Static and Moving Frontiers: The Genetic Landscape of Southern African Bantu-Speaking Populations

Molecular Biology and Evolution

Volumn 32, Issue 1, 2015, Pages 29-43

  Marks, Sarah J ^a   Montinaro, Francesco ^a,b   Levy, Hila ^a   Brisighelli, Francesca ^b   Ferri, Gianmarco ^c   Bertoncini, Stefania ^d   Batini, Chiara ^e   Busby, George B J ^a   Arthur, Charles ^f   Mitchell, Peter ^f,g   Stewart, Brian A ^h   Oosthuizen, Ockie ⁱ   Oosthuizen, Erica ⁱ   D'Amato, Maria Eugenia ^j   Davison, Sean ^j   Pascali, Vincenzo ^b   Capelli, Cristian ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b CATHOLIC UNIVERSITY   (Italy)

^c UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^d UNIVERSITY OF PISA   (Italy)

^e UNIVERSITY OF LEICESTER   (United Kingdom)

^f UNIVERSITY OF OXFORD   (United Kingdom)

^g UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^h UNIVERSITY OF MICHIGAN   (United States)

ⁱ UNIVERSITY OF NAMIBIA   (Namibia)

^j UNIVERSITY OF THE WESTERN CAPE   (South Africa)

more..

Author keywords

"Bantu expansion"; Admixture; Frontier model; MtDNA; Y chromosome

Indexed keywords

MITOCHONDRIAL DNA;

AGRICULTURAL WORKER; ARTICLE; CONSENSUS; CULTURAL FACTOR; DEMOGRAPHY; FORAGER; FORAGING; GENE FLOW; GENE FREQUENCY; GENETIC DISTANCE; GENETIC VARIABILITY; HUMAN; LANDSCAPE; LANGUAGE; MIGRATION; MUTATION RATE; ORGANIZATION; POPULATION GENETICS; POPULATION STRUCTURE; SEX DIFFERENCE; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTHERN AFRICAN; SPEECH; Y CHROMOSOME HAPLOGROUP; AFRICA; BLACK PERSON; ETHNOLOGY; FEMALE; GENETICS; MALE; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; Y CHROMOSOME;

AFRICA, SOUTHERN; AFRICAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; EMIGRATION AND IMMIGRATION; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MALE; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS;

EID: 84922358781     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msu263     Document Type: Article

References (102)

