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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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A New Comparative Framework for Estimating Selection on Synonymous Substitutions.

Hannah Verdonk¹, Alyssa Pivirotto², Vitor Pavinato²

¹Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.

Molecular Biology and Evolution

|March 25, 2025

Summary

This summary is machine-generated.

This study introduces multiclass synonymous substitution (MSS) models to account for selection on codon usage. These models reveal significant variation in substitution rates, offering new insights into evolutionary processes.

Keywords:

codon substitution models codon usage bias molecular evolution synonymous substitutions

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Area of Science:

Evolutionary Biology
Population Genetics
Bioinformatics

Background:

Selection on synonymous codon usage is a known evolutionary phenomenon.
Existing models often fail to incorporate this selection or its impact on substitution rates.
This gap hinders a comprehensive understanding of molecular evolution.

Purpose of the Study:

To develop and enhance multiclass synonymous substitution (MSS) models.
To accurately estimate relative synonymous substitution rates while accounting for mutation bias.
To investigate selection on codon usage across diverse taxa.

Main Methods:

Developed multiclass synonymous substitution (MSS) models.
Partitioned synonymous substitutions into multiple classes with estimated relative rates.
Validated model performance using population genetic simulations and analyzed empirical Drosophila data.

Main Results:

Identified extensive heterogeneity in relative synonymous substitution rates across ~12,000 gene alignments in Drosophila.
Demonstrated MSS model robustness to model misspecification through simulations.
Found significant correlations between MSS rates and codon usage selection covariates (polymorphism and tRNA data).

Conclusions:

MSS models effectively detect signatures of selection on codon usage.
These models provide a powerful tool for studying synonymous substitutions across diverse species.
Allows for analysis independent of prior assumptions about evolutionary forces.