BACKGROUND: Chad Basin, lying within the bidirectional corridor of African Sahel, is one of the most populated places in Sub-Saharan Africa today. The origin of its settlement appears connected with Holocene climatic ameliorations (aquatic resources) that started ~10,000 years before present (YBP). Although both Nilo-Saharan and Niger-Congo language families are encountered here, the most diversified group is the Chadic branch belonging to the Afro-Asiatic language phylum. In this article, we investigate the proposed ancient migration of Chadic pastoralists from Eastern Africa based on linguistic data and test for genetic traces of this migration in extant Chadic speaking populations. RESULTS: We performed whole mitochondrial genome sequencing of 16 L3f haplotypes, focused on clade L3f3 that occurs almost exclusively in Chadic speaking people living in the Chad Basin. These data supported the reconstruction of a L3f phylogenetic tree and calculation of times to the most recent common ancestor for all internal clades. A date ~8,000 YBP was estimated for the L3f3 sub-haplogroup, which is in good agreement with the supposed migration of Chadic speaking pastoralists and their linguistic differentiation from other Afro-Asiatic groups of East Africa. As a whole, the Afro-Asiatic language family presents low population structure, as 92.4% of mtDNA variation is found within populations and only 3.4% of variation can be attributed to diversity among language branches. The Chadic speaking populations form a relatively homogenous cluster, exhibiting lower diversification than the other Afro-Asiatic branches (Berber, Semitic and Cushitic). CONCLUSION: The results of our study support an East African origin of mitochondrial L3f3 clade that is present almost exclusively within Chadic speaking people living in Chad Basin. Whole genome sequence-based dates show that the ancestral haplogroup L3f must have emerged soon after the Out-of-Africa migration (around 57,100 +/- 9,400 YBP), but the "Chadic" L3f3 clade has much less internal variation, suggesting an expansion during the Holocene period about 8,000 +/- 2,500 YBP. This time period in the Chad Basin is known to have been particularly favourable for the expansion of pastoralists coming from northeastern Africa, as suggested by archaeological, linguistic and climatic data.

Archaeogenetics Laboratory Institute of Archaeology of the Academy of Sciences of the Czech Republic Prague The Czech Republic

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Cavalli-Sforza LL, Cavalli-Sforza F, eds . The great human diasporas: the history of diversity and evolution. Reading, Mass.: Addison-Wesley; 1995.

Pereira L, Macaulay V, Torroni A, Scozzari R, Prata MJ, Amorim A. Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Ann Hum Genet. 2001;65:439–458. doi: 10.1046/j.1469-1809.2001.6550439.x. PubMed DOI

Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, Sanchez-Diz P, Macaulay V, Carracedo A. The making of the African mtDNA landscape. Am J Hum Genet. 2002;71:1082–1111. doi: 10.1086/344348. PubMed DOI PMC

Beleza S, Gusmao L, Amorim A, Carracedo A, Salas A. The genetic legacy of western Bantu migrations. Hum Genet. 2005;117:366–375. doi: 10.1007/s00439-005-1290-3. PubMed DOI

Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D, et al. The dawn of human matrilineal diversity. Am J Hum Genet. 2008;82:1130–1140. doi: 10.1016/j.ajhg.2008.04.002. PubMed DOI PMC

Blench R. The westward wandering of Cushitic pastoralists. Explorations in the prehistory of Central Africa. In: Baroin C, Boutrais J, editor. L'Homme et l'animal dans le bassin du lac Tchad. IRD edn. Paris; 1999. pp. 39–80.

Blench R. Archaeology, languages, and the African past. Lanham: Alta Mira Press; 2006. PubMed

Ehret C. The Civilizations of Africa: A History to 1800. Virginia: The University Press of Virginia; 2002.

Kuper R, Kröpelin S. Climate-Controlled Holocene Occupation in the Sahara: Motor of Africa's Evolution. Science. 2006;313:803–807. doi: 10.1126/science.1130989. PubMed DOI

Ehret C. Language and History. In: Heine B, Nurse, D, editor. African Languages: An Introduction. Cambridge: Cambridge University Press; 2000.

