The space of tree-based phylogenetic networks

TL;DR

This paper proves the connectivity of the space of unrooted tree-based phylogenetic networks under NNI operations, introduces new concepts like shoat networks, and provides bounds on the size of this network space.

Contribution

It establishes the connectivity of unrooted tree-based networks under NNI and introduces new concepts, enhancing understanding of network transformations.

Findings

The space of unrooted tree-based networks is connected under NNI.

Introduces shoat networks and explores their properties.

Provides an upper bound on the size of the network space.

Abstract

Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these, tree-based phylogenetic networks, have been introduced to capture the extent to which reticulate evolution nevertheless broadly follows tree-like patterns. Several important operations that change a general phylogenetic network have been developed in recent years, and are important for allowing algorithms to move around spaces of networks; a vital ingredient in finding an optimal network given some biological data. A key such operation is the Nearest Neighbor Interchange, or NNI. While it is already known that the space of unrooted phylogenetic networks is connected under NNI, it has been unclear whether this also holds for the subspace of tree-based networks. In this paper we show that the space of unrooted tree-based phylogenetic networks is indeed connected under the NNI operation. We do so by explicitly showing how to get from one such network to another one without losing tree-basedness along the way. Moreover, we introduce some new concepts, for instance ``shoat networks'', and derive some interesting aspects concerning tree-basedness. Last, we use our results to derive an upper bound on the size of the space of tree-based networks.