The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans

Current Biology

Volumn 26, Issue 9, 2016, Pages 1241-1247

  Sankararaman, Sriram ^a,b   Mallick, Swapan ^c,d,e   Patterson, Nick ^d   Reich, David ^c,d,e  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANCESTRY GROUP; ANIMAL; BIOLOGICAL MODEL; DEMOGRAPHY; GENETICS; HOMO NEANDERTHALENSIS; HUMAN; HUMAN GENOME; TIME FACTOR;

ANIMALS; CONTINENTAL POPULATION GROUPS; DEMOGRAPHY; GENOME, HUMAN; HUMANS; MODELS, GENETIC; NEANDERTHALS; TIME FACTORS;

EID: 84975474808     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2016.03.037     Document Type: Article

References (24)

1. D. Reich, R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L. Johnson, and et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia Nature 468 2010 1053 1060
2. R.E. Green, J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H. Fritz, and et al. A draft sequence of the Neandertal genome Science 328 2010 710 722
3. Q. Fu, H. Li, P. Moorjani, F. Jay, S.M. Slepchenko, A.A. Bondarev, P.L. Johnson, A. Aximu-Petri, K. Prüfer, C. de Filippo, and et al. Genome sequence of a 45,000-year-old modern human from western Siberia Nature 514 2014 445 449
4. S. Sankararaman, N. Patterson, H. Li, S. Pääbo, and D. Reich The date of interbreeding between Neandertals and modern humans PLoS Genet. 8 2012 e1002947
5. A. Seguin-Orlando, T.S. Korneliussen, M. Sikora, A.S. Malaspinas, A. Manica, I. Moltke, A. Albrechtsen, A. Ko, A. Margaryan, V. Moiseyev, and et al. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years Science 346 2014 1113 1118
6. K. Prüfer, F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, and et al. The complete genome sequence of a Neanderthal from the Altai Mountains Nature 505 2014 43 49
7. J.D. Wall, M.A. Yang, F. Jay, S.K. Kim, E.Y. Durand, L.S. Stevison, C. Gignoux, A. Woerner, M.F. Hammer, and M. Slatkin Higher levels of neanderthal ancestry in East Asians than in Europeans Genetics 194 2013 199 209
8. M. Meyer, M. Kircher, M.T. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, and et al. A high-coverage genome sequence from an archaic Denisovan individual Science 338 2012 222 226
9. B. Vernot, and J.M. Akey Complex history of admixture between modern humans and Neandertals Am. J. Hum. Genet. 96 2015 448 453
10. P. Skoglund, and M. Jakobsson Archaic human ancestry in East Asia Proc. Natl. Acad. Sci. USA 108 2011 18301 18306
11. D. Reich, N. Patterson, M. Kircher, F. Delfin, M.R. Nandineni, I. Pugach, A.M. Ko, Y.C. Ko, T.A. Jinam, M.E. Phipps, and et al. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania Am. J. Hum. Genet. 89 2011 516 528
12. E. Huerta-Sánchez, X. Jin, Asan, Z. Bianba, B.M. Peter, N. Vinckenbosch, Y. Liang, X. Yi, M. He, M. Somel, and et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA Nature 512 2014 194 197
13. C. Jeong, G. Alkorta-Aranburu, B. Basnyat, M. Neupane, D.B. Witonsky, J.K. Pritchard, C.M. Beall, and A. Di Rienzo Admixture facilitates genetic adaptations to high altitude in Tibet Nat. Commun. 5 2014 3281
14. S. Sankararaman, S. Mallick, M. Dannemann, K. Prüfer, J. Kelso, S. Pääbo, N. Patterson, and D. Reich The genomic landscape of Neanderthal ancestry in present-day humans Nature 507 2014 354 357
15. B. Vernot, and J.M. Akey Resurrecting surviving Neandertal lineages from modern human genomes Science 343 2014 1017 1021
16. Juric, I., Aeschbacher, S., and Coop, G. (2015). The strength of selection against Neanderthal introgression. BioRxiv, doi: http://dx.doi.org/10.1101/030148.
17. Harris, K., and Nielsen, R. (2015). The genetic cost of Neanderthal introgression. BioRxiv, doi: http://dx.doi.org/10.1101/030148.
18. K. Prüfer, B. Muetzel, H.H. Do, G. Weiss, P. Khaitovich, E. Rahm, S. Pääbo, M. Lachmann, and W. Enard FUNC: a package for detecting significant associations between gene sets and ontological annotations BMC Bioinformatics 8 2007 41
19. C.S. Lai, S.E. Fisher, J.A. Hurst, F. Vargha-Khadem, and A.P. Monaco A forkhead-domain gene is mutated in a severe speech and language disorder Nature 413 2001 519 523
20. G. McVicker, D. Gordon, C. Davis, and P. Green Widespread genomic signatures of natural selection in hominid evolution PLoS Genet. 5 2009 e1000471
21. M. Currat, and L. Excoffier Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression Proc. Natl. Acad. Sci. USA 108 2011 15129 15134
22. D.C. Presgraves Sex chromosomes and speciation in Drosophila Trends Genet. 24 2008 336 343
23. T. Derrien, R. Johnson, G. Bussotti, A. Tanzer, S. Djebali, H. Tilgner, G. Guernec, D. Martin, A. Merkel, D.G. Knowles, and et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression Genome Res. 22 2012 1775 1789
24. J. Lafferty, A. McCallum, and F. Pereira Conditional random fields: probabilistic models for segmenting and labeling sequence data C.E. Brodley, A.P. Danyluk, Proceedings of the Eighteenth International Conference on Machine Learning 2001 Morgan Kaufmann Publishers 282 289