Genome-wide and paternal diversity reveal a recent origin of human populations in north africa

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Fadhlaoui Zid, Karima ^a,b   Haber, Marc ^a,c   Martínez Cruz, Begoña ^a   Zalloua, Pierre ^c   Elgaaied, Amel Benammar ^b   Comas, David ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b FACULTÉ DES SCIENCES DE TUNIS   (Tunisia)

^c LEBANESE AMERICAN UNIVERSITY   (Lebanon)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA, NORTHERN; CHROMOSOMES, HUMAN, Y; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; GENETIC LINKAGE; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE;

EID: 84894244106     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080293     Document Type: Article

References (67)

1. Smith TM, Tafforeau P, Reid DJ, Grun R, Eggins S, et al. (2007) From the cover: earliest evidence of modern human life history in North African early Homo sapiens. Proc Natl Acad Sci USA 104: 6128-6133.
2. Barton RNE, Bouzouggar A, Collcutt SN, Schwenninger J-L, Clark-Balzan L (2009) OSL dating of the Aterian levels at Grotte de Dar es-Soltan I (Rabat, Morocco) and possible implications for the dispersal of modern Homo sapiens. Quaternary Sci Rev 28.
3. Garcea EAA (2010) The spread of Aterian peoples in North Africa. In: GarceaEAA, editor. South-Eastern Mediterranean Peoples Between 130,000 and 10,000 years ago. Oxford: Oxbow Books.
4. Debénath A (2000) Le peuplement préhistorique du Maroc: données récentes et problèmes. L'anthropologie 104: 131-145.
5. Camps G (1974) Les civilisations préhistoriques de l'Afrique du Nord et du Sahara. Paris: Doin.
6. Camps G (1982) Beginnings of pastoralism and cultivation in north-west Africa and the Sahara: origins of the Berbers. In: The Cambridge History of Africa Vol1: from the earliest times to c500 BC, JD . Clark, ed Cambridge: Cambridge University Press: 548-612.
7. Murdock GP (1959) Africa, Its Peoples and their Culture History. New York, Toronto, London: McGraw-Hill Book Company.
8. Hiernaux J (1975) The people of Africa. New York: Charles Scribner's Sons.
9. Barbujani G, Pilastro A, De Domenico S, Renfrew C (1994) Genetic variation in North Africa and Eurasia: neolithic demic diffusion vs. Paleolithic colonisation. Am J Phys Anthropol 95: 137-154.
10. Bosch E, Calafell F, Perez-Lezaun A, Comas D, Mateu E, et al. (1997) Population history of north Africa: evidence from classical genetic markers. Hum Biol 69: 295-311.
11. Chaabani H, Helal AN, van Loghem E, Langaney A, Benammar Elgaaied A, et al. (1984) Genetic study of Tunisian Berbers. I. Gm, Am and Km immunoglobulin allotypes and ABO blood groups. J Immunogenet 11: 107-113.
12. Loveslati BY, Sanchez-Mazas A, Ennafaa H, Marrakchi R, Dugoujon JM, et al. (2001) A study of Gm allotypes and immunoglobulin heavy gamma IGHG genes in Berbers, Arabs and sub-Saharan Africans from Jerba Island, Tunisia. Eur J Immunogenet 28: 531-538.
13. Fadhlaoui-Zid K, Dugoujon JM, Elgaaied A, Amor MB, Yacoubi B, et al. (2004a) Genetic diversity in Tunisia: a study based on the GM polymorphism of human immunoglobulins. Hum Biol 76: 559-567.
14. Abdennaji Guenounou B, Loueslati BY, Buhler S, Hmida S, Ennafaa H, et al. (2006) HLA class II genetic diversity in southern Tunisia and the Mediterranean area. Int J Immunogenet 33: 93-103.
15. Fadhlaoui-Zid K, Buhler S, Dridi A, Benammar El Gaaied A, Sanchez-Mazas A (2010) Polymorphism of HLA class II genes in Berbers from Southern Tunisia. Tissue Antigens 76: 416-420.
16. Bosch E, Calafell F, Perez-Lezaun A, Clarimon J, Comas D, et al. (2000) Genetic structure of north-west Africa revealed by STR analysis. Eur J Hum Genet 8: 360-366.
