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Systematic Biology 2007 56(5):767-775; doi:10.1080/10635150701627304
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© 2007 Society of Systematic Biologists

Phylogenetic Mixtures on a Single Tree Can Mimic a Tree of Another Topology

Frederick A. Matsen and Mike Steel

Biomathematics Research Centre, University of Canterbury Private Bag 4800, Christchurch, New Zealand E-mail: ematsen{at}gmail.com

Edited by Cécile Ané, Jack Sullivan


  Abstract

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data are generated by a mixture model has stimulated considerable recent debate. Much of the controversy stems from simulations of mixture model data on a given tree topology for which reconstruction algorithms output a tree of a different topology; these findings were held up to show the shortcomings of particular tree reconstruction methods. In so doing, the underlying assumption was that mixture model data on one topology can be distinguished from data evolved on an unmixed tree of another topology given enough data and the "correct" method. Here we show that this assumption can be false. For biologists, our results imply that, for example, the combined data from two genes whose phylogenetic trees differ only in terms of branch lengths can perfectly fit a tree of a different topology.

Keywords: Mixture model; model identifiability; phylogenetics; sequence evolution

Received April 25, 2007; Revised June 1, 2007; Accepted June 26, 2007
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