Nature Reviews Microbiology - Reviews: "Bacterial genomes are increasingly viewed in terms of the integration of accessory and dispensable genetic elements into a conserved genomic core. This duality provides both the evolutionary stability that is required for the maintenance of essential functions and the flexibility that is needed for rapid exploitation of new niches. This review focuses on combining genome sequencing, microarray and multilocus sequence data to explore microevolutionary divergence in single species and genera.

Bacterial genomes are composed of essential 'core' genes, encoding functions relating to central metabolism and informational processing, and 'accessory' genes that commonly encode supplementary metabolic pathways and virulence factors. 'Foreign' genes in bacterial genomes can be identified by atypical base composition; these might have been imported from quite distant bacterial taxa.

Three main tools for examining the microevolution (evolution within species) of bacteria are complete genome sequencing, microarray analysis (which detects changes in gene content) and multi-locus sequencing of 'core' genes. These three approaches have advantages and disadvantages and are most powerfully used in combination.

Most bacterial populations consist of a limited number of widespread clonal complexes on the basis of sequence variation in a sample of core genes. These clonal complexes are generally robust with respect to gene choice and are meaningful biological units. These clusters might represent adaptations to specific microniches, and be set on independent evolutionary trajectories.

Despite high degrees of clonality, analysis of clonal diversification and phylogenetic approaches examining the relationships between clones both indicate that homologous recombination is an important evolutionary force in many bacterial populations. It is possible that sampling bias leads to an artificially high degree of clonality, but also that the selective origin of clones allows them to withstand the homogenizing effects of recombination.

Given the clonal structure of bacterial populations, comparative genomic analysis is most fruitfully carried out with reference to clonal assignments. Such an approach allows a consideration of likely ecological adaptations between isolates and a broad temporal perspective to microevolutionary studies."

Edward J. Feil SMALL CHANGE: KEEPING PACE WITH MICROEVOLUTION Nature Reviews Microbiology 2, 483-495 (2004); doi:10.1038/nrmicro904

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