DOI: 10.5061/dryad.61pd6
title: Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

description: 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.
description: Voucher information for
 LPWG matK sequencesSupplemental 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.TableS1_LPWG_matK2016_vouchers.xlsRAxML Bootstrap Consensus Phylogenetic TreeSupplemental 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.Fig.Supp.RAXML.pdfPoster illustrating the new LPWG Legume ClassificationSupplemental Data: Figure S2. Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.Poster_LPWG_LD_final_v2.pdfHigh Resolution Poster illustrating the new LPWG Legume ClassificationSupplemental Data: Figure S3. Schematic diagram illustrating the six new subfamilies of Leguminosae and their floral diversity.Poster_LPWG_HD_final_v2.pdfAligned matK matrixSupplemental Data: Data File A. The aligned matK DNA sequence matrix of 3,744 legume sequences and 100 outgroup taxa spanning core Eudicots. Nexus format.A_LPWG_matK2016_aligned_matrix.nexBayesian Majority Rule Phylobayes Consensus TreeSupplemental 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.B_LPWG_matK2016_Bayesian_majority-rule_consensus_tree_Phylobayes.treBootstrap Majority-rule RAxML Consensus TreeSupplemental 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.C_LPWG_matK2016_bootstrap_majority-rule_consensus_tree_RAxML.treBest-scoring Maximum Likelihood RAxML TreeSupplemental 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.D_LPWG_matK2016_best-scoring_maximum_likelihood_tree_RAxML.treSample of 1000 Phylobayes Posterior TreesSupplemental 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.E_LPWG_matK2016_1000_posterior_trees_Phylobayes.treSample of 1000 RAxML Bootstrap TreesSupplemental 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.F_LPWG_matK2016_1000_bootstrap_trees_RAxML.tre