A Likelihood Framework to Measure Horizontal Gene Transfer

@article{citeulike:2475329, 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/). 10.1093/molbev/msm052}, author = {Linz, Simone and Radtke, Achim and von Haeseler, Arndt }, citeulike-article-id = {2475329}, doi = {10.1093/molbev/msm052}, journal = {Mol Biol Evol}, keywords = {master}, month = {June}, number = {6}, pages = {1312--1319}, posted-at = {2008-03-09 23:58:57}, priority = {2}, title = {A Likelihood Framework to Measure Horizontal Gene Transfer}, url = {http://dx.doi.org/10.1093/molbev/msm052}, volume = {24}, year = {2007} }

TY - JOUR ID - citeulike:2475329 L3 - citeulike-article-id:2475329 TI - A Likelihood Framework to Measure Horizontal Gene Transfer JF - Mol Biol Evol VL - 24 IS - 6 SP - 1312 EP - 1319 N2 - 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/). 10.1093/molbev/msm052 KW - master AU - Linz, Simone AU - Radtke, Achim AU - von Haeseler, Arndt PY - 2007/06/01/ UR - http://dx.doi.org/10.1093/molbev/msm052 ER -