17. Cherni L, Loueslati Yaacoubi B, Pereira L, Alves C, Khodjet-El-Khil H, et al. (2005a) Data for 15 autosomal STR markers (Powerplex 16 System) from two Tunisian populations: Kesra (Berber) and Zriba (Arab). Forensic Sci Int 147: 101-106.
18. Coudray C, Calderon R, Guitard E, Ambrosio B, Gonzalez-Martin A, et al. (2007) Allele frequencies of 15 tetrameric short tandem repeats (STRs) in Andalusians from Huelva (Spain). Forensic Sci Int 168: e21-24.
19. Khodjet-El-Khil H, Fadhlaoui-Zid K, Gusmao L, Alves C, Benammar-Elgaaied A, et al. (2008) Substructure of a Tunisian Berber population as inferred from 15 autosomal short tandem repeat loci. Hum Biol 80: 435-448.
20. Comas D, Calafell F, Benchemsi N, Helal A, Lefranc G, et al. (2000) Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits. Hum Genet 107: 312-319.
21. Flores C, Maca-Meyer N, Gonzalez AM, Cabrera VM (2000) Northwest African distribution of the CD4/Alu microsatellite haplotypes. Ann Hum Genet 64: 321-327.
22. Gonzalez-Perez E, Via M, Esteban E, Lopez-Alomar A, Mazieres S, et al. (2003) Alu insertions in the Iberian Peninsula and north west Africa-genetic boundaries or melting pot? Coll Antropol 27: 491-500.
23. Ennafaa H, Amor MB, Yacoubi-Loueslati B, Khodjet el-khil H, Gonzalez-Perez E, et al. (2006) Alu polymorphisms in Jerba Island population (Tunisia): comparative study in Arab and Berber groups. Ann Hum Biol 33: 634-640.
24. Frigi S, Ennafaa H, Ben Amor M, Cherni L, Ben Ammar-Elgaaied A (2011) Assessing human genetic diversity in Tunisian Berber populations by Alu insertion polymorphisms. Ann Hum Biol 38: 53-58.
25. Henn BM, Botigue LR, Gravel S, Wang W, Brisbin A, et al. (2012) Genomic ancestry of North Africans supports back-to-Africa migrations. PLoS Genet 8: e1002397.
26. Haber M, Gauguier D, Youhanna S, Patterson N, Moorjani P, et al. (2013) Genome-wide diversity in the levant reveals recent structuring by culture. PLoS Genet 9: e1003316.
27. Botigué LR, Henn BM, Gravel S, Maples BK, Gignoux CR, et al. (2013) Gene flow from North Africa contributes to differential human genetic diversity in Southern Europe. Proceedings of the National Academy of Sciences USA: in press.
28. Bosch E, Calafell F, Comas D, Oefner PJ, Underhill PA, 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.
29. Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, et al. (2004) A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. Am J Hum Genet 75: 338-345.
30. Cruciani F, La Fratta R, Santolamazza P, Sellitto D, Pascone R, et al. (2004) 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.
31. Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, et al. (2007) Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12. Mol Biol Evol 24: 1300-1311.
32. Cruciani F, Trombetta B, Sellitto D, Massaia A, Destro-Bisol G, et al. (2010) Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. Eur J Hum Genet 18: 800-807.
33. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, et al. (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74: 1023-1034.
34. Ottoni C, Larmuseau MH, Vanderheyden N, Martinez-Labarga C, Primativo G, et al. (2011) Deep into the roots of the Libyan Tuareg: a genetic survey of their paternal heritage. Am J Phys Anthropol 145: 118-124.
35. Pereira L, Cerny V, Cerezo M, Silva NM, Hajek M, et al. (2010) Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel. Eur J Hum Genet 18: 915-923.
36. Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, et al. (2008) Y-chromosomal diversity in Lebanon is structured by recent historical events. Am J Hum Genet 82: 873-882.
37. Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, et al. (2011) Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. Eur J Hum Genet 19: 334-340.
38. Zalloua PA, Platt DE, El Sibai M, Khalife J, Makhoul N, et al. (2008) Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. Am J Hum Genet 83: 633-642.
