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MBE Advance Access originally published online on August 29, 2003
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Mol. Biol. Evol. 21(1):86-89. 2004
DOI: 10.1093/molbev/msg234
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes

Vincent Daubin and Howard Ochman

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

E-mail: daubin{at}email.arizona.edu.

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 treelike 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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