cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.61pd6.1/1.1
title: Aligned matK matrix

description: Supplemental Data: Data File A.  The aligned matK DNA sequence matrix of 3,744 legume sequences and 100 outgroup taxa spanning core Eudicots. Nexus format.
DOI: 10.5061/dryad.61pd6.1/10.1
title: High Resolution Poster illustrating the new LPWG Legume Classification

description: Supplemental Data: Figure S3.  Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.
DOI: 10.5061/dryad.61pd6.1/7.1
title: Voucher information for LPWG matK sequences

description: Supplemental Data:  Table S1. Voucher information and GenBank numbers for all accessions included in the phylogenetic analyses of matK gene sequences.  Specimens identified with an asterisk (*) are included in the phylogenetic analyses presented in Fig. 1 and in Supplemental Data Fig. S1.  The remaining sequences are not included in the final analyses but are listed here to indicate that they were validated by LPWG. A total of 5,560 legume sequences were verified.  Phylogenetic analyses of all sequences listed allowed us to ascertain that the sequences are of good quality, properly identified taxonomically, and that they are not contaminants.
DOI: 10.5061/dryad.61pd6.1/8.1
title: RAxML Bootstrap Consensus Phylogenetic Tree

description: Supplemental Data: Figure S1.  Phylogeny of Leguminosae based on a RAxML analysis of 3,844 matK sequences representing 3,696 of the c. 19,500 species and 698 of the 765 genera of the family, including 100 outgroup taxa (uncoloured) spanning core Eudicots. Branch lengths are proportional to numbers of matK substitutions. All subfamilies are supported with 100% bootstrap. The phylogenetic tree can be visualised (e.g., with FigTree (http://tree.bio.ed.ac.uk/software/figtree/) or Dendroscope (http://dendroscope.org/; Huson & Scornavacca, 2012), and downloaded from Supplemental Data: Data file C.
DOI: 10.5061/dryad.61pd6.1/9.1
title: Poster illustrating the new LPWG Legume Classification

description: Supplemental Data: Figure S2.  Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.
DOI: 10.5061/dryad.61pd6.2/5.2
title: Sample of 1000 Phylobayes Posterior Trees

description: Supplemental Data: Data File E.  Sample of 1000 Bayesian posterior trees (newick format) resulting from a PhyloBayes analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa. This sample of posterior trees can be used to account for phylogenetic uncertainty in comparative analyses.
DOI: 10.5061/dryad.61pd6.2/6.2
title: Sample of 1000 RAxML Bootstrap Trees

description: Supplemental Data: Data File F.  Sample of 1000 bootstrapped trees (newick format) resulting from a RAxML analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa. This sample of posterior trees can be used to account for phylogenetic uncertainty in comparative analyses.
DOI: 10.5061/dryad.62275/1
title: Reproductive traits of resident mother plants

description: Data underlying tables and figures in the main manuscript and supporting information comprising explanatory variables from the Jena experimental setup and reproductive trait variables of resident K. arvensis mother plants (i.e., number of viable seeds, number of aborted seeds and total number of seeds per seed capsule per mother, mean seed mass (g) and final germination rate (%)).
DOI: 10.5061/dryad.62275/2
title: Performance traits of offspring under common garden conditions

description: Data underlying tables and figures in the main manuscript and supporting information comprising explanatory variables from the Jena experimental setup and K. arvensis offspring growth and reproduction traits in the common garden experiment (i.e., biomass (g), maximum plant height (cm), both leaf length and width (cm), as well as the total number of buds, capitula and infructescences; as well as naturally occurring powdery mildew presence and severity(%)).
DOI: 10.5061/dryad.8t8dh/1
title: Wax moth - Serratia marcescens dose response

description: The data contains times until death in hours of wax moth (Galleria mellonella) larvae injected with a certain dose (colony forming units, CFU) of Serratia marcescens db11.
DOI: 10.5061/dryad.b3d03/2
title: CypriniformesFullTree
DOI: 10.5061/dryad.b3d03/3
title: LociPartitions

