Analysis of one million base pairs of Neanderthal DNA

Nature

Volumn 444, Issue 7117, 2006, Pages 330-336

  Green, Richard E ^a   Krause, Johannes ^a   Ptak, Susan E ^a   Briggs, Adrian W ^a   Ronan, Michael T ^b   Simons, Jan F ^b   Du, Lei ^b   Egholm, Michael ^b   Rothberg, Jonathan M ^b   Paunovic, Maja ^c   Pääbo, Svante ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b 454 Life Sciences ^*  (United States)

^c CROATIAN ACADEMY OF SCIENCES AND ARTS   (Croatia)

Author keywords

[No Author keywords available]

Indexed keywords

CONTAMINATION; DNA; GENES; GENETIC ENGINEERING; THROUGHPUT;

CHIMPANZEE GENOMES; DNA EXTRACTS; GENOME SEQUENCING; NEANDERTHAL FOSSIL;

HUMAN ENGINEERING;

CELL NUCLEUS DNA; MITOCHONDRIAL DNA; NUCLEOTIDE;

DNA; FOSSIL; FOSSIL RECORD; GENETIC ANALYSIS; GENOME; NEANDERTHAL;

ANTHROPOLOGY; ARTICLE; BASE PAIRING; CHIMPANZEE; COMPARATIVE GENE MAPPING; DNA DETERMINATION; DNA EXTRACTION; DNA SEQUENCE; FOSSIL; GENETIC POLYMORPHISM; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HOMINID; HUMAN; HUMAN GENOME; HUMAN VERSUS ANIMAL COMPARISON; NONHUMAN; PRIORITY JOURNAL;

HOMINIDAE; HOMINOIDEA; PAN TROGLODYTES;

EID: 33751077282     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature05336     Document Type: Article

References (50)

