Experts in ancient DNA from McMaster University (Canada) have teamed up with genome researchers from Penn State University (USA) for the investigation of permafrost bone samples from Siberia. The project also involved paleontologists from the American Museum of Natural History (USA) and researchers from Russia, the United Kingdom, France, and Germany. The researchers' report on the first genomic sequences from a woolly mammoth will be published on 22 December 2005 by the journal Science on the Science Express website, <http://www.sciencexpress.org>. This majestic mammal roamed grassy plains of the Northern Hemisphere until it became extinct about 10,000 years ago. The scientific breakthrough allows for the first time comparion of this ancient species with today's populations of African and Indian elephants, not just at the level of mitochondrial sequences, but also encompassing information from the nuclear genome.
Analyzing organellar DNA from mitochondria has been the only method of studying ancient DNA in the past, as it is more tractable due to its 1000-fold higher copy number per cell. 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. In contrast, most hereditary information is organized on chromosomes located in the cell's nucleus (nuclear DNA). A mammoth was chosen for 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.
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 jaws. The bone material used in this study is approximately 28,000 years old, as was shown by beta-carbon dating analysis. 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 computational approach to demonstrate that an unprecedented 50 perecent of the bone DNA was indeed mammoth DNA, while the remaining genetic material was shown to belong to microorganisms living the tundra soil.
The study indicates that any organism that has been trapped in frozen ice or a permafrost environment for up to one million years will be an open book to the researchers. The search is now on for more specimens from plant, animal, and man that can illuminate the route evolution took on its way from the past to the present, and that can perhaps clarify the role environmental changes did play in the extinction of an entire species.
Initial funding for this study was provided by McMaster University, The Natural Sciences and Engineering Research Council of Canada, and Penn State University. The researchers now 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.
IMAGES:
High-resolution images are on the web at http://www.science.psu.edu/alert/Schuster12-2005.htm.
CONTACTS:
Jane Christmas (PIO at McMaster University): phone (+1) 905-525-9140 ext. 27988, fax (+1) 905-521-1504, e-mail chrisja@mcmaster.ca
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
Hendrik N. Poinar: phone (+1) 905 525 -9140 x 26331, cell phone (+1) 905 741 0896, e-mail poinarh@mcmaster.ca
Stephan C. Schuster: phone (+1) 814 863 9278, cell phone (+1) 814 441 3513, e-mail scs@bx.psu.edu
Webb Miller: phone (+1) 814 865 4551, e-mail webb@bx.psu.edu
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 Auch7, 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
Journal
Science