To network or not to network, that is the question

Abstract

The evolutionary history of a set of taxa usually assumes a tree, but naturally phylogenies that involve reticulations cannot be described with a tree. Phylogenetic networks hold the potential to explore these interesting and previously undetected signals in phylogenetic analysis. Largely based on the conflicting signals in datasets, a growing interest in phylogenetic networks has developed. These methods allow the presentation of non-treelike evolutionary histories. Recently, several methods and excellent applications have been developed to reconstruct network-like evolutionary events. Short-comings of applied algorithms have also been described. Based on these findings future prospects can be summarized for phylogenetic analyses.