1. Alexander JA. 1977. Hunters: gatherers and first farmers beyond Europe: an archaeological survey. Leicester (United Kingdom): Leicester University Press.
2. Alexander JA. 1984. Early frontiers in southern Africa. In: Hall M, Avery G, Avery DM, Wilson ML, Humphreys AJB, editors. Frontiers: Southern African archaeology today. Oxford: B.A.R. International Series. p. 12-23.
3. Alves C, Gusm~ao L, Barbosa J, Amorim A. 2003. Evaluating the informative power of Y-STRs: A comparative study using European and new African haplotype data. Forensic Sci Int. 134: 126-133.
4. Ammerman A, Cavalli-Sforza L. 1973. The explanation of culture change: models in prehistory: proceedings. Pittsburgh (PA): University of Pittsburgh Press.
5. Barbieri C, Butthof A, Bostoen K, Pakendorf B. 2013. Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia. Eur J Hum Genet. 21: 430-436.
6. Barbieri C, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Stoneking M, Pakendorf B. 2014. Unraveling the complex maternal history of Southern African Khoisan populations. Am J Phys Anthropol. 153: 435-448.
7. Barbieri C, Vicente M, Rocha J, Mpoloka SW, Stoneking M, Pakendorf B. 2013. Ancient substructure in early mtDNA lineages of southern Africa. Am J Hum Genet. 92: 285-292.
8. Batini C, Ferri G, Destro-Bisol G, et al. 2011. Signatures of the preagricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Mol Biol Evol. 28: 2603-2613.
9. Behar DM, Villems R, Soodyall H, et al. 2008. The dawn of human matrilineal diversity. Am J Hum Genet. 82: 1130-1140.
10. Bohannan P, Plog F. 1967. Beyond the frontier: social process and cultural change. Garden City (NY): Published for the American Museum of Natural History [by] Natural History Press.
11. Bosch E, Calafell F, González-Neira A, et al. 2006. Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns. Ann Hum Genet. 70: 459-487.
12. Bostoen K, Sands B. 2012. Clicks in south-western Bantu languages: contact-induced vs. language-internal lexical change. In: Brenzinger M, editor. In: Proceedings of the 6th World Congress of African
13. Linguistics Cologne 2009. Köln (Germany): Rüdiger Köppe Verlag. p. 129-140.
14. Burt AL. 1940. The frontier in the history of New France. Rep AnnuMeet. 19: 93-99.
15. Carter PL, Vogel JC. 1974. The dating of industrial assemblages from stratified sites in Eastern Lesotho. Man 9: 557-570.
16. Castrí L, Tofanelli S, Garagnani P, Bini C, Fosella X, Pelotti S, Paoli G, Pettener D, Luiselli D. 2009. mtDNA variability in two Bantu-speaking populations (Shona and Hutu) from Eastern Africa: implications for peopling and migration patterns in sub-Saharan Africa. Am J Phys Anthropol. 140: 302-311.
17. Cavalli-Sforza LL. 1986. African pygmies. New York: Academic Press. Cerezo M, Bandelt HJ, Martín-Guerrero I, Ardanaz M, Vega A, Carracedo
18. A, García-Orad A, Salas A. 2009. High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 4: e7902.
19. Challis S. 2012. Creolisation on the nineteenth-century frontiers of Southern Africa: A case study of the AmaTola "Bushmen" in the Maloti-Drakensberg. J S Afr Stud. 38: 265-280.
20. Chen YS, Olckers A, Schurr TG, Kogelnik AM, Huoponen K,Wallace DC. 2000. mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations. Am J Hum Genet. 66: 1362-1383.
21. Coelho M, Sequeira F, Luiselli D, Beleza S, Rocha J. 2009. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol Biol. 9: 80.
22. 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.
23. Currat M, Ruedi M, Petit RJ, Excoffier L. 2008. The hidden side of invasions: massive introgression by local genes. Evolution 62: 1908-1920.
24. de Filippo C, Barbieri C, Whitten M, et al. 2011. Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups. Mol Biol Evol. 28: 1255-1269.
25. de Filippo C, Bostoen K, Stoneking M, Pakendorf B. 2012. Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc Biol Sci. 279: 3256-3263.
26. de Filippo C, Heyn P, Barham L, StonekingM, Pakendorf B. 2010. Genetic perspectives on forager-farmer interaction in the Luangwa valley of Zambia. Am J Phys Anthropol. 141: 382-394.
27. Destro-Bisol G. 2005. Genetic variation and social structure: A case-study from Africa. Hum Evol. 20: 93-98.
28. Destro-Bisol G, Donati F, Coia V, Boschi I, Verginelli F, Cagliá A, TofanelliS, Spedini G, Capelli C. 2004. Variation of female and male lineages in sub-Saharan populations: the importance of sociocultural factors. Mol Biol Evol. 21: 1673-1682.
29. Diamond JM. 1997. Guns, germs, and steel: the fates of human societies. New York: W.W. Norton &Co.
30. Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour. 10: 564-567.
31. Fenner JN. 2005. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol. 128: 415-423.
32. Gill SJ. 1993. A short history of Lesotho from the late stone age until the 1993 elections. Morija (Lesotho): Morija Museum &Archives.
33. Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusm~ao L. 2010. Digging deeper into East African human Y chromosome lineages. Hum Genet. 127: 603-613.
34. Güldemann T, Stoneking M. 2008. A historical appraisal of clicks: A linguistic and genetic population perspective. Ann Rev Anthropol. 37: 93-109.
