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 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 website. 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.
"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 1000-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.
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