Revised timeline and distribution of the earliest diverged human maternal lineages in southern Africa

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Chan, Eva K F ^a,b   Hardie, Rae Anne ^a,b   Petersen, Desiree C ^a,b,c   Beeson, Karen ^c   Bornman, Riana M S ^d   Smith, Andrew B ^e   Hayes, Vanessa M ^a,b,c,d,f  

^a GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c J CRAIG VENTER INSTITUTE   (United States)

^d UNIVERSITY OF PRETORIA   (South Africa)

^e UNIVERSITY OF CAPE TOWN   (South Africa)

^f UNIVERSITY OF SYDNEY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLADISTICS; CONTROLLED STUDY; EXTRACHROMOSOMAL INHERITANCE; GENE EXPRESSION PROFILING; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME ANALYSIS; GEOGRAPHICAL VARIATION (SPECIES); HUMAN; MITOCHONDRIAL GENOME; MITOCHONDRIAL HAPLOGROUP; PHYLOGENETIC TREE; PHYLOGENY; POPULATION DISTRIBUTION; POPULATION MIGRATION; PREHISTORIC PERIOD; SOUTH AFRICA; AFRICA; BLACK PERSON; EVOLUTION; FEMALE; GENETICS; HAPLOTYPE; MOLECULAR GENETICS; POPULATION GENETICS;

MITOCHONDRIAL DNA;

AFRICA, SOUTHERN; AFRICAN CONTINENTAL ANCESTRY GROUP; BIOLOGICAL EVOLUTION; DNA, MITOCHONDRIAL; FEMALE; GENETICS, POPULATION; GENOME, MITOCHONDRIAL; HAPLOTYPES; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY;

EID: 84926333178     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0121223     Document Type: Article

References (55)

