Probabilistic inference of lateral gene transfer events

BMC Bioinformatics

Research

Jens Lagergren¹  Owais Mahmudi¹  Mehmood Alam Khan¹  Ikram Ullah¹  Lars Arvestad² 

[1] KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, 171 21, Solna, Sweden;Science for Life Laboratory, Box 1031, 171 21, Solna, Sweden;Stockholm University, Dept. of Numerical Analysis and Computer Science, Box 1031, 171 21, Solna, Sweden;Swedish e-Science Research Centre, Solna, Sweden;Science for Life Laboratory, Box 1031, 171 21, Solna, Sweden;

关键词: Evolution;    Bayesian inference;    Phylogeny;    Lateral gene transfer;   

DOI  :  10.1186/s12859-016-1268-2

来源: Springer

【 摘 要 】

BackgroundLateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge.ResultsIn this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify “highways” of LGT.ConclusionsBased on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.

【 授权许可】

CC BY   
© The Author(s) 2016

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