The nearest neighbor interchange proximity measure for the tree-basedness of rooted binary phylogenetic networks

Abstract: Tree-based networks are a broad graph class in phylogenetics which posit a model of evolution composed of tree-like processes and hybridization events. Hence, for any non-tree-based phylogenetic network, it is meaningful to study the magnitude of violation of the tree-based model assumptions. For rooted networks, we introduce the proximity measure delta_rNNI, defined by the minimum number of rooted nearest neighbor interchanges (NNIs) required to transform a network into a tree-based network. For binary networks, we prove that delta_rNNI is pairwise distinct from all previously known proximity measures in the literature and that no approximation guarantees between delta_rNNI and other known proximity measures holds. In addition, we characterize a family of networks for which a linear time lower bound on delta_rNNI is tight. Moreover, we analyze upper bounds and give an exact solution algorithm to compute delta_rNNI.