cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t5v58/13
title: FigureS6

description: Supplementary Figure 6: Comparison of evolutionary rates. Boxplots of inferred evolutionary rates (in expected mutations per site per billion years) are shown for plastid markers (top row) and nuclear markers (bottom row) under calibration #1. Rates are sorted by phylogenetic groups: basal angiosperms (“basal”), eudicots, monocots without graminids, graminids without BEP-PACMAD and BEP-PACMAD. The results obtained with four different methods are shown: BEAST, PB_ug = uncorrelated gamma method implemented in PHYLOBAYES, PB_ln = log-normal autocorrelated method implemented in PHYLOBAYES, MD = MULTIDIVTIME.
DOI: 10.5061/dryad.t5v58/14
title: FigureS7

description: Supplementary Figure 7: Age for the BEP-PACMAD crown estimated by MULTIDIVTIME under different priors. The age for the node (in million years ago) is indicated as a function of the prior for the mean of the Brownian motion constant mean. Results are aggregated for different values of the other priors. Analyses with a value of 0.01 for the Brownian motion constant standard deviation are in black.
DOI: 10.5061/dryad.t5v58/15
title: FigureS8

description: Supplementary Figure 8: Detailed comparison of methods and datasets. For calibration #1, the age estimates (in million years ago) are represented for nodes that were shared between phylogenetic trees of plastid and nuclear markers. The ages are represented independently when produced by BEAST and MULTIDIVTIME. Black circles are ages based on the whole plastid dataset, red squares are ages based on plastid markers for 28 species only, black triangles are aged based on the whole nuclear dataset, and red bars indicate the interval between the 1st and 3rd quartiles of 100 replicates of the nuclear dataset decreased to the size of the plastid dataset. Taxonomic groups are indicated on the bottom. The last point corresponds to the crown of BEP, and the horizontal bar indicates the minimal age for the clade that would be congruent with the 67 Ma phytolith fossil (Prasad et al. 2011). Numbers can be used to identify the corresponding nodes in Supplementary Figure 9.
DOI: 10.5061/dryad.t5v58/16
title: FigureS9

description: Supplementary Figure 9: Node identity. Nodes represented in Figure 2 and Supplementary Figure 8 are indicated on the phylogenetic tree showing the expected relationships among nuclear genes without branch lengths. Taxonomic groups represented in the tips are delimited on the right.
DOI: 10.5061/dryad.v0v58gd5/1
title: Mutator frequencies during propagation

description: The dataset contains mutator frequencies measured during propagation of the five sets of experimental populations mentioned in the manuscript.
DOI: 10.5061/dryad.vt562/1
title: PlaybackExperimentLumped_130720

description: Results of a playback experiment testing the effect of three different peacock calls on the probability that females would approach the playback speaker. 'Success' gives the number of time intervals when at least one female was near the speaker. 'Fail' gives the number of time intervals when no females were near the speaker.
DOI: 10.5061/dryad.vt562/2
title: NaturalHoots_130720

description: Observations of female presence before and after peacock solo hoot calls.
DOI: 10.5061/dryad.vt562/3
title: RatesHootCallsMatingSuccess_120720

description: Male call rates, mating success, and ornamental traits.
DOI: 10.5061/dryad.vt8t7/4
title: DIYABC reftable.header for ABC demographic analysis in Silene vulgaris

description: This file contains the metadata necessary to run approximate Bayesian computation in DIYABC for 2 historical demographic scenarios in Silene vulgaris.
DOI: 10.5061/dryad.1154dd89/1
title: Sharpe et al_R argentea collection and morphological data

description: Please see ReadMe file
DOI: 10.5061/dryad.1154dd89/2
title: Sharpe et al_R argentea egg size and fecundity

description: Please see ReadMe file
DOI: 10.5061/dryad.1v8j7/15
title: branch dS values
DOI: 10.5061/dryad.2355t/1
title: Proestou_etal_Killifish_SNP_sequences

description: Fasta format file containing the flanking sequences for validated single nucleotide polymorphisms (SNPs) included in the population genetic analysis.
DOI: 10.5061/dryad.25nt8/1
title: Yalkaparidon morphological matrix - Yalkaparidon scored for craniodental characters only

