cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.933bs/1
title: Haughian&Frego2017_FunctionalEcology_moisture_capacity_&_moss_growth_data

description: Sheet 1 - change in biomass of mosses grown in mesh envelopes over 20 months. Sheet 2 - water potential of air recorded 3-5 mm above the surface of synthetic and natural logs, in the laboratory, under simulated precipitation. Sheet 3 - physical properties of a subset of experimental logs, including porosity, density, and volume. Sheet 4 - ambient moisture availability (water potential) from 9 data loggers in the experimental areas, recorded at 30 minute intervals over the growing season in 2014 (at 1.0 m from the ground).
DOI: 10.5061/dryad.b1q08/1
title: ColorTraitValues

description: Color trait values for associated pairs of blue tits per year and population (column 'pop'). Columns 'mID' and 'fID' refer to metal ring identity for males (m) and females (f) respectively. For full names for columns 5 to 16 ('mBB' to 'fYC') see Table 2 of the article (DOI: 10.1002/ece3.2822).
DOI: 10.5061/dryad.b9h4h/1
title: Objective 1: Comparison of long-term changes in species presence/absence

description: Contemporary species presence/absence obtained from pelagic and/or shoreline tows (2012-2013); taxonomic level matches historical data.
DOI: 10.5061/dryad.b9h4h/2
title: Objective 2: Contemporary drivers of species

description: Contemporary relative abundance of species obtained from pelagic and/or shoreline tows (2012-2013).
DOI: 10.5061/dryad.bp765/1
title: genepop_wood_river_sockeye

description: Genepop formatted file containing genotypes from the 6,254 filtered SNPs and 286 individuals with &gt;80% genotyping rate used in this study. SNP names are radtag_snp position i.e. a SNP named 12_46 would be on radtag number 12 and the SNP would be at position 46 in the tag. Population abbreviations are identical to those in Table S1 of the publication.
DOI: 10.5061/dryad.c5t6v/1
title: Soil Sample Data with 4 Site Codes

description: Soil Sample Data documentation.
137 records, each representing a point at which soil samples were obtained. 

Variables are "SITECODE", "SITENUM", "TDIST" (m), "X" (m), 	"Y" (m), "EL.CA.MOL" (mol/m2), "EL.MG.MOL" (mol/m2), "EL.K.MOL" (mol/m2), "EX.CA.MOL" (mol/m2), "EX.MG.MOL" (mol/m2), "EX.K.MOL" (mol/m2)

"SITECODE", values 1-4, is code indicating area of landscape where samples were taken. In the accompanying manuscript, corresponding locations and codes are 1=Camps Pond (A), 2=Wangum (D), 3 = #4 Trail (B), 4 = Backgate (C).

"SITENUM", values 1-104 (not inclusive). SITENUM 1-18 and 52-95 are at Camps Pond. SITENUM 19-30 are at Wangum, SITENUM 31-36 are at #4 Trail. SITENUM 101 is at Backgate, and SITENUM 104 is at #4 Trail. 

"TDIST" indicates distance along transect, in meters. SITENUM 101 consists of two parallel transects: the first transect has distances from 0-100, and second, from 200-300 (i.e., the different transect is indicated by adding 200 to each distance along it). SITENUM 104 consists of a single 200 m transect with soil sample sites at 5 m intervals. Every record is defined by a unique combination of "SITENUM" and "TDIST".

"X" and "Y" are xy coordinates (in m) where soil sample was taken. There is a unique XY coordinate reference system at each value of "SITENUM".

"EL.CA.MOL" (mol/m2), "EL.MG.MOL" (mol/m2), "EL.K.MOL" (mol/m2), "EX.CA.MOL" (mol/m2), "EX.MG.MOL" (mol/m2), "EX.K.MOL" (mol/m2) are values of exchangeable calcium, magnesium and potassium.
DOI: 10.5061/dryad.cb2d2/1
title: BHEF_ALL

description: This file contains individual tree ring records, in Tucson format, for each tree sampled at the Black Hill Experimental Forest thinning experiment included in the study.
DOI: 10.5061/dryad.cb2d2/2
title: CEF_all