description: Partition identifiers for all loci
DOI: 10.5061/dryad.b3d03/4
title: ProbeDesignFiles
DOI: 10.5061/dryad.b3d03/5
title: Alignment
DOI: 10.5061/dryad.nt890/3
title: CapeCod_NarrBay_GISdata_2015

description: GIS Area Calculations and Site Identifiers
DOI: 10.5061/dryad.nt890/4
title: ExperimentalSite_BurrowData_2015

description: Experimental plot burrow data 2015
DOI: 10.5061/dryad.nt890/5
title: ExperimentalSite_PenetrometerData_2015

description: Experimental plot substrate hardness data
DOI: 10.5061/dryad.r48vj/1
title: Flower and pollen production

description: Data on flower and pollen production for three natural populations of each study species, i.e., Armeria maritima, A. pubigera and Limonium vulgare.
DOI: 10.5061/dryad.r48vj/2
title: Morphological measurements

description: Pollen and stigmatic papillae morphological measurements for Armeria maritima, A. pubigera and Limonium vulgare.
DOI: 10.5061/dryad.r48vj/3
title: Pollen loads

description: Compatible and incompatible stigmatic pollen loads in natural populations of Armeria maritima, A. pubigera and Limonium vulgare.
DOI: 10.5061/dryad.r48vj/4
title: Hand pollination experiments

description: Data on pollen adherence, germination and pollen tube growth in the upper part of the style after self-, legitimate and mixed pollinations of Armeria maritima.
DOI: 10.5061/dryad.s6v4p/1
title: Java sparrow behavioral data (dance and mating)
DOI: 10.5061/dryad.sk81k/10
title: zip of primate phylogeny inference

description: Zip file containing all input, intermediate, and output files from the inference of the primate phylogeny using the SUPERSMART pipleine. See README.txt for details.
DOI: 10.5061/dryad.sk81k/11
title: zip of palm phylogeny inference

description: Zip file containing all input, intermediate, and output files from the inference of the palm phylogeny using the SUPERSMART pipleine. See README.txt for details.
DOI: 10.5061/dryad.sk81k/12
title: zip of simulation study data

description: Zip file containing all input, intermediate, and output files from the simulation study described in the manuscript. See README.txt for details.
DOI: 10.5061/dryad.sk81k/13
title: Supplementary Figure S1

description: Backbone supermatrix dimensions for varying minimum marker coverage in the case of the Primates. For each value for minimum marker coverage we varied the maximum divergence for a marker to be accepted in the set from 0.05 to 0.19 in increments of 0.02, hence the scatter around each value. Higher values of maximum accepted divergence mean that more markers are included, which consequently results in more characters as well as more taxa in the supermatrix.
DOI: 10.5061/dryad.sk81k/14
title: Supplementary Figure S2

description: Average nodal posterior probabilities p as a function of varying minimum marker coverage and varying maximum divergence. Values are binned as p&lt;0.8 (red), 0.8 &lt; p &lt; 0.95 (green), p&gt;0.95 (blue).
DOI: 10.5061/dryad.sk81k/15
title: Supplementary Figure S3

description: Fully annotated primate phylogeny visualized with FigTree. Posterior support values are displayed on the internal nodes. Family names are displayed on the branches of the respective clades. Taxon names and branches are colour-coded by family. The scale bar on the bottom represents the time relative to the root node in Million years.
DOI: 10.5061/dryad.0618v/1
title: empirical data(psmcfa files)

description: The zip file contains the input files for PSMC from the empirical data of threespine sticklebacks in the study. Seventeen of them are from RAD data, and one of them is from whole genome sequencing data.
DOI: 10.5061/dryad.0618v/2
title: Generating PSMC input files from simulated data

description: The file contains a function written in R. This function randomly samples RAD loci from chromosomes simulated by ms (Hudson 2002), and transforms the RAD data into a ".psmcfa" file for PSMC analysis.
DOI: 10.5061/dryad.0618v/3
title: Generating PSMC input files from empirical RAD data

description: The files contains a script written in R. The script creates input files for PSMC from empirical RAD data using tag files and allele files. Tag files and allele files are generated through pstacks in Stacks v1.13.
DOI: 10.5061/dryad.0618v/4
title: Plot PSMC results

description: The file contains functions written in R. The functions are used to visualize the results from PSMC.
DOI: 10.5061/dryad.14811/1
title: Sampling locations and sample sizes.

