Figure 5.

Bootstrap support and the SH-test p-value for the Amborella-sister or grasses-sister topologies as a function of (A) the gamma distribution α parameter value or (B) the proportion of invariable sites. The left vertical line in A and right line in B indicate the rate-heterogeneity parameter estimated from the data. The right vertical line in A and left line in B indicate the boundary where the topology of the best tree transitions between Amborella-sister and grasses-sister. All analyses were performed using the 61-gene first- and second-position matrix of Goremykin et al. [19] and the ML HKY85 model with the α parameter or proportion of invariant sites indicated on the X-axis. The transition-transversion parameter was estimated for each specified rate-heterogeneity parameter. p(Δ|L_Amb-L_grasses|) signifies the SH-test p-value for the difference between the likelihood scores of the two topologies. Bootstrap searches and SH-tests were performed as described in Methods.