Fig. 2.

Five-taxon anomaly zones. (A) The only ranked five-taxon species tree topology that produces ARGTs. The same species tree, with a gene tree evolving inside, is shown in figure 1A. (B) Slices of the unranked (on the left side) and ranked (on the right side) anomaly zones for the topology in (A). For fixed values of t₄, each shaded region represents pairs of speciation interval lengths (t₂, t₃) for which the most probable unranked (ranked) gene tree topology does not match the unranked (ranked) species tree topology. Each slice was generated by computing the probability distribution of gene tree topologies on a grid with $t_2\in [0.01,3]$ and $t_3\in [0.01,1]$, with increments of 0.01 for both variables. In the ranked case, the shaded region for a smaller t₄ contains the shaded region for a larger t₄. In the unranked case, the shaded region for a larger t₄ contains the shaded region for a smaller t₄.