Inferring horizontal gene transfer.

Matt Ravenhall,Christophe Dessimoz,Nives Škunca,Florent Lassalle,Shoshana Wodak

doi:10.1371/journal.pcbi.1004095

Abstract

Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages [1]. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.

Highlights

Horizontal gene transfer (HGT) was first observed in 1928, in Frederick Griffith’s experiment
Showing that virulence was able to pass from virulent to nonvirulent strains of Streptococcus pneumoniae, Griffith demonstrated that genetic information can be horizontally transferred between bacteria via a mechanism known as transformation [2]
While weakly-supported differences between gene and species trees can be due to inference uncertainty, statistically significant differences can be suggestive of HGT events

Summary

Introduction

Horizontal gene transfer (HGT) was first observed in 1928, in Frederick Griffith’s experiment. Genomic segments of foreign origin are subject to the same mutational processes as the rest of the host genome, and so the difference between the two tends to vanish over time, a process referred to as amelioration [9] This limits the ability of parametric methods to detect ancient HGTs. Phylogenetic methods benefit from the recent availability of many sequenced genomes. As for all comparative methods, phylogenetic methods can integrate information from multiple genomes and in particular integrate them using a model of evolution This lends them the ability to better characterize the HGT events they infer—notably by designating the donor species and time of the transfer. Combining inferences from multiple methods entails a risk of an increased false positive rate [14]

Parametric Methods

Phylogenetic Methods

Evaluation