Fence decompositions and cherry covers in non-binary phylogenetic networks

TL;DR

This paper explores the relationship between fence decompositions and cherry covers in non-binary phylogenetic networks, providing new characterizations and enumeration methods for semi-binary tree-based networks.

Contribution

It generalizes fence decompositions to non-binary networks and links them with cherry covers, offering new characterizations and enumeration techniques for semi-binary tree-based networks.

Findings

Number of cherry covers equals the number of support trees in semibinary networks

Fence decompositions are extended to non-binary networks

Characterizations of semi-binary tree-based networks via forbidden structures and cherry covers

Abstract

Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories with an underlying tree structure. To better understand tree-based networks, numerous characterizations have been proposed, based on tree embeddings, matchings, and arc partitions. Here, we build a bridge between two arc partition characterizations, namely maximal fence decompositions and cherry covers. Results on cherry covers have been found for general phylogenetic networks. We first show that the number of cherry covers is the same as the number of support trees (underlying tree structure of tree-based networks) for a given semibinary network. Maximal fence decompositions have only been defined thus far for binary networks (constraints on vertex degrees). We remedy this by generalizing fence decompositions to non-binary networks, and using this, we characterize semi-binary tree-based networks in terms of forbidden structures. Furthermore, we give an explicit enumeration of cherry covers of semi-binary networks, by studying its fence decomposition. Finally, we prove that it is possible to characterize semi-binary tree-child networks, a subclass of tree-based networks, in terms of the number of their cherry covers.