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

Area of Science:

• Microbiology
• Evolutionary Biology
• Genetics

Background:

• Synonymous codons are used unequally within genes, a phenomenon known as codon usage bias (CUB).
• CUB varies across species and reflects a balance of microevolutionary forces like natural selection and mutation bias.
• CUB is closely linked to molecular processes, especially mRNA translation.

Purpose of the Study:

• To quantify natural selection and mutation biases on a per-codon basis across budding yeasts.
• To investigate how microevolutionary processes and molecular mechanisms interact to shape CUB variation.
• To understand the link between tRNA evolution and natural selection in codon usage.

Main Methods:

• Employed a population genetics model to analyze codon usage bias.
• Quantified per-codon natural selection and mutation biases across 327 budding yeast species.
• Correlated CUB variations with tRNA gene copy number and genome-wide GC content.

Main Results:

• Significant variation in natural selection and mutation biases was observed even between closely related yeasts.
• Changes in natural selection on CUB were linked to the evolution of tRNA gene copy number.
• Evidence suggests tRNA modification expression influences natural selection on CUB independently of tRNA gene copy number.
• Changes in tRNA gene copy number often correlated with genome-wide GC content, indicating a link to mutation bias.

Conclusions:

• The evolution of the tRNA pool, including gene copy number and modifications, is a key driver of natural selection in codon usage.
• Changes in microevolutionary processes, such as mutation bias, can influence the tRNA pool and subsequently affect CUB.
• This study elucidates how molecular mechanisms and microevolutionary dynamics interact to shape macroevolutionary variation in traits like codon usage bias.