An article published in Genome Biology assesses the pitfalls of sequencing ancient DNA and presents a new approach for improved identification of ancient DNA sequences.

The DNA sequence of extinct species are of enormous value in determining evolutionary relationships to living species. However, ancient DNA from fossil is notoriously difficult to sequence due to the presence of bacterial contamination and DNA damage. Kay Prüfer and colleagues at the Max-Planck Institute for Evolutionary Anthropology investigated the biases inherent in short read sequencing of ancient DNA samples with an analysis of Neandertal (Homo neanderthalensis) DNA, generated as part of the Neandertal genome project, from 38,000-year-old fossil bone. The full draft Neandertal genome sequence is published today in Science by the Neandertal Genome Analysis Consortium.

To identify the endogenous Neandertal sequence from the contaminating bacterial sequences Prüfer and colleagues perform pairwise comparisons of the sequence data to the genomes of  closely related living primate and mammalian species. The authors discuss other ancient extinct species to which their approach for ancient DNA shotgun sequencing could be applied, such as mammoth, cave bear, sabre tooth cat and  ground sloth. It could also be used to study living species when no reference genome sequence is available.

Read the Prüfer and colleagues method here in Genome Biology.