The phylogenetic and geographic structure of Y-chromosome haplogroup R1a

European Journal of Human Genetics

Volumn 23, Issue 1, 2015, Pages 124-131

  Underhill, Peter A ^a   Poznik, G David ^b   Rootsi, Siiri ^c   Järve, Mari ^c   Lin, Alice A ^a   Wang, Jianbin ^d   Passarelli, Ben ^d   Kanbar, Jad ^d   Myres, Natalie M ^e   King, Roy J ^a   Di Cristofaro, Julie ^f   Sahakyan, Hovhannes ^c,g   Behar, Doron M ^c,h   Kushniarevich, Alena ^c   Šarac, Jelena ^c,i   Šaric, Tena ^c,i   Rudan, Pavao ^i,j   Pathak, Ajai Kumar ^c   Chaubey, Gyaneshwer ^c   Grugni, Viola ^k   Semino, Ornella ^k   Yepiskoposyan, Levon ^g   Bahmanimehr, Ardeshir ^l   Farjadian, Shirin ^m   Balanovsky, Oleg ⁿ   Khusnutdinova, Elza K ^o,p   Herrera, Rene J ^q   Chiaroni, Jacques ^f   Bustamante, Carlos D ^a   Quake, Stephen R ^d,r   Kivisild, Toomas ^c,s   Villems, Richard ^c,t   more..

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD LAW SCHOOL   (United States)

^c UNIVERSITY OF TARTU   (Estonia)

^d Stanford University   (United States)

^e Ancestry   (United States)

^f AIX MARSEILLE UNIVERSITÉ   (France)

^g INSTITUTE OF MOLECULAR BIOLOGY   (Armenia)

^h Molecular Medicine Laboratory   (Israel)

ⁱ INSTITUTE FOR ANTHROPOLOGICAL RESEARCH   (Croatia)

^j CROATIAN ACADEMY OF SCIENCES AND ARTS   (Croatia)

^k UNIVERSITY OF PAVIA   (Italy)

^l SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

^m SHIRAZ UNIVERSITY OF MEDICAL SCIENCES   (Iran)

ⁿ RESEARCH CENTRE FOR MEDICAL GENETICS   (Russian Federation)

^o INSTITUTE OF BIOCHEMISTRY AND GENETICS   (Russian Federation)

^p Birsk Branch of Federal State Budgetary Educational Establishment of Higher Education Bashkir State University   (Russian Federation)

^q FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^r STANFORD UNIVERSITY   (United States)

^s UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^t ESTONIAN ACADEMY OF SCIENCES   (Estonia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; MICROSATELLITE DNA;

AFGHAN; AFGHANISTAN; ARTICLE; BELARUS; BRONZE AGE; CHROMOSOME ANALYSIS; CZECH REPUBLIC; GENETIC VARIABILITY; HUMAN; HUMAN EXPERIMENT; INDIA; KYRGYZSTAN; MALE; MUTATION RATE; NORMAL HUMAN; PAKISTAN; PEDIGREE; PHYLOGENY; PHYLOGEOGRAPHY; POLAND; PRIORITY JOURNAL; RUSSIAN FEDERATION; SEQUENCE ANALYSIS; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; TIME PERCEPTION; UKRAINE; Y CHROMOSOME; Y CHROMOSOME HAPLOGROUP; Y CHROMOSOME HAPLOGROUP R1A; ALLELE; ASIA; ETHNIC GROUP; EUROPE; GENE FREQUENCY; GENETIC LINKAGE; GENETICS; HAPLOTYPE; MOLECULAR EVOLUTION; SPATIAL ANALYSIS;

ALLELES; ASIA; CHROMOSOMES, HUMAN, Y; ETHNIC GROUPS; EUROPE; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC LINKAGE; HAPLOTYPES; HUMANS; MALE; MICROSATELLITE REPEATS; PHYLOGENY; PHYLOGEOGRAPHY; POLYMORPHISM, SINGLE NUCLEOTIDE; SPATIAL ANALYSIS;

EID: 84927035659     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.50     Document Type: Article

References (63)

