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Originally published in Science Express on 20 December 2005
Science 20 January 2006:
Vol. 311. no. 5759, pp. 392 - 394
DOI: 10.1126/science.1123360
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Reports

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Hendrik N. Poinar,1,2,3* Carsten Schwarz,1,2 Ji Qi,4 Beth Shapiro,5 Ross D. E. MacPhee,6 Bernard Buigues,7 Alexei Tikhonov,8 Daniel H. Huson,9 Lynn P. Tomsho,4 Alexander Auch,9 Markus Rampp,10 Webb Miller,4 Stephan C. Schuster4*

We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics.

1 McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
2 Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
3 Department of Pathology and Molecular Medicine, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada.
4 Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA.
5 Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK.
6 Division of Vertebrate Zoology/Mammalogy, American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024, USA.
7 #2 Avenue de la Pelouse, F-94160 St. Mandé, France.
8 Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.1, Saint Petersburg 199034, Russia.
9 Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany.
10 Garching Computing Center (RZG), Boltzmannstrasse 2, D-85748 Garching, Germany.

* To whom correspondence should be addressed. E-mail: poinarh{at}mcmaster.ca (H.N.P.); scs{at}bx.psu.edu (S.C.S.)

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