Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding...

Area of Science:

• Evolutionary Biology
• Genomics
• Molecular Biology

Background:

• Synonymous codons are used unequally within genomes, a phenomenon known as codon usage bias (CUB).
• CUB varies significantly across species and reflects a balance between adaptive and nonadaptive microevolutionary processes.
• Understanding the link between CUB and molecular/biophysical processes is crucial for deciphering evolutionary mechanisms.

Purpose of the Study:

• To quantify natural selection and mutation biases on a per-codon basis in Saccharomycotina budding yeasts.
• To investigate how microevolutionary processes shape codon usage bias across species.
• To establish the link between microevolutionary changes and molecular mechanisms influencing CUB.

Main Methods:

• Employed a population genetics model to analyze codon usage bias.
• Quantified natural selection and mutation biases per codon.
• Examined the evolution of tRNA gene copy number (tGCN) and tRNA modification expression.

Main Results:

• Significant variation in natural selection and mutation biases was observed even between closely related yeasts.
• Across-species variation in natural selection correlated with the evolution of tRNA gene copy number (tGCN).
• Changes in tRNA modification expression also influenced natural selection on codon usage, independent of tGCN.
• Changes in tGCN often reflected alterations in genome-wide GC content, indicating a link to mutation biases.

Conclusions:

• The evolution of the tRNA pool, through changes in tGCN and tRNA modifications, directly impacts natural selection on codon usage.
• Changes in translation efficiency, driven by the tRNA pool, are a key mechanism linking microevolutionary processes to CUB.
• Alterations in microevolutionary processes, including mutation biases reflected in GC content, shape molecular mechanisms and ultimately influence macroevolutionary trait variation.