Kuper R. Untersuchungen zur Besiedlunsgeschiche der östlichen Sahara. Vorbericht über die Expedition 1980. Beitrage zur Allgemeinen und Vergleichenden Archäologie. 1981;3:215–275.

Keding B. Leiterband sites in the Wadi Howar, North Sudan. In: Krzyzaniak L, Kobusiewicz L, Alexander J, editor. Environmental change and human culture in the Nile Basin and Northern Africa until the Second millennium BC. Poznan Archaeological Museum; 1993. pp. 371–380.

Holl AFC. The land of Houlouf. Genesis of a Chadic polity, 1900 B.C.-A.D. 1800. Vol. 35. Ann Arbor, Michigan: Museum of Anthropology; 2002.

Maley J. Etudes palynologiques dans le bassin du Tchad et paléoclimatologie de l'Afrique nord-tropicale de 30.000 ans a l'epoque actuelle. Paris: Editions ORSTOM; 1981.

David N, MacEachern S. The Mandara Archaeological Project: preliminary results of the 1984 season. In: Barreteau DTH, editor. Le millieu et les hommes, recherches comparatives et historiques dans le bassin du Lac Tchad. Paris: ORSTOM; 1988. pp. 51–80.

Rapp J. [PhD dissertation] Université Bordeaux I; 1984. Quelques aspects des civilisations Néolithiques et post-Néolithiques de l'extreme Nord-Cameroun. Etude des décors céramiques et essai de chronologie.

Delneuf M. Les recherches archéologiques menées par l'Orstom au Cameroun septentrional. In: Delneuf M, Essomba J-M, Froment A, editor. Paléo-anthropologie en Afrique centrale: un bilan de l'archéologie au Cameroun. Paris L'Harmattan; 1998. pp. 91–124.

Marliac A, Langlois O, Delneuf M. Archéologie de la région Mandara-Diamaré. In: Seignobos C, Iyébi-Mandjek O, editor. Atlas de la province Extreme-Nord Cameroun. Paris: Editions IRD; 2000. pp. 71–76.

Breunig PA. The Dufuna dugout: Africa's oldest boat. Abstracts: 10th congress of the Pan African Association for Prehistory and Related Studies Harare. 1995. p. 16.

David N, Sterner S. The Mandara archaeological project, 1984–87. Nyame Akuma. 1987;29:2–8.

David N, Sterner S. The Mandara archaeological project, 1988–89. Nyame Akuma. 1989;32:5–9.

Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, et al. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science. 2005;308:1034–1036. doi: 10.1126/science.1109792. PubMed DOI

Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L. Reconstructing the origin of Andaman Islanders. Science. 2005;308:996. doi: 10.1126/science.1109987. PubMed DOI

Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, Lee ZY, Lin M. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 2005;3:e247. doi: 10.1371/journal.pbio.0030247. PubMed DOI PMC

Pierson MJ, Martinez-Arias R, Holland BR, Gemmell NJ, Hurles ME, Penny D. Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes. Mol Biol Evol. 2006;23:1966–1975. doi: 10.1093/molbev/msl063. PubMed DOI PMC

Friedlaender JS, Friedlaender FR, Hodgson JA, Stoltz M, Koki G, Horvat G, Zhadanov S, Schurr TG, Merriwether DA. Melanesian mtDNA complexity. PLoS ONE. 2007;2:e248. doi: 10.1371/journal.pone.0000248. PubMed DOI PMC

Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhadanov SI, Ossipova LP, Damba L, Voevoda MI, Dipierri JE, Villems R, Malhi RS. Beringian standstill and spread of Native American founders. PLoS ONE. 2007;2:e829. doi: 10.1371/journal.pone.0000829. PubMed DOI PMC

Kitchen AMMM, Mulligan CJ. A three-stage colonization model for the peopling of the Americas. PLoS ONE. 2008;13:e1596. doi: 10.1371/journal.pone.0001596. PubMed DOI PMC

