MBE Advance Access published online on December 23, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh049
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room 6N611R, 8600 Rockville Pike, Bethesda, MD, USA
* To whom correspondence should be addressed. E-mail: gascuel{at}lirmm.fr.
Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (Desper and Gascuel 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Pauplin (2000). Initial simulations suggested that FASTME, our program implementing the BME principle, was more accurate than or equivalent to all other distance methods we tested, with running time significantly faster than Neighbor-Joining (NJ). This article further explores the properties of the BME principle, and explains and illustrates its impressive topological accuracy. We prove that the BME principle is a special case of the weighted least-squares approach, with biologically meaningful variances of the distance estimates. We show that the BME principle is statistically consistent. We demonstrate that FASTME only produces trees with positive branch lengths, a feature that separates this approach from NJ (and related methods) that may produce trees with branches with biologically meaningless negative lengths. Finally, we consider a large simulated data set, with 5000 100-taxon trees generated by the Aldous beta-splitting distribution encompassing a range of distributions from Yule-Harding to uniform, and using a covarion-like model of sequence evolution. FASTME produces trees faster than NJ, and much faster than WEIGHBOR and the weighted least-squares implementation of PAUP*. Moreover, FASTME trees are consistently more accurate at all settings, ranging from Yule-Harding to uniform distributions, and all ranges of maximum pairwise divergence and departure from molecular clock. Interestingly, the covarion parameter has little effect on the tree quality for any of the algorithms. Key Words:
minimum evolution, least-squares, distance-based phylogenetic inference, consistency, method comparison using simulations
© 2003 Society for Molecular Biology and Evolution
Original Articles
Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting
2 Equipes Méthodes et Algorithmes pour la Bioinformatique LIRMM, 161 rue Ada, 34392 Montpellier, France
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