Phylogenetic networks are used to represent evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We study two network classes in this paper: tree-based networks and orchard networks. Tree-based networks are those that can be obtained by inserting edges between the edges of an underlying tree. Orchard networks are a recently introduced generalization of the class of tree-child networks. Structural characterizations have already been discovered for tree-based networks; this is not the case for orchard networks. In this paper, we introduce cherry covers—a unifying characterization of both network classes—in which we decompose the edges of the networks into so-called cherry shapes and reticulated cherry shapes. We show that cherry covers can be used to characterize the class of tree-based networks as well as the class of orchard networks. Moreover, we also generalize these results to non-binary networks.

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Advances in Applied Mathematics
Centrum Wiskunde & Informatica, Amsterdam, The Netherlands

van Iersel, L.J.J, Janssen, R, Jones, M.E.L, Murakami, Y, & Zeh, N. (2021). A unifying characterization of tree-based networks and orchard networks using cherry covers. Advances in Applied Mathematics, 129. doi:10.1016/j.aam.2021.102222