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James P. Noonan,1,2Michael Hofreiter,3Doug Smith,1James R. Priest,2Nadin Rohland,3Gernot Rabeder,4Johannes Krause,3J. Chris Detter,1,5Svante Pääbo,3Edward M. Rubin1,2*
Despite the greater information content of genomic DNA, ancientDNA studies have largely been limited to the amplification ofmitochondrial sequences. Here we describe metagenomic librariesconstructed with unamplified DNA extracted from skeletal remainsof two 40,000-year-old extinct cave bears. Analysis of 1 megabaseof sequence from each library showed that despite significantmicrobial contamination, 5.8 and 1.1% of clones contained cavebear inserts, yielding 26,861 base pairs of cave bear genomesequence. Comparison of cave bear and modern bear sequencesrevealed the evolutionary relationship of these lineages. Themetagenomic approach used here establishes the feasibility ofancient DNA genome sequencing programs.
1 United States Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. 2 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. 3 Max Planck Institute for Evolutionary Anthropology, Leipzig, D-04103, Germany. 4 Institute of Paleontology, University of Vienna, Vienna, A-1010 Austria. 5 Biosciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Published online 2 June 2005
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* To whom correspondence should be addressed. E-mail: emrubin{at}lbl.gov
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1 megabase of sequence from each library showed that despite significant microbial contamination, 5.8 and 1.1% of clones contained 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 used here establishes the feasibility of ancient DNA genome sequencing programs. 
