Abstract
The higher genetic diversity present in African human groups is the result of our African origin and the subsequent bottleneck that took place during the colonization of the rest of the continents. However, the genetic diversity within Africa is structured by geography, lifestyle, and culture. The analysis of the genetic structure within Africa might reveal the population history of human groups, including some controversial issues such as the geographic origin of our species, some population splits and admixtures among groups, and the dating of several demographic events. In addition, adaptation to broad environmental landscapes within Africa has left a genetic signal in some human groups. In the present chapter, we summarize part of the vast genetic complexity described in African populations, focusing in the genetic structure in extant groups and emphasizing the urgent need to enlarge our knowledge at continental level.
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References
Atkinson QD (2011) Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science 332:346–349
Barton RNE, Bouzouggar A, Collcutt SN et al (2009) OSL dating of the Aterian levels at Dar es-Soltan I (Rabat, Morocco) and implications for the dispersal of modern Homo sapiens. Quat Sci Rev 28:1914–19431
Batini C, Coia V, Battaggia C et al (2007) Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. Mol Phylogenet Evol 43:635–644
Batini C, Ferri G, Destro-Bisol G et al (2011a) Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Mol Biol Evol 28:2603–2613
Batini C, Lopes J, Behar DM et al (2011b) Insights into the demographic history of African pygmies from complete mitochondrial genomes. Mol Biol Evol 28:1099–1110
Behar DM, Villems R, Soodyall H et al (2008) The dawn of human matrilineal diversity. Am J Hum Genet 82:1130–1140
Berniell-Lee G, Calafell F, Bosch E et al (2009) Genetic and demographic implications of the bantu expansion: insights from human paternal lineages. Mol Biol Evol 26:1581–1589
Bersaglieri T, Sabeti PC, Patterson N et al (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74:1111–1120
Bigham A, Bauchet M, Pinto D et al (2010) Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet 6:e1001116. https://doi.org/10.1371/journal.pgen.1001116
Bosch E, Calafell F, Pérez-Lezaun A et al (1997) Population history of North Africa: evidence from classical genetic markers. Hum Biol 69:295–311
Bosch E, Calafell F, Comas D et al (2001) High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula. Am J Hum Genet 68:1019–1029
Botigué LR, Henn BM, Gravel S et al (2013) Gene flow from North Africa contributes to differential human genetic diversity in southern Europe. Proc Natl Acad Sci USA 110:11791–11796
Cann R, Stoneking M, Wilson AC (1987) Mitochondrial DNA and human evolution. Nature 325:31–36
Cavalli-Sforza LL (1986) African pygmies. Academic Press, Orlando
Cavalli-Sforza LL, Menozzi P, Piazza A (1994) History and geography of human genes. Princeton University Press, Princeton
Cruciani F, Santolamazza P, Shen P et al (2002) A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes. Am J Hum Genet 70:1197–1214
Cruciani F, Trombetta B, Massaia A et al (2011) A revised root for the human y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa. Am J Hum Genet 88:814–818
Destro-Bisol G, Donati F, Coia V et al (2004) Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors. Mol Biol Evol 21:1673–1682
Diamond JD (1991) Anthropology. Why are pygmies small? Nature 354:111–112
Diamond JD (1997) Guns, germs, and steel: the fates of human societies. W.W.Norton & Company, New York
Ehret C (2001) Bantu expansions: re-envisioning a central problem of early African history. Int J Afr Hist Stud 34:5–41
Elhaik E, Tatarinova TV, Klyosov AA, Graur D (2014) The “extremely ancient” chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. Eur J Hum Genet 22:1111. https://doi.org/10.1038/ejhg.2013.303
Enattah NS, Trudeau A, Pimenoff V et al (2007) Evidence of still-ongoing convergence evolution of the lactase persistence T-13910 alleles in humans. Am J Hum Genet 81:615–625. https://doi.org/10.1086/520705
Enattah NS, Jensen TGK, Nielsen M et al (2008) Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture. Am J Hum Genet 82:57–72. https://doi.org/10.1016/j.ajhg.2007.09.012