description: Sampling locations and initial species designations are provided for each sampling location. Site name abbreviations correspond to Figure 3. Sample sizes are given for each sampling location with mtDNA given on the first line, microsatellites the second, scale morphology the third and the forth row has additional individuals from Haenel 2007 and a manuscript that is in preparation included in figure 1 and body size analyses.
DOI: 10.5061/dryad.14811/2
title: Arlequin input file microsatellites

description: Formatted input file of microsatellite data used in Arlequin.
DOI: 10.5061/dryad.14811/3
title: STRUCTURE input: microsatellites

description: STRUCTURE input file of microsatellite alleles.Seven Microsatellites are provided in columns. The first column has individual Ids.
DOI: 10.5061/dryad.14811/4
title: STRUCTURE summary: deltaK

description: Graph of output of summary for STRUCTURE analyses. Evanno’s K and individual assignment probabilities were used to assess the best value of K (Evanno et al. 2005). This figure shows the results as DeltaK = mean(|L"(K)|)/sd(L(K)).
DOI: 10.5061/dryad.14811/5
title: Input file MrBayes mtDNA sequences.

description: Input file used to run phylogenetic analyses in MrBayes including mtDNA sequences. U. nigricaudus included as outgroup. MrBayes block included at bottom of the file.
DOI: 10.5061/dryad.14811/6
title: Summary of MrBayes analyses.

description: Table of summary of run from MrBayes phylogenetic analyses. This is the .mcmc output file.
DOI: 10.5061/dryad.14811/7
title: Arlequin input U. orantus mtDNA sequences.

description: Arlequin input file for population genetic analyses of U. orantus mtDNA sequences. Includes geographic structure.
DOI: 10.5061/dryad.17tp1/1
title: BMJopen-Role of Broadband Ultrasound Attenuation Measured by Calcaneal Quantitative Ultrasound in the Fall Incidence in Middle-Aged and Old People

description: This data file was the raw data of the article which is submitted to BMJ open journal with the article title named as:Role of Broadband Ultrasound Attenuation Measured by Calcaneal Quantitative Ultrasound in the Fall Incidence in Middle-Aged and Old People. Thanks!
DOI: 10.5061/dryad.1b5t7/1
title: Arrhenaterum_quantitative_data

description: Quantitative responses (biomass, height, flowering) of Arrhenatherum elatius in response to different winter temperature scenarios.
DOI: 10.5061/dryad.1r45h/1
title: Abrahamczyk_et_al_JEB_DataS1

description: Literature sources consulted for generating the asterid summary phylogeny
DOI: 10.5061/dryad.515c6/1
title: Phenotype data

description: Excel file containing two sheets, one with the phenotypic data, the other with explanations of all variables
DOI: 10.5061/dryad.52636/2
title: OnlineAppendixV2

description: We provide here the full, uncut, Online Appendix to our paper entitled "A unifying comparative phylogenetic framework including traits coevolving across interacting lineages". The first section is exposed in the attached appendix of the paper, but we let it here for the sake of self-containment. Note that simple equation numbering (e.g. equation (5)) refers to equations printed in the main text, whereas equations exposed in this appendix are designated as, e.g. equation (S5).
DOI: 10.5061/dryad.5c4rk/1
title: life-history data C. obscurior queens
DOI: 10.5061/dryad.61pd6.1/2.1
title: Bayesian Majority Rule Phylobayes Consensus Tree

