Phylogenetic reconstruction methods remain the only way to reliably infer historical events from gene sequences as they are the only methods that are based on a large body of work (Eisen, 2000). For example, phylogenetic methods

are designed to accommodate buy 5-Fluoracil variation in evolutionary rates and patterns within and between taxa (Ragan et al., 2006). However, it is not easy to extend phylogenetic methods to all genes, for example some gene families evolve so rapidly that orthologs cannot be confidently identified (Ragan, 2001). Other problems that may arise are the computational difficulties in inferring trees and assessing confidence intervals for large data sets. It is not surprising therefore that there is considerable interest in developing methods that can rapidly identify HGT without the need of phylogenetic trees. These heuristic methods have been referred to as surrogate methods (Ragan, 2001). An example of a surrogate method includes the examination of the patterns of best matches to different species using similarity search techniques to determine the best match for each gene in a genome. This approach has the advantage of speed and automation but does not have a high degree of accuracy. Some notable failures of this approach include the unsupported claim that

223 genes have been transferred from bacterial pathogens to humans (Lander et al., AZD6244 nmr 2001). These Quinapyramine findings were based on top hits from a blast database search; however, rigorous phylogenetic analyses showed these initial claims to be unsupportable (Stanhope et al., 2001). Similarly, another study based on blast database searches also reported

that Mycobacterium tuberculosis has 19 genes that originate from various eukaryotes (Gamieldien et al., 2002); again using phylogenetic analyses, this hypothesis was shown to be unsupportable (Kinsella & McInerney, 2003). Reasons for low levels of accuracy with these similarity searches include hidden paralogy, distant slowly evolving genes being detected as best matches or two closely related genes not matching well if they have evolved rapidly (Eisen, 1998). Other surrogate methods identify the regions within genomes that have atypical genomic characteristics (Fig. 1d,e). In theory when a gene is introduced into a recipient genome, it takes time for it to ameliorate to the recipients’ base composition. Therefore, foreign genes in a genome can be detected by identifying genes with unusual phenotypes such as atypical nucleotide composition or codon usage patterns (Lawrence & Ochman, 1998; Fig. 1d). This approach is attractive as it only requires one genome but does suffer from some obvious flaws. For example, atypical composition may be the result of selection or mutation bias. Furthermore, this approach cannot detect the transfers between species with similar base compositions.