Sample of 1000 Phylobayes Posterior Trees

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

Aligned matK matrix

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

Bayesian Majority Rule Phylobayes Consensus Tree

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

Sample of 1000 Phylobayes Posterior Trees

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

Aligned matK matrix

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

RAxML Bootstrap Consensus Phylogenetic Tree

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

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

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircum-scribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use

Poster illustrating the new LPWG Legume Classification

Supplemental Data: Figure S2. Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity

Best-scoring Maximum Likelihood RAxML Tree

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

Voucher information for LPWG matK sequences

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