1. Ingman M, Kaessmann H, Pääbo S, Gyllensten U. Mitochondrial genome variation and the origin of modern humans. Nature. 2000 Dec 7; 408(6813):708-13. PMID: 11130070
2. Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, et al. The dawn of human matrilineal diversity. Am J Hum Genet. 2008 May; 82(5):1130-40. doi: 10.1016/j.ajhg.2008.04.002 PMID: 18439549
3. Gonder MK, Mortensen HM, Reed FA, de Sousa A, Tishkoff SA. Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages. Mol Biol Evol. 2007 Mar 1; 24(3):757-68. PMID: 17194802
4. Tishkoff SA, Gonder MK, Henn BM, 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. 2007 Oct 1; 24(10):2180-95. PMID: 17656633
5. Barbieri C, Vicente M, Rocha J, Mpoloka SW, Stoneking M, Pakendorf B. Ancient Substructure in Early mtDNA Lineages of Southern Africa. Am J Hum Genet. 2013 Jul 2; 92(2):285-92. doi: 10.1016/j.ajhg.2012.12.010 PMID: 23332919
6. Morris AG, Heinze A, Chan EKF, Smith AB, Hayes VM. First Ancient Mitochondrial Human Genome from a Prepastoralist Southern African. Genome Biol Evol. 2014 Oct 1; 6(10):2647-53. doi: 10.1093/gbe/evu202 PMID: 25212860
7. Brown KS, Marean CW, Herries AIR, Jacobs Z, Tribolo C, Braun D, et al. Fire As an Engineering Tool of Early Modern Humans. Science. 2009 Aug 14; 325(5942):859-62. doi: 10.1126/science.1175028 PMID: 19679810
8. Marean CW. Pinnacle Point Cave 13B (Western Cape Province, South Africa) in context: The Cape Floral kingdom, shellfish, and modern human origins. J Hum Evol. 2010 Oct; 59(3-4):425-43. doi: 10.1016/j.jhevol.2010.07.024 PMID: 20880568
9. Brown KS, Marean CW, Jacobs Z, Schoville BJ, Oestmo S, Fisher EC, et al. An early and enduring advanced technology originating 71,000 years ago in South Africa. Nature. 2012 Nov 22; 491(7425):590-3. doi: 10.1038/nature11660 PMID: 23135405
10. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Rohl A, et al. Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. Am J Hum Genet. 2009 Jun 12; 84(6):740-59. doi: 10.1016/j.ajhg.2009.05.001 PMID: 19500773
11. Mishmar D, Ruiz-Pesini E, Golik P, Macaulay V, Clark AG, Hosseini S, et al. Natural selection shaped regional mtDNA variation in humans. Proc Natl Acad Sci. 2003 Jan 7; 100(1):171-6. PMID: 12509511
12. Güldemann T, Vossen R. Khoisan. In: Heine B, Nurse D, editors. African Languages: An Introduction. Cambridge University Press; 2000.
13. Güldemann T. A linguist's view: Khoe-Kwadi speakers as the earliest food-producers of southern Africa. South Afr Humanit. 2008; 20(1):93-132.
14. Robbins LH, Campbell AC, Murphy ML, Brook GA, Srivastava P, Badenhorst S. The Advent of Herding in Southern Africa: Early AMS Dates on Domestic Livestock from the Kalahari Desert. Curr Anthropol. 2005 Aug 1; 46(4):671-7.
15. Smith AB. African Herders: Emergence of Pastoral Traditions. Rowman Altamira; 2005. 270 p.
16. Pleurdeau D, Imalwa E, Détroit F, Lesur J, Veldman A, Bahain J-J, et al. "Of Sheep and Men": Earliest Direct Evidence of Caprine Domestication in Southern Africa at Leopard Cave (Erongo, Namibia). PLoS ONE. 2012 Jul 11; 7(7):e40340. doi: 10.1371/journal.pone.0040340 PMID: 22808138
17. Henshilwood C. A revised chronology for pastoralism in southernmost Africa: new evidence of sheep at c. 2000 b.p. from Blombos Cave, South Africa. Antiquity. 1996; 70(270):945-9.
18. Smith AB. Excavations at Kasteelberg and the Origins of the Khoekhoen in the Western Cape, South Africa. Archaeopress; 2006. 124 p.
19. Huffman TN. Southern Africa to the south of the Zambesi. In: F s M, Africa UISC for the D of a GH of, Hrbek I, editors. UNESCO General History of Africa - Volume III - Africa from the Seventh to the Eleventh Century. Heinemann Educational Books; 1988. doi: 10.1016/S2214-109X(13)70069-X PMID: 25104346
20. Sandelowsky BH. Kapako and Vungu Vungu: Iron Age Sites on the Kavango River. Goodwin Ser. 1979 Jan 1;(3:) :52-61.
21. Smith AB, Yates R, Miller D, Jacobson L, Evans G. Excavations at Geduld and the Appearance of Early Domestic Stock in Namibia. South Afr Archaeol Bull. 1995 Jun 1; 50(161):3-20.
22. Van der Ross RE. Up from slavery: slaves at the Cape: their origins, treatment and contribution. Ampersand Press in association with the University of the Western Cape; 2005. 180 p.
23. Schlebusch CM, Lombard M, Soodyall H. MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa. BMC Evol Biol. 2013 Feb 27; 13(1):56.
24. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18; 463(7283):943-7. doi: 10.1038/nature08795 PMID: 20164927
25. Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, et al. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci. 2011 Mar 29; 108 (13):5154-62. doi: 10.1073/pnas.1017511108 PMID: 21383195
26. Schlebusch CM, de Jongh M, Soodyall H. Different contributions of ancient mitochondrial and Y-chromosomal lineages in "Karretjie people" of the Great Karoo in South Africa. J Hum Genet. 2011 Sep; 56 (9):623-30. doi: 10.1038/jhg.2011.71 PMID: 21776000
