Computational challenges in the analysis of ancient DNA
1 Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
2 Evolutionary Biology and Ecology, Department of Biology, University of York, York YO10 5YW, UK
Genome Biology 2010, 11:R47 doi:10.1186/gb-2010-11-5-r47Published: 6 May 2010
High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.