Figure 2.

Homologous gene quartets and inference of conversion based on phylogenetic topology changes. (A) Colinear genes and quartets of homologous genes. Squares show genes, and the same color ones show homologous genes. If conversion does not occur, the expected phylogenetic relationship of a homologous quartet is shown in (B); (C) if a D_h gene is converted by an A_h paralog; (D) if an A_h gene is converted by a D_h paralog; (E) if an Ah gene is converted by a B_h paralog; (F) if a B_h gene is converted by an A_h paralog; (G) if a B_h gene is converted by a D_h paralog; (H) if a D_h gene is converted by a B_h paralog. Places without squares indicate gene loss.