Different contributions of ancient mitochondrial and Y-chromosomal lineages in Karretjie people of the Great Karoo in South Africa

Journal of Human Genetics

Volumn 56, Issue 9, 2011, Pages 623-630

  Schlebusch, Carina M ^a   De Jongh, Michael ^b   Soodyall, Himla ^a  

^a UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^b UNIVERSITY OF SOUTH AFRICA   (South Africa)

Author keywords

Karretjie people; Khoe; KhoeSan; L0d; mitochondrial DNA haplogroup; San; Y chromosome haplogroup

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; ETHNIC GROUP; GENE FREQUENCY; GENE SEQUENCE; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; GREAT KAROO; HAPLOTYPE; HUMAN; KARRETJIE PEOPLE; NUCLEOTIDE SEQUENCE; SOUTH AFRICA; Y CHROMOSOME;

AFRICAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; FEMALE; GENETIC VARIATION; HAPLOTYPES; HUMANS; MALE; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA;

OVIS ARIES;

EID: 80053248597     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/jhg.2011.71     Document Type: Article

References (60)

1. De Jongh, M. No fixed abode: the poorest of the poor and elusive identities in rural South Africa. J South Afr Stud. 28, 441-460 (2002). (Pubitemid 34789344)
2. De Jongh, M. Human agency, asymmetrical relations and sociocultural systems, itinerancy and sedentarism in the Great Karoo of South Africa. Int J Human. 3, 199-208 (2005/2006).
3. DeJongh,M.inCustomary Strangers. New Perspectives On Peripatetic Peoples in the Middle East, Africa and Asia, (eds. Berland J. C., Rao A.), 155-178, (Praeger, London, 2004).
4. Kivisild, T., Shen, P., Wall, D. P., Do, B., Sung, R., Davis, K. et al. The role of selection in the evolution of human mitochondrial genomes. Genetics. 172, 373-387 (2006). (Pubitemid 43345499)
5. Behar, D. M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E. et al. The dawn of human matrilineal diversity. Am. J. Hum. Genet. 82, 1130-1140 (2008).
6. Chen, Y. S., Olckers, A., Schurr, T. G., Kogelnik, A. M., Huoponen, K. & Wallace, D. C. mtDNA variation in the South African Kung and Khwe and their genetic relationships to other African populations. Am. J. Hum. Genet. 66, 1362-1383 (2000). (Pubitemid 30468791)
7. Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K. & Wilson, A. C. African populations and the evolution of human mitochondrial DNA. Science. 253, 1503-1507 (1991). (Pubitemid 21917299)
8. Schlebusch, C. M., Naidoo, T. & Soodyall, H. SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa. Electrophoresis. 30, 3657-3664 (2009).
9. Tishkoff, S. A., Gonder, M. K., Henn, B. M.,Mortensen, H., Knight, A., Gignoux, C. et al. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Mol. Biol. Evol. 24, 2180-2195 (2007). (Pubitemid 47574725)
10. Pereira, L., Macaulay, V., Torroni, A., Scozzari, R., Prata, M. J. & Amorim, A. Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Ann. Hum. Genet. 65, 439-458 (2001). (Pubitemid 33149889)
11. Salas, A., Richards, M., De la Fe, T., Lareu, M. V., Sobrino, B., Sanchez-Diz, P. et al. The making of the African mtDNA landscape. Am. J. Hum. Genet. 71, 1082-1111 (2002). (Pubitemid 35305228)
12. Cruciani, F., Santolamazza, P., Shen, P., Macaulay, V., Moral, P., Olckers, A. et al. 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 (2002). (Pubitemid 34450570)
13. Cruciani, F., La Fratta, R., Santolamazza, P., Sellitto, D., Pascone, R., Moral, P. et al. Phylogeographic analysis of haplogroup E3b (E-M215). Y chromosomes reveals multiple migratory events within and out of Africa. Am. J. Hum. Genet. 74, 1014-1022 (2004). (Pubitemid 38568971)
