Mutational Patterns Cannot Explain Genome Composition: Are There Any Neutral Sites in the Genomes of Bacteria?

The dissection of natural selection and neutral processes remains a core problem for molecular evolutionary biologists. One of the longest-standing controversies concerns the causes of genome base composition, notably the variation in the sum of G and C content (GC) between 17% and 75% in bacteria. Sueoka argued very early that GC content variation is driven by mutational biases and, as this bias affects non-synonymous sites, protein evolution might also be largely driven by neutral forces [1]. Later, Muto and Osawa showed that 4-fold degenerate positions in codons exhibit the largest range of GC content (GC4), whereas the non-degenerate second codon positions (GC2) exhibit the narrowest (Figure 1) [2]. As the footprint of genomic GC variation is most evident in those sites under the least selective constraint for amino acid composition, it has become accepted that GC content variation is primarily driven by neutral mutational effects and has little adaptive relevance [2]. Two papers in the current issue of PLoS Genetics aim to test whether the variation in bacterial genomic GC content results directly from mutation biases. Far from observing variation in mutational patterns concordant with the range of GC content, Hildebrand et al. [3], and Hershberg and Petrov [4] independently point to a strong and consistent AT pressure on bacterial genomes, whereby de novo GC R AT mutations arise much more commonly than the reverse. Hershberg predicts that most bacterial genomes, if left entirely vulnerable to mutation, would approach an equilibrium GC content of 20%–30%, close to the highly reduced genomes of endosymbionts [5]. Discounting a rather implausible scenario whereby nearly all diverse GC-rich taxa are converging towards a low GC content, one is forced to conclude that the excess A and T generated by mutation bias (AT pressure) is lost over time. If so, mutational patterns are not strongly shaping genomes after all, and something else is keeping GC contents up. Hildebrand and co-workers analyze polymorphism data from 149 phylogenetically diverse species corresponding to a wide range of GC content. A major strength of this analysis is that it tests for a number of possible confounders that might explain the excess of GC R AT changes, including variation in mutation rates, sequencing errors, and violations of the infinite sites assumption. The proportion of GC « AT changes that are GC R AT (Z) is almost always .0.5, and is positively correlated with GC4. This means that AT pressure is strongest in GC-rich genomes. For the most GC-poor genomes, the ratio is reversed (Z,0.5), but this might result from violation of the infinite sites assumption at extreme GC content. In fact, the extreme AT-rich genomes of Buchnera do have Z = 0.5 [6]. Hershberg and Petrov exploit full genome data of five very recently evolved ‘‘clonal pathogens’’, presumably under relaxed selection, allowing precise detection of mutational patterns. This more limited dataset includes no extreme GCpoor genomes. On the other hand, the availability of a large number of SNPs and of an outgroup allows the comparison of patterns within and between species. Consistent with the results of Hildebrand et al., Hershberg and Petrov find an excess of GC R AT mutations in synonymous, non-synonymous, and intergenic sites. Comparisons with the outgroup species suggest this is not caused by loss of repair genes, and that it abates over greater phylogenetic distances (i.e., between ‘‘species’’). This pattern is similar to that previously found in E. coli [7], and reflects the action of purifying selection (or a process that mimics selection) preferentially removing AT-enriching mutations over time. Hershberg and Petrov’s study also highlights the significance of weaker purifying selection in newly emerged pathogens, as shown in Shigella strains [7]. Strikingly, they find no evidence for a correlation between predicted GC contents at mutational equilibrium and extant base composition, suggesting that mutational bias might have no role in shaping genome composition. Hildebrand et al. show a similar qualitative bias, but predicted equilibrium values vary between 5% and 90% GC. As methods and datasets differ in the two studies, further analyses will be required to shed light on this issue. Taken together, the evidence for a common mutational pressure towards low GC is clear. The process maintaining base composition in GC-rich genomes must be very strong, because a genomic GC content of 75% corresponds to a GC4 of nearly 100% (Figure 1). This represents a ,70% gap with Hershberg and Petrov’s predicted mutational equilibrium. Two distinct processes might be at work: biased gene conversion (BGC) and natural selection. In certain eukaryotes, BGC results from recombination between heterologous sequences preferentially removing AT polymorphisms [8]. Contrary to sexual eukaryotes, allelic recombination in bacteria requires horizontal transfer. As a result, rates of recombination between, and even