1. Altshuler D, Durbin RM, Abecasis GR et al: A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-1073.
2. Altshuler DM, Durbin RM, Abecasis GR et al: An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491: 56-65.
3. Wei W, Ayub Q, Chen Y et al: A calibrated human Y-chromosomal phylogeny based on resequencing. Genome Res 2013; 23: 388-395.
4. Poznik GD, Henn BM, Yee MC et al: Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 2013; 341: 562-565.
5. Francalacci P, Morelli L, Angius A et al: Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 2013; 341: 565-569.
6. Sims LM, Garvey D, Ballantyne J: Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs. Hum Mutat 2007; 28: 97.
7. Niederstätter H, Berger B, Erhart D, Parson W: Recently introduced Y-SNPs improve the resolution within Y-chromosome haplogroup R1b in a central European population sample (Tyrol, Austria). Forensic Sci Int Genet Suppl Series 2008; 1: 226-227.
8. Sims LM, Garvey D, Ballantyne J: Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs. PLoS One 2009; 4: e5792.
9. Rocca RA, Magoon G, Reynolds DF et al: Discovery of Western European R1b1a2 Y chromosome variants in 1000 Genomes Project Data: an online community approach. PLoS One 2012; 7: e41634.
10. International Society of Genetic Genealogy. http://www.isogg.org/tree/, 2013.
11. Rootsi S, Magri C, Kivisild T et al: Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. Am J Hum Genet 2004; 75: 128-137.
12. Rootsi S, Zhivotovsky LA, Baldovic M et al: A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. Eur J Hum Genet 2007; 15: 204-211.
13. Rootsi S, Myres NM, Lin AA et al: Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 2012; 20: 1275-1282.
14. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF: New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 2008; 18: 830-838.
15. Myres NM, Rootsi S, Lin AA et al: A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. Eur J Hum Genet 2011; 19: 95-101.
16. Chiaroni J, Underhill PA, Cavalli-Sforza LL: Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci USA 2009; 106: 20174-20179.
17. Kayser M, Lao O, Anslinger K et al: Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis. Hum Genet 2005; 117: 428-443.
18. Arredi B, Poloni ES, Tyler-Smith C: The peopling of Europe; in Crawford MH (ed) Anthropological Genetics: Theory, Methods and Applications. Cambridge: Cambridge University Press, 2007; pp 380-408.
19. Balaresque P, Bowden GR, Adams SM et al: A predominantly neolithic origin for european paternal lineages. PLoS Biol 2010; 8: e1000285.
20. Gignoux CR, Henn BM, Mountain JL: Rapid, global demographic expansions after the origins of agriculture. Proc Natl Acad Sci USA 2011; 108: 6044-6049.
21. Pinhasi R, Thomas MG, Hofreiter M, Currat M, Burger J: The genetic history of Europeans. Trends Genet 2012; 28: 496-505.
22. Underhill PA, Myres NM, Rootsi S et al: Separating the post-Glacial coancestry of European and Asian Y chromosomes within haplogroup R1a. Eur J Hum Genet 2010; 18: 479-484.
23. Cruciani F, Trombetta B, Antonelli C et al: Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152. Forensic Sci Int Gentic 2011; 5: E49-E52.
24. Busby GB, Brisighelli F, Sanchez-Diz P et al: The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci 2012; 279: 884-892.
25. Larmuseau MH, Vanderheyden N, Van Geystelen A, van Oven M, Kayser M, Decorte R: Increasing phylogenetic resolution still informative for Y chromosomal studies on West-European populations. Forensic Sci Int Genet 2013; 9: 179-185.
26. Balanovsky O, Dibirova K, Dybo A et al: Parallel evolution of genes and languages in the Caucasus region. Mol Biol Evol 2011; 28: 2905-2920.
27. Rebala K, Martinez-Cruz B, Tonjes A et al: Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. Eur J Hum Genet 2013; 21: 415-422.
28. Varzari A, Kharkov V, Nikitin AG et al: Paleo-Balkan and Slavic contributions to the genetic pool of Moldavians: insights from the Y chromosome. PLoS One 2013; 8: e53731.
29. Karachanak S, Grugni V, Fornarino S et al: Y-chromosome diversity in modern Bulgarians: new clues about their ancestry. PLoS One 2013; 8: e56779.
30. Kushniarevich A, Sivitskaya L, Danilenko N et al: Uniparental genetic heritage of Belarusians: encounter of rare Middle Eastern Matrilineages with a Central European mitochondrial DNA pool. PLoS One 2013; 8: e66499.
31. Pamjav H, Feher T, Nemeth E, Padar Z: Brief communication: new Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1. Am J Phys Anthropol 2012; 149: 611-615.
