Related Experiment Video
Updated: May 24, 2025
06:12
Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
Published on: October 25, 2018
8.6K
A Short-Term View of Protein Sequence Evolution from Salmonella
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Genome Biology and Evolution
|March 6, 2025
Summary
Analyzing recent Salmonella genome changes reveals weak purifying selection and identifies 151 genes under positive selection, including those for antibiotic resistance and transcriptional regulation.
Area of Science:
- Evolutionary biology
- Genomics
- Microbial genetics
Background:
- Protein sequence evolution studies typically use distantly related sequences, where purifying selection's effects are pronounced.
- This approach infers past evolutionary events under varied conditions.
Purpose of the Study:
- To investigate recent evolutionary changes using closely related Salmonella genome sequences.
- To discern the effects of weak purifying selection on short evolutionary timescales.
- To identify genes under positive selection and understand the selective pressures involved.
Main Methods:
- Comparative analysis of a large number of closely related Salmonella genome sequences.
- Quantification of nonsynonymous to synonymous substitution ratios.
- Assessment of gene essentiality and expression levels in relation to nonsynonymous change rates.
- Inference of positive selection acting on specific genes.
Main Results:
- Purifying selection is weakly but detectably active on short evolutionary timescales.
- Essential genes show lower nonsynonymous change rates, even after controlling for expression.
- Positive selection was inferred for 151 genes, often associated with loss of function, altered antibiotic sensitivity, or transcriptional regulation.
- Many positively selected variants appear favored only under specific, short-term conditions.
Conclusions:
- Close sequence comparisons provide a complementary view to distant comparisons for understanding protein evolution.
- Recent evolutionary events reveal subtle selective pressures and identify specific adaptive changes in Salmonella.
- The study highlights the dynamic nature of gene evolution and adaptation in microbial populations.
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