description: Supplemental Data: Data File B.  Bayesian phylogenetic consensus tree (newick format) resulting from a PhyloBayes analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa.
DOI: 10.5061/dryad.61pd6.1/3.1
title: Bootstrap Majority-rule RAxML Consensus Tree

description: Supplemental Data: Data File C.  Bootstrap consensus tree, based on 1000 replicates (newick format) resulting from the RAxML analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa.
DOI: 10.5061/dryad.61pd6.1/4.1
title: Best-scoring Maximum Likelihood RAxML Tree

description: Supplemental Data: Data File D.  Best-scoring Maximum Likelihood tree (newick format) resulting from the RAxML phylogenetic analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa.
DOI: 10.5061/dryad.61pd6.1/5.1
title: Sample of 1000 Phylobayes Posterior Trees

description: Supplemental Data: Data File E.  Sample of 1000 Bayesian posterior trees (newick format) resulting from a PhyloBayes analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa. This sample of posterior trees can be used to account for phylogenetic uncertainty in comparative analyses.
DOI: 10.5061/dryad.61pd6.1/6.1
title: Sample of 1000 RAxML Bootstrap Trees

description: Supplemental Data: Data File F.  Sample of 1000 bootstrapped trees (newick format) resulting from a RAxML analysis of matK DNA sequences for 3,744 legume sequences and 100 outgroup taxa. This sample of posterior trees can be used to account for phylogenetic uncertainty in comparative analyses.
DOI: 10.5061/dryad.62275/3
title: Germination experiment

description: Data underlying supporting information S2, comprising explanatory variables from the Jena experimental setup and germination rate (%) of K. arvensis for all six sampling times of the germination experiment.
DOI: 10.5061/dryad.66jd4/1
title: Ostrom et al Hawaiian Petrel amino acid N isotope data

description: Amino acid specific nitrogen isotope data from Hawaiian petrel gelatin
DOI: 10.5061/dryad.7c57r/1
title: Ruaha dry season 2013 camera trap records of mammal species

description: Camera trap records of mammal species (including the study species) collected in the Msembe area of Ruaha National Park, Tanzania, between September and December 2013. The file includes the camera trap location name (Station), the species common name (Species), the date and time of the capture (DateTime), the sampling day (SampDay - useful with reference to the effort matrix), and a decimal capture time (CapTime).
DOI: 10.5061/dryad.7c57r/2
title: Ruaha dry season 2014 camera trap records of mammal species

description: Camera trap records of mammal species (including the study species) collected in the Msembe area of Ruaha National Park, Tanzania, between September and December 2014. The file includes the camera trap location name (Station), the species common name (Species), the date and time of the capture (DateTime), the sampling day (SampDay - useful with reference to the effort matrix), and a decimal capture time (CapTime).
DOI: 10.5061/dryad.7c57r/3
title: Ruaha dry season 2013 camera trap sampling effort

description: Location (rows) by sampling day (columns) camera trap effort matrix for the dry season of 2013 (Sep-Dec).
DOI: 10.5061/dryad.7c57r/4
title: Ruaha dry season 2014 camera trap sampling effort

description: Location (rows) by sampling day (columns) camera trap effort matrix for the dry season of 2014.
DOI: 10.5061/dryad.7c57r/5
title: Ruaha dry season 2013 camera trap location covariates

description: Variables recorded for each camera location and used to model species co-occurrence in Ruaha NP during the dry season of 2013. The file includes the camera trap location name (Station), the elevation (Altitude), an index of vegetation density (VegDens), an encounter rate for lion prey (LionPrey), and encounter rate for spotted hyaena prey (HyenaPrey), and the distance to the Great Ruaha River (Dist2Water).
DOI: 10.5061/dryad.831g1/1
title: Raw DArT-seq data

