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MBE Advance Access published online on August 29, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg234
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted August 8, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes

Vincent Daubin 1* and Howard Ochman 1

1 Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona, 85721

* To whom correspondence should be addressed. E-mail: daubin{at}email.arizona.edu.


  Abstract

Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of tree-like evolution might be abandoned in favor of a net or web. Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa.

Key Words: Bacterial phylogeny, maximum likelihood, quartet trees, lateral gene transfer


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