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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.〔 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. ==Overview== Horizontal gene transfer was first observed in 1928, in Frederick Griffith's experiment: showing that virulence was able to pass from virulent to non-virulent strains of ''Streptococcus pneumoniae'', Griffith demonstrated that genetic information can be horizontally transferred between bacteria via a mechanism known as transformation.〔 Similar observations in the 1940s〔 and 1950s〔 showed evidence that conjugation and transduction are additional mechanisms of horizontal gene transfer. To infer HGT events, which may not necessarily result in phenotypic changes, most contemporary methods are based on analyses of genomic sequence data. These methods can be broadly separated into two groups: parametric and phylogenetic methods (see Figure 1). Parametric methods search for sections of a genome that significantly differ from the genomic average, such as GC content or codon usage.〔 Phylogenetic methods examine evolutionary histories of genes involved and identify conflicting phylogenies. Phylogenetic methods can be further divided into those that reconstruct and compare phylogenetic trees explicitly, and those that use surrogate measures in place of the phylogenetic trees.〔 The main feature of parametric methods is that they only rely on the genome under study to infer HGT events that may have occurred on its lineage. It has been a considerable advantage at the early times of the sequencing era, when few closely related genomes were available for comparative methods. However, because they rely on the uniformity of the host's signature to infer HGT events, not accounting for the host's intra-genomic variability will result in overpredictions—flagging native segments as possible HGT events.〔 Similarly, the transferred segments need to exhibit the donor's signature and to be significantly different from the recipient's.〔 Furthermore, 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.〔 This limits the ability of parametric methods to detect ancient HGTs. Phylogenetic methods benefit from the recent availability of many sequenced genomes. Indeed, 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. However, models have limits and need to be used cautiously. For instance, the conflicting phylogenies can be the result of events not accounted for by the model, such as unrecognized paralogy due to duplication followed by gene losses. Also, many approaches rely on a reference species tree that is supposed to be known, when in many instances it can be difficult to obtain a reliable tree. Finally, the computational costs of reconstructing many gene/species trees can be prohibitively expensive. Phylogenetic methods tend to be applied to genes or protein sequences as basic evolutionary units, which limits their ability to detect HGT in regions outside or across gene boundaries. Because of their complementary approaches—and often non-overlapping sets of HGT candidates—combining predictions from parametric and phylogenetic methods can yield a more comprehensive set of HGT candidate genes. Indeed, combining different parametric methods has been reported to significantly improve the quality of predictions.〔〔 Moreover, in the absence of a comprehensive set of true horizontally transferred genes, discrepancies between different methods〔〔 might be resolved through combining parametric and phylogenetic methods. However, combining inferences from multiple methods also entails a risk of an increased false-positive rate.〔 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Inferring horizontal gene transfer」の詳細全文を読む スポンサード リンク
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