INTRODUCTION

Intracellular bacteria (symbionts and parasites) are characterized by a genome reduction syndrome that, when compared to their free-living relatives, leads us to the conclusion that they are evolving anomalously. Is this right? The notion of anomaly has an anthropocentric connotation, and from such a viewpoint we cannot state that genome reduction is an evolutionary anomaly; likewise we cannot state that parasitic organisms represent a degenerate stage of evolution as compared to their non-parasitic ancestors. By contrast, we can affirm that they represent an anomaly if we are unable to explain their origin and evolution, given there is no suitable theory to explain both the increase in genome size and evolutionary complexity as well as the genome reduction process in endosymbionts. The question is: Do we have such a theory? In the past few years Michel Lynch and collaborators have published a series of papers on this particular issue, trying to integrate the evolution of genome size and concomitantly genome complexity of prokaryotes and eukaryotes into a single theoretical framework following the basic principles of population genetics.

In this chapter, we would like to deal with how basic principles, such as mutation, selection, and effective population size, can give us an acceptable explanation, empirically founded, of the genome reduction process in endosymbiotic bacteria. We propose a model that both explains the huge transformation of endosymbiotic genomes at nucleotide level and accounts for genome reduction.