60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Mitochondrial DNA (mtDNA) haplogroup L2 originated in Western Africa but is nowadays spread across the entire continent. L2 movements were previously postulated to be related to the Bantu expansion, but L2 expansions eastwards probably occurred much earlier. By reconstructing the phylogeny of L2 (44 new complete sequences) we provide insights on the complex net of within-African migrations in the last 60 thousand years (ka). Results show that lineages in Southern Africa cluster with Western/Central African lineages at a recent time scale, whereas, eastern lineages seem to be substantially more ancient. Three moments of expansion from a Central African source are associated to L2: (1) one migration at 70-50 ka into Eastern or Southern Africa, (2) postglacial movements (15-10 ka) into Eastern Africa; and (3) the southward Bantu Expansion in the last 5 ka. The complementary population and L0a phylogeography analyses indicate no strong evidence of mtDNA gene flow between eastern and southern populations during the later movement, suggesting low admixture between Eastern African populations and the Bantu migrants. This implies that, at least in the early stages, the Bantu expansion was mainly a demic diffusion with little incorporation of local populations.

This research received support from the European project “A European Initial Training Network on the History, Archaeology, and New Genetics of the Trans-Atlantic Slave Trade (EUROTAST)” (EU project: 290344). PSo is supported by FCT (the Portuguese Foundation for Science and Technology), European Social Fund, Programa Operacional Potencial Humano and the FCT Investigator Programme (IF/01641/2013). IPATIMUP integrates the i3S Research Unit, which is partially supported by FCT. This work is funded by FEDER funds through the Operational Programme for Competitiveness FactorsCOMPETE and National Funds through FCT, under the project “PEst-C/SAU/LA0003/2013”. FCT/MEC supports CBMA through Portuguese funds (PIDDAC) - PEst-OE/BIA/UI4050/2014. NORTE-07-0162FEDER-00018 (Contributos para o reforço da capacidade do IPATIMUP enquanto actor do sistema regional de inovação) and NORTE-07-0162-FEDER-000067 (Reforço e consolidação da capacidade infraestrutural do IPATIMUP para o sistema regional de inovação), both supported by Programa Operacional Regional do Norte (ON.2 – O Novo Norte), through FEDER funds under the Quadro de Referência Estratégico Nacional (QREN).