Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

American Journal of Human Genetics

Volumn 99, Issue 1, 2016, Pages 163-173

  Ilumäe, Anne Mai ^a   Reidla, Maere ^a   Chukhryaeva, Marina ^b,k   Järve, Mari ^a   Post, Helen ^a   Karmin, Monika ^a   Saag, Lauri ^a   Agdzhoyan, Anastasiya ^b   Kushniarevich, Alena ^a,c   Litvinov, Sergey ^a,d   Ekomasova, Natalya ^e   Tambets, Kristiina ^a   Metspalu, Ene ^a   Khusainova, Rita ^d   Yunusbayev, Bayazit ^a   Khusnutdinova, Elza K ^d,e   Osipova, Ludmila P ^f,g   Fedorova, Sardana ^h   Utevska, Olga ⁱ   Koshel, Sergey ^j   Balanovska, Elena ^k   Behar, Doron M ^a   Balanovsky, Oleg ^b,k   Kivisild, Toomas ^a,l   Underhill, Peter A ^m   Villems, Richard ^a,n   Rootsi, Siiri ^a   more..

^a UNIVERSITY OF TARTU   (Estonia)

^b VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

^c INSTITUTE OF GENETICS AND CYTOLOGY   (Belarus)

^d INSTITUTE OF BIOCHEMISTRY AND GENETICS   (Russian Federation)

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

^f INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^g NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^h Russian Academy of Sciences   (Russian Federation)

ⁱ V N KARAZIN KHARKIV NATIONAL UNIVERSITY   (Ukraine)

^j MOSCOW STATE UNIVERSITY   (Russian Federation)

^k RESEARCH CENTRE FOR MEDICAL GENETICS   (Russian Federation)

^l UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^m STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁿ ESTONIAN ACADEMY OF SCIENCES   (Estonia)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLADISTICS; DEMOGRAPHY; FEMALE; GENE SEQUENCE; GEOGRAPHIC DISTRIBUTION; HUMAN; LANGUAGE; MAJOR CLINICAL STUDY; MALE; MULTIGENE FAMILY; PHYLOGENETIC TREE; PHYLOGEOGRAPHY; PREHISTORIC PERIOD; PRIORITY JOURNAL; Y CHROMOSOME; Y CHROMOSOME HAPLOGROUP; ASIA; EUROPE; GENETICS; HAPLOTYPE; TIME FACTOR;

ASIA; CHROMOSOMES, HUMAN, Y; EUROPE; HAPLOTYPES; HUMANS; LANGUAGE; PHYLOGEOGRAPHY; TIME FACTORS;

EID: 84989849271     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2016.05.025     Document Type: Article

References (57)