27. Haacke WHG. Linguistic Evidence in the Study of Origins: The Case of the Namibian Khoekhoe-speakers: Inaugural Lecture Delivered at the University of Namibia on 7 September 2000. University of Namibia; 2002. 38 p.
28. Schlebusch CM, Naidoo T, Soodyall H. SNaPshot minisequencing to resolve mitochondrial macro-haplogroups found in Africa. Electrophoresis. 2009 Nov; 30(21):3657-64. doi: 10.1002/elps.200900197 PMID: 19810027
29. 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. 2010 Apr 9; 86(4):611-20. doi: 10.1016/j.ajhg.2010.02.014 PMID: 20346436
30. Schlebusch CM, Skoglund P, Sjödin P, Gattepaille LM, Hernandez D, Jay F, et al. Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science. 2012 Oct 19; 338 (6105):374-9. doi: 10.1126/science.1227721 PMID: 22997136
31. Petersen DC, Libiger O, Tindall EA, Hardie R-A, Hannick LI, Glashoff RH, et al. Complex Patterns of Genomic Admixture within Southern Africa. PLoS Genet. 2013 Mar 14; 9(3):e1003309. doi: 10.1371/journal.pgen.1003309 PMID: 23516368
32. Van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 2009 Feb; 30(2):E386-394. doi: 10.1002/humu.20921 PMID: 18853457
33. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32(5):1792-7. PMID: 15034147
34. Pages H, Aboyoun P, Gentleman R, DebRoy S. Biostrings: String objects representing biological sequences, and matching algorithms. R package.
35. Price MN, Dehal PS, Arkin AP. FastTree 2 - Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE. 2010 Mar 10; 5(3):e9490. doi: 10.1371/journal.pone.0009490 PMID: 20224823
36. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012 Aug; 29(8):1969-73. doi: 10.1093/molbev/mss075 PMID: 22367748
37. R Development Core Team. R Development Core Team (2013). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. R Foundation for Statistical Computing, Vienna, Austria;
38. Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004 Jan 22; 20(2):289-90. PMID: 14734327
39. Friederich R, Lempp H. Verjagt verweht vergessen. Die Hai||om und das Etoschagebiet im Namibiana Buchdepot. Macmillan Education Namibia; 2009. doi: 10.1586/erp.09.53 PMID: 19817525
40. Meyer S, Weiss G, von Haeseler A. Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics. 1999 Jul; 152(3):1103-10. PMID: 10388828
41. Henshilwood CS, d'Errico F, Watts I. Engraved ochres from the Middle Stone Age levels at Blombos Cave, South Africa. J Hum Evol. 2009 Jul; 57(1):27-47. doi: 10.1016/j.jhevol.2009.01.005 PMID: 19487016
42. Henshilwood CS, d'Errico F, van Niekerk KL, Coquinot Y, Jacobs Z, Lauritzen S-E, et al. A 100,000- Year-Old Ochre-Processing Workshop at Blombos Cave, South Africa. Science. 2011 Oct 14; 334 (6053):219-22. doi: 10.1126/science.1211535 PMID: 21998386
43. 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. 2002 Nov; 71(5):1082-111. PMID: 12395296
44. Chen YS, Torroni A, Excoffier L, Santachiara-Benerecetti AS, Wallace DC. Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am J Hum Genet. 1995 Jul; 57(1):133-49. PMID: 7611282
45. Atkinson QD, Gray RD, Drummond AJ. Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proc Biol Sci. 2009 Jan 22; 276(1655):367-73. doi: 10.1098/rspb.2008.0785 PMID: 18826938
46. Rosa A, Brehem A. African human mtDNA phylogeography at-a-glance. J Anthropol Sci Riv Antropol JASS Ist Ital Antropol. 2011; 89:25-58.
47. Price TD, Bar-Yosef O. The Origins of Agriculture: New Data, New Ideas: An Introduction to Supplement 4. Curr Anthropol. 2011 Oct 1; 52(S4):S163-S174.
48. Chen Y-S, Olckers A, Schurr TG, Kogelnik AM, Huoponen K, Wallace DC. mtDNA Variation in the South African Kung and Khwe - and Their Genetic Relationships to Other African Populations. Am J Hum Genet. 2000 Apr; 66(4):1362-83. PMID: 10739760
49. Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27; 253(5027):1503-7. PMID: 1840702
50. Barbieri C, Vicente M, Oliveira S, Bostoen K, Rocha J, Stoneking M, et al. Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in Southern Africa. PloS One. 2014; 9(6): e99117. doi: 10.1371/journal.pone.0099117 PMID: 24901532
51. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, et al. Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. Science. 2008 Feb 22; 319(5866):1100-4. doi: 10.1126/science.1153717 PMID: 18292342
52. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet. 2011 Oct; 43(10):1031-4. doi: 10.1038/ng.937 PMID: 21926973
53. Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, et al. The Last Glacial Maximum. Science. 2009 Aug 7; 325(5941):710-4. doi: 10.1126/science.1172873 PMID: 19661421
54. Mithen S. After the ice: a global human history, 20,000-5000 BC. Harvard University Press; 2006. 670 p.
55. Morris AG. Isolation and the origin of the khoisan: Late pleistocene and early holocene human evolution at the southern end of Africa. Hum Evol. 2002 Jul 1; 17(3-4):231-40.