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Mol Biol Evol. 2007 Jun;24(6):1312-9. Epub 2007 Mar 20.

A likelihood framework to measure horizontal gene transfer.

Author information

  • 1Department of Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany. linz@cs.uni-duesseldorf.de

Erratum in

  • Mol Biol Evol. 2007 Jul;24(7):1576.

Abstract

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/).

PMID:
17374878
DOI:
10.1093/molbev/msm052
[PubMed - indexed for MEDLINE]
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