Locating a tree in a phylogenetic network

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider the restriction of these problems to several well-studied classes of phylogenetic networks. We show that Tree Containment is polynomial-time solvable for normal networks, for binary tree-child networks, and for level-k networks. On the other hand, we show that, even for tree-sibling, time-consistent, regular networks, both Tree Containment and Cluster Containment remain NP-complete.

Research highlights► Tree containment polynomial time for normal networks. ► Tree containment polynomial time for binary tree-child networks. ► Tree containment NP-complete for tree-sibling, time-consistent, regular networks. ► Cluster containment NP-complete for tree-sibling, time-consistent, regular networks.