sory elements, such as plasmids and prophages of temperate viruses. Some of these islands and virulence-encoding accessory elements may have had a long history with one or a few specific pathogenic species of bacteria (Groisman and Ochman, 1997). On the other hand, many are distributed among bacteria that, based on their less mobile chromosomal loci, are phylogenetically quite different (Czeczulin et al., 1999). Plasmids and their running dogs, transposons, also bear many of the genes responsible for antibiotic resistance and, all too commonly, multiple antibiotic resistance (Falkow, 1975), and many of the other characters that make the lives of prokaryotic organisms as interesting and exciting as they are. Included among these plasmid-borne genes are those that code for the fermentation of exotic carbon sources, the detoxification of heavy metals, and the production of allelopathic agents, such as bacteriocins (Summers, 1996). Bacteria also commonly carry integrons, elements that acquire, accumulate, and control the expression of genes acquired from external sources (Hall, 1997, 1998; Mazel et al., 1998; Row-Magnus and Mazel, 1999).
All of these islands and accessory genetic elements and even some seemingly ordinary chromosomal genes, like those for the resistant forms of the penicillin-binding proteins of Streptococcus pneumoniae (Dowson et al., 1989), were acquired from other organisms (primarily, but possibly not exclusively, other bacteria). They were picked up in a number of ways: as free DNA (transformation), through bacteriophage (transduction), or by intimate contact with other bacteria (conjugation). Although genetic exchange may occur less frequently in bacteria than in sexual eukaryotes (for which recombination is an integral part of the reproductive process), the phylogenetic range across which genetic exchange can occur in bacteria is far broader than that in extant eukaryotes. From a prokaryotic perspective, sexual eukaryotes like ourselves are incestuous nymphomaniacs: we do “it” too far often and almost exclusively with partners that, from a phylogenetic perspective, are essentially identical to ourselves. To be sure, genes acquired by horizontal transfer can be a source of variation for adaptive evolution in “higher” eukaryotes, up to and including those high enough to publish (Courvalin et al., 1995; Grillot-Courvalin et al., 1998). However, for at least contemporary eukaryotes, it is sufficient (and sufficiently problematic) to develop a comprehensive genetic theory of adaptive evolution based on variation generated from within by mutation (broadly defined to include transposition and chromosomal rearrangement) and recombination among members of the same species. By contrast, in contemporary as well as ancient bacteria, the horizontal transfer of genes (and accessory genetic elements) from other species is a major source of variation and is fundamental to the genetic theory of adaptive evolution in these prokaryotes.