description: Yalkaparidon morphological matrix - Yalkaparidon scored for craniodental characters only
DOI: 10.5061/dryad.25nt8/2
title: Yalkaparidon morphological matrix - Yalkaparidon scored for craniodental and tarsal characters

description: Yalkaparidon morphological matrix - Yalkaparidon scored for craniodental and tarsal characters
DOI: 10.5061/dryad.25nt8/3
title: Yalkaparidon total evidence matrix - Yalkaparidon scored for craniodental characters only

description: Yalkaparidon total evidence matrix - Yalkaparidon scored for craniodental characters only
DOI: 10.5061/dryad.25nt8/4
title: Yalkaparidon total evidence matrix - Yalkaparidon scored for craniodental and tarsal characters

description: Yalkaparidon total evidence matrix - Yalkaparidon scored for craniodental and tarsal characters
DOI: 10.5061/dryad.3488j/1
title: Biomass and yield data of monocultures and mixtures for the different treatment combinations
DOI: 10.5061/dryad.5922k/1
title: HenryObleser_PLOSONE_rawdata

description: These four data files constitute a single large file that has been split to facilitate download and reuse. To recombine the files, please follow these instructions: On Unix, Linux, or Mac OSX, recombine files with the "cat" command, like this: cat xaa xab xac xad &gt; dataFile.zip  On Windows, recombine files with the "copy" command, like this: copy /B xaa+xab+xac+xad dataFile.zip
DOI: 10.5061/dryad.5922k/2
title: part b
DOI: 10.5061/dryad.5922k/3
title: part c
DOI: 10.5061/dryad.5922k/4
title: part d
DOI: 10.5061/dryad.5bd50/1
title: Ferenci_Heredity_data

description: The file includes all primary data for Figures 1-5. The file is an .xls spreadsheet with all the columns/labels as described in the axes/legends to the figures.
DOI: 10.5061/dryad.5fn76/1
title: Hannides_LO13042_Data
DOI: 10.5061/dryad.5m96v/1
title: Study 1 - numerical analyses

description: This zip file contains a set of data files This study is comprised of an ensemble of 10 simulations for each of the 4 focal grid cells listed in Table 4 of the manuscript. The outputs were used to generate Figure 2 of the manuscript. Refer to the ReadMe-Study1.txt for a detailed description of output files and ReadMe-ModelSetup.txt file for a more detailed description of the model setup files.
DOI: 10.5061/dryad.5m96v/2
title: Study 2 - Individual and community predictions

description: Data outputs generated by the Madingley General Ecosystem Model for single simulations in the four focal grid cells listed in Table 4 of the manuscript. These outputs were used to generate Figures 3 and 4 of the manuscript. A comprehensive description of the outputs is given in the ReadMe-Study1.txt file. Refer to ReadMe-ModelSetup.txt for a description of the model setup files.
DOI: 10.5061/dryad.5m96v/3
title: Study 3 - community predictions at observation locations

description: Outputs from the Madingley model for Study 3 listed in Table 3 of the manuscript. The data file is comprised of an ensemble of 10 simulations for each of the 13 focal grid cells listed in Table S3. Model outputs files are described in detail in 'ReadMe-Study3.txt', whilst model setup files are detailed in the 'ReadMe-ModelSetup.txt'.
DOI: 10.5061/dryad.62j0q/1
title: Quantitative proteomics data set

description: The folder 'Mannitol' contains data from the two mixtures (M1, M2) in the mannitol background. The folder 'Fructose' contains data from the two mixtures (M1, M2) in the fructose background. Mixtures were prepared as shown in Fig. 1a of the main paper: | Label: Strain, Carbon source (X = fructose or mannitol) | M1: | Light (L): M145, G+X | Medium (M): M145, X | Heavy (H): dGlkA, G+X | M2: | Light (L): dGlkA, X | Medium (M): M145, X | Heavy (H): dGlkA, G+X | Normalized ratios as found in proteinGroups.txt were used to create the data tables in the main paper. Descriptions of all tables and column headers can be found in 'tables.pdf'. All tables were created using MaxQuant 1.2.2.5.
DOI: 10.5061/dryad.6cv06/1
title: raw data
DOI: 10.5061/dryad.8n8v3/1
title: Panda_FEA_models_BioLett

