Genomic Sequencing of Pleistocene Cave Bears
Abstract
Despite the greater information content of genomic DNA, ancient DNA studies have largely been limited to the amplification of mitochondrial sequences. Here we describe metagenomic libraries constructed with unamplified DNA extracted from skeletal remains of two 40,000-year-old extinct cave bears. Analysis of ∼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.
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References and Notes
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We cannot formally exclude alternative topologies, given the small number of nucleotide sites in the analysis and the limited divergence among these bear species, which also accounts for the low percent support for the internal nodes. Damage-induced substitutions in cave bears also perturb the phylogeny. The topology with the next-best likelihood score has cave bears as the outgroup to the modern bears due to an excess of GC–AT substitutions in several library CB2 sequences.
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Data have been deposited into GenBank with accession numbers CZ551658 to CZ552046. We thank members of the Rubin and Pääbo laboratories for insightful discussions and support. This work was performed under the auspices of the U.S. Department of Energy's Office of Science Biological and Environmental Research Program and by the University of California; Lawrence Berkeley National Laboratory; Lawrence Livermore National Laboratory; and Los Alamos National Laboratory under contract numbers DE-AC03-76SF00098, W-7405-Eng-48, and W-7405-ENG-36, respectively, with support from NIH grants U1 HL66681B and T32 HL07279 and at the Max Planck Institute for Evolutionary Anthropology.
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Published In
Science
Volume 309 | Issue 5734
22 July 2005
22 July 2005
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American Association for the Advancement of Science.
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Submission history
Received: 12 April 2005
Accepted: 26 May 2005
Published in print: 22 July 2005
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