In a recent investigation, we, along with Marc Lipsitch (Bergstrom et al., 2000), addressed this question from a slightly different angle, that of the existence conditions for plasmids. We demonstrated that, under broad conditions, if host-expressed genes have higher fitness when carried on the chromosome than on an infectiously transmitted plasmid, then those genes will be sequestered eventually by the chromosome. These usurpings of genes from the plasmid by the chromosome will be the case even when selection for those genes is intermittent, as is the case for antibiotic resistance and most other plasmid-encoded characters. A broader interpretation of this result is that, if the mobility of host-adaptive genes has a cost, that mobility will be lost eventually. Plasmids, transposons, and temperate phages, or the genes they carry will give up their vagabond lifestyle and become islands.
On the other side, using primarily simulation methods, we demonstrated two seemingly realistic situations under which those genes can be maintained for extended periods on infectiously transmitted accessory elements. The first of these is the continuous entry into that population of lineages that are more fit than existing ones. By being infectiously transmitted, those favored (or occasionally favored) genes will be able to make their way to the rising stars rather than being lost along with their has-been hosts. The second situation involves movement among two or more distinct bacterial ecotypes in an ecologically heterogeneous environment. Although the accessory element may be lost from any particular ecotype at any particular time, it can return via horizontal transfer, and in the long term, the host-beneficial genes can persist on accessory elements.
In this interpretation, genes originally carried on accessory elements (and even the elements themselves) are in a continuous state of flux with respect to their mobility and within-host stability. As the habitat of a bacterial population becomes more stable and/or the opportunities for its accessory elements to move to uninfected populations decline, selection will favor the incorporation of those elements or the favored genes they carry into the chromosome. The opposite will occur in more interesting times and places. Selection will favor the mobility of accessory elements, and broadly favored but narrowly available genes and former elements will be seduced back into a vagabond lifestyle. A corollary of this interpretation, if interpretations are allowed to have corollaries, is that genes that become widely popular for some environmental reason—such as the genes for antibiotic resistance after the human use of antibiotics—will be borne initially by more mobile accessory elements. Whether the mobile elements bearing these genes will be phages, conjugative or nonconjugative plasmids, or transposons or whether those genes would be acquired by transformation will depend on a variety of historical, genetic,