Horizontal transfer beyond genes

Horizontal gene transfer (HGT) is a major process in the evolution of bacteria and archaea (1⇓–3) that is thought to be the principal source of functional innovation in microbial evolution (4, 5). The signal of vertical, tree-like evolution is detectable primarily among genes encoding components of information processing systems, whereas evolution of the operational genes (primarily, metabolic enzymes, transporters, and regulators of these processes) effectively shows network-type evolutionary dynamics (6, 7). Quantification of HGT across the diversity of bacteria reveals extremely high characteristic rates of gene transfer in most groups of bacteria, with multiple HGT events detectable per nucleotide substitution per gene, indicating that HGT is indeed the dominant mode of microbial evolution (8). Many HGT events involve individual genes, but transfer of larger portions of genomes, in particular operons, is common as well, leading to the selfish operon hypothesis under which operons represent self-contained and hence readily transferable units of evolution (9, 10). Accordingly, evolution of bacterial metabolic networks has been modeled as a process of acquisition of operons encoding distinct metabolic pathways, complete with the cognate regulatory elements (11). In PNAS, Oren et al. (12) add an unexpected, potentially important facet to the already extensive evidence of the dominance of …