Fig. 5 Phylogenomic trees estimated using RAxML from 122 concatenated nuclear single-copy genes. Numbers above the branches represent ML bootstrap/Bayesian posterior probability (BS/PP), and “*” indicates that the clade is supported by BS/PP value 100/1. Numbers next to the species names correspond to the numbered plant photographs at the right. Fabids as defined here are shown with green branches; the expanded malvid clade is shown with blue branches.
Under the coalescence method, some backbone nodes had lower LPP compared to the two concatenation analyses, but the three analyses were topologically highly similar (Fig. 6 ). Vitales was sister to Saxifragales + core rosids (LPP = 0.77). The phylogenetic positions of COM clade members, Picramniales, Huerteales, Zygophyllales, and Myrtales were completely consistent in the coalescence and concatenation trees; incongruences between the two approaches were mainly observed for the positions of Crossosomatales and Geraniales. In the coalescence phylogeny, after the successive branching of Vitales and Saxifragales, Crossosomatales was sister to all other core rosids with maximum local branch support (LPP = 1.0). Subsequently, Geraniales was sister to a clade comprising Zygophyllales, Myrtales, fabids, and malvids, with moderate support (LPP = 0.55). Fabids comprised nitrogen-fixing clade orders (LPP = 1), and malvids consisted of Picramniales, Malpighiales, Celastrales, Huerteales, Brassicales, Malvales, Oxalidales, and Sapindales (LPP = 0.99).