Phylogenetic network

Phylogenetic Network

The evolutionary history of a set of taxa is most often represented by a phylogenetic tree, and this model has greatly benefited the discussion and testing of hypotheses. However, it is clear that more complex evolutionary scenarios are poorly described by such models. Indeed, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step.

A phylogenetic network is any graph used to visualize evolutionary relationships between species or organisms. It should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks may have a valuable role to play.

This tutorial reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, their definition and interpretation. SplitsTree4 is an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees, free download here. For a recent article on the subject, see D. H. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Mol. BIol. Evol., 23(2):254-267, 2006.