Genetic encapsulation among Near Eastern populations

Journal of Human Genetics

Volumn 51, Issue 5, 2006, Pages 467-476

  Shepard, Erica M ^a,b   Herrera, Rene J ^a  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b Federal Bureau of Investigation   (United States)

Author keywords

Allele; Autosomal; Phylogeny; Population genetics; STRs

Indexed keywords

AFRICA; ARTICLE; ASIA; DESERT; ENCAPSULATION; GENE FLOW; GENE FREQUENCY; GENETIC MARKER; GENETIC VARIABILITY; GEOGRAPHY; HUMAN; INDIA; LANDSCAPE; MIDDLE EAST; PHYLOGENY; POPULATION; POPULATION GENETICS;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETICS, POPULATION; HUMANS; PHYLOGENY; TANDEM REPEAT SEQUENCES; VARIATION (GENETICS);

EID: 33744970289     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-006-0387-4     Document Type: Article

References (74)

1. 1 URL for linguistic affiliation web resource in Table 1: http://www.ethnologue.com
2. 2 URL for geographical co-ordinate web resource in Table 1: http://www.nationalgeographic.com/xpeditions/atlas/index.html
3. Alves C, Gusmao L, Damasceno A, Soares B, Amorim A (2004) Contribution for an African autosomal STR database (AmpFISTR Identifiler and Powerplex 16 system) and a report on genotypic variations. Forensic Sci Int 139:201-205
4. Arredi B, Poloni ES, Paracchini S, Zerjal T, Fathallah DM, Makrelouf M, Pascali VL, Novelletto A, Tyler-Smith C (2004) A predominantly Neolithic origin for Y chromosomal DNA variation in North Africa. Am J Hum Genet 75:338-345
5. Bar-Yosef O (2002) The upper paleolithic revolution. Annu Rev Anthropol 31:363-393
6. Beleza S, Alves C, Reis F, Amorim A, Carracedo A, Gusmao L (2004) 17 STR (AmpFISTR Identifiler and Powerplex 16 system) from Cabinda (Angola). Forensic Sci Int 141:193-196
7. Bosch E, Calalfell F, Perez-Lezaun A, Comas D, Mateu E, Betranpetit J (1997) Population history of north Africa: evidence from classical genetic markers. Hum Biol 69:295-311
8. Bosch E, Calafell F, Perez-Lezaun A, Clarimon J, Comas D, Mateu E, Martinez-Arias R, Morera B, Brakez Z, Akhayat O, Sefiani A, Hariti G, Cambon-Thomsen A, Bertranpetit J (2000) Genetic structure of north-west Africa revealed by STR analysis. Eur J Hum Genet 8:360-366
9. Bowcock A, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457
10. Brenner C, Morris J (1990) Paternity index calculations in single locus hypervariable DNA probes: validation and other studies. Proceedings for the International Symposium on Human Identification 1989. Promega Corporation, Madison, WI, pp 21-53
11. Butler JM, Schoske R, Vallone PM, Redman JW, Kline MC (2003) Allele frequencies for 15 autosomal STR loci on U.S. Caucasian, African American and Hispanic populations. J Forensic Sci 48(4):908-911
12. Cavalli-Sfroza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton Unviersity Press, Princeton, NJ
13. Chen YS, Torroni A, Excoffier L, Santachiara-Benerecetti AS, Wallace DC (1995) Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am J Hum Genet 57:133-149
14. Chretein JP (2003) The Great Lakes of Africa: two thousand years of history. Urzone Inc., New York, NY
15. Cruciani F, Santolamazza P, Shen P, Macaulay V, Moral P, Olckers A, Modiano D, Holmes S, Destro-Bisol G, Coia V, Wallace DC, Oefner PJ, Torroni A, Cavalli-Sforza LL, Scozzari R, Underhill PA (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
16. Decorte R, Engelen M, Larno L, Nelissen K, Gilissen A, Cassiman JJ (2004) Belgian population data for 15 STR loci (AmpFISTR SGM Plus and AmpFISTR Profiler PCR amplification kit). Forensic Sci Int 139:211-213
17. Diamond J, Bellwood P (2003) Farmers and their languages: the first expansions. Science 300:597-603
18. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491
19. Felsenstein J (2002) Phylogeny Inference Package (PHYLIP) Version 3.6a3 distributed by author, Department of Genetics, University of Washington, Seattle, WA
20. Guo S, Thompson E (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361-372
21. Hadi S, Vanezis P, Goodwin W (2004) The autosomal STR frequencies in Pakistani populations. J For Sci 49:868-869
22. Hammer MF, Karafet T, Rasanayagam A, Wood ET, Altheide TK, Jenkins T, Griffiths RC, Templeton AR, Zegura SL (1998) Out of Africa and back again: nested cladistic analysis of Human Y chromosome variation. Mol Biol Evol 15:427-441
