DESCRIPTION (provided by applicant): Comparative approaches for the annotation of mammalian genomes rely on sequences from extant taxa to identify functionally conserved elements and lineage-specific sequence changes. However, such analyses would benefit from ancient DNA sequence from extinct species. Previous ancient DNA studies have relied on mitochondrial rather than genomic DNA due to technical hurdles such as microbial contamination and degradation of ancient DNAs. This proposal outlines a way to surmount these hurdles through the development of methods for the construction, sequencing and analysis of small-insert ancient nuclear DNA libraries. These methods will be refined using abundant cave bear ancient DNA and then extended to Neandertal genomic DNA. Analysis of a pilot cave bear library indicates that ancient DNA sequences can be recovered using these methods. Cave bear genomic sequence will be used to assess the phylogeny of cave bear and modern bear species obtained with mitochondrial DNA. With our collaborators, who will provide ancient DNAs, we will then construct Neandertal ancient DNA libraries and recover Neandertal orthologs of rapidly evolving human genes involved in human traits such as language.