Scientists Sequence DNA of Woolly Mammoth

Genomicists Webb Miller and Stephan C. Schuster in front of the Roche / 454 Life Sciences' Genome Sequencer 20 System that was used to sequence mammoth nuclear DNA. Credit: Penn State University

A team of genome researchers at Penn State University and experts in ancient DNA at McMaster University in Canada has obtained the first genomic sequences from a woolly mammoth, a mammal that roamed the grassy plains of the Northern Hemisphere until it became extinct about 10,000 years ago. The team's research on bones preserved in Siberian permafrost will be published on 22 December 2005 by the journal Science on the Science Express Web site. The project also involved paleontologists from the American Museum of Natural History (USA) and researchers from Russia, the United Kingdom, France, and Germany.

"We demonstrated that 50 percent of the total DNA extracted from the bone was mammoth," says Stephan C. Schuster, associate professor at Penn State’s Center for Comparative Genomics and Bioinformatics. "This allowed us to compare hereditary information from the cell’s nucelus of today's African elephants with the one from this ancient species."

The project became possible through the discovery of exceptionally well preserved remains of a mammoth skeleton in the permafrost soil of northern Siberia, in combination with a novel high-throughput sequencing technique that could cope with the heavily fragmented DNA retrieved from the organism's mandible, its jaw bone. "The bone material used in this study is approximately 28,000 years old, as was shown by beta carbon dating analysis," said Hendrik N. Poinar, associate professor of anthropology at McMaster University. "This was a surprising finding, as it demonstrated that the analyzed material was frozen for more than 10,000 years before the maximum of the last ice age." The research team used a comparative computational approach to demonstrate that an unprecedented large percentage of the bone DNA was indeed mammoth DNA, while the remaining genetic material was shown to belong to microorganisms and plants living the tundra soil.

Large numbers of tusks in the permafrost museum in Khatanga demonstrate the abundance mammoth once had in the Northern hemisphere. Credit: Debi Poinar, McMaster University

"Analyzing DNA from the organelles of mitochondria has been the only method of studying ancient DNA in the past, as it is more tractable due to its 1,000-fold higher copy number per cell," Schuster explains. However, the mitochondrial genome codes for only a tiny fraction of an organism's genetic information — 0.0006 percent in the case of a mammal. "We focused on sequencing nuclear DNA in this study because most hereditary information is organized on chromosomes located in the cell's nucleus," Schuster says.

A mammoth was chosen for the study, in part, because of its close evolutionary relationship to the African elephant, whose nuclear DNA sequence has been made publicly available by the Broad Institute in Cambridge, Massachusetts (USA). Using comparisons with elephant DNA, the researchers identified 13-million base pairs as being nuclear DNA from the mammoth, which they showed to be 98.5 percent identical to nuclear DNA from an African elephant.

Collaborator Webb Miller of Penn State believes the study indicates that any organism conserved in frozen ice or a permafrost environment will be an open book to the researchers. The search is now on for more specimens from animal, plant, and man that can illuminate the route evolution took on its way from the past to the present, and can clarify the role that environmental changes may have played in the extinction of an entire species.

"We currently are seeking funding for the completion of the mammoth-genome sequence and hope to conduct detailed comparative studies that include the genomes of African and Indian elephants," Schuster says.

Initial funding for this study was provided by McMaster University, The Natural Sciences and Engineering Research Council of Canada, and Penn State University.

CONTACTS:

Barbara Kennedy (PIO at Penn State University): phone (+1) 814-863-4682, fax (+1) 814-863-2246, cell phone (+1) 814-883-6930, e-mail science@psu.edu

Stephan C. Schuster: phone (+1) 814-863-9278, e-mail scs@bx.psu.edu

Webb Miller: phone (+1) 814-865-4551, e-mail webb@bx.psu.edu

Jane Christmas (PIO at McMaster University): phone (+1) 905-525-9140 ext. 27988, fax (+1) 905-521-1504, e-mail  chrisja@mcmaster.ca

Hendrik N. Poinar: phone (+1) 905-525 –9140 x 26331, cell phone (+1) 905-741-0896, e-mail poinarh@mcmaster.ca

TITLE AND AUTHORS OF RESEARCH PAPER

"Metagenomics to paleogenomics: Large scale sequencing of Mammoth DNA"

* Authors to whom correspondence should be addressed are Hendrik N. Poinar and Stephan C. Schuster.

Hendrik N. Poinar1*, Carsten Schwarz1, Ji Qi2, Beth Shapiro3, Ross D. E. MacPhee4, Bernard Buigues5, Alexei Tikhonov6, Daniel Huson7, Lynn P. Tomsho2, Alexander Auch2, Markus Rampp8, Webb Miller2 and Stephan C. Schuster2*.

1. McMaster ancient DNA center, Department of Anthropology, Pathology & Molecular Medicine, McMaster University, 1280 Main St. West. Hamilton ON. L8S 4L9 Canada.

2. Penn State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, PA 16802, USA

3. Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, South Parks Road, Oxford, OX1 3PS, UK

4. Division of Vertebrate Zoology/Mammalogy American Museum of Natural History, 79th Street and Central Park West, New York, NY 10024 USA

5. #2 Avenue de la Pelouse, F- 94160 St Mandé France.

6. Zoological Institute, Russian Academy of Sciences, Universitetskaya nab.1, Saint-Petersburg 199034, Russia.

7. Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany

8. Garching Computing Center (RZG), Boltzmannstr. 2, D-85748 Garching, Germany

© Debi Poinar, McMaster University 

Paleontologists Alexei Tikhonov, Hendrik N. Poinar, Ross D. E. MacPhee, and Clair Flemming in the ice cave.

© Debi Poinar, McMaster University 

Permafrost ice cave in Khatanga, Siberia.

© Debi Poinar, McMaster University 

A frozen mammoth skull in the ice cave displays its excellent state of preservation. 

© Debi Poinar, McMaster University 

Paleontologists Hendrik N. Poinar and Ross D. E. MacPhee taking a sample from a permafrost bone.