Disentangling Positive Selection from Relaxed Selection in Animal Mitochondrial Genomes

AbstractDisentangling different types of selection is a common goal in molecular evolution. Elevated d_N/d_S ratios (the ratio of nonsynonymous to synonymous substitution rates) in focal lineages are often interpreted as signs of positive selection. Paradoxically, relaxed purifying selection can also result in elevated d_N/d_S ratios, but tests to distinguish these two causes are seldomly implemented. Here, we reevaluated seven case studies describing elevated d_N/d_S ratios in animal mitochondrial DNA (mtDNA) and their accompanying hypotheses regarding selection. They included flightless lineages versus flighted lineages in birds, bats, and insects and physiological adaptations in snakes, two groups of electric fishes, and primates. We found that elevated d_N/d_S ratios were often not caused by the predicted mechanism, and we sometimes found strong support for the opposite mechanism. We discuss reasons why energetic hypotheses may be confounded by other selective forces acting on mtDNA and caution against overinterpreting singular molecular signals, including elevated d_N/d_S ratios.