Genomic Sequencing of Pleistocene Cave Bears:

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.

Mitochondrial DNA is plentiful because cells are stuffed to the brim with mitochondria, but it isn't much to work with in terms of quantity of data and it is only a matrilineage (the lack of a lot of sequence means that deep time depth is problematic because of turnover at all the base pairs). This piece in the Scientific American makes clear the relevance to human evolution, we could actually get functional if some autosomal stretches could be extracted, see if MC1R jumped from Neandertals (OK, that's aiming high). PCR, microarrays, distributed computing, so much change in 15 years. Let's see what the future holds.

Related: Ancient DNA comes of age.