description: This file contains individual tree ring records, in Tucson format, for each tree sampled at the Cutfoot Experimental Forest thinning experiment included in the study.
DOI: 10.5061/dryad.cb2d2/3
title: FVEF_ALL

description: This file contains individual tree ring records, in Tucson format, for each tree sampled at the Fort Valley Experimental Forest thinning experiment included in the study.
DOI: 10.5061/dryad.cm28r.2
title: Data from: Phylogenomics using formalin-fixed and 100+ year old intractable natural history specimens
DOI: 10.5061/dryad.cm28r.2/1.2
title: Phylips&trees

description: Includes the 50% missing data alignment/resulting tree and the 35% missing data (i.e., 65% complete) alignment/resulting tree .
DOI: 10.5061/dryad.cm28r.2/2.2
title: Extraction_protocol

description: Extraction protocol followed in the manuscript.
DOI: 10.5061/dryad.cv4r7/10
title: Daucus_carota_subsp._carota_Ames_27395

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/11
title: Daucus_carota_subsp._gummifer_478883

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/12
title: Daucus_carota_subsp._gummifer_Ames_26381

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/13
title: Daucus_carota_subsp._gummifer_Ames_26383

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/14
title: Daucus_carota_subsp._gummifer_Ames_31194

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/15
title: Daucus_carota_subsp._maximus_Ames_26408

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/16
title: Daucus_conchitae_652367

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/8
title: Daucus_carota_subsp._carota_502244

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.cv4r7/9
title: Daucus_carota_subsp._carota_652393

description: Bam file containing all reads that mapped to individual plastid reference. This reference contains only 1 inverted repeat.

Commands used to create bam file is as follows:
bwa mem -a -M -t 8 -R "@RG\tID:Accession\tLB:barcode\tPL:illumina\tSM:accession_number\tPI:350" reference.fa fastq1 fastq2 | awk '$3 != "*"' &gt;name.sam
samtools view -bt reference.fa.fai -o name.bam name.sam
samtools sort name.bam name.s
samtools view -b -q 30 -f 2 name.s.bam &gt;name.sq.bam
samtools index name.sq.bam
java -Xmx4g -jar /usr/local/bin/picard-tools/picard.jar MarkDuplicates I=name.sq.bam M=metrics.name.txt TMP_DIR=/tmp MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=900 O=Final.bam

bwa version 0.7.15-r1140
samtools version 0.1.19-44428cd
java version 1.8.0_111
picard version 2.7.1
DOI: 10.5061/dryad.g6m44/1
title: Gordonetal_2016_JAE_DataDryad

description: Data relating to the publication: "Shrub encroachment is linked to extirpation of an apex predator"
DOI: 10.5061/dryad.gg5k0/1
title: SCC_MorphoDataMatrix

description: Data matrix of morphological characters used to evaluate the phylogeny of the Stachys coccinea complex based in morphological data.
DOI: 10.5061/dryad.gj14q/1
title: X virginica genotypes

description: Genotypes and population data for female X. virginica.
DOI: 10.5061/dryad.h45mr/1
title: Nongrazed_konza_lter_lowlands_dominant_veg_cover

description: This data-set reports results from long-term experimental treatments manipulating fire frequency in a native tallgrass prairie in the Central Great Plains, U.S.A. (39’05” N, 96’35” W). All plots are from lowland locations and were not grazed by large grazers during the experiments. Methods for calculating cover are described in the “Methods” section of the main text and in Appendix S1. The column “Watershed_designation” uses the same watershed designations as Table 1 in the main text. “Fire_treatment” refers to the fire frequency treatment a plot was grouped into for all calculations (see Table 1). For each watershed there were twenty plots (see “Plot_number”) arrayed over four transects per watershed (see “Transect_number”). Note that from year 2000 onwards, plots in 4B were sometimes visited in a different order, leading to some mislabeling of “Plot_number”. Therefore, the plot labels might not be consistent between locations in 4b after year 2000, but the same physical locations were measured each year. “Grass_cover” is the summed cover of the four dominant C4 grasses species. “Shrub_cover” is the summed cover of shrub and tree species that consistently maintain foliage above the grass layer. Cover within both functional groups is in units of “the sum of plant canopy cover per species per unit ground area” and can therefore exceed 100%, due to the presence of multiple overlapping canopies of different species. “NA” in the “Grass_cover” or “Shrub_cover” indicates that data were not available due to a disruption of the fire frequency treatment (see Table 1). For more information, including updates to the data-set, see description of PVC02 on the Konza Prairie LTER website: http://www.konza.ksu.edu/knz/pages/home/home.aspx
DOI: 10.5061/dryad.j03q3/1
title: Alignment_ITS_4.11