23. Hashiyada M, Itakura Y, Nagashima T, Nata M, Funayama M (2003) Polymorphism of 17 STRs by multiplex analysis in Japanese population. Forensic Sci Int 133:250-253
24. Hassan F (2002) Archeology and linguistic diversity in North Africa. In: Bellwood P, Renfrew C (eds) Examining the farming/language dispersal hypothesis. McDonald Institute for Archeological Research, Cambridge, England, pp 127-133
25. http://www.bartleby.com
26. http://www.nationalgeographic.com/xpeditions/atlas/index.html
27. Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708-713
28. Jones DA (1972) Blood samples: probability of discrimination. J Forensic Sci Soc 12:355-359
29. Jorde L, Bamsgad M, Watkins W, Zenger R, Fraley A, Krakowiak P, Carpenter K, Soodyall H, Jenkins T, Rogers A (1995) Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am J Hum Genet 57:523-538
30. Jorde LB, Watkins WS, Bamshad MJ, Dizon ME, Ricker CE, Seielstad MT, Batzer MA (2000) The distribution of human genetic diversity: a comparison of mitochondrial, auotsomal and Y-chromosome data. Am J Hum Genet 66:979-988
31. July RW (1992) A history of the African people, 4th edn. East African Educational Publishers Ltd., Nairobi, Kenya
32. Ke Y, Su B, Song X, Lu D, Chen L, Li H, Qi C, Marzuki S, Deka R, Underhill P, Xiao C, Shriver M, Lell J, Wallace D, Wells RS, Seielstad M, Oefner P, Zhu D, Jin J, Huang W, Chakraborty R, Chen Z, Jin L (2001) African origins of modern humans in East Asia: a tale of 12,000 Y-chromosomes. Science 292:1151-1153
33. Kivisilid T, Bamshad M, Kaldma K, Metspalu M, Metspalu E, Reidla M, Laos S, Parik J, Watkins W, Dixon M, Papiha S, Mastana S, Mir M, Ferak V, Villems R (1999) Deep common ancestry of Indian and Western-Eurasian mitochondrial DNA lineages. Curr Biol 9:1331-1334
34. Kivisilid 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
35. Klintschar M, Al-Hammadi N, Reichenpfader B (2001) Significant differences between Yemenite and Egyptian STR profiles and the influence on frequency estimations in Arabs. Int J Legal Med 114:211-214
36. Levene H (1949) On a matching problem arising in genetics. Ann Mathm Stat 20:91-94
37. Li CC (1976) First course in population genetics. Boxwood Press, Pacific Grove, CA
38. Luis JR, Rowold DJ, Regueiro M, Caeiro B, Cinnioglu C, Roseman C, Underhill PA, Cavalli-Sforza LL, Herrera RJ (2004) The Levant vesus the Horn of Africa: evidence for bi-directional corridors of human migrations. Am J Hum Genet 74:532-544
39. Lum JK, Jorde LB, Schiefenhovel W (2002) Affinities among Melanisians, Micronesians and Polynesians: a neutral biparental genetic perspective. Hum Biol 74(3):413-430
40. Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM (2001) Major genomic mitochondrial lineages delineate early human expansions. BMC Genet 2:13-20
41. Maca-Meyer N, Gonzalez AM, Pestano J, Flores C, Larruga JM, Cabrera VM (2003) Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 4:15-25
42. Manni F, Leonardi P, Barakat A, Rouba H, Heyer E, Klintschar M, McElreavey K, Quintana-Murci L (2002) Y chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa. Hum Biol 74:645-658
43. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, Kaldma K, Serk P, Karmin M, Behar DM, Gilbert MT, Endicott P, Mastana S, Papiha SS, Skorecki K, Torroni A, Villems R (2004) Most of the extant mtDNA boundaries in the south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet 5:26-50
44. Militarev A (2002) The prehistory of a dispersal: the proto-Afrasain (Afroasiatic) farming lexicon. In: Bellwood P, Renfrew C (eds) Examining the farming/language dispersal hypothesis. McDonald Institute for Archeological Research, Cambridge, England, pp 135-150
45. Nebel A, Nadau-Tasseron E, Filon D, Oppenheim A, Faerman M (2004) Genetic evidence for the expansion of Arabian tribes into the Southern Levant and North Africa. Am J Hum Genet 74:532-544
46. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, NY
47. Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, Mansoor A, Zerjal T, Tyler-Smith C, Mehdi SQ (2002) Y-chromosomal DNA variation in Pakistan. Am J Hum Genet 23:437-441
48. Quintana-Murci L, Semino O, Bandelt H, Passarino G, McElreavey K, Santachiara-Benerecetti A (1999) Genetic evidence of an early exit of Homo sapiens sapiens from Africa through eastern Africa. Nat Genet 23:437-441
