Trading in trees

D. Huson, D. Bryant, "Application of phylogenetic networks in evolutionary studies," Mol Biol Evol, 23:254-67, 2006. (Cited in 120 papers)

In this review paper, Daniel Huson, a bioinformatician at the University of Tbingen, Germany, and David Bryant, from the University of Auckland, explained the rationale of using web-like phylogenetic networks instead of traditional trees to represent evolutionary relationships. This paper also introduced a new version of computer software, SplitsTree4, designed to handle phylogenetic data and build complex networks.

Though phylogenetic networks have been used since the 1990s, this paper attempted to demystify the process. "It does provide a very lucid summary, in no-nonsense terms of what these networks are," says Bill Martin, University of Dusseldorf botanist and the editor-in-chief of Molecular Biology and Evolution when the paper was published.

According to Martin, phylogenetic networks illustrate the vagaries of molecular evolution more faithfully than simple trees, but there has been some resistance to supplanting those longstanding evolutionary metaphors. The Huson and Bryant paper "does a great deal to bridge the gap between the networking community and the tree community," he says.

Huson says that he is now working on a computer program called Dendroscope that might smooth the transition into networks for researchers who have built careers using trees. Dendroscope melds the concepts underlying phylogenetic networks with a more familiar tree-like presentation. "The future direction is trying to make the networks more palatable for people who are tree believers," he says.