Although in any given bacterial population, the absolute rate of chromosomal gene change by recombination may be as low or lower than that of mutation, the consequences of recombination for adaptive evolution in bacteria can be far more profound than those of mutation. By legitimate (homologous) or illegitimate (nonhomologous) recombination, bacteria can acquire new genes that have evolved in other often phylogenetically and ecologically distant populations. These genes can code for phenotypes that can expand or alter the ecological niche of their host bacterium (Cohan, 1996), and if they are favored in the recipient population, they will ascend. Given sufficient time and sufficiently intense selection, bacteria will acquire whatever genes they need either directly or indirectly through intermediate species. And, as we have learned from the evolution of antibiotic resistance, “sufficient time” need not be very long. For this reason, bacterial ecosystems have been characterized as a “global gene pool” (Maiden et al., 1996). From the perspective of adaptive evolution, it is generally not the rate of recombination that is important but rather the existence of mechanisms for gene exchange, the range of “species” with which a populations of bacteria can (and do) exchange genes, and the intensity of selection for those genes.
From one perspective, the accessory genetic elements of bacteria are parasites and symbionts, and their population and evolutionary biology can be—and has been—treated in that context with little or no reference to their role as sources of variation for their host bacteria. However, as we have discussed above, much of the real “action” in adaptive evolution in bacteria is through genes borne on, transmitted by, and sequestered from these elements. And, from this perspective, the population and evolutionary dynamics of these elements form an integral part of the process of adaptive evolution in bacteria.
Traditionally, we classify the accessory genetic elements of bacteria into functional, rather than phylogenetic groups: primarily as plasmids, transposons, and temperate phages. Furthermore, we typically draw a distinction between these peregrine elements and those with less mobile and autonomous life styles such as islands and integrons. However, the distinction between plasmids, phages, and transposons is somewhat arti-