description: Alignment of ITS region
DOI: 10.5061/dryad.j03q3/2
title: Alignment_trnL_trnLF_4.11

description: Alignment of trnL and trnL-F
DOI: 10.5061/dryad.j03q3/3
title: Alignment_ndhF_4.11

description: Alignment of ndhF
DOI: 10.5061/dryad.j03q3/4
title: Alignment_rbcL_4.11

description: Alignment of rbcL
DOI: 10.5061/dryad.j03q3/5
title: Alignment_matK_4.11

description: Alignment of matK
DOI: 10.5061/dryad.k0q1n/1
title: Raw data on plant-pollinator interactions

description: File showing all sites and every individual pollinator surveyed and the plant it interacted with.
DOI: 10.5061/dryad.k7t20/1
title: Amplicon_Sequence_Jan2017

description: Amplicon mapping markers reference sequences
DOI: 10.5061/dryad.k7t20/13
title: Male_Counts_2016

description: Male reproductive tissue raw transcript counts for 6 E and 6 Z RNA-seq libraries.
DOI: 10.5061/dryad.mv5t7/1
title: PONE-D-16-28880R1_FTC1_data2
DOI: 10.5061/dryad.pf0s5/1
title: AFLP

description: AFLP loci
DOI: 10.5061/dryad.pf0s5/2
title: MSAFLP

description: MSAFLP loci
DOI: 10.5061/dryad.q14c1/1
title: Galápagos sea lion reference genomes

description: Reference genomes of the Galápagos sea lion in fasta format. One is derived from the CLC workbench and the other from mapping to the Antarctic fur seal.
DOI: 10.5061/dryad.q6s1m/1
title: Cichlids_representative_OTUs_aligned

description: 16S V3-V4 alignment of 22869 representative OTUs, without lanemask
DOI: 10.5061/dryad.rq5ht/1
title: microsat_data

description: microsatellite genotype of samples from Belgium, England and France
DOI: 10.5061/dryad.s1v34/10
title: Supplementary File 10 - BEAST_7 analysis

description: Supplementary File 10. BEAST .xml input file used for analysis of the ‘BEAST_7’ dataset.
DOI: 10.5061/dryad.s1v34/11
title: Supplementary File 11 - FULL analysis MrBayes topology detail

description: Supplementary File 11. Bayesian majority-rule consensus tree (presented as two parts) resulting from a partitioned phylogenetic analysis of the ‘FULL’ (12-gene) dataset (129 taxa; 9,601 bp; 20 million generations). Non-idiopid outgroups have been omitted for ease of presentation, and posterior probability values are &gt; 0.98 unless otherwise stated. The type species of valid genera are shown in red, and the type species of junior generic synonyms are shown in dark blue; specimens of named species from their respective type localities are highlighted (#). The schematic summary phylogeny of Figure 5 is shown at left for comparison, and clades not recovered as presented in the Bayesian and/or likelihood analyses of the ‘MAJORITY’ dataset are highlighted (*).
DOI: 10.5061/dryad.s1v34/12
title: Supplementary File 12 - Parsimony ancestral states

description: Supplementary File 12. Mesquite input file of characters and the tree resulting from Bayesian analysis of the ‘FULL’ dataset, used for parsimony ancestral state reconstruction. Character coding is as follows: CHARACTER 1 (distribution): 0 = south-western Western Australia; 1 = arid zone; 2 = temperate south-eastern Australia; 3 = eastern Australia. CHARACTER 2 (phragmosis): 0 = unmodified abdomen; 1 = phragmotic abdominal morphology. CHARACTER 3 (burrow morphology): 0 = closed, with a hinged trapdoor lid; 1 = open burrow; 2 = semi-closed burrow, with a sock-like entrance.
DOI: 10.5061/dryad.s1v34/5
title: Supplementary File 5 - Specimen & laboratory data

