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).