A Class of Unrooted Phylogenetic Networks Inspired by the Properties of Rooted Tree-Child Networks

TL;DR

This paper introduces new classes of undirected phylogenetic networks called q-cuttable networks, which are computationally tractable and useful for phylogenetic analysis, inspired by properties of rooted tree-child networks.

Contribution

The paper proposes q-cuttable networks as a new class of undirected phylogenetic networks that are polynomial-time recognizable and facilitate efficient solutions to complex problems.

Findings

Recognition of q-cuttable networks is polynomial-time for all q≥1.

Tree Containment problem is polynomial-time solvable on q-cuttable networks for q≥3.

Class of tree-child-orientable networks is NP-hard to recognize.

Abstract

A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example, several computationally difficult problems in phylogenetics become tractable when restricted to tree-child networks. At the same time, the class itself is rich enough to contain quite complex networks. Furthermore, checking whether a directed network is tree-child can be done in polynomial time. In this paper, we seek a class of undirected phylogenetic networks that is rich and computationally useful in a similar way to the class tree-child directed networks. A natural class to consider for this role is the class of tree-child-orientable networks which contains all those undirected phylogenetic networks whose edges can be oriented to create a tree-child network. However, we show here that recognizing such networks is NP-hard, even for binary networks, and as such this class is inappropriate for this role. Towards finding a class of undirected networks that fills a similar role to directed tree-child networks, we propose new classes called $q$-cuttable networks, for any integer $q\geq 1$. We show that these classes have many of the desirable properties, similar to tree-child networks in the rooted case, including being recognizable in polynomial time, for all $q\geq 1$. Towards showing the computational usefulness of the class, we show that the NP-hard problem Tree Containment is polynomial-time solvable when restricted to $q$-cuttable networks with $q\geq 3$.