Figure 1
Adjacency evolution. The evolution of an adjacency within a dated species tree, along reconciled gene phylogenies. The gene trees are blue and purple, while red horizontal edges are adjacencies. The time slices t0, ..., t3 indicate in which order the speciation nodes (big green nodes) occur, and are used to localize genes in the species tree (a branch and a time slice give the coordinates of a gene or an event). Red crosses mean gene losses, for example in the branches leading to A or C(adjacencies are lost when one extremity is lost), or an adjacency breakage, for example in the branch leading to D(gene loss and adjacency breakages are different events, since a gene loss is not a rearrangement while a breakage is, and only rearrangements are counted in the objective function). Here one adjacency is gained in the branch leading to species C, one is broken in the branch leading to species D, and one is transferred from the branch leading to B to the branch leading to C. The transfer implies first a speciation outside the species phylogeny, and then a transfer which can be in another time slice. A tandem duplication in the branch leading to A gives a new adjacency between the two copies.