Variable heteroplasmy of the Common 9-bp Deletion in the Human Mitochondrial Genome in Ancient and Present-Day Populations

The recurrent 9-bp deletion in the intergenic region between COII and tRNA _Lys genes of the human mitochondrial genome is present in various world populations and has been linked to disease. The heteroplasmy of this deletion in the different carrier mitochondrial lineages, however, has remained largely unexplored. Employing deep sequencing mitochondrial DNA data, we quantified the deletion in diverse ancient and present-day human populations. We observed low 9-bp deletion heteroplasmy in specific haplogroups of ancient populations from various continents, high levels in their closely-related present-day populations, and independent emergence at high levels in isolated present-day lineages, always without reaching complete homoplasmy.