Phylogenetic patterns and diversification in the caesalpinioid legumesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Subfamily Caesalpinioideae is a paraphyletic grade of 171 genera that comprises the first branches of the Leguminosae and from which are derived the monophyletic subfamilies Mimosoideae and Papilionoideae. We have sequenced the chloroplast matK gene, and the trnL and 3′-trnK introns for 153 genera of caesalpinioid legumes. Parsimony and Bayesian phylogenetic analyses of these data support the monophyly of several major groups within the caesalpinioid legumes: the Cercideae, Detarieae, Detarieae s. str., Prioria , Amherstieae, Dialiinae, Cassia , Caesalpinia , Peltophorum , and Tachigali clades. Relationships among the first branching lineages of the legumes are not well supported, with Cercideae, Detarieae, and the genus Duparquetia alternatively resolved as sister group to all of the legumes. The division of certain large genera (e.g., Caesalpinia s. l., Bauhinia s. l.) into segregate genera generally is supported by our molecular data. Using 18 well-documented fossils as calibration points, fixing the stem node of the legumes at 65 Ma, and using the Penalised Likelihood method, we estimate the crown node of the Leguminosae at 64 Ma and the crown age of each of the major caesalpinioid lineages varying from 34 to 56 Ma. Fossil cross-validation suggests that none of the 18 fossil calibrations is internally inconsistent. Analyses done without fossil calibrations yield much younger divergence times. The age estimates for the Detarieae clade are more sensitive to the presence of calibration points than other caesalpinioid clades, a situation which we attribute to the slow rate of chloroplast DNA evolution in this group.