Are mitochondrial DNA mutations under purifying selection in somatic tissues?

The extent to which somatic mitochondrial DNA (mtDNA) mutations are subject to selection is a fundamental question relevant to development, mitochondrial disease, cancer, and aging. Recently a study from the Sudmant laboratory that used an advanced, high fidelity mutational analysis reported that somatic mutations in protein-coding genes exhibit signatures of negative selection. This report came as surprise as several other studies including those that used same technology reported either lack of selection or positive (destructive) selection on somatic mutations. We hypothesized that these discrepancies may stem, in part, from the inclusion of germline mutations in addition to somatic ones, which could bias selection analyses due to the high synonymity of the latter. To test this, we reanalyzed the Sudmant dataset by separating mutations into germline (defined as shared between related animals) and somatic (not shared between tissues of an animal). We then employed a cumulative curve approach to assess selection without bias. Our analysis reveals that, indeed, an apparent purifying selection signal is driven by an admixture of synonymous germline mutations and disappears upon their removal. The remaining somatic mutations for most part show overall dynamics consistent with neutral drift. However, mutations at higher mutant fractions show positive selection trend, most compatible with a low proportion of mutations experiencing positive selection. While we do not exclude rare or context-specific selection events, our results argue against pervasive somatic selection and highlight the importance of rigorous stratification when interpreting mtDNA mutational patterns.