Sequencing and Analysis of Neanderthal Genomic DNA
Abstract
Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor ∼706,000 years ago, and that the human and Neanderthal ancestral populations split ∼370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.
Get full access to this article
View all available purchase options and get full access to this article.
Supplementary Material
References and Notes
1
P. Mellars, Nature432, 461 (2004).
2
F. H. Smith, E. Trinkaus, P. B. Pettitt, I. Karavanic, M. Paunovic, Proc. Natl. Acad. Sci. U.S.A.96, 12281 (1999).
3
M. Krings et al., Cell90, 19 (1997).
4
M. Krings et al., Proc. Natl. Acad. Sci. U.S.A.96, 5581 (1999).
5
S. Pääbo et al., Annu. Rev. Genet.38, 645 (2004).
6
D. Serre et al., PLoS Biol.2, e57 (2004).
7
M. Currat, L. Excoffier, PLoS Biol.2, e421 (2004).
8
S. G. Tringe et al., Science308, 554 (2005).
9
S. G. Tringe, E. M. Rubin, Nat. Rev. Genet.6, 805 (2005).
10
J. P. Noonan et al., Science309, 597 (2005).
11
M. Margulies et al., Nature437, 376 (2005).
12
H. N. Poinar et al., Science311, 392 (2006).
13
Materials and methods are available as supporting material on Science Online.
14
S. F. Altschul et al., Nucleic Acids Res.25, 3389 (1997).
15
Chimpanzee Sequencing and Analysis Consortium, Nature437, 69 (2005).
16
M. Hofreiter et al., Nucleic Acids Res.29, 4793 (2001).
17
S. Kumar, A. Filipski, V. Swarna, A. Walker, S. B. Hedges, Proc. Natl. Acad. Sci. U.S.A.102, 18842 (2005).
18
N. Patterson, D. Richter, S. Gnerre, E. Lander, D. Reich, Nature, in press; published online 17May2006.
19
The International HapMap Consortium et al., Nature437, 1299 (2005).
20
B. F. Voight et al., Proc. Natl. Acad. Sci. U.S.A.102, 18508 (2005).
21
A. M. Adams, R. R. Hudson, Genetics168, 1699 (2004).
22
I. McDougall et al., Nature433, 733 (2005).
23
V. Plagnol, J. D. Wall, PLoS Genet., in press.
24
S. Bashiardes et al., Nat. Methods2, 63 (2005).
25
P. Mellars, Nature439, 931 (2006).
26
Neanderthal sequences reported in this study have been deposited in GenBank under accession numbers DX935178 to DX936503. We thank E. Green, M. Lovett, and members of the Rubin, Pääbo, and Pritchard laboratories for insightful discussions and support. J.P.N. was supported by NIH National Research Service Award fellowship 1-F32-GM074367. G.C. and S.K. were supported by grant R01 HG002772-1 (NIH) to J.K.P. This work was supported by grant HL066681, NIH Programs for Genomic Applications, funded by the National Heart, Lung and Blood Institute; and by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract number DE-AC02-05CH11231.
(0)eLetters
eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.
Log In to Submit a ResponseNo eLetters have been published for this article yet.
Information & Authors
Information
Published In
Science
Volume 314 | Issue 5802
17 November 2006
17 November 2006
Copyright
American Association for the Advancement of Science.
Submission history
Received: 16 June 2006
Accepted: 17 August 2006
Published in print: 17 November 2006
Notes
Supporting Online Material
www.sciencemag.org/cgi/content/full/314/5802/1113/DC1
Materials and Methods
Figs. S1 to S6
Tables S1 to S12
References
Authors
Metrics & Citations
Metrics
Article Usage
Altmetrics
Citations
Cite as
- James P. Noonan et al.
Export citation
Select the format you want to export the citation of this publication.
Cited by
- Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal, Cureus, (2023).https://doi.org/10.7759/cureus.35721
- Balancing selection on genomic deletion polymorphisms in humans, eLife, 12, (2023).https://doi.org/10.7554/eLife.79111
- Proteomics and Genomics as Identification Procedures in Human Anthropology, Gene, Cell and Tissue, In Press, In Press, (2022).https://doi.org/10.5812/gct-131402
- Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598, Biology, 11, 8, (1177), (2022).https://doi.org/10.3390/biology11081177
- Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA, Frontiers in Genetics, 13, (2022).https://doi.org/10.3389/fgene.2022.1000123
- Metagenomics: A New Direction in Ecology, Biology Bulletin, 48, S3, (S107-S117), (2022).https://doi.org/10.1134/S1062359022010150
- Escherichia Coli: What Is and Which Are ? , Molecular Biology and Evolution, 40, 1, (2022).https://doi.org/10.1093/molbev/msac273
- Extended longevity of DNA preservation in Levantine Paleolithic sediments, Sefunim Cave, Israel, Scientific Reports, 12, 1, (2022).https://doi.org/10.1038/s41598-022-17399-2
- Patterns of genomic diversity and linkage disequilibrium across the disjunct range of the Australian forest tree Eucalyptus globulus, Tree Genetics & Genomes, 18, 3, (2022).https://doi.org/10.1007/s11295-022-01558-7
- Worldwide research trends on Neanderthals, Journal of Quaternary Science, 38, 2, (208-220), (2022).https://doi.org/10.1002/jqs.3476
- See more
Loading...
View Options
Check Access
Log in to view the full text
AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.
- Become a AAAS Member
- Activate your AAAS ID
- Purchase Access to Other Journals in the Science Family
- Account Help
Log in via OpenAthens.
Log in via Shibboleth.
More options
Purchase digital access to this article
Download and print this article for your personal scholarly, research, and educational use.
Buy a single issue of Science for just $15 USD.