description: DArT-seq genotypes for 86 individuals of Acropora. These data include the raw sequences (~100 bp) for each of 10,034 loci, and show the position and variation of each single nucleotide polymorphism (SNP).
DOI: 10.5061/dryad.831g1/2
title: PaxC sequence alignment

description: Aligned DNA sequences from PaxC 46/47 intron, including indels, for 85 individuals of Acropora from Western Australia. Sequence length ~ 1067 bp. File is in FASTA format.
DOI: 10.5061/dryad.bp7s3/1
title: Rio Grande silvery minnow MHC_Microsatellites_Parasites

description: Rio Grande silvery minnow  microsatellite, MHC and parasite data. Sample site collection information is also included.
DOI: 10.5061/dryad.cd6tv/1
title: eichhorn_woodmad

description: Terrestrial Laser Scanning data from woods surveyed in the WoodMAD (Woodland Management And Deer) project. Columns give plot name (site and compartment number), region (s: Weald, w: Welsh Marches), UK county, deer density (high or low), records of management within the last 20 years (yes or no), dominant tree species, height of canopy layer (10 cm bands), subplot (five of 10 x 10 m, labelled a--e), foliage and stem density (number of 1 cm3 voxels filled per m3).
DOI: 10.5061/dryad.d47fm/5
title: PGM_SequencingRuns

description: The table presents the strategy used for multiplexing samples.
DOI: 10.5061/dryad.d47fm/6
title: Metabarcode_OTUrepresentatives

description: This file contains one representative sequence per OTU
DOI: 10.5061/dryad.d47fm/7
title: Metabarcode_OTUtables

description: This file contains an OTU table from each experiment and identifications for each OTU from Biocode, NCBI, BOLD and SAP.
DOI: 10.5061/dryad.h5486/1
title: Behavioral Data

description: Observations of wolves hunting bison in Yellowstone National Park. State ID is nested within Encounter ID, which is nested within Observation ID. Analysis refers to whether the data were associated with bison being attacked or captured by wolves. Outcome (1 = attacked/captured). Bison flight response (1 = fled).
DOI: 10.5061/dryad.h5486/2
title: Prey Switching Data
DOI: 10.5061/dryad.j6kb2/1
title: Data_ZF_Boucaud_2016
DOI: 10.5061/dryad.jm60b/1
title: Japan_herring_genepop

description: Microsatellite genotypes for 20 samples (n=3,784) collected from nine major spawning sites in Japan during the spawnng season before and after the Great Tohoku earthquake
DOI: 10.5061/dryad.nf781/1
title: Dryad_Nerophis_lumbriciformis

description: Microsatellite data from the Viana (Portugal) Nerophis lumbriciformis population. On the first page, the unique adult genotypes are presented (used for the construction of Table 1, using GENALEX and CERVUS). The second page contains the genotypes of embryos and potential parents, including recaptures (used in PARFEX for the parentage analysis).
DOI: 10.5061/dryad.q58hr/1
title: Table S1. F2 Spawning decisions of F2 hybrid females

description: Table S1 contains a summary of the spawning decisions of all F2 hybrid females, including their IDs, brood numbers and fathers.
1-32 is the experimental round and each round may include more than one spawning decision per female.
0 = spawning decision with P. sp. "pundamilia-like"
1 = spawning decision with P. sp. "nyererei-like"
out = female isolated in a tank with a male of the non-preferred species
in = female re-introduced into the experiment

out = female isolated in a tank with a male of the non-preferred species
in = female re-inroduced into the experiment
DOI: 10.5061/dryad.q58hr/2
title: Table S2.  Spawning decisions of wild type females and F1 females

description: Table S2 contains a summary of the spawning decisions of all wild type females and F1 hybrid females
1-32 is the experimental round and each round may include more than one spawning decision per female.
Species:
p = P. sp. "pundamilia like"
n = P. sp. "nyererei-like"
pn = F1 hybrid between female P. sp. "pundamilia like" and male P. sp. "nyererei-like"
np = F1 hybrid between female P. sp. "nyererei-like" and male P. sp. "pundamilia like"
0 = spawning decision with P. sp. "pundamilia-like"
1 = spawning decision with P. sp. "nyererei-like"
DOI: 10.5061/dryad.q58hr/3
title: Table S3. Males used in the spawning experiment: Microsatellite genotypes and experimental round