description: Three-dimensional models for FE analysis of the Ailurus and Ailuropoda skulls. Open .st7 files with Strand7 software.
DOI: 10.5061/dryad.b68hr/1
title: Bicyclus data_Saastamoinen et al. 2012_JEB

description: The file data.xls includes all data needed to fit the animal model.
DOI: 10.5061/dryad.b68hr/2
title: MATHEMATICA6_estimate

description: MATHEMATICA6_estimate.nb includes the source code needed to fit the model to data. It also illustrates the obtained parameter estimates and the mixing of the algorithm.
DOI: 10.5061/dryad.b68hr/3
title: MathLinkLDL

description: The file MathLinkLDL.exe is a linear solver that is called from the Mathematica file.
DOI: 10.5061/dryad.f37km/2
title: ReadMe

description: ReadMe file describing the contents of this dataset.
DOI: 10.5061/dryad.f37km/3
title: Results_Main_Experiment

description: Original (anonymized) score sheets, labeled with the numbers of the subject.
DOI: 10.5061/dryad.f37km/5
title: Walkthrough_virtual_environment

description: A WMV movie file showing a walkthrough of the virtual environment used in this study.
DOI: 10.5061/dryad.ft56mn76/1
title: Blown vs unblown color
DOI: 10.5061/dryad.ft56mn76/2
title: Spatial data for color
DOI: 10.5061/dryad.ft56mn76/3
title: Spatial data for pattern
DOI: 10.5061/dryad.g8h42/1
title: Microsatellite data and sequence data of R.affinis-
DOI: 10.5061/dryad.g8h42/2
title: Morphology data of R. affinis
DOI: 10.5061/dryad.g8h42/3
title: DIY ABC-input file of R.affinis
DOI: 10.5061/dryad.g8h42/4
title: DIY ABC-input file of R.affinis-microsatellite
DOI: 10.5061/dryad.hd300/22
title: RatDems-House15-ML-RELATE

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 15 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/23
title: RatDems-House16-ML-RELATE

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 16 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/24
title: RatDems-House19-ML-RELATE

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 19 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/25
title: SalvadorRatMsatGenotypes

description: Rat microsatellite genotypes for 17 loci in 146 individuals captured in Salvador, Brazil. Individuals are grouped by sites and sampling year or by cluster in different sheets in the workbook. All data files used in analyses were converted for specialized software from these excel sheets in CREATE (Coombs, Letcher, & Nislow 2009).
DOI: 10.5061/dryad.hg6st/1
title: Trigonoderus repeated measures data.txt

description: Three measurements for each morphometric character (23 characters on 86 females). Column names: sp.id - specimen identity; repeat - repeated measures; sp.name - group name; spm.code - specimen code; cntry.fact - country code, descriptions of all other abbreviations in the paper Table 1. Cells with "NA" - missing data.
DOI: 10.5061/dryad.hv75h/12
title: InfiniumFWSW_fst

description: Fst calculations between all freshwater and all saltwater L. parva (18 freshwater, 21 saltwater individuals: Florida Atlantic = 5 fresh, 6 salt; Florida Gulf = 8 fresh, 7 salt; Texas Gulf = 5 fresh, 8 salt) genotyped on the Infinium Chip.  Calculations done in hierfstat in R.
DOI: 10.5061/dryad.jh4dr/1
title: oxyura_jamaicensis_files.zip

description: arlequin, IMa2, nexus, and structure infiles
DOI: 10.5061/dryad.jh4dr/3
title: genbank_accessions_seqids

description: Genbank accessions and sequence IDs
DOI: 10.5061/dryad.k7686/1
title: Supplementary Table 1
DOI: 10.5061/dryad.k7686/2
title: Supplementary Table 2
DOI: 10.5061/dryad.k7686/3
title: Supplementary Table 3
DOI: 10.5061/dryad.k7686/4
title: Supplementary Table 4
DOI: 10.5061/dryad.m5g7d/1
title: FIA_data_derived

