A biologically consistent model for comparing molecular phylogenies.

In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived.