Comparison of orchard networks using their extended $μ$-representation

Abstract: Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much different for phylogenetic networks. Some classes of phylogenetic networks, mainly tree-child networks, are known to be classified efficiently by their $\mu$-representation, which essentially counts, for every node, the number of paths to each leaf. In this paper, we introduce the extended $\mu$-representation of networks, where the number of paths to reticulations is also taken into account. This modification allows us to distinguish orchard networks and to define a sound metric on the space of such networks that can, moreover, be computed efficiently. The class of orchard networks, as well as being one of the classes with biological significance (one such network can be interpreted as a tree with extra arcs involving coexisting organisms), is one of the most generic ones (in mathematical terms) for which such a representation can (conjecturally) exist, since a slight relaxation of the definition leads to a problem that is Graph Isomorphism Complete.