Positive germline selection of mtDNA Mutations: evidence from the oocyte

Purifying selection of mtDNA mutations is a vital process that cleanses the mitochondrial genome of detrimental variants that may endanger individuals and populations. A common measure of purifying selection is the increase of average synonymity by reduction the proportion of mostly detrimental non-synonymous mutations. The mechanisms underlying purifying selection are still debated. The Makova group has recently published high-fidelity analysis of mtDNA mutations in individual human oocytes (Arbeithuber et al., 2025). The authors observed a decrease in the proportion of potentially detrimental coding and conservative mutations at higher mutant fractions (MFs) and interpreted this as purifying selection removing detrimental mutations at higher MFs. We noted, however, that, in contrast to what would be expected under purifying selection, the synonymity of oocyte mutations was very low and decreased, rather than increased, at higher MFs. We hypothesized that this inconsistency resulted from non-synonymous mutations being prone to strong positive selection which erroneously made coding mutations appear negatively selected in comparison. In support of our hypothesis, we show that non-coding oocytes mutations indeed are under strong positive selection. To alleviate this setback, we reanalyzed the data using a new metric of intracellular clonal selection and neutral synonymous mutations as the reference. We demonstrated that coding mutations are in fact under prevailing positive selection. This is in line with previous estimates of positive selection in primordial germ cells (PGCs) and in mother-child pairs. Importantly, “prevailing positive selection” does not imply the absence of negative selection. We show that specific types of mutations may be under prevailing purifying selection (e.g., the Co1 gene). Of note, this prevailing positive selection pertains only to the most recent, germline mtDNA mutations which have not been yet inherited into the next generation. Purifying selection steps in as germline mutations proceed to subsequent generations. The implications of these findings and the potential benefits of positive selection of detrimental mtDNA mutations are discussed. Graphical summary Germline mtDNA mutations fuel evolution, shape population genomics, and cause mitochondrial disease. Yet it remains unresolved whether mtDNA selection in the germline is predominantly purifying or positive. A recent high-fidelity single-oocyte study (Arbeithuber et al., 2025) reported purifying(negative) selection on germline mutations at elevated mutant fractions (MFs). However, the low synonymity of oocyte mutations and concerns about using non-coding mutations as a reference for estimating selection prompted us to reanalyze the data. In single cells, mtDNA mutations are subject to genetic drift which randomly expands mtDNA clones. In this context, selection means that some mutant clones expand systematically faster (positive selection), or slower/get lost (p