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MBE Advance Access published online on August 1, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl075
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted July 25, 2006

Research Article

The Evolutionary Origin of Xanthomonadales Genomes and the Nature of the Horizontal Gene Transfer Process

Iñaki Comas 1 *, Andrés Moya 1, Rajeev K. Azad 2, Jeffrey G. Lawrence 2, and Fernando Gonzalez-Candelas 1

1 Instituto Cavanilles de Biodiversidad y Biología Evolutiva. Universidad de Valencia. Apartado Oficial 22085, Valencia E-46071, Spain
2 Department of Biological Sciences. University of Pittsburgh. Pittsburgh, PA 15260, Pennsylvania, USA

* To whom correspondence should be addressed.
Iñaki Comas, E-mail: inaki.comas{at}uv.es


  Abstract

Determining the influence of horizontal gene transfer on phylogenomic analyses and the retrieval of a tree of Life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from horizontal gene transfer. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present horizontal gene transfers during their evolution. The scenario derived from this analysis and other recently published reports reflects the confounding effects on bacterial phylogenomics of past and present HGT. While transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.

Keywords: phylogenomics; microbial evolution; conflicting phylogenetic signals; horizontal gene transfer.
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