32. King RJ, Ozcan SS, Carter T et al: Differential Y-chromosome Anatolian influences on the Greek and Cretan Neolithic. Ann Hum Genet 2008; 72: 205-214.
33. Martinez L, Underhill PA, Zhivotovsky LA et al: Paleolithic Y-haplogroup heritage predominates in a Cretan highland plateau. Eur J Hum Genet 2007; 15: 485-493.
34. Cinnioglu C, King R, Kivisild T et al: Excavating Y-chromosome haplotype strata in Anatolia. Hum Genet 2004; 114: 127-148.
35. Luis JR, Rowold DJ, Regueiro M et al: The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations. Am J Hum Genet 2004; 74: 532-544.
36. Cadenas AM, Zhivotovsky LA, Cavalli-Sforza LL, Underhill PA, Herrera RJ: Y-chromosome diversity characterizes the Gulf of Oman. Eur J Hum Genet 2008; 16: 374-386.
37. Regueiro M, Cadenas AM, Gayden T, Underhill PA, Herrera RJ: Iran: tricontinental nexus for Y-chromosome driven migration. Hum Hered 2006; 61: 132-143.
38. Di Cristofaro J, Pennarun E, Mazieres S et al: Afghan Hindu Kush: Where Eurasian sub-continent gene flows converge. PLoS One 2013; 8: e76748.
39. Grugni V, Battaglia V, Hooshiar Kashani B et al: Ancient migratory events in the Middle East: new clues from the Y-chromosome variation of modern Iranians. PLoS One 2012; 7: e41252.
40. Chiaroni J, King RJ, Myres NM et al: The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations. Eur J Hum Genet 2010; 18: 348-353.
41. Sengupta S, Zhivotovsky LA, King R et al: 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 2006; 78: 202-221.
42. Fornarino S, Pala M, Battaglia V et al: Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 2009; 9: 154.
43. Behar DM, Thomas MG, Skorecki K et al: Multiple origins of Ashkenazi Levites: Y chromosome evidence for both near Eastern and European ancestries. Am J Hum Genet 2003; 73: 768-779.
44. Behar DM, Yunusbayev B, Metspalu M et al: The genome-wide structure of the Jewish people. Nature 2010; 466: 238-242.
45. Rootsi S, Behar DM, Jarve M et al: Phylogenetic applications of whole Y-chromosome sequences and the Near Eastern origin of Ashkenazi Levites. Nat Commun 2013; 4: 2928.
46. Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10: R25.
47. Nei M: Molecular Evolutionary Genetics. New York: Columbia University Press, 1987.
48. Zhivotovsky LA, Underhill PA, Cinnioglu C et al: The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet 2004; 74: 50-61.
49. Goedbloed M, Vermeulen M, Fang RN et al: Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR Yfiler PCR amplification kit. Int J Legal Med 2009; 123: 471-482.
50. Underhill PA, Passarino G, Lin AA et al: The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet 2001; 65: 43-62.
51. Chennakrishnaiah S, Perez D, Gayden T, Rivera L, Regueiro M, Herrera RJ: Indigenous and foreign Y-chromosomes characterize the Lingayat and Vokkaliga populations of Southwest India. Gene 2013; 526: 96-106.
52. Derenko M, Malyarchuk B, Denisova GA et al: Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions. Hum Genet 2006; 118: 591-604.
53. Haak W, Brandt G, de Jong HN et al: Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age. Proc Natl Acad Sci USA 2008; 105: 18226-18231.
54. Haak W, Balanovsky O, Sanchez JJ et al: Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol 2010; 8: e1000536.
55. Sherratt A: The transformation of early agrarian Europe: the later Neolithic and Copper Ages 4500-2500 BC; in: Cunliffe B (ed): Prehistoric Europe: An Illustrated History. Oxford: Oxford University Press, 1998, pp 167-201.
56. Mielnik-Sikorska M, Daca P, Malyarchuk B et al: The history of Slavs inferred from complete mitochondrial genome sequences. PLoS One 2013; 8: e54360.
57. Anthony DW: The horse, the wheel and language. How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World. Princeton, NJ: Princeton University Press, 2007.
58. Xue Y, Wang Q, Long Q et al: Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol 2009; 19: 1453-1457.
59. Mendez FL, Krahn T, Schrack B et al: An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet 2013; 92: 454-459.
60. Brotherton P, Haak W, Templeton J et al: Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 2013; 4: 1764.
61. Gray RD, Atkinson QD: Language-tree divergence times support the Anatolian theory of Indo-European origin. Nature 2003; 426: 435-439.
62. Lamberg-Karlovsky C: Archaeology and language: The Indo-Iranians. Curr Anthrop 2002; 43: 63-88.
63. Y Chromosome Consortium. A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 2002; 12: 339-348.