Fadhlaoui-Zid K, Rodríguez-Botigué L, Naoui N et al (2011) Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. Am J Phys Anthropol 145:107–117. https://doi.org/10.1002/ajpa.21472
Fadhlaoui-Zid K, Haber M, Martínez-Cruz B et al (2013) Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa. PLoS One 8:e80293. https://doi.org/10.1371/journal.pone.0080293
Francalacci P, Morelli L, Angius A et al (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341:565–569
Garcea EAA (2010) The spread of Aterian peoples in North Africa. Oxbow Books, Oxford
Gonder MK, Mortensen HM, Reed FA et al (2007) Whole-mtDNA genome sequence analysis of ancient African lineages. Mol Biol Evol 24:757–768
Green RE, Krause J, Briggs AW et al (2010) A draft sequence of the Neandertal genome. Science 328:710–722
Greenberg J (1963) The languages of Africa. Indiana University Press, Bloomington
Hamblin MT, Di Rienzo A (2000) Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet 66:1669–1679. https://doi.org/10.1086/302879
Hammer MF, Woerner AE, Mendez FL et al (2011) Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci USA 108:15123–15128
Hart TB, Hart JA (1986) The ecological basis of hunter-gatherer subsistence in African rain forest. The Mbuti of eastern Zaire. Hum Ecol 14:29–55
Heeney JL, Dalgleish AG, Weiss RA (2006) Origins of HIV and the evolution of resistance to AIDS. Science 313:462–466. https://doi.org/10.1126/science.1123016
Henn BM, Gignoux CR, Jobin M et al (2011) Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci USA 108:5154–5162
Henn BM, Botigue LR, Gravel S et al (2012a) Genomic ancestry of north Africans supports back-to-Africa migrations. PLoS Genet 8:e1002397
Henn BM, Cavalli-Sforza LL, Feldman MW (2012b) The great human expansion. Proc Natl Acad Sci USA 109:17758–17764
Hiernaux J (1974) The peoples of Africa. Weidenfeld & Nicholson, London
Ingman M, Kaessmann H, Gyllensten U, Pääbo S (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713
Jakobsson M, Scholz SW, Scheet P et al (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451:998–1003
Jarvis JP, Scheinfeldt LB, Soi S et al (2012) Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies. PLoS Genet 8:e1002641. https://doi.org/10.1371/journal.pgen.1002641
Keinan A, Mullikin JC, Patterson N, Reich D (2009) Accelerated genetic drift on chromosome X during the human dispersal out of Africa. Nat Genet 41:66–70. https://doi.org/10.1038/ng.303
Lachance J, Vernot B, Elbers CC et al (2012) Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150:457–469
Li JZ, Absher DM, Tang H et al (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319:1100–1104
Luzzatto L (2012) Sickle cell anaemia and malaria. Mediterr J Hematol Infect Dis 4:e2012065. https://doi.org/10.4084/MJHID.2012.065
Lwanga-Lunyiigo S (1976) The Bantu problem reconsidered. Curr Anthropol 17:282–286
Macaulay V, Hill C, Achilli A et al (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036
Melé M, Javed A, Pybus M et al (2012) Recombination gives a new insight in the effective population size and the history of the old world human populations. Mol Biol Evol 29:25–30. https://doi.org/10.1093/molbev/msr213
Mendez FL, Krahn T, Schrack B et al (2013) An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet 92:454–459
Mendizabal I, Marigorta UM, Lao O, Comas D (2012) Adaptive evolution of loci covarying with the human African Pygmy phenotype. Hum Genet 131:1305–1317
Migliano AB, Vinicius L, Lahr MM (2007) Life history trade-offs explain the evolution of human pygmies. Proc Natl Acad Sci USA 104:20216–20219
Montano V, Ferri G, Marcari V et al (2011) The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa. Mol Ecol 20:2693–2708
Newman J (1995) The peopling of Africa: a geographic interpretation. Yale University Press, New Haven
Patin E, Laval G, Barreiro LB et al (2009) Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet 5:e1000448
Pereira L, Macaulay V, Torroni A et al (2001) Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Ann Hum Genet 65:439–458
Perry GH, Dominy NJ (2009) Evolution of the human pygmy phenotype. Trends Ecol Evol 24:218–225
Phillipson DW (1993) African archaeology. Cambridge University Press, Cambridge
Pickrell JK, Patterson N, Barbieri C et al (2012) The genetic prehistory of southern Africa. Nat Commun 3:1143
