Prokaryote genome fluidity is dependent on effective population size

Abstract

Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size N_e. No effects of genome size, phylogeny or homologous recombination rate on genome fluidity were found. Our findings are consistent with a scenario where accessory gene content turnover is for a large part dictated by neutral evolution.

Figure 1

The genome fluidity statistic φ as a function of synonymous core genome nucleotide variation π for 90 free-living prokaryote species on a ln-ln scale. White dots: Proteobacteria, black dots: Terrabacteria (Actinobacteria, Firmicutes and Cyanobacteria), grey dots: other taxa.