Genomic Flux: Genome Evolution by Gene Loss and Acquisition

Abstract

This chapter describes methods for assessing the frequency of successful gene acquisition and the fraction of modern genomes that has been acquired by horizontal transfer of useful phenotypic information. Although both loss and acquisition strongly influence genome evolution, the authors suggest that the two processes are synergistic due to the limits on genome expansion. To assess the contribution of genomic flux to genome evolution and speciation, one must measure rates of gene loss and acquisition. All novel phenotypes were conferred by horizontally transferred genes. Therefore, genes for the diverse metabolic pathways have formed slowly at earlier times and not during the course of competitive invasion of novel ecological niches. Regardless of the relative rates of these two processes, it is clear that gene loss and acquisition have facilitated exploration of novel environments and allowed more rapid divergence of bacterial types in competitive situations. The authors propose that the prevalence of gene clusters stands as evidence that genomic flux has historically been a primary contributor to genome evolution. They have outlined a model for the evolution of bacterial genomes through the synergistic processes of gene acquisition and gene loss. The organization of genes into operons reflects the important role in bacterial evolution and speciation played by genomic flux—the development of bacterial genomes by gene loss and gene acquisition.