Sequence evolution in bacterial endosymbionts having extreme base compositions

A major limitation on ability to reconstruct bacterial evolution is the lac k of dated ancestors that might be used to evaluate and calibrate molecular clocks. Vertically transmitted symbionts that have cospeciated with animal hosts offer a firm basis for calibrating sequence evolution in bacteria, s ince fossils of the hosts can be used to date divergence events. Sequences for a functionally diverse set of genes have been obtained for bacterial en dosymbionts (Buchnera) from two pairs of aphid host species, each pair dive rging 50-70 MYA. Using these dates and estimated numbers of Buchnera genera tions per year, we calculated rates of base substitution for neutral and se lected sites of protein-coding genes and overall fates for rRNA genes. Buch nera shows homogeneity among loci with regard to synonymous rate. The Buchn era synonymous rate is about twice that for low-codon-bias genes of Escheri chia coli-Salmonella typhimurium on an absolute timescale, and fourfold hig her on a generational timescale. Nonsynonymous substitutions show a greater rate disparity in favor of Buchnera, a result consistent with a genomewide decrease in selection efficiency in Buchnera. Ratios of synonymous to nons ynonymous substitutions differ for the two pairs of Buchnera, indicating th at selection efficiency varies among lineages. Like numerous other intracel lular bacteria, such as Rickettsia and Wolbachia, Buchnera has accumulated amino acids with codons rich in A or T. Phylogenetic reconstruction of amin o acid replacements indicates that replacements yielding increased A+T pred ominated early in the evolution of Buchnera, with the trend slowing or stop ping during the last 50 Myr. This suggests that base composition in Buchner a has approached a limit enforced by selective constraint acting on protein function.