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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
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Reversions mask the contribution of adaptive evolution in microbiomes
Paul A Torrillo1,2, Tami D Lieberman1,2,3,4
1Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, United States.
Elife
|September 6, 2024
Summary
Bacterial genome evolution depends on mutational distance. An adaptive reversion model, not weak purifying selection, better explains dN/dS decay in microbiomes, suggesting caution when interpreting long-term evolutionary data.
Area of Science:
- Evolutionary Biology
- Genomics
- Microbiome Research
Background:
- The interpretation of bacterial genome evolution relies on mutational distance.
- The ratio of nonsynonymous to synonymous mutations (dN/dS) is a key indicator of selection.
- Existing models struggle to explain observed dN/dS patterns in gut microbiome data.
Purpose of the Study:
- To challenge the classical interpretation of dN/dS decay as weak purifying selection.
- To propose and validate an alternative model for bacterial genome evolution in microbiomes.
- To re-evaluate the implications of dN/dS ratios for understanding bacterial adaptation.
Main Methods:
- Analysis of bacterial genome data, focusing on mutational distance.
- Development and application of an adaptive reversion model.
- Utilizing analytical and simulation approaches to test the model.
- Examining dN/dS ratios in the context of gut microbiome dynamics.
Main Results:
- The classical interpretation of dN/dS decay is problematic for microbiome data.
- An adaptive reversion model accurately explains dN/dS decay with fluctuating selection.
- Adaptive reversions are likely in microbiomes due to large populations and rapid evolution.
- The model is particularly relevant for bacteria like *Bacteroides*.
Conclusions:
- Low dN/dS values over long timescales may result from frequent adaptive sweeps, not just weak selection.
- Mutational reversions play a significant role in shaping bacterial genomic landscapes.
- Studying bacterial evolution on shorter timescales is crucial for accurate interpretation.
Keywords:
Bacteroidalesevolutionary biologyhuman microbiomeinfectious diseasemicrobiologymolecular evolutionwithin-person evolutionMore Related Videos
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