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MBE Advance Access published online on March 20, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm052
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© The Author 2007. 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

Research Article

A Likelihood Framework to Measure Horizontal Gene Transfer

Simone Linz*, Achim Radtke* and Arndt von Haeseler{dagger},{ddagger},$,¶

* Department of Bioinformatics, Heinrich-Heine-University, Universitätsstr. 1, 40225 Düsseldorf, Germany
{dagger} Center for Integrative Bioinformatics Vienna, Max F. Preutz Laboratories, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
{ddagger} University of Vienna
$ Medical University of Vienna
University of Veterinary Medicine Vienna

Corresponding author: Simone Linz, Department of Bioinformatics, Heinrich-Heine-University, Universitätsstr. 1, 40225 Düsseldorf, Germany, Tel.: +49 (0)211 8112163, Fax: +49 (0)211 8115767, Email: linz{at}cs.uni-duesseldorf.de

Received for publication November 27, 2006. Revision received February 28, 2007. Accepted for publication March 15, 2007.

We suggest a likelihood based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees representing a set of taxa. As an illustrative example, we use the "Clusters of Orthologous Groups of proteins (COGs)". We also perform a correction of the estimated rate taking into account the inaccuracies due to gene tree reconstructions. The results suggest a corrected HGT rate of about 0.36 per gene and unit time, in other words eleven HGT events have occurred on average among the 44 taxa of the COG species tree. A software package to estimate an HGT rate is available online (http://www.cibiv.at/software/hgt/).

Key Words: horizontal gene transfer • gene tree • species tree • non-tree-like evolution


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