Mulligan CJ, Kitchen A, Miyamoto MM. Updated three-stage model for the peopling of the Americas. PLoS ONE. 2008;3:e3199. doi: 10.1371/journal.pone.0003199. PubMed DOI PMC

Perego UA, Achilli A, Angerhofer N, Accetturo M, Pala M, Olivieri A, Kashani BH, Ritchie KH, Scozzari R, Kong Q-P, et al. Distinctive Paleo-Indian migration routes from Beringia marked by two rare mtDNA haplogroups. Current Biology. 2009;19:1–8. doi: 10.1016/j.cub.2008.11.058. PubMed DOI

Černý V, Salas A, Hájek M, Žaloudková M, Brdička R. A bidirectional corridor in the Sahel-Sudan belt and the distinctive features of the Chad Basin populations: a history revealed by the mitochondrial DNA genome. Ann Hum Genet. 2007;71:433–452. PubMed

Abu-Amero KK, Gonzalez AM, Larruga JM, Bosley TM, Cabrera VM. Eurasian and African mitochondrial DNA influences in the Saudi Arabian population. BMC Evol Biol. 2007;7:32. doi: 10.1186/1471-2148-7-32. PubMed DOI PMC

Černý V, Mulligan CJ, Rídl J, Žaloudková M, Edens CM, Hájek M, Pereira L. Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen. Am J Phys Anthropol. 2008;136:128–137. doi: 10.1002/ajpa.20784. PubMed DOI

Brooks N, Chiapello I, Di Lernia S, Drake N, Legrand M, Moulin C, Prospero J. The climate-environment nexus in the Sahara from prehistoric times to present day. The Journal of North African Studies. 2005;10:253–292. doi: 10.1080/13629380500336680. DOI

Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E, et al. A signal, from human mtDNA, of postglacial recolonization in Europe. Am J Hum Genet. 2001;69:844–852. doi: 10.1086/323485. PubMed DOI PMC

Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R, Cruciani F, Zeviani M, Briem E, Carelli V, et al. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet. 2004;75:910–918. doi: 10.1086/425590. PubMed DOI PMC

Loogvali EL, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, Tambets K, Reidla M, Tolk HV, Parik J, et al. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol Biol Evol. 2004;21:2012–2021. doi: 10.1093/molbev/msh209. PubMed DOI

Pereira L, Richards M, Goios A, Alonso A, Albarran C, Garcia O, Behar DM, Golge M, Hatina J, Al-Gazali L, et al. High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res. 2005;15:19–24. doi: 10.1101/gr.3182305. PubMed DOI PMC

Černý V, Hájek M, Čmejla R, Brůžek J, Brdička R. mtDNA sequences of Chadic-speaking populations from northern Cameroon suggest their affinities with eastern Africa. Ann Hum Biol. 2004;31:554–569. doi: 10.1080/03014460412331287182. PubMed DOI

Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999;23:147. doi: 10.1038/13779. PubMed DOI

Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM. Major genomic mitochondrial lineages delineate early human expansions. BMC Genet. 2001;2:13. doi: 10.1186/1471-2156-2-13. PubMed DOI PMC

Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999;41:95–98.

Bandelt HJ, Forster P, Sykes BC, Richards MB. Mitochondrial portraits of human populations using median networks. Genetics. 1995;141:743–753. PubMed PMC

Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997;13:555–556. PubMed

Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, Brandon M, Easley K, Chen E, Brown MD, et al. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci USA. 2003;100:171–176. doi: 10.1073/pnas.0136972100. PubMed DOI PMC

Saillard J, Forster P, Lynnerup N, Bandelt HJ, Norby S. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet. 2000;67:718–726. doi: 10.1086/303038. PubMed DOI PMC

Forster P, Harding R, Torroni A, Bandelt HJ. Origin and evolution of Native American mtDNA variation: a reappraisal. Am J Hum Genet. 1996;59:935–945. PubMed PMC

Excoffier LGL, Schneider S. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online. 2005;1:47–50. PubMed PMC

Circum-Saharan Prehistory through the Lens of mtDNA Diversity

Extensive Admixture and Selective Pressure Across the Sahel Belt

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