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The region in Africa where Tishkoff found the greatest level of mitochondrial diversity (green) and the region Behar et al. postulated the most ancient division in the human population began to occur (light brown)
L0 is one of two branches from the most recent common ancestor (MRCA) for the shared human maternal lineage. The haplogroup consists of five main branches (L0a, L0b, L0d, L0f, L0k). Four of them were originally classified into L1 subclades, L1a, L1d, L1f and L1k.
In 2014, ancient DNA analysis of a 2,330 year old male forager's skeleton in Southern Africa found that the specimen belonged to the L0d2c1c mtDNA subclade. This maternal haplogroup is today most closely associated with the Ju, a subgroup of the indigenous San people, which points to population continuity in the region. In 2016, a Late Iron Age desiccated mummy from the Tuli region in northern Botswana was also found to belong to haplogroup L0.
Haplogroup L0d is the most divergent ("ancient") haplogroup of global mitochondrial DNA haplogroups. It is found at highest frequencies in the Khoisan groups of Southern Africa. L0d is also commonly found in the Coloured population of South Africa and frequencies range from 60%  to 71%. This illustrates the massive maternal contribution of Khoisan people to the Coloured population of South Africa.
Haplogroups L0k is the second most common haplogroup in the Khoisan groups (following L0d) and is largely restricted to the Khoisan. Although the Khoisan associated L0d haplogroup were found in high frequencies in the coloured population of South Africa, L0k were not observed in two studies involving large groups of Coloured individuals.
Haplogroup L0a is most prevalent in South-East African populations (25% in Mozambique).
Among Guineans, it has a frequency between 1% and 5%, with the Balanta group showing increased frequency of about 11%. Haplogroup L0a has a Paleolithic time depth of about 33,000 years and likely reached Guinea between 10,000 and 4,000 years ago. It also is often seen in the Mbuti and Biaka Pygmies. L0a is found at a frequency of almost 25% in Hadramawt (Yemen).
This phylogenetic tree of haplogroup L0 subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation and subsequent published research.
Age estimates (ka, 95% CI in angular brackets):
ML whole-mtDNA age estimate: 128.2 [95% CI: 107.9-148.9],
? whole-mtDNA age estimate: 121.3 [99.2;143.7],
? synonymous age estimate (ka): 131.0 [97.8;164.2]:
Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P., "The first modern human dispersals across Africa", PLoS One 2013 Nov 13; 8(11):e80031. doi: 10.1371/journal.pone.0080031.
^ abVan Oven, Mannis; Kayser, Manfred (2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386-94. doi:10.1002/humu.20921. PMID18853457.
^ abRosa, Alexandra; Brehm, Antonio; Kivisild, Toomas; Metspalu, Ene; Villems, Richard (2004). "MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region". Annals of Human Genetics. 68 (4): 340-52. doi:10.1046/j.1529-8817.2004.00100.x. PMID15225159.
^ abcTishkoff, S. A.; Gonder, M. K.; Henn, B. M.; Mortensen, H.; Knight, A.; Gignoux, C.; Fernandopulle, N.; Lema, G.; Nyambo, T. B. (2007). "History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation". Molecular Biology and Evolution. 24 (10): 2180-95. doi:10.1093/molbev/msm155. PMID17656633.
^ abKnight, Alec; Underhill, Peter A.; Mortensen, Holly M.; Zhivotovsky, Lev A.; Lin, Alice A.; Henn, Brenna M.; Louis, Dorothy; Ruhlen, Merritt; Mountain, Joanna L. (2003). "African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages". Current Biology. 13 (6): 464-73. doi:10.1016/S0960-9822(03)00130-1. PMID12646128.
^ abcdSchlebusch, Carina M.; Naidoo, Thijessen; Soodyall, Himla (2009). "SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa". Electrophoresis. 30 (21): 3657-64. doi:10.1002/elps.200900197. PMID19810027.
^Rídl, Jakub; Edens, Christopher M.; ?erný, Viktor (2009). "Mitochondrial DNA Structure of Yemeni Population: Regional Differences and the Implications for Different Migratory Contributions". The Evolution of Human Populations in Arabia. Vertebrate Paleobiology and Paleoanthropology. pp. 69-78. doi:10.1007/978-90-481-2719-1_5. ISBN978-90-481-2718-4.
Rosa, Alexandra; Brehm, Antonio; Kivisild, Toomas; Metspalu, Ene; Villems, Richard (2004). "MtDNA Profile of West Africa Guineans: Towards a Better Understanding of the Senegambia Region". Annals of Human Genetics. 68 (4): 340-52. doi:10.1046/j.1529-8817.2004.00100.x. PMID15225159. Based on the previous knowledge of African complete sequences paraphyletic clade L1 is split into two monophyletic units L0, capturing previously defined L1a and L1d lineages, and L1 clade that includes L1b and L1c clades...
Pavesi, A. (2005). "Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times". Journal of General Virology. 86 (5): 1315-26. doi:10.1099/vir.0.80650-0. PMID15831942. The first axis of mtDNA, on the other hand, places the ancestral haplogroup L0 at the extreme left, since it gave rise to one sole lineage...
Mishmar, Dan; Ruiz-Pesini, Eduardo; Brandon, Martin; Wallace, Douglas C. (2004). "Mitochondrial DNA-like sequences in the nucleus (NUMTs): Insights into our African origins and the mechanism of foreign DNA integration". Human Mutation. 23 (2): 125-33. doi:10.1002/humu.10304. PMID14722916. haplogroup L0 mtDNAs, the haplogroup that we had previously concluded lies at the base of the human mtDNA. tree based on phylogenetic analysis...
Knight, Alec; Underhill, Peter A.; Mortensen, Holly M.; Zhivotovsky, Lev A.; Lin, Alice A.; Henn, Brenna M.; Louis, Dorothy; Ruhlen, Merritt; Mountain, Joanna L. (2003). "African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages". Current Biology. 13 (6): 464-73. doi:10.1016/S0960-9822(03)00130-1. PMID12646128.