Positive germline selection of mtDNA: evidence from the oocyte

Abstract Purifying selection is the removal of detrimental mutations. Nuclear DNA mutations are purged by removing mutant individuals, embryos, or germline cells. Because mtDNA is present in numerous copies per cell, purifying selection of mtDNA mutations introduces an additional layer of complexity. The intracellular mutant fraction can change due to clonal expansion/reduction of mutant mtDNA molecules in germline cells. Different research groups have reported either negative (purifying), or positive (destructive) germline mtDNA selection. In this study, we use recently published high-fidelity data on mtDNA mutations in individual human oocytes from the Makova laboratory (Arbeithuber et al., 2025) to resolve this disagreement. To assess selection, we used the “selective expansion” metric S t , which compares the average weighted rate of clonal expansion in a set of mutations tested for selection (e.g. non-synonymous mutations) to that of the set of synonymous mutations. We found that, on average, noncoding oocyte mutations in the control region expand faster than synonymous mutations, i.e., are under positive selection. Intriguingly, mutations in the coding region, the detrimental ones in particular, were also on average under positive selection. The prescence of average positive selection does not preclude purifying selection against individual mutations; it only indicates that positive selection dominates in aggregate mutational dynamics. Positive selection impacts the dynamics of de novo germline mutations that arise in primordial germ cells or oocytes and have not yet been inherited by the next generation. Contrastly, mutations that are passed to subsequent generations are under average purifying selection. We suggest that initial positive selection begets subsequent purifying selection by increasing intracellular mutant fractions to levels at which their deleterious effects become phenotypically apparent and can be efficiently removed.