Phylogenetic age is associated with mitochondrial heteroplasmy in African and diaspora populations

Background: Mitochondrial DNA (mtDNA) heteroplasmy—the co-existence of multiple mtDNA variants within an individual—has been linked to ageing, disease susceptibility, and cellular dysfunction. However, the evolutionary and population-level factors governing heteroplasmy burden remain poorly understood. Recent work in green sea turtles demonstrated that individuals carrying phylogenetically derived mtDNA haplotypes accumulate more heteroplasmic variants than those carrying ancestral haplotypes, suggesting that lineage age may influence heteroplasmy burden. Here, we test whether a similar phylogenetic age effect exists in humans using whole mitochondrial genome sequencing data from 1,306 individuals representing African and diaspora populations. Using negative binomial and Poisson generalised linear models with L0—the most ancestral human mtDNA macrohaplogroup—as the reference, we find that carriers of L1, L2, and L3 haplogroups exhibit significantly higher heteroplasmy counts (incidence rate ratios 2.71–3.41, all FDR-adjusted p < 10⁻³⁹). This pattern persists after controlling for broad geographic region and is replicated in a diaspora-only subset with shared demographic history. Importantly, using calibrated sub-haplogroup age estimates, we identify a significant negative relationship between sub-haplogroup age and heteroplasmy burden within L0 itself (IRR = 0.978 per thousand years, p = 3.8 × 10⁻¹⁴). Each additional 1,000 years of lineage age is associated with approximately 2.2% fewer heteroplasmic variants. This within-lineage gradient provides strong evidence that phylogenetic age contributes to shaping mtDNA heteroplasmy burden in humans.