49. Quintana-Murci L, Krausz C, Zerjal T, Sayar H, Hammer M, Mehdi SQ, Ayub Q, Qamar R, Mohyuddin A, Radhakrishna U, Jobling MA, Tyler-Smith C, McElreavey K (2001) Y chromosome lineages trace diffusion of peoples and languages in Southwestern Asia. Am J Hum Genet 68:537-542
50. Quintana-Murci L, Chaix R, Spencer Wells R, Behar DM, Sayar H, Scozzari R, Rengo C, Al-Zahery N, Semino O, Santachiara-Benerecetti AS, Coppa A, Ayub Q, Mohyuddin A, Tyler-Smith C, Mehdi SQ, Torroni A, McElreavey K (2004) Where west meets east: the complex mtDNA landscape of the Southwest and Central Asian corridor. Am J Hum Genet 74:827-845
51. Regueiro M (2004): personal communication
52. Renfrew C (1996) Language families and the spread of farming. In: Harris D (ed) The origins and spread of agriculture and pastoralism in Eurasia. University College of London Press, London, England, pp 70-92
53. Renfrew C (2000) At the edge of knowability: towards a prehistory of languages. Camb Archeol J 10:7-34
54. Rowold DJ, Herrera RJ(2003) Inferring recent human phylogenies using forensic STR technology. For Sci Int 133:260-265
55. Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, Sanchez-Diaz P, Macaulay V, Carracedo A (2002) The making of the African mtDNA landscape. Am J Hum Genet 71:1082-1111
56. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
57. Schneider S, Kueffer J-M, Roessli D, Excoffier L (2000) Arlequin v.2000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland
58. Semino O, Santachiara-Benerecetti AS, Falaschi F, Cavalli-Sforza LL, Underhill PA (2002) Ethiopians and Khosians share the deepest clades of the human y-chromosome phylogeny. Am J Hum Genet 70:265-268
59. Shepard EM, Herrera RJ (2005) Iranian STR variation at the fringes of biogeographical demarcation. Forensic Sci Int (in press)
60. SPSS for Windows, Rel. 11.0.1.2001. Chicago: SPSS Inc
61. STRBase (http://www.cstl.nist.gov/biotech/strbase/)
62. Stringer C (2000) Paleoanthropology: coasting out of Africa. Nature 405:24-25, 27
63. Tahir MA, Balamurugan K, Tahir UA, Amjad M, Awin MB, Chaudhary OR, Hamby JE, Budowle B, Herrera RJ (2000a) Allelic distribution of nine short tandem repeat (STR), HLA-DQA1 and polymarker loci in an Omani sample population. Forensic Sci Int 109:81-85
64. Tahir MA, Herrera RJ, Khan AA, Kashyap VK, Duncan G, Barna C, Budowle B, Rowold DJ, Amjad M, Sinha S (2000b) Distribution of HLA-DQA1, polymarker CSF1PO, vWA, TH01, TPOX, D16S539, D7S820, D13S317 and D5S818 alleles in East Bengali and West Punjabi populations from the Indo-Pak subcontinent. J Forensic Sci 45:1320-1323
65. Tahir MA, Herrera RJ, el-Gohary M, Granoff M, Amjad M (2003) Allele frequency distribution of Power Plex 1.2 and Profiler Plus short tandem repeat (STR) loci in Egyptian population. J Forensic Sci 48:889-890
66. Tereba A (1999) Tools for analysis of population statistics. Profiles in DNA, v.2, Promega Corporation pp14-16
67. Tishkoff SA, Dietzsch E, Speed W, Pakstis AJ, Kidd JR, Cheung K, Bonne-Tamir B, Santachiara-Benerecetti AS, Moral P, Krings M (1996) Global patterns of linkage disequilibrium at the CD4 locus in modern human origins. Science 271:1380-1387
68. Tofanelli S, Boschi I, Bertoneri S, Coia V, Taglioli L, Franceschi MG, Destro-Bisol G, Pascali V, Paoli G (2003) Variation at 16 STR loci in Rwandan (Hutu) and implications on profile frequency estimation in Bantu-speakers. Int J Legal Med 117:121-126
69. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertrapetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358-361
70. Wang C-W, Chen D-P, Chen C-Y, Lu S-C, Sun C-F (2003) STR data for the AmpFISTR SGM Plus and Profiler loci from Taiwan. Forensic Sci Int 138:119-122
71. Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB (2001) Patterns of ancestral human diversity: an analysis of Aluinsertions and restriction site polymorphisms. Am J Hum Genet 68:738-752
72. Watson E, Forster P, Richards M, Bandelt HJ (1997) Mitochondrial footprints of human expansions in Africa. Am J Hum Genet 61:691-704
73. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B et al (2001) The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci USA 98:10244-10249
74. Zvelebil M (1980) The rise of the nomads in Central Asia. In: Sherratt A (ed) The Cambridge encyclopedia of archeology Crown, NY, pp 252-256