description: FIA plots: species richness, commmunity mean trait values and trait diversity (seed mass, leaf nitrogen content, wood density), phylogenetic diversity, water deficit, soil nutrient availability, and geographic coordinates.
DOI: 10.5061/dryad.m5g7d/2
title: CVS_data_derived

description: Community and environmental data for CVS plots.
DOI: 10.5061/dryad.m5g7d/3
title: FIA_siteXsp_matrix

description: Tree species abundance matrix for FIA plots.
DOI: 10.5061/dryad.m5g7d/4
title: CVS_siteXsp_matrix

description: Tree species abundance matrix for CVS plots.
DOI: 10.5061/dryad.m5g7d/5
title: CVS_phylogeny

description: Phylogenetic tree of taxa in CVS plots.
DOI: 10.5061/dryad.m5g7d/6
title: FIA_phylogeny

description: Phylogenetic tree of taxa in FIA plots.
DOI: 10.5061/dryad.mk364/1
title: Description of files deposited to Dryad

description: Description of files deposited to Dryad
DOI: 10.5061/dryad.mk364/2
title: R script: 1_Slacks

description: This script allows testing multiple values for two stacks parameters used in the denovo_map command: M and n. It runs both denovo_map and populations commands.
DOI: 10.5061/dryad.mk364/3
title: R script: 2_RAD_Parse_tags

description: This script was used to retrieve and sort sequences from the stacks outputs (after applying the populations command) into variable versus invariable sequences. These sequences were then blasted using Blast2GO.
DOI: 10.5061/dryad.mk364/4
title: R script: 3_RAD_Similarity_evalue_blastn

description: This script retrieves the similarity scores from Blast results obtained using Blast2GO, calculates the median and range, and builds a histogram of these similarity values.
DOI: 10.5061/dryad.mk364/5
title: R script: 4_RAD_Parse_blast_xml_Pp_Dd

description: This script was used to summarize Blast hits results from Blast2GO (number of hits belonging to each organism) and to retrieve and export in fasta format the whole sequence from the best hits (these longer sequences were subsequently used in Blast2GO).
DOI: 10.5061/dryad.mk364/6
title: R script: 5_Getting_info_on_best_Ttru_hit_sequences

description: This script retrieves the length of the best Blast hit sequences obtained using the previous R script.
DOI: 10.5061/dryad.mk364/7
title: R script: 6_Annotation_analysis_DelphinusTursiops_RADtag_08-13-2013

description: This script was used to make histograms of the Blast2GO annotation results.
DOI: 10.5061/dryad.mk364/8
title: sequence file for individual 9902012

description: Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
DOI: 10.5061/dryad.mk364/9
title: sequence file for individual 10201010

description: Individual identifiers are listed in Table 1. These sequences have been filtered for quality (post process_radtags).
DOI: 10.5061/dryad.nd853/1
title: Quality filtered genotypes of Pacific lamprey in GENEPOP format

description: GENEPOP file: 518 Pacific lamprey individuals from 21 collections, genotyped with a set of 4,439 quality filtered SNPs from a larger dataset of 8,772 unique SNP loci identified using methods described by Hess et al. 2013. "POP" headings delineate collections of individuals and include collections names listed in Table 1, Hess et al. 2013.
DOI: 10.5061/dryad.q2c86hb2/1
title: Table_1

description: Summary of the the technical characteristics of the 83 polymorphic microsatellite loci validated from the turbot (Scophthalmus maximus) EST database.
DOI: 10.5061/dryad.q2c86hb2/2
title: Table_S1

description: Comparative analysis of turbot microsatellites with Senegalese sole (Solea senegalensis), bastard halibut (Paralichthys olivaceus) and Atlantic halibut (Hippoglossus hippoglossus).
DOI: 10.5061/dryad.qg67c/1
title: AC_regScores_BJLS-2861.R1

description: Regression Scores (RegScore1) obtained from an Ordinary Least Square regression between Procrustes Coordinates (original data: 43 landmarks from caviomorph crania) and ln-CS. These were obtained using MorphoJ (Klingenberg, 2011).
DOI: 10.5061/dryad.qg67c/2
title: caviomorh_phy_BJLS-2861.R1