Pierron D, Razafindrazaka H, Pagani L et al (2014) Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar. Proc Natl Acad Sci USA 111:936–941. https://doi.org/10.1073/pnas.1321860111
Plaza S, Calafell F, Helal A et al (2003) Joining the pillars of Hercules: mtDNA sequences show multidirectional gene flow in the western Mediterranean. Ann Hum Genet 67:312–328
Plaza S, Salas A, Calafell F et al (2004) Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola. Hum Genet 115:439–447
Quintana-Murci L, Semino O, Bandelt HJ et al (1999) Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat Genet 23:437–441. https://doi.org/10.1038/70550
Quintana-Murci L, Quach H, Harmant C et al (2008) Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci USA 105:1596–1601
Ranciaro A, Campbell MC, Hirbo JB et al (2014) Genetic origins of lactase persistence and the spread of pastoralism in Africa. Am J Hum Genet 94:496–510. https://doi.org/10.1016/j.ajhg.2014.02.009
Rando JC, Pinto F, Gonzÿlez AM et al (1998) Mitochondrial DNA analysis in Northwestern African populations reveals genetic exchanges with European, near-Eastern, and sub-Saharan populations. Ann Hum Genet 62:531–550
Reich D, Green RE, Kircher M et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060
Ruhlen M (1994) The origin of language: tracing the evolution of the mother tongue. John Wiley and Sons, New York
Sabeti PC, Reich DE, Higgins JM et al (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832–837. https://doi.org/10.1038/nature01140
Salas A, Richards M, De la Fe T et al (2002) The making of the African mtDNA landscape. Am J Hum Genet 71:1082–1111
Sánchez-Quinto F, Botigue LR, Civit S et al (2012) North African populations carry the signature of admixture with Neandertals. PLoS One 7:e47765
Sands B (2009) Africa’s linguistic diversity. Lang Linguist Compass 3(2):559–580
Scheinfeldt LB, Tishkoff SA (2012) Living the high life: high-altitude adaptation. Genome Biol 11:133
Schlebusch CM, Skoglund P, Sjodin P et al (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338:374–379
Schoenbrun D (2001) Representing the Bantu expansions: What’s at stake? Int J Afr Hist Stud 34:1–4
Schuster SC, Miller W, Ratan A et al (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943–947
Scozzari R, Massaia A, D’Atanasio E et al (2012) Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree. PLoS One 7:e49170. https://doi.org/10.1371/journal.pone.0049170
Sikora M, Laayouni H, Calafell F et al (2011) A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. Eur J Hum Genet 19:84–88. https://doi.org/10.1038/ejhg.2010.141
Stringer CB, Andrews P (1988) Genetic and fossil evidence for the origin of modern humans. Science 239:1263–1268
Tishkoff SA, Dietzch E, Speed W et al (1996) Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271:1380–1387
Tishkoff SA, Goldman A, Calafell F et al (1998) A global haplotype analysis of the myotonic dystrophy locus: implications for the evolution of modern humans and for the origin of myotonic dystrophy mutations. Am J Hum Genet 62:1389–1402
Tishkoff SA, Reed FA, Ranciaro A et al (2007) Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39:31–40
Tishkoff SA, Reed FA, Friedlaender FR et al (2009) The genetic structure and history of Africans and African Americans. Science 324:1035–1044
Tofanelli S, Bertoncini S, Castri L et al (2009) On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages. Mol Biol Evol 26:2109–2124
Underhill PA, Shen P, Lin AA et al (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361
Vansina J (1995) New linguistic evidence and the “Bantu expansion”. J Afr Hist 36:173–195
Verdu P, Austerlitz F, Estoup A et al (2009) Origins and genetic diversity of pygmy hunter-gatherers from Western Central Africa. Curr Biol 19:312–318
Vigilant L, Stoneking M, Harpending H et al (1991) African populations and the evolution of mitochondrial DNA. Science 253:1503–1507
Wood ET, Stover DA, Ehret C et al (2005) Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes. Eur J Hum Genet 13:867–876
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Comas, D., Calafell, F. (2021). Africa. In: Saitou, N. (eds) Evolution of the Human Genome II. Evolutionary Studies. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56904-6_6
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