Figure 2.

Gene trees connecting (A) PHO and PHOL and (B) YY1, YY2 and REX1. Alignments were first created using a subset of sequences, the protein sequences of which are available or can be predicted with certainty. Later, the trees were constructed with the neighbor-joining method using the Mega3 program. In each tree, the bootstrap values calculated from 1000 replicates are indicated above each branch. The trees constructed with the maximum parsimony method are also available as Supplementary Data 6.