Paper: Application of Phylogenetic Networks in Evolutionary Studies

Application of Phylogenetic Networks in Evolutionary Studies
Daniel H. Huson and David Bryant

Molecular Biology and Evolution 2006 23(2):254-267 [link]

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, 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. Thus, phylogenetic networks 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 have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.


Found today while adding sites to the Link List at the side:

PhyloTaxis, a nifty visualisation thing, that gathers science news headlines and turns them into this geometric flash array.

Surname Profiler. A UCL GIS project which produces a spatial map of the frequency of your surname in the UK. The wonders of GIS! My surname increased in frequency quite dramatically in the last century, and according to this, is pretty much confined to English and (in a minor way) Irish persons – which makes sense, given that Ireland is where my dad’s father’s family are from.

The different categories at visualcomplexity have fascinating topics. I like this one: London Connections, which is a spatial representation of a social network of one person in London.

Am well impressed with the bloggers at ScienceBlogs. Am assuming that joining the hosting service requires some sort of proof of science blogging, which I should get further underway with before knocking on the door.


I, Fiona Jordan, being of obvious unsound mind by the mere fact of enrolment in a PhD program, do declare this blog to henceforth be a repository of somewhat useful, mostly relevant, occasionally trivial, hopefully entertaining and always diverting anthropological and biological… stuff.

For a nearly up-to-date precis of what goes on in my tiny corner of academe, visit my UCL website.