35. Guthrie M. 1971. Comparative Bantu: an introduction to the comparative linguistics and prehistory of the Bantu languages. Bantu prehistory, inventory and indexes. Farnborough (United Kingdom): Gregg Press.
36. Hall TD. 1987. Native Americans and incorporation: patterns and problems. Am Indian Cult Res J. 11: 1-30.
37. Hammond-TookeWD. 1998. Selective borrowing. The possibility of San shamanistic influence on Southern Bantu divination and healing practices. S Afr Archaeol Bull. 53: 9-15.
38. Hammond-Tooke WD. 1999. Divinatory animals: further evidence of San/Nguni borrowing. S Afr Archaeol Bull. 54: 128-132.
39. Hellenthal G, Busby GBJ, Band G, Wilson JF, Capelli C, Falush D, Myers S. 2014. A genetic atlas of human admixture history. Science 343: 747-751.
40. Herbert RK. 1990. The sociohistory of clicks in Southern Bantu. In: Mesthrie R, editor. Language in South Africa. Cambridge (MA): Cambridge University Press. p. 297-315.
41. Holden CJ. 2002. Bantu language trees reflect the spread of farming across sub-Saharan Africa: A maximum-parsimony analysis. Proc R Soc Lond Biol Sci. 269: 793-799.
42. Huffman TN. 1988. Ngwenani ya themeli. In: Evers TM, Huffman TN, Wadley L, editors. Guide to archaeological sites in the transvaal. Johannesburg (South Africa): University of the Witwatersrand. p. 52-55.
43. Huffman TN. 2007. Handbook to the iron age: the archaeology of precolonial farming societies in Southern Africa. Scottsville (South Africa): University of KwaZulu-Natal Press.
44. Jombart T, Devillard S, Balloux F. 2010. Discriminant analysis of principal components: A newmethod for the analysis of genetically structured populations. BMC Genet. 11: 94.
45. Jombart T, Pontier D, Dufour AB. 2009. Genetic markers in the playground of multivariate analysis. Heredity (Edinb) 102: 330-341.
46. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF. 2008. New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 18: 830-838.
47. Kido A, Fujitani N, Hara M, Kimura H. 2006. Genetic data of 16 Ychromosomal short tandem repeat loci in Africans from South Africa. J Forensic Sci. 51: 1414-1416.
48. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik J, Geberhiwot T, Usanga E, Villems R. 2004. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet. 75: 752-770.
49. Kloss-Brandstätter A, Pacher D, Schönherr S, Weissensteiner H, Binna R, Specht G, Kronenberg F. 2011. HaploGrep: A fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum Mutat. 32: 25-32.
50. Knight A, Underhill PA, Mortensen HM, Zhivotovsky LA, Lin AA, HennBM, Louis D, Ruhlen M, Mountain JL. 2003. African Y chromosome and mtDNA divergence provides insight into the history of click languages. Curr Biol. 13: 464-473.
51. Leat N, Benjeddou M, Davison S. 2004. Nine-locus Y-chromosome STR profiling of Caucasian and Xhosa populations from Cape Town, South Africa. Forensic Sci Int. 144: 73-75.
52. Leat N, Ehrenreich L, BenjeddouM, Cloete K, Davison S. 2007. Properties of novel and widely studied Y-STR loci in three South African populations. Forensic Sci Int. 168: 154-161.
53. Lewis MP. 2009. Ethnologue: languages of the world. Dallas (TX): SIL International.
54. Loubser J, Laurens G. 1994. Depictions of domestic ungulates and shields: hunter-gatherers and agro-pastoralists in the Caledon Valley area. In: Dowson T, Lewis-Williams JD, editors. Contested images: diversity in southern African rock art research. Johannesburg: Wits University Press. p. 83-118.
55. Maggs T. 1976. Iron age communities of the southern Highveld. Pietermaritzburg (South Africa): Council of the Natal Museum.
56. Maggs T. 1980. The iron age sequence south of the Vaal and Pongola rivers: some historical implications. J Afr Hist. 21: 1-15.
57. Maggs T. 1994. The early iron age in the extreme south: some patterns and problems. Azania 29/30: 171-178.
58. Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
59. Mantel N, Valand RS. 1970. A technique of nonparametric multivariate analysis. Biometrics 26: 547-558.
60. Marks SJ, Levy H, Martinez-Cadenas C, Montinaro F, Capelli C. 2012. Migration distance rather than migration rate explains genetic diversity in human patrilocal groups. Mol Ecol. 21: 4958-4969.
61. Mazel AD. 1986. Mbabane Shelter and eSinhlonhlweni Shelter: the last two thousand years of hunter-gatherer settlement in the central Thukela Basin, Natal, South Africa. Ann Natal Museum. 27: 389-453.
62. Mazel AD. 1989. People making history: the last ten thousand years of hunter-gatherer communities in the Thukela Basin. Natal Museum J Human. 1: 1-168.
63. Melo MM, CarvalhoM, Lopes V, AnjosMJ, Serra A, Vieira DN, Sequeiros, Corte-Real F. 2010. Genetic study of 15 STRs loci of Identifiler system in Angola population. Forensic Sci Int Genet. 4: e153-e157.
64. Mitchell P. 2002. The archaeology of Southern Africa. Cambridge (MA): Cambridge University Press.
65. Mitchell P. 2009. Hunter-gatherers and farmers: some implications of 2000 years of interaction in the Maloti-Drakensberg region of southern Africa. Senri Ethnol Stud. 73: 15-46.
66. Mitchell PJ, Plug I, Balley GN, Woodborne S 2008. Bringing the Kalahari debate to the mountains: late first millennium AD hunter-gatherer/ farmer interaction in highland Lesotho., Before Farming [Internet], 2008/2 article 4.
