Reversions mask the contribution of adaptive evolution in microbiomes

Area of Science:

• Evolutionary Biology
• Microbial Genomics
• Population Genetics

Background:

• The interpretation of bacterial genome evolution relies on mutational distance.
• The normalized ratio of nonsynonymous to synonymous mutations ($$) typically indicates purifying selection, but this interpretation is scale-dependent.

Purpose of the Study:

• To challenge the classical interpretation of scale-dependence in $$ values.
• To propose and validate an alternative model for understanding $$ decay in microbial genomes.

Main Methods:

• Analytical modeling
• Computer simulations
• Analysis of gut microbiome data (specifically *Bacteroides* genomes)

Main Results:

• The classical interpretation of weak purifying selection leads to problematic mutation accumulation in microbiome data.
• An adaptive reversion model effectively explains the observed $$ decay with realistic environmental fluctuations.
• Adaptive sweeps, driven by reversions, can explain low $$ values even with frequent selection.

Conclusions:

• Low $$ values from long evolutionary timescales should be interpreted with caution, as they may result from frequent adaptive sweeps.
• Mutational reversions play a significant role in shaping bacterial genomic landscapes over time.
• Studying bacterial genomic evolution on shorter timescales is crucial for accurate interpretation.