Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies

• DOI: 10.1111/nph.16290
• Publication Date: 2019-10-30T22:31:30Z
• Authors: Erik J. M. Koenen; Dario I. Ojeda; Royce Steeves; Jérémy Migliore; Freek T. Bakker; Jan J. Wieringa; Catherine Kidner; Olivier J. Hardy; R. Toby Pennington; Anne Bruneau; Colin E. Hughes
• Keywords: Coalescent theory; Phylogenomics; Introgression; Nuclear gene; Lineage (genetic)

Summary Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate among subfamilies Leguminosae (or Fabaceae), third largest angiosperm family. Despite their ecological economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data lacking. generated alignments 72 chloroplast genes 7621 homologous nuclear‐encoded proteins, 157 76 taxa, respectively. analysed these with maximum likelihood, Bayesian inference, multispecies coalescent summary method, evaluated support alternative topologies across gene trees. resolve deepest divergences in legume phylogeny despite lack signal all majority nuclear genes. Strongly supported conflict remainder suggestive sorting. All six originated nearly simultaneously, suggesting that prevailing view some ‘basal’ or ‘early‐diverging’ respect others should be abandoned, which has important implications understanding evolution diversity traits. Our study highlights limits resolution relation rapid successive speciation.