1. Bischoff, J. L. et al. The Sima de los Huesos hominids date to beyond U/Th equilibrium (>350 kyr) and perhaps to 400-500 kyr: New radiometric dates. J. Archaeol. Sci. 30, 275-280 (2003).
2. Hublin, J-J. (ed.) Climatic Changes, Paleogeography, and the Evolution of the Neandertals (Plenum Press, New York, 1998).
3. Franciscus, R. G. (ed.) Neanderthals (Oxford Univ. Press, Oxford, 2002).
4. Hublin, J. J., Spoor, F., Braun, M., Zonneveld, F. & Condemi, S. A late Neanderthal associated with Upper Palaeolithic artefacts. Nature 381, 224-226 (1996).
5. Krings, M. et al. Neandertal DNA sequences and the origin of modern humans. Cell 90, 19-30 (1997).
6. Krings, M., Geisert, H., Schmitz, R. W., Krainitzki, H. & Pääbo, S. DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl Acad. Sci. USA 96, 5581-5585 (1999).
7. Schmitz, R. W. et al. The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany. Proc. Natl Acad. Sci. USA 99, 13342-13347 (2002).
8. Ovchinnikov, I. V. et al. Molecular analysis of Neanderthal DNA from the northern Caucasus. Nature 404, 490-493 (2000).
9. Krings, M. et al. A view of Neandertal genetic diversity. Nature Genet. 26, 144-146 (2000).
10. Serre, D. et al. No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. 2, 313-317 (2004).
11. Orlando, L. et al. Revisiting Neandertal diversity with a 100,000 year old mtDNA sequence. Curr. Biol. 16, R400-R402 (2006).
12. Caramelli, D. et al. A highly divergent mtDNA sequence in a Neandertal individual from Italy. Curr. Biol. 16, R630-R632 (2006).
13. Lalueza-Fox, C. et al. Neandertal evolutionary genetics: mitochondrial DNA data from the Iberian peninsula. Mol. Biol. Evol. 22, 1077-1081 (2005).
14. Currat, M. & Excoffier, L. Modern humans did not admix with Neanderthals during their range expansion into Europe. PLoS Biol. 2, e421 (2004).
15. Stringer, C. Modern human origins: progress and prospects. Phil. Trans. R. Soc. Lond. B 357, 563-579 (2002).
16. Takahata, N., Lee, S. H. & Satta, Y. Testing multiregionality of modern human origins. Mol. Biol. Evol. 18, 172-183 (2001).
17. Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87 (2005).
18. Pääbo, S. et al. Genetic analyses from ancient DNA. Annu. Rev. Genet. 38, 645-679 (2004).
19. Greenwood, A. D., Capelli, C., Possnert, G. & Paabo, S. Nuclear DNA sequences from late Pleistocene megafauna. Mol. Biol. Evol. 16, 1466-1473 (1999).
20. Noonan, J. P. et al. Genomic sequencing of Pleistocene cave bears. Science 309, 597-599 (2005).
21. Rompler, H. et al. Nuclear gene indicates coat-color polymorphism in mammoths. Science 313, 62 (2006).
22. Poinar, H. N. et al. Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311, 392-394 (2006).
23. Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. & Pääbo, S. Ancient DNA. Nature Rev. Genet. 2, 353-359 (2001).
24. Malmstrom, H., Stora, J., Dalen, L., Holmlund, G. & Gotherstrom, A. Extensive human DNA contamination in extracts from ancient dog bones and teeth. Mol. Biol. Evol. 22, 2040-2047 (2005).
25. Pääbo, S. Human evolution. Trends Cell Biol. 9, M13-M16 (1999).
26. Poinar, H. N., Höss, M., Bada, J. L. & Pääbo, S. Amino acid racemization and the preservation of ancient DNA. Science 272, 864-866 (1996).
27. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
28. Stiller, M. et al. Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc. Natl Acad. Sci. USA 103, 13578-13584 (2006).
29. Pääbo, S. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc. Natl Acad. Sci. USA 86, 1939-1943 (1989).
30. Höss, M., Dilling, A., Currant, A. & Pääbo, S. Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc. Natl Acad. Sci. USA 93, 181-185 (1996).
31. Hofreiter, M., Jaenicke, V., Serre, D., Haeseler Av, A. & Pääbo, S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 29, 4793-4799 (2001).
32. International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
33. Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
34. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Wheeler, D. L. GenBank. Nucleic Acids Res. 34, D16-D20 (2006).
35. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
36. Beja, O. et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2, 516-529 (2000).
37. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
38. Ingman, M. & Gyllensten, U. mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res. 34, D749-D751 (2006).
39. Krause, J. et al. Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature 439, 724-727 (2006).
40. Kumar, S., Filipski, A., Swarna, V., Walker, A. & Blair Hedges, S. Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc. Natl Acad. Sci. USA 102, 18842-18847 (2005).
41. Patterson, N., Richter, D. J., Gnerre, S., Lander, E. S. & Reich, D. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441, 1103-1108 (2006).
42. Wall, J. D. Estimating ancestral population sizes and divergence times. Genetics 163, 395-404 (2003).
43. Yang, Z. & Yoder, A. D. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 48, 274-283 (1999).
44. Innan, H. & Watanabe, H. The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population. Mol. Biol. Evol. 23, 1040-1047 (2006).
45. Kaessmann, H., Wiebe, V., Weiss, G. & Pääbo, S. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nature Genet. 27, 155-156 (2001).
46. Yu, N., Jensen-Seaman, M. I., Chemnick, L., Ryder, O. & Li, W-H. Nucleotide diversity in gorillas. Genetics 166, 1375-1383 (2004).
47. Fischer, A., Pollack, J., Thalmann, O., Nickel, B. & Pääbo, S. Demographic history and genetic differentiation in apes. Curr. Biol. 16, 1133-1138 (2006).
48. Rannala, B. & Yang, Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656 (2003).
49. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
50. Hinds, D. A. et al. Whole genome patterns of common DNA variation in diverse human populations. Science 307, 1072-1079 (2005).