Apparent longevity-related adaptation of mitochondrial amino acid content is due to nucleotide compositional shifts

Recent studies across animal phyla have suggested a possible link between amino acid compositional shifts and adaptive evolution across mitochondrial proteomes enabling longer lifespans. These studies examined associations of a gradual loss of cysteine (Cys) residues, increased usage of methionine (Met), and increased usage of threonine (Thr), with the evolution of longevity. Here, we examine all three hypotheses in a framework that considers nucleotide composition. We find that nucleotide composition is strongly correlated across codon positions, and with the above amino acid frequency patterns. We also find that the ND6 gene, which in vertebrates is the only mitochondrial gene situated on the "light-strand" shows no significant pattern for any of the amino acid associations. We also reasoned that if the mitochondrially-encoded proteins of oxidative phosphorylation (OXPHOS) were under selection for such shifts, then nuclear-encoded components should also reflect such pressure. However, we found non-correspondence of these patterns in the nuclear genes when compared to the mitochondrial genes previously associated with positive selection. These results are strongly suggestive of mutational bias, or less efficient purifying selection, as the primary driver of whole proteome shifts in amino acid composition.