description: Supplementary File 5. Collection and repository data for every specimen sequenced as part of this study, along with conditions for polymerase chain reaction (PCR) amplification of amplicons and GenBank accession numbers. F = forward primer; R = reverse primer; Ta = annealing temperate.
DOI: 10.5061/dryad.s1v34/6
title: Supplementary File 6 - Loci

description: Supplementary File 6. Locus summaries for genes used in the final optimised 12-gene ‘FULL’ dataset (see Tables 1-2). Genes are organised according to their phylogenetic informativeness over three epochs (see Table 2, Supplementary File 3), followed by additional unranked nuclear loci from previous studies. Test taxa listed are those sequenced as part of Phase 6 (see Materials and Methods).
DOI: 10.5061/dryad.s1v34/7
title: Supplementary File 7 - FULL dataset MrBayes

description: Supplementary File 7. Concatenated alignment of nucleotide sequence data for the final 12-gene 129-taxon (FULL) dataset, including Bayesian command block. See character set partitions at end of matrix for the gene- and partition-specific breakdowns.
DOI: 10.5061/dryad.s1v34/8
title: Supplementary File 8 - MAJORITY dataset MrBayes

description: Supplementary File 8. Concatenated alignment of nucleotide sequence data for the reduced representation 12-gene 120-taxon (MAJORITY) dataset, including Bayesian command block. See character set partitions at end of matrix for the gene- and partition-specific breakdowns.
DOI: 10.5061/dryad.s1v34/9
title: Supplementary File 9 - BEAST_9 analysis

description: Supplementary File 9. BEAST .xml input file used for analysis of the ‘BEAST_9’ dataset.
DOI: 10.5061/dryad.td771/1
title: Consumption Data

description: Data used in a meta-analysis of the effects of low dissolved oxygen on fish consumption.
DOI: 10.17632/p3ts9p2gc8.2
title: Metal Transmission Calculator

description: Tool to calculate metal transmission in mass cytometry instruments (CyTOF)
DOI: 10.5061/dryad.24q8p/1
title: Fulton_etal_Thalassoma_global_success

description: Density of reef fishes of the family Labridae within the reef crest habitat at 11 global locations. Density of reef fishes of the family Labridae within the reef crest and back reef habitats across six reefs of the northern Great Barrier Reef. Maximum flow velocity data within reef crest and back reef habitats across six reefs of the northern Great Barrier Reef.
DOI: 10.5061/dryad.4b6d3/1
title: Phylogenetic alignments, tree sets, and summary trees

description: 13 files corresponding to the multiple sequence alignments, partition files, tree sets (bootstrap replicates and post burn-in posterior probabilities), and summary trees (maximum-likelihood trees and majority rule consensus trees) for multiple phylogenetic analyses.
DOI: 10.5061/dryad.4c117/1
title: Code to draw figures

description: The code here allows the figures in the main paper to be reproduced.
DOI: 10.5061/dryad.53b58/1
title: TOB VS STW populations_text

description: raw dataset with 3980 SNP genotypes for two wild Atlantic salmon populations from the Tobique River and the Stewiacke River in the Bay of Fundy, Canada.
DOI: 10.5061/dryad.562bg/1
title: ChandlerMcGraw_matrices

description: Matrices for each disturbance type, labelled by location as is done in manuscript (NY - tent caterpillar defoliation, WKY - ice storm, and EKY - lightning strike)  Matrices are presented for  nine transition periods (2004-2013) for each disturbance.
DOI: 10.5061/dryad.60k68.1/6.1
title: BF37.sync

description: Synchronized pileup file created with PoPoolation2 containing the allelic information of all populations used in the analysis of the comparison between Base and generation 37. P-Values of the Cochran Mantel Haenzel Test are attached to each SNP in the last column. The order of the population is as follows: BR1,BR3,BR2,F15R4,F15R5,F23R1,F27R5,F37R4,F37R5,F37R1
DOI: 10.5061/dryad.60k68/7
title: Pairwise Comparisons for CMH test

description: Populations used for the pairwise CMH tests
DOI: 10.5061/dryad.61pd6/1
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.61pd6/2
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.61pd6/3
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.61pd6/4
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.61pd6/5
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.61pd6/6
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.