Since the establishment of the symbiosis between the ancestor of modern aphids and their primary endosymbiont, Buchnera aphidicola, insects and bacteria have coevolved. Due to this parallel evolution, the analysis of bacterial genomic features constitutes a useful tool to understand their evolutionary history. Here we report, based on data from B. aphidicola, the molecular evolutionary analysis, the phylogenetic relationships among lineages and a comparison of sequence evolutionary rates of symbionts of four aphid species from three subfamilies. Our results support previous hypotheses of divergence of B. aphidicola and their host lineages during the early Cretaceous and indicate a closer relationship between subfamilies Eriosomatinae and Lachninae than with the Aphidinae. They also reveal a general evolutionary pattern among strains at the functional level. We also point out the effect of lifecycle and generation time as a possible explanation for the accelerated rate in B. aphidicola from the Lachninae. 1. Introduction Aphids constitute a diversified group of insects widespread and of economical relevance as crop pests. The underlying reason of their ecological success is their novel capability to exploit ecological niches with little competitors, mainly due to their diet based on phloem, which is abundant and of easy access but represents an unbalanced source of nutrients, rich in sugars and poor in amino acids [1]. The clue to the use of new resources lies in the establishment of an obligate endosymbiotic relationship between the ancestor of aphids and a gamma-proteobacterium, the ancestor of Buchnera aphidicola. This single event of infection has been dated at least 150–200 million years ago (MYA) [2] according to the fossil record or to 80–150 MYA based on molecular data [3]. As a result of millions of years of cospeciation of host and endosymbiont, the current species of aphids carrying their specific strains of B. aphidicola emerged. The vertical mode of transmission of B. aphidicola, from mother to eggs and embryos, together with the location in specific host cells (the bacteriocytes), determines a population scenario for this bacterium characterized by their low effective population size, with frequent bottlenecks and little chance of genetic recombination with other bacteria. As a result, the genome reductive process undergone by B. aphidicola encompasses a decrease in the genomic size due to the loss of unnecessary genes in the new intracellular context, the increase in A+T content compared to its free-living relatives, a significant
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