Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

Legume Phylogeny Working Group (LPWG)

Date Published: March 3, 2017

DOI: http://dx.doi.org/10.5061/dryad.61pd6.2

 

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Title Voucher information for LPWG matK sequences
Downloaded 84 times
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.
Download TableS1_LPWG_matK2016_vouchers.xls (914.9 Kb)
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Title RAxML Bootstrap Consensus Phylogenetic Tree
Downloaded 114 times
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.
Download Fig.Supp.RAXML.pdf (1.967 Mb)
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Title Poster illustrating the new LPWG Legume Classification
Downloaded 76 times
Description Supplemental Data: Figure S2. Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.
Download Poster_LPWG_LD_final_v2.pdf (2.109 Mb)
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Title High Resolution Poster illustrating the new LPWG Legume Classification
Downloaded 43 times
Description Supplemental Data: Figure S3. Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.
Download Poster_LPWG_HD_final_v2.pdf (590.5 Mb)
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Title Aligned matK matrix
Downloaded 25 times
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.
Download A_LPWG_matK2016_aligned_matrix.nex (11.00 Mb)
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Title Bayesian Majority Rule Phylobayes Consensus Tree
Downloaded 49 times
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.
Download B_LPWG_matK2016_Bayesian_majority-rule_co...es.tre (235.9 Kb)
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Title Bootstrap Majority-rule RAxML Consensus Tree
Downloaded 34 times
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.
Download C_LPWG_matK2016_bootstrap_majority-rule_c...ML.tre (186.6 Kb)
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Title Best-scoring Maximum Likelihood RAxML Tree
Downloaded 16 times
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.
Download D_LPWG_matK2016_best-scoring_maximum_like...ML.tre (286.2 Kb)
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Title Sample of 1000 Phylobayes Posterior Trees
Downloaded 28 times
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.
Download E_LPWG_matK2016_1000_posterior_trees_Phyl...es.tre (262.1 Mb)
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Title Sample of 1000 RAxML Bootstrap Trees
Downloaded 24 times
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.
Download F_LPWG_matK2016_1000_bootstrap_trees_RAxML.tre (178.5 Mb)
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When using this data, please cite the original publication:

Legume Phylogeny Working Group (LPWG) (2017) A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon 66(1): 44-77. http://dx.doi.org/10.12705/661.3

Additionally, please cite the Dryad data package:

Legume Phylogeny Working Group (LPWG) (2017) Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.61pd6.2
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