Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Di Cristofaro, Julie ^a   Pennarun, Erwan ^b   Mazières, Stéphane ^a   Myres, Natalie M ^c   Lin, Alice A ^d   Temori, Shah Aga ^e   Metspalu, Mait ^b   Metspalu, Ene ^b   Witzel, Michael ^f   King, Roy J ^d   Underhill, Peter A ^d   Villems, Richard ^b,g   Chiaroni, Jacques ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b UNIVERSITY OF TARTU   (Estonia)

^c Sorenson Molecular Genealogy Foundation   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e Kabul Medical University   (Afghanistan)

^f HARVARD UNIVERSITY   (United States)

^g ESTONIAN ACADEMY OF SCIENCES   (Estonia)

Author keywords

[No Author keywords available]

Indexed keywords

AFGHANISTAN; ARTICLE; ASIA; AUTOSOME; ETHNIC GROUP; GENE CLUSTER; GENE FLOW; GENE POOL; GENETIC ANALYSIS; GENETIC VARIABILITY; HAPLOIDY; HUMAN; HUMAN CELL; IRAN; KYRGYZSTAN; MITOCHONDRIAL GENE; MONGOLIA; PAKISTAN; PHYLOGEOGRAPHY; PLESIOMORPHY; Y CHROMOSOME;

AFGHANISTAN; ANALYSIS OF VARIANCE; ASIA; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, Y; DNA, MITOCHONDRIAL; ETHNIC GROUPS; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; HUMANS; PHYLOGENY; PHYLOGEOGRAPHY; PRINCIPAL COMPONENT ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 84885782165     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076748     Document Type: Article

References (94)

