Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes. 1. Introduction Genomic science has brought about the possibility of disclosing the genetic underpinnings of entire organisms, and, for microbes, even of complex populations and communities. In doing so, it has unearthed a good number of surprising facts regarding the structure, organization, and variability of genomes, with strong evolutionary implications. In bacteria, the relatively small size of genomes has warranted the obtention of entire genomic sequences for a vast number of organisms, including numerous sets of sequences of closely related taxa. As genome sequences of closely related bacteria have accumulated, our view of bacterial genomes has radically changed. Genome comparisons have demonstrated that little 16S rRNA sequence divergence can be accompanied by large differences in total gene repertoire [1–7], and that even populations of a single 16S rRNA species can be made up of vast numbers of genomic varieties [8]. Much of the observed variation among closely related bacterial genomes has been attributed to gains and losses of genes that are acquired horizontally, often by way of mobile genetic elements (MGEs) as well as to a variety of genomic rearrangements that include gene duplications and large gene
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