67. Montano V, Marcari V, Pavanello M, Anyaele O, Comas D, Destro-Bisol G, Batini C. 2013. The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation. BMC Evol Biol. 13: 24.
68. Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, Hennessy LK. 2006. Development and validation of the AmpFISTR Yfiler PCR amplification kit: A male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci. 51: 64-75.
69. Nenadic O, Greenacre M. 2007. Correspondence analysis in R, with twoand three-dimensional graphics: the ca package. J Stat Softw. 20: 1-13.
70. Newman JL. 1995. The peopling of Africa: A geographic interpretation. New Haven (CT): Yale University Press.
71. Nychka D, Furrer R, Sain S. 2013. fields: tools for spatial data. Available from: http: //cran.r-project.org/web/packages/fields/index.html.
72. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH, Wagner H. 2013. vegan: community ecology package. R package version 2.0-3. Available from: http: //cran.r-project.org/web/packages/vegan/index.html.
73. Onofri V, Alessandrini F, Turchi C, Pesaresi M, Buscemi L, Tagliabracci A. 2006. Development of multiplex PCRs for evolutionary and forensic applications of 37 human Y chromosome SNPs. Forensic Sci Int. 157: 23-35.
74. Ownby CP. 1988. Early Nguni history: the linguistic evidence and its correlation with archaeology and oral tradition [Ph.D. thesis].[California (LA)]: University of California.
75. Patin E, Siddle KJ, Laval G, et al. 2014. The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. Nat Commun. 5: 3163.
76. Pereira L, Gusm~ao L, Alves C, Amorim A, Prata MJ. 2002. Bantu and European Y-lineages in sub-Saharan Africa. Ann Hum Genet. 66: 369-378.
77. Pereira L, Macaulay V, Torroni A, Scozzari R, Prata MJ, Amorim A. 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.
78. Phillipson DW. 2005. African archaeology. Cambridge (MA): Cambridge University Press.
79. Pickrell JK, Patterson N, Barbieri C, et al. 2012. The genetic prehistory of southern Africa. Nat Commun. 3: 1143.
80. Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D. 2014. Ancient west Eurasian ancestry in southern and eastern Africa. Proc Natl Acad Sci U S A. 111: 2632-2637.
81. Pickrell JK, Pritchard JK. 2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: e1002967.
82. Quintana-Murci L, Harmant C, Quach H, Balanovsky O, Zaporozhchenko V, Bormans C, van Helden PD, Hoal EG, Behar DM. 2010. Strong maternal Khoisan contribution to the South African coloured population: A case of gender-biased admixture. Am J Hum Genet. 86: 611-620.
83. 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 U S A. 105: 1596-1601.
84. Reynolds J, Weir BS, Cockerham CC. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
85. Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, Sánchez-Diz P, Macaulay V, Carracedo A. 2002. The making of the African mtDNA landscape. Am J Hum Genet. 71: 1082-1111.
86. Schlebusch CM, de Jongh M, Soodyall H. 2011. Different contributions of ancient mitochondrial and Y-chromosomal lineages in "Karretjie people" of the Great Karoo in South Africa. J Hum Genet. 56: 623-630.
87. Schlebusch CM, Lombard M, Soodyall H. 2013. MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa. BMC Evol Biol. 13: 56.
88. Sikora M, Laayouni H, Calafell F, Comas D, Bertranpetit J. 2011. A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. Eur J Hum Genet. 19: 84-88.
89. Sturrock K, Rocha J. 2000. A multidimensional scaling stress evaluation table. Field Method. 12: 49-60.
90. Tesele TF. 1994. Symbols of power: beads and flywhisks in traditional healing in Lesotho [BA thesis]. [Cape Town (South Africa)]: University of Cape Town.
91. Thioulouse J, Chessel D, Dolédec S, Olivier JM. 1997. ADE-4: A multivariate analysis and graphical display software. Stat Comput. 7: 75-83.
92. Tishkoff SA, Gonder MK, Henn BM, et al. 2007. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Mol Biol Evol. 24: 2180-2195.
93. Tishkoff SA, Reed FA, Friedlaender FR, et al. 2009. The genetic structure and history of Africans and African Americans. Science 324: 1035-1044.
94. Turner FJ. 1962. The frontier in American history. New York: Henry Holt.
95. Underhill PA, Shen P, Lin AA, et al. 2000. Y chromosome sequence variation and the history of human populations. Nat Genet. 26: 358-361.
96. van Oven M, Kayser M. 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 30: E386-E394.
97. Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC. 1991. African populations and the evolution of human mitochondrial DNA. Science 253: 1503-1507.
98. Wadley L. 1996. Changes in the social relations of precolonial hunter-gatherers after agropastoralist contact: an example from the Magaliesberg, South Africa. J Anthropol Archaeol. 15: 205-217.
99. Walker NJ. 1995. Late Pleistocene and Holocene hunter-gatherers of the Matopos: an archaeological study of change and continuity in Zimbabwe. Uppsala (Sweden): Societas Archaeologica Upsaliensis.
100. Wood ET, Stover DA, Ehret C, et al. 2005. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sexbiased demographic processes. Eur J Hum Genet. 13: 867-876.
101. Y Chromosome Consortium. 2002. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res. 12: 339-348.
102. Zalloua PA, Xue Y, Khalife J, et al. 2008. Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet. 82: 873-882