1. 1 Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S.M., Bondarev, A.A., Johnson, P.L., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514 (2014), 445–449.
2. 2 Zerjal, T., Dashnyam, B., Pandya, A., Kayser, M., Roewer, L., Santos, F.R., Schiefenhövel, W., Fretwell, N., Jobling, M.A., Harihara, S., et al. Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am. J. Hum. Genet. 60 (1997), 1174–1183.
3. 3 Hammer, M.F., Karafet, T.M., Park, H., Omoto, K., Harihara, S., Stoneking, M., Horai, S., Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes. J. Hum. Genet. 51 (2006), 47–58.
4. 4 Karafet, T.M., Osipova, L.P., Gubina, M.A., Posukh, O.L., Zegura, S.L., Hammer, M.F., High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life. Hum. Biol. 74 (2002), 761–789.
5. 5 Rootsi, S., Zhivotovsky, L.A., Baldovic, M., Kayser, M., Kutuev, I.A., Khusainova, R., Bermisheva, M.A., Gubina, M., Fedorova, S.A., Ilumäe, A.M., et al. A counter-clockwise northern route of the Y-chromosome haplogroup N from Southeast Asia towards Europe. Eur. J. Hum. Genet. 15 (2007), 204–211.
6. 6 Shi, H., Qi, X., Zhong, H., Peng, Y., Zhang, X., Ma, R.Z., Su, B., Genetic evidence of an East Asian origin and paleolithic northward migration of Y-chromosome haplogroup N. PLoS ONE, 8, 2013, e66102.
7. 7 Xue, Y., Zerjal, T., Bao, W., Zhu, S., Lim, S.K., Shu, Q., Xu, J., Du, R., Fu, S., Li, P., et al. Recent spread of a Y-chromosomal lineage in northern China and Mongolia. Am. J. Hum. Genet. 77 (2005), 1112–1116.
8. 8 Kayser, M., The human genetic history of Oceania: near and remote views of dispersal. Curr. Biol. 20 (2010), R194–R201.
9. 9 Zhong, H., Shi, H., Qi, X.B., Duan, Z.Y., Tan, P.P., Jin, L., Su, B., Ma, R.Z., Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Mol. Biol. Evol. 28 (2011), 717–727.
10. 10 Cui, Y., Li, H., Ning, C., Zhang, Y., Chen, L., Zhao, X., Hagelberg, E., Zhou, H., Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. BMC Evol. Biol., 13, 2013, 216.
11. 11 Gao, S.Z., Zhang, Y., Wei, D., Li, H.J., Zhao, Y.B., Cui, Y.Q., Zhou, H., Ancient DNA reveals a migration of the ancient Di-qiang populations into Xinjiang as early as the early Bronze Age. Am. J. Phys. Anthropol. 157 (2015), 71–80.
12. 12 Zhao, Y.B., Zhang, Y., Li, H.J., Cui, Y.Q., Zhu, H., Zhou, H., Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago. Am. J. Hum. Biol. 26 (2014), 813–821.
13. 13 Gamba, C., Jones, E.R., Teasdale, M.D., McLaughlin, R.L., Gonzalez-Fortes, G., Mattiangeli, V., Domboróczki, L., Kővári, I., Pap, I., Anders, A., et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun., 5, 2014, 5257.
14. 14 Tambets, K., Rootsi, S., Kivisild, T., Help, H., Serk, P., Loogväli, E.L., Tolk, H.V., Reidla, M., Metspalu, E., Pliss, L., et al. The western and eastern roots of the Saami–the story of genetic “outliers” told by mitochondrial DNA and Y chromosomes. Am. J. Hum. Genet. 74 (2004), 661–682.
15. 15 Derenko, M., Malyarchuk, B., Denisova, G., Wozniak, M., Grzybowski, T., Dambueva, I., Zakharov, I., Y-chromosome haplogroup N dispersals from south Siberia to Europe. J. Hum. Genet. 52 (2007), 763–770.
16. 16 Karlsson, A.O., Wallerström, T., Götherström, A., Holmlund, G., Y-chromosome diversity in Sweden - a long-time perspective. Eur. J. Hum. Genet. 14 (2006), 963–970.
17. 17 Lappalainen, T., Koivumäki, S., Salmela, E., Huoponen, K., Sistonen, P., Savontaus, M.L., Lahermo, P., Regional differences among the Finns: a Y-chromosomal perspective. Gene 376 (2006), 207–215.
18. 18 Lappalainen, T., Laitinen, V., Salmela, E., Andersen, P., Huoponen, K., Savontaus, M.L., Lahermo, P., Migration waves to the Baltic Sea region. Ann. Hum. Genet. 72 (2008), 337–348.
