Fig. 6 Phylogenomic trees estimated using ASTRAL based on 122 nuclear
single-copy genes. Branch support was calculated using local posterior
probabilities (LPP), and the LPP value less than 1.0 are shown on
branches. Fabids as defined here are shown with green branches; the
expanded malvid clade is shown with blue branches.
Coalescent simulations demonstrated a significant role of the ILS in the
backbone of the superrosids (Fig. S5 ). The branch subtending
(core rosids + Saxifragales), the critical node for examining the
relative placement of Vitales versus Saxifragales with respect to the
core rosids, had a clade probability of 0.31. This value is close to the
theoretical minimum probability (0.33 for the species tree clade under
the ILS in the three-taxon case (Pamilo & Nei, 1988 ),
suggesting that this branch is in the anomaly zone (Degnan &
Rosenberg, 2006 ). Therefore, these results are consistent with the
primary role of the ILS in conflicting interpretations of superrosid
relationships. However, the expected clade probabilities were lower (≤
0.1) in the backbone of the rosids, suggesting high discord compared to
ILS expectations. Statistical tests suggest that ILS alone cannot
explain gene tree incongruence; observed gene tree Robinson-Foulds
distances were significantly higher than expected (p <
1e-20), and the observed gene tree clade probabilities were lower than
the ILS expectation (p = 0.0043). These results are therefore
consistent with a potential role for early reticulation in the radiation
of rosids.