A likelihood framework to measure horizontal gene transfer.
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/).
Linz
Simone
S
Department of Bioinformatics, Heinrich-Heine-University, Düsseldorf, Germany. linz@cs.uni-duesseldorf.de
Radtke
Achim
A
von Haeseler
Arndt
A
D001419:Bacteria / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D005658:Fungi / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016013:Likelihood Functions; D008957:Models, Genetic