Figure_S7

The reliability of the eigengap heuristic versus MEDUSA in recovering shifts in speciation rate and diversification pattern in simulated trees. The absolute deviation of shifts recovered by the eigengap (red) and MEDUSA (blue) from the known number of shifts for trees with 0–10 shifts in (a) speciation rate and (b) diversification pattern. In (a), only when five or ten shifts were simulated, MEDUSA performed significantly better (T > 2, P < 0.05) than the eigengap. (a, Inset) The average deviation across all trees is slightly lower for MEDUSA (2.89) than for the eigengap heuristic (3.10), although this is not significant (T = 1.88, P > 0.05). In (b), the eigengap heuristic outperformed MEDUSA for all trees with > 2 shifts and (b, inset) overall (T = 10.44, P < 0.01). In (a) and (b), only eigengaps supported by BIC post-hoc analysis were computed in the means. Asterisks indicate a significantly lower deviation for MEDUSA (blue) or the eigengap heuristic (red).