1. Witzel M (2003) Linguistic Evidence for Cultural Exchange in Prehistoric Western Central Asia. Philadelphia: Sino-Platonic Papers 129.
2. Frachetti MD, (2012) Multiregional Emergence of Mobile Pastoralism and Nonuniform Institutional Complexity across Eurasia. Current Anthropology 53: 2.
3. Ali I, Zahir M, Qasim M, (2005) Archaeological survey of district Chitral. Frontier Archaeology 3: 91.
4. Hiebert FT (1994) Origins of the Bronze Age Oasis Civilization of Central Asia. Cambridge: Harvard University Press.
5. Lamberg-Karlovsky CC, (2002) Archaeology and language: The Indo-Iranians. Current Anthropology 43: 63.
6. Witzel M (1999) Early Sources for South Asian Substrate Languages. Mother Tongue (extra number) October 1.
7. Lubotsky A (2001) Uralic and Indo-European: Linguistic and Archaeological Considerations. In Carpelan C, Parpola A, Koskikallio P (eds): Suomalais-Ugrilaisen Seuran Toimituksia. Tvärminne Research Station, University of Helsinki.
8. Sims-Williams N (2002) Indo-Iranian Languages and Peoples. Oxford, Oxford University Press.
9. Pinault G-J, (2003) Une nouvelle connexion entre le substrat indo-iranien et le tokharien commun. Historische Sprachforschung 116: 175.
10. Bengtson J, (1997) Ein vergleich von buruschaski und nordkaukasisch. Georgica 20: 88.
11. Bengtson J, (2003) Linguistic Databases and Linguistic Taxonomy Workshop. Mother Tongue 8: 131.
12. Oranskij IM (1977) Les Langues Iraniennes. trad. J. Blau, ibid., Paris.
13. Hintze A (1996) The Migrations of the Indo-Aryans and the Iranian Sound-Change s>h. In Meid W (ed). Innsbruck, 22.-28. p 139.
14. Redei K (1986) Zu den indogermanisch-uralischen Sprachkontakten. Sitzungsberichte der Ö-sterreichischen Akademie der Wissenschaften, Philosophisch-Historische Klasse, vol 468. Wien.
15. Carpelan CP, Koskikallio A, P(2001) Uralic and Indo-European: Linguistic and Archaeological Considerations.
16. Kuz'mina EE (2012) Early contacts between Uralic and Indo-European: Linguistic and Archaeological Considerations. Helsinki, Memoires de la Societe Finno-Ougrienne 242, 2001, p 289.
17. Ahmed KM (2012) The beginnings of ancient Kurdistan (c. 2500-1500 BC): a historical and cultural synthesis. Leiden, Leiden University.
18. Anthony D (2007) The Horse, the Wheel and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Princeton, Princeton University Press.
19. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, et al. (2002) Genetic structure of human populations. Science 298: 2381.
20. Morgenstierne G (1973) Indo-Iranian frontier languages. vol 4, The Kalasha language. Oslo, Universitetsforlaget.
21. Bashir E (1998) Topics in Kalasha syntax: An areal and typological perspective. Chicago, Ann Arbor: University of Michigan.
22. Holt FL (2006) Into the Land of Bones: Alexander the Great in Afghanistan. Berkeley, University of California Press.
23. Elisseeff V (2001) The Silk Roads: Highways of Culture and Commerce, UNESCO Publishing.
24. Kuz'mina EE (2007) The Prehistory of the Silk Road. Pennsylvania, Penn Press.
25. Holster CW (1993) The Turks of Central Asia. Westport, CT., Praeger.
26. Findley CV (2005) The Turks in World History. Oxford, Oxford University Press.
27. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton, Princeton University Press.
28. Jackson P (2005) The Mongols and the West, 1221-1410. Harlow, Longman, p 448.
29. Elfenbein JH, (1987) A periplous of the 'Brahui problem'. Studia Iranica 16: 215.
30. Lacau H, Bukhari A, Gayden T, La Salvia J, Regueiro M, et al. (2011) Y-STR profiling in two Afghanistan populations. Leg Med (Tokyo) 13: 103.
31. Lacau H, Gayden T, Regueiro M, Chennakrishnaiah S, Bukhari A, et al. (2012) Afghanistan from a Y-chromosome perspective. Eur J Hum Genet.
32. Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, et al. (2012) Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS One 7: e34288.
33. Zerjal T, Wells RS, Yuldasheva N, Ruzibakiev R, Tyler-Smith C, (2002) A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia. Am J Hum Genet 71: 466.
34. Keyser-Tracqui C, Crubezy E, Ludes B, (2003) Nuclear and mitochondrial DNA analysis of a 2,000-year-old necropolis in the Egyin Gol Valley of Mongolia. Am J Hum Genet 73: 247.
35. Keyser-Tracqui C, Crubezy E, Pamzsav H, Varga T, Ludes B, (2006) Population origins in Mongolia: genetic structure analysis of ancient and modern DNA. Am J Phys Anthropol 131: 272.
36. Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, et al. (2001) The Eurasian heartland: a continental perspective on Y-chromosome diversity. Proc Natl Acad Sci U S A 98: 10244.
37. Calafell F, Underhill P, Tolun A, Angelicheva D, Kalaydjieva L, (1996) From Asia to Europe: mitochondrial DNA sequence variability in Bulgarians and Turks. Ann Hum Genet 60: 35.
38. Comas D, Calafell F, Mateu E, Perez-Lezaun A, Bosch E, et al. (1998) Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations. Am J Hum Genet 63: 1824.
39. Comas D, Calafell F, Bendukidze N, Fananas L, Bertranpetit J, (2000) Georgian and kurd mtDNA sequence analysis shows a lack of correlation between languages and female genetic lineages. Am J Phys Anthropol 112: 5.
40. Comas D, Plaza S, Wells RS, Yuldaseva N, Lao O, et al. (2004) Admixture, migrations, and dispersals in Central Asia: evidence from maternal DNA lineages. Eur J Hum Genet 12: 495.
41. Quintana-Murci L, Chaix R, Wells RS, Behar DM, Sayar H, et al. (2004) Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor. Am J Hum Genet 74: 827.
42. Irwin JA, Ikramov A, Saunier J, Bodner M, Amory S, et al. (2010) The mtDNA composition of Uzbekistan: a microcosm of Central Asian patterns. Int J Legal Med 124: 195.
43. Metspalu M, Romero IG, Yunusbayev B, Chaubey G, Mallick CB, et al. (2011) Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet 89: 731.
44. Fuller DQ, (2007) Contrasting patterns in crop domestication and domestication rates: recent archaeobotanical insights from the Old World. Ann Bot 100: 903.
45. Fuller DQ (2009) Framing a Middle Asian corridor of crops exchange and agricultural innovation. 13th Harvard University Round Table. Ethnogenesis of South and Central Asia (ESCA), Kyoto session. Kyoto, Research Institute for Humanity and Nature (RHIN), p 3.
46. Underhill PA, Myres NM, Rootsi S, Metspalu M, Zhivotovsky LA, et al. (2010) Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 18: 479.
47. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, et al. (2002) A human genome diversity cell line panel. Science 296: 261.