14. Knight, A., Underhill, P. A., Mortensen, H. M., Zhivotovsky, L. A., Lin, A. A., Henn, B. M. et al. African Y chromosome and mtDNA divergence provides insight into the history of click languages. Curr. Biol. 13, 464-473 (2003). (Pubitemid 36345720)
15. Jobling, M. A. & Tyler-Smith, C. The human Y chromosome: an evolutionary marker comes of age. Nat. Rev. Genet. 4, 598-612 (2003). (Pubitemid 36917502)
16. Scozzari, R., Cruciani, F., Santolamazza, P., Malaspina, P., Torroni, A., Sellitto, D. et al. Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations. Am. J. Hum. Genet. 65, 829-846 (1999). (Pubitemid 30468728)
17. Underhill, P. A., Passarino, G., Lin, A. A., Shen, P., Mirazon Lahr, M., Foley, R. A. et al. The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann. Hum. Genet. 65, 43-62 (2001). (Pubitemid 32390189)
18. Semino, O., Santachiara-Benerecetti, A. S., Falaschi, F., Cavalli-Sforza, L. L. & Underhill, P. A. Ethiopians and Khoisan share the deepest clades of the human Y-chromosome phylogeny. Am. J. Hum. Genet. 70, 265-268 (2002). (Pubitemid 34031716)
19. Naidoo, T., Schlebusch, C. M., Makkan, H., Patel, P., Mahabeer, R., Erasmus, J. C. et al. Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations. Investig. Genet. 1, 6 (2010).
20. Henn, B. M., Gignoux, C., Lin, A. A., Oefner, P. J., Shen, P., Scozzari, R. et al. Y-chromosomal evidence of a pastoralist migration through Tanzania to southern Africa. Proc. Natl Acad. Sci. USA. 105, 10693-10698 (2008).
21. Census 2001 Census in brief. Statistics South Africa, http://www.statssa.gov.za/ census01/HTML/CInBrief/CIB2001pdf.
22. Miller, S. A., Dykes, D. D. & Polesky, H. F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988).
23. Behar, D. M., Rosset, S., Blue-Smith, J., Balanovsky, O., Tzur, S., Comas, D. et al. The Genographic Project public participation mitochondrial DNA database. PLoS Genet. 3, e104 (2007).
24. Andrews, R. M., Kubacka, I., Chinnery, P. F., Lightowlers, R. N., Turnbull, D. M. & Howell, N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23, 147 (1999). (Pubitemid 29455385)
25. Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994). (Pubitemid 24354800)
26. Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41, 95-98 (1999).
27. Nei, M. Molecular Evolutionary Genetics. (Columbia University Press: New York, USA, 1987).
28. Tajima, F. Evolutionary relationship of DNA sequences in finite populations. Genetics. 105, 437-460 (1983). (Pubitemid 14247444)
29. Rozas, J., SanchezDelBarrio, J. C., Messeguer, X. & Rozas, R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19, 2496-2497 (2003). (Pubitemid 38016658)
30. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123, 585-595 (1989). (Pubitemid 19274682)
31. Fu, Y. X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147, 915-925 (1997).
32. Excoffier, L., Smouse, P. E. & Quattro, J. M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131, 479-491 (1992).
33. Raymond, M. & Rousset, F. An exact test for population differentiation. Evolution. Int. J. Org. Evolution. 49, 1280-1283 (1995). (Pubitemid 3025486)
34. Excoffier, L., Laval, G. & Schneider, S. Arlequin ver. 30: An integrated software package for population genetics data analysis. Evol. Bioinfor. Online. 1, 47-50 (2005).
35. Network v.4500 Fluxus engineering. http://www.fluxus-engineering.com/.
36. Bandelt, H. J., Forster, P. & Rohl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37-48 (1999). (Pubitemid 29024937)
37. Polzin, T. & Daneschmand, S. V. On Steiner trees and minimum spanning trees in hypergraphs. Operations Res. Lett. 31, 12-20 (2003). (Pubitemid 35432900)
38. Ronquist, F. & Huelsenbeck, J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 19, 1572-1574 (2003). (Pubitemid 37038874)
