Genomes on the shrink

Because genetic events do not fossilize, we are forced to deduce the evolution of bacterial genomes by comparing the features of contemporary organisms. This comparative approach has exposed many of the alterations endured by bacterial genomes (bouts of expansion and contraction or changes in base compositions), but such reconstructions are often imprecise, and sometimes incorrect, because they are limited by the spectrum and relationships of the sequenced genomes that are available. Determining whether changes in gene repertoires and genome size were gradual or episodic is not feasible when the genomes being considered diverged several hundred million years ago. Fortunately, the results reported by Nilsson et al. (1) in this issue of PNAS indicate how such transformations proceed and help to explain one of the most interesting and pervasive trends in the evolution of bacterial genomes.

When analyzed in a molecular phylogenetic perspective, every clade of bacteria with genome sizes of <2 Mb was derived from ancestors with substantially larger genomes (Fig. 1). This pattern dispels the long-held notion that bacteria evolved by the successive doubling of small-genomed progenitors (2, 3) and raises numerous questions about an evolutionary process that seems to affect all bacterial lineages. Among the groups best suited for investigating the progression toward reduced genomes are the γ-proteobacteria, due principally to the large number of fully sequenced constituents (53 at last count). Within this phylum, which includes the workhorses of bacterial genetics and pathogenesis, Escherichia coli and Salmonella typhimurium, the sizes of already-sequenced genomes vary over an order …