19. 19 Balanovsky, O., Rootsi, S., Pshenichnov, A., Kivisild, T., Churnosov, M., Evseeva, I., Pocheshkhova, E., Boldyreva, M., Yankovsky, N., Balanovska, E., Villems, R., Two sources of the Russian patrilineal heritage in their Eurasian context. Am. J. Hum. Genet. 82 (2008), 236–250.
20. 20 Pimenoff, V.N., Comas, D., Palo, J.U., Vershubsky, G., Kozlov, A., Sajantila, A., Northwest Siberian Khanty and Mansi in the junction of West and East Eurasian gene pools as revealed by uniparental markers. Eur. J. Hum. Genet. 16 (2008), 1254–1264.
21. 21 Mirabal, S., Regueiro, M., Cadenas, A.M., Cavalli-Sforza, L.L., Underhill, P.A., Verbenko, D.A., Limborska, S.A., Herrera, R.J., Y-chromosome distribution within the geo-linguistic landscape of northwestern Russia. Eur. J. Hum. Genet. 17 (2009), 1260–1273.
22. 22 Dulik, M.C., Osipova, L.P., Schurr, T.G., Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS ONE, 6, 2011, e17548.
23. 23 Dulik, M.C., Zhadanov, S.I., Osipova, L.P., Askapuli, A., Gau, L., Gokcumen, O., Rubinstein, S., Schurr, T.G., Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am. J. Hum. Genet. 90 (2012), 229–246.
24. 24 Fedorova, S.A., Reidla, M., Metspalu, E., Metspalu, M., Rootsi, S., Tambets, K., Trofimova, N., Zhadanov, S.I., Hooshiar Kashani, B., Olivieri, A., et al. Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): implications for the peopling of Northeast Eurasia. BMC Evol. Biol., 13, 2013, 127.
25. 25 Poznik, G.D., Henn, B.M., Yee, M.C., Sliwerska, E., Euskirchen, G.M., Lin, A.A., Snyder, M., Quintana-Murci, L., Kidd, J.M., Underhill, P.A., Bustamante, C.D., Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341 (2013), 562–565.
26. 26 Francalacci, P., Morelli, L., Angius, A., Berutti, R., Reinier, F., Atzeni, R., Pilu, R., Busonero, F., Maschio, A., Zara, I., et al. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341 (2013), 565–569.
27. 27 Hallast, P., Batini, C., Zadik, D., Maisano Delser, P., Wetton, J.H., Arroyo-Pardo, E., Cavalleri, G.L., de Knijff, P., Destro Bisol, G., Dupuy, B.M., et al. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol. Biol. Evol. 32 (2015), 661–673.
28. 28 Lippold, S., Xu, H., Ko, A., Li, M., Renaud, G., Butthof, A., Schröder, R., Stoneking, M., Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences. Investig. Genet., 5, 2014, 13.
29. 29 Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M.A., Järve, M., Talas, U.G., Rootsi, S., Ilumäe, A.M., Mägi, R., Mitt, M., et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25 (2015), 459–466.
30. 30 Batini, C., Hallast, P., Zadik, D., Delser, P.M., Benazzo, A., Ghirotto, S., Arroyo-Pardo, E., Cavalleri, G.L., de Knijff, P., Dupuy, B.M., et al. Large-scale recent expansion of European patrilineages shown by population resequencing. Nat. Commun., 6, 2015, 7152.
31. 31 Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., Hammer, M.F., New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 18 (2008), 830–838.
32. 32 Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
33. 33 Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 (2009), 2078–2079.
34. 34 Drummond, A.J., Suchard, M.A., Xie, D., Rambaut, A., Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29 (2012), 1969–1973.
35. 35 Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.C., Remm, M., Rozen, S.G., Primer3–new capabilities and interfaces. Nucleic Acids Res., 40, 2012, e115.
36. 36 Koressaar, T., Remm, M., Enhancements and modifications of primer design program Primer3. Bioinformatics 23 (2007), 1289–1291.
37. 37 Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T.L., Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, 13, 2012, 134.
38. 38 Andreson, R., Reppo, E., Kaplinski, L., Remm, M., GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics, 7, 2006, 172.
