Upper Palaeolithic genomes reveal deep roots of modern Eurasians

Nature Communications

Volumn 6, Issue , 2015, Pages

  Jones, Eppie R ^a   Gonzalez Fortes, Gloria ^b,c   Connell, Sarah ^d   Siska, Veronika ^e   Eriksson, Anders ^e,f   Martiniano, Rui ^a   McLaughlin, Russell L ^a   Gallego Llorente, Marcos ^e   Cassidy, Lara M ^a   Gamba, Cristina ^a,d,g   Meshveliani, Tengiz ^h   Bar Yosef, Ofer ⁱ   Müller, Werner ^j,k   Belfer Cohen, Anna ^l   Matskevich, Zinovi ^m   Jakeli, Nino ^h   Higham, Thomas F G ⁿ   Currat, Mathias ^o   Lordkipanidze, David ^h   Hofreiter, Michael ^b   Manica, Andrea ^e   Pinhasi, Ron ⁿ   Bradley, Daniel G ^a   more..

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b UNIVERSITY OF POTSDAM   (Germany)

^c UNIVERSITY OF FERRARA   (Italy)

^d UNIVERSITY COLLEGE DUBLIN   (Ireland)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^f KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

^h Georgian National Museum   (Georgia)

ⁱ HARVARD UNIVERSITY   (United States)

^j UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^k Section Archéologie   (Switzerland)

^l HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^m ISRAEL ANTIQUITIES AUTHORITY   (Israel)

ⁿ UNIVERSITY OF OXFORD   (United Kingdom)

^o UNIVERSITY OF GENEVA   (Switzerland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANATOMY; ANCESTRY; GENOME; LANGUAGE; LAST GLACIAL MAXIMUM; MESOLITHIC; PALEOLITHIC;

ADOLESCENT; AGRICULTURAL WORKER; BRONZE AGE; CHILD; CLADISTICS; GENOME; HUMAN; HUMAN EXPERIMENT; LANGUAGE; LAST GLACIAL MAXIMUM; MALE; MESOLITHIC; NEOLITHIC; PALEOLITHIC; SOUTH ASIA; STEPPE; SWITZERLAND; ASIA; ASIAN CONTINENTAL ANCESTRY GROUP; CAUCASIAN; EUROPE; GENETICS; GENOMICS; HUMAN GENOME; MIGRATION;

EURASIA; GEORGIA; UNITED STATES;

ASIA; ASIAN CONTINENTAL ANCESTRY GROUP; EUROPE; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENOME, HUMAN; GENOMICS; HUMAN MIGRATION; HUMANS; MALE;

EID: 84947563586     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms9912     Document Type: Article

References (51)

1. Lazaridis, I. et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513, 409-413 (2014).
2. Olalde, I. et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225-228 (2014).
3. Gamba, C. et al. Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun 5, 5257 (2014).
4. Skoglund, P. et al. Genomic diversity and admixture differs for stone-age Scandinavian foragers and farmers. Science 344, 747-750 (2014).
5. Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207-211 (2015).
6. Raghavan, M. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87-91 (2013).
7. Allentoft, M. E. et al. Population genomics of Bronze Age Eurasia. Nature 522, 167-172 (2015).
8. Seguin-Orlando, A. et al. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science 346, 1113-1118 (2014).
9. Keller, A. et al. New insights into the Tyrolean Icemans origin and phenotype as inferred by whole-genome sequencing. Nat. Commun. 3, 698 (2012).
10. Fu, Q. et al. Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514, 445-449 (2014).
11. Patterson, N., Price, A. L. and Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).
12. Alexander, D. H., Novembre, J. and Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655-1664 (2009).
13. Green, R. E. et al. ADraft Sequenceofthe Neandertal Genome. Science 328, 710-722 (2010).
14. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065-1093 (2012).
15. Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G. and Siepel, A. Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43, 1031-1034 (2011).
16. Pinhasi, R., Thomas, M. G., Hofreiter, M., Currat, M. and Burger, J. The genetic history of Europeans. Trends Genet. 28, 496-505 (2012).
17. Lamason, R. L. et al. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310, 1782-1786 (2005).
18. Mathieson, I. et al. Eight thousand years of natural selection in Europe. Preprint at http://dx.doi.org/10.1101/016477 (2015).
19. Morin, E. Evidence for declines in human population densities during the early Upper Paleolithic in western Europe. Proc. Natl. Acad. Sci. USA 105, 48-53 (2008).
20. Kirin, M. et al. Genomic runs of homozygosity record population history and consanguinity. PLoS ONE 5, e13996 (2010).
21. Pemberton, T. J. et al. Genomic patterns of homozygosity in worldwide human populations. Am. J. Hum. Genet. 91, 275-292 (2012).
22. Semino, O. et al. 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 (2004).
23. Derenko, M. et al. Complete mitochondrial DNA diversity in Iranians. PLoS ONE 8, e80673 (2013).
24. Balanovsky, O. et al. Parallel evolution of genes and languages in the Caucasus region. Mol. Biol. Evol. 28, 2905-2920 (2011).
25. Reich, D., Thangaraj, K., Patterson, N., Price, A. L. and Singh, L. Reconstructing Indian population history. Nature 461, 489-494 (2009).
26. Mallory, J. P. Yamna Culture. (Encyclopedia of Indo-European Culture, 1997).
27. Kohl, P. L. The Making of Bronze Age Eurasia (Cambridge University Press (2007).
28. Moorjani, P. et al. Genetic evidence for recent population mixture in India. Am. J. Hum. Genet. 93, 422-438 (2013).
29. Metspalu, M. et al. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am. J. Hum. Genet. 89, 731-744 (2011).
30. Yang, D. Y., Eng, B., Waye, J. S., Dudar, J. C. and Saunders, S. R. Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am. J. Phys. Anthropol. 105, 539-543 (1998).
31. Meyer, M. and Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, db.prot5448 (2010).
32. Rohland, N., Siedel, H. and Hofreiter, M. A rapid column-based ancient DNA extraction method for increased sample throughput. Mol. Ecol. Resour. 10, 677-683 (2010).
33. Bollongino, R. et al. 2000 years of parallel societies in Stone Age Central Europe. Science 342, 479-481 (2013).
34. Fortes, G. G. and Paijmans, J. L. A. Analysis of whole mitogenomes from ancient samples. Methods Mol. Biol. 1347, 179-195 (2015).
35. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10-12 (2011).
36. Briggs, A. W. et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA 104, 14616-14621 (2007).
37. Brotherton, P. et al. Novel high-resolution characterization of ancient DNA reveals C4U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 35, 5717-5728 (2007).
38. Li, H. and Durbin, R. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
39. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
40. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
41. Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F. and Orlando, L. mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682-1684 (2013).
42. Sánchez-Quinto, F. et al. Genomic affinities of two 7,000-year-old Iberian hunter-gatherers. Curr. Biol. 22, 1494-1499 (2012).
43. Skoglund, P., Storå, J., Götherström, A. and Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477-4482 (2013).
44. Jostins, L. et al. YFitter: Maximum likelihood assignment of Y chromosome haplogroups from low-coverage sequence data. Preprint at http://arxiv.org/abs/1407.7988 (2014).
45. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
46. Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156-2158 (2011).
47. Skoglund, P. et al. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336, 466-469 (2012).
48. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43-49 (2013).
49. - 1000 Genomes Project Consortium et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012).
50. Hart, K. L. et al. Improved eye- and skin-color prediction based on 8 SNPs. Croat. Med. J. 54, 248-256 (2013).
51. Walsh, S. et al. The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA. Forensic Sci. Int. Genet. 7, 98-115 (2013).