Figure 2

The tree of possible adjacencies. A tree of possible adjacencies is constructed from two reconciled gene trees (top trees). The nodes of the tree are annotated as speciation nodes (grey nodes), duplication nodes (white squares), or losses (crossed grey nodes). A binary state is attributed to each leaf according to the presence/absence pattern of the adjacency in extant species (light blue square). The true evolutionary history of the adjacency is represented on the blue tree. An adjacency exists between genes a₁ and a₂, c₁ and c₂, d₁ and d₂. It is absent between genes a₁ and $a_2^{\prime }$ and genes $c_1^{\prime }$ and c₂. If one extremity of the adjacency is lost (species B), the adjacency node is given an undefined state "?".