39. 39 Balanovsky, O., Dibirova, K., Dybo, A., Mudrak, O., Frolova, S., Pocheshkhova, E., Haber, M., Platt, D., Schurr, T., Haak, W., et al., Genographic Consortium. Parallel evolution of genes and languages in the Caucasus region. Mol. Biol. Evol. 28 (2011), 2905–2920.
40. 40 Nei, M., Molecular Evolutionary Genetics. 1987, Columbia University Press.
41. 41 Atkinson, Q.D., Gray, R.D., Drummond, A.J., mtDNA variation predicts population size in humans and reveals a major Southern Asian chapter in human prehistory. Mol. Biol. Evol. 25 (2008), 468–474.
42. 42 Kitchen, A., Miyamoto, M.M., Mulligan, C.J., A three-stage colonization model for the peopling of the Americas. PLoS ONE, 3, 2008, e1596.
43. 43 Pakendorf, B., Novgorodov, I.N., Osakovskij, V.L., Danilova, A.P., Protod'jakonov, A.P., Stoneking, M., Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts. Hum. Genet. 120 (2006), 334–353.
44. 44 Monserud, R.A., Tchebakova, N.M., Denissenko, O.V., Reconstruction of the mid-Holocene palaeoclimate of Siberia using a bioclimatic vegetation model. Palaeogeog. Palaeoclimat. Palaeoecol. 139 (1998), 15–36.
45. 45 Andreev, A.A., Tarasov, P.E., Siegert, C., Ebel, T., Klimanov, V.A., Melles, M., Bobrov, A.A., Dereviagin, A.Y., Lubinski, D.J., Hubberten, H.W., Late Pleistocene and Holocene vegetation and climate on the northern Taymyr Peninsula, Arctic Russia. Boreas 32 (2003), 484–505.
46. 46 Anderson, P.M., Lozhkin, A.V., Brubaker, L.B., Implications of a 24,000-yr palynological record for a Younger Dryas cooling and for boreal forest development in northeastern Siberia. Quat. Res. 57 (2002), 325–333.
47. 47 Nazarova, L., Lupfert, H., Subetto, D., Pestryakova, L., Diekmann, B., Holocene climate conditions in central Yakutia (Eastern Siberia) inferred from sediment composition and fossil chironomids of Lake Temje. Quat. Int. 290 (2013), 264–274.
48. 48 Weber, A.W., Link, D.W., Katzenberg, M.A., Hunter-gatherer culture change and continuity in the Middle Holocene of the Cis-Baikal, Siberia. J. Anthropol. Archaeol. 21 (2002), 230–299.
49. 49 Weber, A., Katzenberg, M.A., Schurr, T.G., Prehistoric Hunter-Gatherers of the Baikal Region, Siberia: Bioarchaeological Studies of Past Life Ways. 2010, University of Pennsylvania Press.
50. 50 Mooder, K.P., Schurr, T.G., Bamforth, F.J., Bazaliiski, V.I., Savel'ev, N.A., Population affinities of Neolithic Siberians: a snapshot from prehistoric Lake Baikal. Am. J. Phys. Anthropol. 129 (2006), 349–361.
51. 51 Chernykh, E., The “Steppe Belt” of stockbreeding cultures in Eurasia during the Early Metal Age. Trab. Prehist. 65 (2008), 73–93, 10.3989/tp.2008.08004.
52. 52 Der Sarkissian, C., Balanovsky, O., Brandt, G., Khartanovich, V., Buzhilova, A., Koshel, S., Zaporozhchenko, V., Gronenborn, D., Moiseyev, V., Kolpakov, E., et al., Genographic Consortium. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe. PLoS Genet., 9, 2013, e1003296.
53. 53 Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P.H., Schraiber, J.G., Castellano, S., Lipson, M., et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513 (2014), 409–413.
54. 54 Raghavan, M., Skoglund, P., Graf, K.E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford, T.W. Jr., Orlando, L., Metspalu, E., et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505 (2014), 87–91.
55. 55 Allentoft, M.E., Sikora, M., Sjögren, K.G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P.B., Schroeder, H., Ahlström, T., Vinner, L., et al. Population genomics of Bronze Age Eurasia. Nature 522 (2015), 167–172.
56. 56 Anthony, D., The horse, the wheel and language. How Bronze-Age riders from the Eurasian steppes shaped the modern world. 2007, Princeton University Press, Princeton, NJ.
57. 57 Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522 (2015), 207–211.