Figure 8.

Competing hypotheses for the rooting of angiosperms showing the same underlying angiosperm topology when outgroups are excluded. A. Rooting within monocots (Mono), on the branch between grasses and all other angiosperms (see Fig. 2C, whose BS values are shown here, and also Fig. 2F; also see Goremykin et al. [19]). B. Unrooted network, with arrow showing alternative rootings as in A and C. C. Canonical rooting on the branch between Amborella and the rest of angiosperms (see Fig. 2I, whose BS values are shown here, and also Fig. 2L). We emphasize that 100% BS was obtained for Amborella-sister and for monocot monophyly (compared to 79% and 78% in C) using ML methods that allow for site-to-site rate heterogeneity (e.g., Additional files 1–3).