39. Fadhlaoui-Zid K, Martinez-Cruz B, Khodjet-el-khil H, Mendizabal I, Benammar-Elgaaied A, et al. (2011b) Genetic structure of Tunisian ethnic groups revealed by paternal lineages. Am J Phys Anthropol 146: 271-280.
40. Ennafaa H, Fregel R, Khodjet-El-Khil H, Gonzalez AM, Mahmoudi HA, et al. (2011) Mitochondrial DNA and Y-chromosome microstructure in Tunisia. J Hum Genet 56: 734-741.
41. Fadhlaoui-Zid K, Plaza S, Calafell F, Ben Amor M, Comas D, et al. (2004b) Mitochondrial DNA heterogeneity in Tunisian Berbers. Ann Hum Genet 68: 222-233.
42. Plaza S, Calafell F, Helal A, Bouzerna N, Lefranc G, et al. (2003) Joining the Pillars of Hercules: mtDNA sequences show multidirectional gene flow in the western Mediterranean. Ann Hum Genet 67: 312-328.
43. González AM, Cabrera VM, Larruga JM, Tounkara A, Noumsi G, et al. (2006) Mitochondrial DNA variation in Mauritania and Mali and their genetic relationship to other Western Africa populations. Ann Hum Genet 70: 631-657.
44. Harich N, Costa MD, Fernandes V, Kandil M, Pereira JB, et al. (2010) The trans-Saharan slave trade-clues from interpolation analyses and high resolution characterization of mitochondrial DNA lineages. BMC Evol Biol 10: 138-156.
45. Fadhlaoui-Zid K, Rodriguez-Botigue L, Naoui N, Benammar-Elgaaied A, Calafell F, et al. (2011a) Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. Am J Phys Anthropol 145: 107-117.
46. Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, et al. (2013) Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations. PLoS One 8: e54616.
47. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, et al. (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18: 830-838.
48. Gill P, Jeffreys AJ, Werrett DJ (1985) Forensic application of DNA 'fingerprints'. Nature 318: 577-579.
49. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16: 37-48.
50. Excoffier L, Lischer HE (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.
51. R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing.
52. Jolliffe I (1986) Principal Coponents Analysis. Second Edition New York, NY: Springer.
53. Wilson IJ, Weale ME, Balding DJ (2003) Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. Journal of the Royal Statistical Society A 166, part 2.
54. Balaresque P, Bowden GR, Adams SM, Leung HY, King TE, et al. (2010) A predominantly neolithic origin for European paternal lineages. PLoS Biol 8: e1000285.
55. Weale ME, Weiss DA, Jager RF, Bradman N, Thomas MG (2002) Y chromosome evidence for Anglo-Saxon mass migration. Mol Biol Evol 19: 1008-1021.
56. Rebala K, Martinez-Cruz B, Tonjes A, Kovacs P, Stumvoll M, et al. (2012) Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. Eur J Hum Genet.
57. 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.
58. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5.
59. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100-1104.
60. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
61. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2: e190.
62. Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967.
63. Reich D, Thangaraj K, Patterson N, Price AL, Singh L (2009) Reconstructing Indian population history. Nature 461: 489-494.
64. Brovkin V, Claussen M (2008) Comment on "Climate-driven ecosystem succession in the Sahara: the past 6000 years". Science 322: 1326; author reply 1326.
65. Kropelin S, Verschuren D, Lezine AM, Eggermont H, Cocquyt C, et al. (2008) Climate-driven ecosystem succession in the Sahara: the past 6000 years. Science 320: 765-768.
66. Bar-Yosef O (1987) Pleistocene Connexions between Africa and Southwest Asia: An Archaeological Perspective. The African Archaeological Review 5: 29-38.
67. Balter M (2011) Was North Africa The Launch Pad For Modern Human Migrations? Science 331: 20-23.