Orienting undirected phylogenetic networks to tree-child network (2305.10162v1)

Abstract: Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene transfer. Distance-based methods such as the Neighbor-Net algorithm are widely used to compute phylogenetic networks from data. However, the output is necessarily an undirected graph, posing a great challenge to deduce the direction of genetic flow in order to infer the true evolutionary history. Recently, Huber et al. investigated two different computational problems relevant to orienting undirected phylogenetic networks into directed ones. In this paper, we consider the problem of orienting an undirected binary network into a tree-child network. We give some necessary conditions for determining the tree-child orientability, such as a tight upper bound on the size of tree-child orientable graphs, as well as many interesting examples. In addition, we introduce new families of undirected phylogenetic networks, the jellyfish graphs and ladder graphs, that are orientable but not tree-child orientable. We also prove that any ladder graph can be made tree-child orientable by adding extra leaves, and describe a simple algorithm for orienting a ladder graph to a tree-child network with the minimum number of extra leaves. We pose many open problems as well.