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MBE Advance Access originally published online on March 20, 2007
Molecular Biology and Evolution 2007 24(6):1312-1319; 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 Articles

A Likelihood Framework to Measure Horizontal Gene Transfer

Simone Linz*, Achim Radtke* and Arndt von Haeseler{dagger},{ddagger},§,||

* Department of Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany
{dagger} Center for Integrative Bioinformatics Vienna, Max F. Preutz Laboratories, Vienna, Austria
{ddagger} University of Vienna, Vienna, Austria
§ Medical University of Vienna, Vienna, Austria
|| University of Veterinary Medicine Vienna, Vienna, Austria

E-mail: linz{at}cs.uni-duesseldorf.de.

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 11 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 • nontree-like evolution

Martin Embley, Associate Editor


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