Revisiting the African mtDNA landscape through complete mitochondrial genomes

Abstract

Africa harbors the richest diversity of mitochondrial DNA lineages, reflecting its central role in human evolutionary history. Early studies of mtDNA variation provided the first genetic evidence for the African origin of modern humans. With complete mitochondrial genome sequencing, we can now reconstruct maternal lineages with high resolution, yet large parts of the continent remain underrepresented. Using a newly developed long-range sequencing assay, we generated 1176 complete mitochondrial genomes from 13 countries across sub-Saharan Africa, focusing on previously understudied regions. We combined these with over 3600 publicly available African mitogenomes to produce a comprehensive dataset and updated overview of maternal genetic diversity across the continent. We contextualized this diversity with autosomal structure and information on major human expansions, integrating archeological and linguistic evidence. Our analyses suggest an initial demographic expansion of Niger-Congo speakers around 17 thousand years ago (kya), and an initial  expansion associated with Bantu-speaking groups around 6 kya. We identify haplogroup L3e as a key marker of this early Bantu expansion, tracking its spread across sub-Saharan Africa. Distinct demographic signatures also emerge for different geographic sub-branches of Bantu speakers. These findings highlight the power of mitochondrial DNA to trace maternal ancestry and demographic history in Africa, while also acknowledging its limitations for phylogeographic reconstruction.