AI Insight
Researchers analyzed how recombination affects the ratio of harmful to neutral mutations in human gut bacteria populations. They discovered that genomic regions inherited without recombination show higher ratios of nonsynonymous to synonymous substitutions, and that the accumulation of recombined DNA segments explains most of the observed decline in this ratio as bacterial strains diverge. The findings reveal that horizontal gene transfer plays a major role in shaping patterns of natural selection across bacterial genomes, with evidence for widespread weak selection affecting a large fraction of protein-coding genes.
Why it matters
This work fundamentally changes how scientists should interpret evolutionary patterns in bacterial populations by accounting for horizontal gene transfer, which has important implications for understanding how natural selection operates in the complex microbial communities inhabiting the human gut and potentially for predicting bacterial evolution and antimicrobial resistance.
Understand the Science
by Zhiru Liu, Benjamin H. Good
The ratio of nonsynonymous to synonymous substitutions (dN/dS) encodes important information about the selection pressures acting on protein-coding genes. In bacterial populations, dN/dS often declines with the sequence divergence between strains, but the mechanisms responsible for this broad empirical trend are still debated. Existing models have primarily focused on de novo mutations, overlooking the older genetic variants that are continually introduced through horizontal gene transfer and recombination. Here we introduce a phenomenological model of dN/dS in recombining populations of bacteria, which allows us to disentangle the effects of recombination among pairs of closely related strains. We find that clonally inherited regions of the genome exhibit consistently higher dN/dS ratios, and that the accumulation of recombined segments can quantitatively explain the majority of the decline in dN/dS. We use these observations to re-examine models of purifying selection and adaptive reversion in human gut bacteria, and uncover evidence for widespread weak selection at a large fraction of protein-coding sites. Our findings show that horizontal gene transfer can be an important factor in shaping genome-wide patterns of selective constraint, and raise new questions about the effectiveness of natural selection in complex bacterial populations.