39. Posada, D. & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14, 817-818 (1998). (Pubitemid 28552116)
40. Nylander, J. A. A. MrModeltest v2 Program Distributed By The Author. Evolutionary Biology Centre, Uppsala University (2004).
41. Forster, P., Harding, R., Torroni, A. & Bandelt, H. J. Origin and evolution of Native American mtDNA variation: a reappraisal. Am. J. Hum. Genet. 59, 935-945 (1996). (Pubitemid 26328092)
42. Drummond, A. J. & Rambaut, A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7, 214 (2007).
43. Ward, R. H., Frazier, B. L., Dew-Jager, K. & Paabo, S. Extensive mitochondrial diversity within a single Amerindian tribe. Proc. Natl Acad. Sci. USA. 88, 8720-8724 (1991). (Pubitemid 21915428)
44. Gonder, M. K., Mortensen, H. M., Reed, F. A., de Sousa, A. & Tishkoff, S. A. WholemtDNA genome sequence analysis of ancient African lineages. Mol. Biol. Evol. 24, 757-768 (2007). (Pubitemid 46355804)
45. Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R. et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 463, 943-947 (2010).
46. Yao, Y. G., Salas, A., Logan, I. & Bandelt, H. J. mtDNA data mining in GenBank needs surveying. Am J Hum Genet. 85, 929-933 (2009); author reply 933
47. de Filippo, C., Heyn, P., Barham, L., Stoneking, M. & Pakendorf, B. Genetic perspectives on forager-farmer interaction in the Luangwa valley of Zambia. Am J Phys Anthropol. 141, 382-94 (2009).
48. Sharp, J. & Douglas, S. in Miscast: Negotiating the Presence of the Bushmen (ed. Skotnes P.) 323-329 (UCT Press, Cape Town, 1996).
49. Gü ldemann, T. A linguist's view: Khoe-Kwadi speakers as the earliest food-producers of southern Africa. South Afr Human. 20, 93-132 (2008).
50. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 40 Mol. Biol. Evol. 24, 1596-1599 (2007). (Pubitemid 47236692)
51. Saillard, J., Forster, P., Lynnerup, N., Bandelt, H. J. & Norby, S. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am. J. Hum. Genet. 67, 718-726 (2000). (Pubitemid 30659601)
52. Ramirez-Soriano, A., Ramos-Onsins, S. E., Rozas, J., Calafell, F. & Navarro, A. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics. 179, 555-567 (2008).
53. Ramos-Onsins, S. E. & Rozas, J. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol. 19, 2092-2100 (2002). (Pubitemid 35440445)
54. de Filippo, C., Barbieri, C., Whitten, M., Mpoloka, S. W., Gunnarsdottir, E. D., Bostoen, K. et al. Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups. Mol. Biol. Evol. 28, 1255-1269 (2011).
55. Underhill, P. A., Shen, P., Lin, A. A., Jin, L., Passarino, G., Yang, W. H. et al. Y chromosome sequence variation and the history of human populations. Nat. Genet. 26, 358-361 (2000).
56. Wood, E. T., Stover, D. A., Ehret, C., Destro-Bisol, G., Spedini, G., McLeod, H. et al. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes. Eur. J. Hum. Genet. 13, 867-876 (2005). (Pubitemid 40946086)
57. Soodyall, H., Makkan, H., Haycock, P. & Naidoo, T. The prehistory of the Khoe and San. South Afr Human. 20, 37-48 (2008).
58. Quintana-Murci, L., Harmant, C., Quach, H., Balanovsky, O., Zaporozhchenko, V., Bormans, C. et al. Strong maternal Khoisan contribution to the South African coloured population: a case of gender-biased admixture. Am. J. Hum. Genet. 86, 611-620 (2010).
59. Patterson, N., Petersen, D. C., van der Ross, R. E., Sudoyo, H., Glashoff, R. H., Marzuki, S. et al. Genetic structure of a unique admixed population: implications for medical research. Hum. Mol. Genet. 19, 411-419 (2010).
60. Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M. et al. From the cover: feature article: hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc. Natl Acad. Sci. USA. 108, 5154-5162 (2011).