description: Males used in the spawning experiment. ID is the identification code. IDs starting with m were lab bred males. All others males were wild caught. Spec is the species. 1&2-30-32 are the experimental rounds. The numbers are the experimental rounds and the positions of the compartments. 11 is the first round and the first compartment, 12 is the first round and the second compartment etc. 21 is the second round and the first compartment, 22 is the second round and the second compartment etc. Ppun7-Ppun32 are the microsatellite genotypes of the males (in bp)
DOI: 10.5061/dryad.q58hr/4
title: Table S4. Raw data and paternal analyses

description: Table S4 includes microsatellite raw data of the offspring of the F2 females (q1-35 and 1-286), the wild type females (p and n) and the F1 hybrid females (pn and np), as well as the paternity analyses.
ID (Blank): The ID of the female used in Table S1-2, 
Brood No: The numer of the brood, 
Prefix: The prefix in the PIT-tag number, 
Suffix: The suffix in the PIT-tag number, 
SL (mm): Standard length (mm), 
TL (mm): Total lenght (mm), 
Weight (g), 
No fry: Number of fry in the brood, 
Date stripped, 
No broods, 
Experimental round: Experimental round in Table S1-2, 
(Blank), 
Mother: Result of maternal analyses (same as ID if left blank), 
Father: Result of the paternity analyses, 
Ppun7a: Microsatellite lengt in base pairs (bp), 
Ppun7b: Microsatellite lengt in base pairs (bp), 
Ppun5a: Microsatellite lengt in base pairs (bp), 
Ppun5b: Microsatellite lengt in base pairs (bp), 
Ppun21a: Microsatellite lengt in base pairs (bp), 
Ppun21b: Microsatellite lengt in base pairs (bp), 
Ppun17a: Microsatellite lengt in base pairs (bp), 
Ppun17b: Microsatellite lengt in base pairs (bp), 
Ppun32a: Microsatellite lengt in base pairs (bp), 
Ppun32b: Microsatellite lengt in base pairs (bp).
DOI: 10.5061/dryad.q5s4v/1
title: eDNA_Picinguaba_unfiltered
DOI: 10.5061/dryad.rc3cp/1
title: Juvenile migration data

description: Contains information about migration of tagged juvenile salmon through the Snake and Columbia River hydropower system
DOI: 10.5061/dryad.rc3cp/2
title: Life history data

description: Contains information about growth rate of juvenile offspring and life history information about their parents
DOI: 10.5061/dryad.rc3cp/3
title: Offspring genotypes

description: Microsatellite genotypes for juveniles used in this study
DOI: 10.5061/dryad.rt8n4/1
title: Salt x Chain Data - Hintz et al. - Ecological Applications

description: Experimental data. Variable descriptions are included in the excel file.
DOI: 10.5061/dryad.sk81k/16
title: Supplementary Figure S4

description: Fully annotated palm phylogeny generated with FigTree. Posterior support values are displayed on the internal nodes. Subfamily names are displayed on the branches of the respective clades. Taxon names and branches are colour-coded by subfamily. The scale bar on the bottom represents the time relative to the root node in million years.
DOI: 10.5061/dryad.sk81k/18
title: Supplementary Figure S6

description: Illustration of how the relative number of dispersals (reported in Fig. 5) is calculated. First, the total branch length within a period (bold branches) is calculated (in this case 17.5 My). In order to account for the decreasing number of lineages towards the root of the tree, the relative number of dispersals is calculated by dividing the total branch length per time bin, thus computing the number of dispersal events in relation to the number of lineages available for dispersal. The green line shows a dispersal event at a node, whereas the red and yellow lines show events at branches that partially fall in another time bin.