Complex reticulation in backbone subfamily relationships in Leguminosae

Contradictory lines of evidence have made it difficult to resolve the phylogenetic history of the legume diversification era; this is true for the backbone topology, and for the number and timing of whole genome duplications (WGDs). By analyzing the transcriptomic data for 473 gene families in 76 species covering all six accepted legume subfamilies, we assessed the phylogenetic relationships of the legume backbone and uncovered evidence of independent whole genome duplications in each of the six legume subfamilies. Three subfamilies - Cercidoideae, Dialioideae, and Caesalpinioideae - bear evidence of an allopolyploid duplication pattern suggestive of ancient hybridization. In Cercidoideae and Dialioideae, the hybridization appears to be within-subfamily, with the genera Cercis and Poeppigia apparently unduplicated descendants of one of the parental lineages. In Caesalpinioideae, the hybridization appears to involve a member of the Papilionoideae lineage, and some other lineage, potentially extinct. Several independent lines of evidence converged on a single backbone hypothesis and the above hypotheses of reticulate evolution: phylogenies calculated from both superalignments and from multi-tree coalescent-based analyses; concordance factor analysis of the set of gene family alignments and topologies; and direct inference of reticulation events via maximum pseudo-likelihood implemented by PhyloNet.