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

Across taxonomical domains, synonymous codons of an amino acid are found to be used at unequal frequencies within genes. This codon usage bias (CUB) is highly variable across species. Genome-wide CUB reflects a balance between adaptive and non-adaptive microevolutionary processes within a species. Variation in microevolutionary processes results in across-species variation in CUB. As CUB is tightly linked to important molecular and biophysical processes, it is critical to understand how changes to these processes are linked to changes in microevolutionary processes. We employed a population genetics model to quantify natural selection and mutation biases on a per-codon basis across the Saccharomycotina budding yeast subphylum. We found that the strength of natural selection and mutation biases varied significantly between closely related yeasts. Across-species variation in natural selection reflected the evolution of tRNA gene copy number. Additionally, we found evidence that changes to tRNA modification expression can contribute to changes in natural selection across species independent of changes to tGCN. Both lines of evidence support the link between the evolution of the tRNA pool and natural selection in codon usage through changes in the translation efficiency of a codon. Furthermore, we found that changes to tGCN often reflected changes to genome-wide GC%, suggesting changes to the tRNA pool reflect changes to mutation bias. Our work establishes how changes in microevolutionary processes impact changes in molecular mechanisms, ultimately shaping the macroevolutionary variation of a trait. Significance statement: Codon usage bias (CUB) - the non-uniform usage of synonymous codons - is a feature of all genomes and varies across closely related species. Differences in CUB imply differences in the underlying microevolutionary processes (natural selection, mutation bias) driving CUB. CUB is hypothesized to be tightly linked to key molecular processes, particularly mRNA translation. We used a population genetics model to quantify natural selection and mutation bias on a per-codon basis across 327 budding yeasts. We found high variability in the microevolution of CUB and showed that changes in natural selection were correlated with the evolution of the tRNA pool. Our work establishes how variation in molecular mechanisms relates to variation in microevolution, shaping variation in a trait across species.