Preemptively following this early online release in PLoS, comes this paper published just now in PNAS, “Patterns of damage in genomic DNA sequences from a Neandertal.” From the abstract, what I can tell is the authors are defending,”Hey, don’t worry we know where and what the damages are. And that’s okay, because we still have reliable sequences!”
Here’s the abstract,
“High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.”
I don’t yet have access to the paper because my school’s library hasn’t updated access to issue number 37 of their year’s volume of the Proceedings of the National Academy of Sciences. But once I do get my hands on the paper, expect a much thorough review of it.