Evidence for genetic drift in endosymbionts (Buchnera): Analyses of protein-coding genes

Buchnera, the bacterial endosymbionts of aphids, undergo severe population bottlenecks during maternal transmission through their hosts. Previous stud ies suggest an increased effect of drift within these strictly asexual, sma ll populations, resulting in an increased fixation of slightly deleterious mutations. This study further explores sequence evolution in Buchnera using three approaches. First, patterns of codon usage were compared across seve ral homologous Escherichia coli and Buchnera loci, in order to test the pre diction that selection for the use of optimal codons is less effective in s mall populations. A chi(2)-based measure of codon bias was developed to adj ust for the overall A+T richness of silent positions in the endosymbionts. In contrast to E. coli homologues, adaptive codon bias across Buchnera loci is markedly low, and patterns of codon usage lack a strong relationship wi th gene expression level. These data suggest that codon usage in Buchnera h as been shaped largely by mutational pressure and drift rather than by sele ction for translational efficiency. One exception to the overall lack of bi as is groEL, which is known to be constitutively overexpressed in Buchnera and other endosymbionts. Second, relative-rate tests show elevated rates of sequence evolution of numerous protein-coding loci across Buchnera, compar ed to E. coli. Finally, consistently higher ratios of nonsynonymous to syno nymous substitutions in Buchnera loci relative to the enteric bacteria stro ngly suggest the accumulation of nonsynonymous substitutions in endosymbion t lineages. Combined, these results suggest a decreased effectiveness of pu rifying selection in purging endosymbiont populations of slightly deleterio us mutations, particularly those affecting codon usage and amino acid ident ity.