The consequences of genetic drift for bacterial genome complexity

Abstract

Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the contribution of genetic drift to genome evolution is problematic because the usual methods, based on intraspecific polymorphisms, can be thwarted by difficulties in delineating species' boundaries. The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.

Figure 1.

Association between genome size and gene count (A) and gene density (B) for 488 bacterial species. Green points represent the 84 genomes considered in the present study; gray points are other published genomes.

Figure 2.

Association between level of genetic drift and genome size (A) and gene density (B) for the 42 pairs of bacterial genomes. The level of genetic drift exhibits a strong negative correlation with genome size (r = –0.72, P = 6.3 × 10⁻⁸). When only strictly free-living bacteria are considered, the correlation remains statistically significant (r = –0.55, P = 0.039), particularly when the anomalous pair of cyanobacteria is excluded (r = –0.86, P = 0.0018; see Results for explanation).