48. Behar DM, Garrigan D, Kaplan ME, Mobasher Z, Rosengarten D, et al. (2004) Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations. Hum Genet 114: 354.
49. 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.
50. Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52.
51. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, et al. (2010) Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463: 757.
52. Chaubey G, Metspalu M, Choi Y, Magi R, Romero IG, et al. (2011) Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture. Mol Biol Evol 28: 1013.
53. Yunusbayev B, Metspalu M, Jarve M, Kutuev I, Rootsi S, et al. (2011) The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations. Mol Biol Evol.
54. 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.
55. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945.
56. Alexander DN, Lange J, K. (2010) ADMIXTURE 1.04 Software Manual.
57. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS Genet 2: e190.
58. Behar DM, van Oven M, Rosset S, Metspalu M, Loogvali EL, et al. (2012) A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90: 675.
59. van Oven M, Kayser M, (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30: E386.
60. Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, et al. (2006) Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 78: 202.
61. Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, et al. (2003) The genetic legacy of the Mongols. Am J Hum Genet 72: 717.
62. Genealogy ISoG (2012) Y-DNA Haplogroup Tree 2012, Version: 7.01.
63. Yao YG, Kong QP, Wang CY, Zhu CL, Zhang YP, (2004) Different matrilineal contributions to genetic structure of ethnic groups in the silk road region in china. Mol Biol Evol 21: 2265.
64. 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.
65. Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, et al. (2002) Y-chromosomal DNA variation in Pakistan. Am J Hum Genet 70: 1107.
66. Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, et al. (2009) Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. Eur J Hum Genet 17: 820.
67. Metspalu M, Kivisild T, Metspalu E, Parik J, Hudjashov G, et al. (2004) Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans. BMC Genet 5: 26.
68. Rosser ZH, Zerjal T, Hurles ME, Adojaan M, Alavantic D, et al. (2000) Y-chromosomal diversity in Europe is clinal and influenced primarily by geography, rather than by language. Am J Hum Genet 67: 1526.
69. Chiaroni J, Underhill PA, Cavalli-Sforza LL, (2009) Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci U S A 106: 20174.
70. Li H, Mukherjee N, Soundararajan U, Tarnok Z, Barta C, et al. (2007) Geographically separate increases in the frequency of the derived ADH1B*47His allele in eastern and western Asia. Am J Hum Genet 81: 842.
71. Bryk J, Hardouin E, Pugach I, Hughes D, Strotmann R, et al. (2008) Positive selection in East Asians for an EDAR allele that enhances NF-kappaB activation. PLoS One 3: e2209.
72. Martinez-Cruz B, Vitalis R, Segurel L, Austerlitz F, Georges M, et al. (2011) In the heartland of Eurasia: the multilocus genetic landscape of Central Asian populations. Eur J Hum Genet 19: 216.
73. Busby GB, Brisighelli F, Sanchez-Diz P, Ramos-Luis E, Martinez-Cadenas C, et al. (2012) The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 279: 884.
74. Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y, et al. (2012) A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 23: 388.
75. Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, et al. (2013) Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341: 562.
76. Francalacci P, Morelli L, Angius A, Berutti R, Reinier F, et al. (2013) Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341: 565.
77. Li H, Cho K, Kidd JR, Kidd KK, (2009) Genetic landscape of Eurasia and "admixture" in Uyghurs. Am J Hum Genet 85: 934.
78. Hodoglugil U, Mahley RW, (2012) Turkish population structure and genetic ancestry reveal relatedness among Eurasian populations. Ann Hum Genet 76: 128.
79. Katoh T, Munkhbat B, Tounai K, Mano S, Ando H, et al. (2005) Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis. Gene 346: 63.
80. Dulik MC, Osipova LP, Schurr TG, (2011) Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS One 6: e17548.
81. Malyarchuk B, Derenko M, Denisova G, Wozniak M, Grzybowski T, et al. (2010) Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann Hum Genet 74: 539.
82. Zhong H, Shi H, Qi XB, Duan ZY, Tan PP, et al. (2011) Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Mol Biol Evol 28: 717.
83. Zhong H, Shi H, Qi XB, Xiao CJ, Jin L, et al. (2010) Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 55: 428.
84. Geppert M, Baeta M, Nunez C, Martinez-Jarreta B, Zweynert S, et al. (2011) Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America. Forensic Sci Int Genet 5: 100.
85. Malyarchuk B, Derenko M, Denisova G, Maksimov A, Wozniak M, et al. (2011) Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. J Hum Genet 56: 583.
86. Dulik MC, Zhadanov SI, Osipova LP, Askapuli A, Gau L, et al. (2012) Mitochondrial DNA and Y chromosome variation provides evidence for a recent common ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet 90: 229.
87. Semino O, Passarino G, Oefner PJ, Lin AA, Arbuzova S, et al. (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective. Science 290: 1155.
88. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, et al. (2005) Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci U S A 102: 15942.
89. Di Cristofaro J, Buhler S, Temori SA, Chiaroni J, (2012) Genetic data of 15 STR loci in five populations from Afghanistan. Forensic Sci Int Genet 6: e44.
90. Mazieres S, Temory SA, Vasseur H, Gallian P, Di Cristofaro J, et al. (2013) Blood group typing in five Afghan populations in the North Hindu-Kush region: implications for blood transfusion practice. Transfus Med.
91. Zeder MA, Hesse B, (2000) The initial domestication of goats (Capra hircus) in the Zagros mountains 10,000 years ago. Science 287: 2254.
92. Golden PB (2011) Central Asia in world history Central Asia in world history. New York, Oxford University Press, p 192.
93. Hegedus I, Blazek V (2010) On the position of Nuristani within Indo-Iranian. In forthc. (ed).
94. Behar DM, Garrigan D, Kaplan ME, Mobasher Z, Rosengarten D, et al. (2004) Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations. Hum Genet 114: 354-365.