5061/dryad.g6r7943/11
title: Fig_S3.tre

description: Fig. S3 tree.  Best tree from the RAxML analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset showing branch lengths, in nexus format. Branch labels show bootstrap values from 1000 bootstrap rep¬licates.
DOI: 10.5061/dryad.g6r7943/12
title: Fig_S4.tre

description: Fig. S4 tree.  MrBayes analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset, in nexus format. Branch labels show Bayesian posterior probabilities.
DOI: 10.5061/dryad.g6r7943/13
title: Fig_1_S5.tre

description: Fig. 1 and S5 tree.  BEAST analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset, in nexus format. Node labels represent median divergence time estimates (Ma).
DOI: 10.5061/dryad.g6r7943/7
title: Fig_S4.pdf

description: Fig. S4. MrBayes analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset. Branch labels show Bayesian posterior probabilities. When more than one accession per species was included, the localities after the names correspond to those in Appendix 1. SAfr refers to South Africa.
DOI: 10.5061/dryad.g6r7943/8
title: Fig_S5.pdf

description: Fig. S5. BEAST analysis of the combined trnK-matK, rbcL, and ITS, core Caryophyllales dataset. Node labels represent median divergence time estimates (Ma). Blue node bars represent 95% HPD. When more than one accession per species was included, the localities after the names correspond to those in Appendix 1. SAfr refers to South Africa.