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.

] Faculdade de Medicina Universidade Eduardo Mondlane 257 Maputo Moçambique [2] Departamento de Saúde Mental Ministério da Saúde 14 Maputo Moçambique

] Faculdade de Medicina Universidade Eduardo Mondlane 257 Maputo Moçambique [2] Hospital Central de Maputo 1164 Maputo Moçambique

] Instituto Gulbenkian Ciência 2780 156 Oeiras Portugal [2] Centro Nacional de Endemias CP 23 São Tomé e Príncipe

] IPATIMUP 4200 465 Porto Portugal [2] General Department of Forensic Sciences and Criminology Dubai Police GHQ 1493 Dubai United Arab Emirates

] IPATIMUP 4200 Porto Portugal

] IPATIMUP Departamento de Biologia Universidade do Minho 4710 057 Braga Portugal

Department of Anthropology and Human Genetics Faculty of Science Charles University 128 43 Prague Czech Republic

IPATIMUP 4200 465 Porto Portugal

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