description: Phylogenetic relationships among caviomorphs studied. Phylogenetic relationships were estimated through Bayesian inference methods implemented in BEAST v1.6.1. Sequences from the Growth Hormone Receptor (GHR), Transtyrethin Hormone (TTH) and mitochondrial subunit 12S (12S rRNA) were used. Values correspond to estimated age of each taxa.
DOI: 10.5061/dryad.qg67c/3
title: CoordProc_3Dskull_BJLS-2861.R1

description: Procrustes coordinates obtained through a Generalized Procrustes Analysis (GPA) on raw coordinates of 43 landmarks representing caviomorph cranial shape. To obtain average ProcCoord for each genus, a separate GPA was carried for each one in Morphologika 2.5.
DOI: 10.5061/dryad.qg67c/4
title: RSCs_BJLS-2861.R1

description: PC scores for caviomorph genera within a morphospace constructed through a Principal Component Analysis on the residuals of an Ordinary Least Square regression between Procrustes Coordinates (raw data: 43 landmarks representing cranial shape) and lnCS (natural-log transformed centroid sizes). This analysis was carried out using MorphoJ (Klingenberg, 2011)
DOI: 10.5061/dryad.qg67c/5
title: RWs_BJLS-2861.R1

description: Relative Warps scores (i.e. PC scores) of caviomorph taxa corresponding to the study of cranial shape variation. RWA was performed on the Procrustes Coordinates of 43 landmarks representing cranial shape. This analysis was carried out using MorphoJ (Klingenberg, 2011)
DOI: 10.5061/dryad.sp2m46f6/1
title: CHC data

description: Please see ReadMe.txt
DOI: 10.5061/dryad.tf8q1/1
title: full_gene_set_12S_16S_CO1_CytB_phylogeny

description: This nexus file contains the sequence data for the full gene set (ND4, CR, 12s, 16s,Cox1, Cytb) used to confirm major nodes and refine bootstrap support for Elseya novaeguineae, with E. branderhorsti as outgroup.
DOI: 10.5061/dryad.tf8q1/2
title: reduced_gene_set_CR_ND4_phylogeny

description: This nexus file contains the sequence data for the reduced gene set (ND4 and CR) used to recover the phylogeny for mitochondrial haplotypes of Elseya novaeguineae, with E. branderhorsti haplotypes as outgroup.
DOI: 10.5061/dryad.tf8q1/3
title: nuclear_emydura_group_beast_input

description: Nuclear data in nexus format used as the input for the Beast analysis.
DOI: 10.5061/dryad.tf8q1/4
title: mtdna_emydura_group_beast_input

description: Mitochondrial data in nexus format used as the input for the Beast analysis.
DOI: 10.5061/dryad.tf8q1/5
title: emydura_group_beast_trees_comb_1-7-5_output

description: Maximum clade credibility tree saved from figtree from the combined output of our Beast runs.
DOI: 10.5061/dryad.tf8q1/6
title: emydura.group

description: XML file used in the BEAST molecular clock analysis using only the RedbankPlains fossil calibration.
DOI: 10.25345/c57659t42
title: MassIVE MSV000097615 - A Comparative Metabolomics Study of Multiple Urological Diseases by Highly Sensitive Dansylation Isotope Labeling LC-MS
title: Urine analysis utilized 12C2/13C2-chemical dansylation labeling was used to explore the urinary amine/phenol-metabolome profiles of eight urological conditions compared with normal profiles from a total of 90 participants, pooling them as representative samples, and constructed metabolite panels to differentiate various urological conditions. IsoMS Pro software was used for the follwoing data processing. Mass spectrometry raw data and a supplementary file exported from IsoMS Pro were uploaded.
DOI: 10.13145/bacdive112145.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112146.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112147.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112148.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112149.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112150.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112151.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112152.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112153.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112154.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112155.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112156.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112157.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112158.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112159.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112160.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive112161.20230509.8
title: Streptomyces sp.

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.