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Published Online June 2, 2005
Science DOI: 10.1126/science.1113485

Reports

Submitted on April 12, 2005
Accepted on May 26, 2005

Genomic Sequencing of Pleistocene Cave Bears

James P. Noonan 1, Michael Hofreiter 2, Doug Smith 3, James R. Priest 4, Nadin Rohland 2, Gernot Rabeder 5, Johannes Krause 2, J Chris Detter 6, Svante Pääbo 2, Edward M. Rubin 1*

1 US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
2 Max Planck Institute for Evolutionary Anthropology, Leipzig, D-04103, Germany.
3 US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
4 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
5 Institute of Paleontology, University of Vienna, Vienna, A-1010 Austria.
6 US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

* To whom correspondence should be addressed.
Edward M. Rubin , E-mail: emrubin{at}lbl.gov

Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to amplification of mitochondrial sequences. We describe metagenomic libraries constructed using unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of ~1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8% and 1.1% of clones contain cave bear inserts, yielding 26,861 base pairs of cave bear genome sequence. Comparison of cave bear and modern bear sequences revealed the evolutionary relationship of these lineages. The metagenomic approach employed here establishes the feasibility of ancient DNA genome sequencing programs.


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