The extent to which genes and accessory genetic elements are exchanged among phylogenetically distant populations raises a number of issues beyond those of the genetic mechanisms of adaptive evolution addressed herein. Perhaps the most fundamental of these other issues are the classical ones of the definition of species and the remarkable discreetness of the genomic clusters of organisms we classify as members of the same species of bacteria. For interesting and appealing considerations of these issues, see Dykhuizen (1998), Dykhuizen and Green (1991), Majewski and Cohan (1999), and Palys et al. (1997).
Although genes and accessory elements acquired from external sources are responsible for many of the interesting adaptations of bacteria to their environments and their seemingly saltational evolution, the mundane processes of mutation and selection at chromosomal loci are by no means inconsequential for the long-term as well as day-to-day evolution of bacteria. On the other hand, at least quantitatively and possibly qualitatively, the chromosomal population genetics of adaptive evolution in bacteria are different from those of sexually reproducing eukaryotes.
The primary differences between the chromosomal population genetics of bacteria and those of sexually reproducing eukaryotes arise as a consequence of the low rates of chromosomal gene recombination in bacterial populations. To be sure, if one looks hard enough, some natural mechanism of chromosomal gene recombination can probably be demonstrated to occur in most species of bacteria. And collectively, the chromosomal genomes of some species of bacteria may even be at or near linkage equilibrium (Maynard Smith et al., 1993; Maynard Smith and Smith, 1998). Nonetheless, because bacteria reproduce clonally, by binary fission, any given population will be composed of relatively few genetically distinct lineages, with recombination between them occurring only on rare occasions. We postulate that for most natural populations of bacteria, the probability of a gene in one lineage (clone) being replaced by homologous recombination with a gene from another lineage of its own or another