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Computational challenges in the analysis of ancient DNA

Kay Prüfer1*, Udo Stenzel1, Michael Hofreiter12, Svante Pääbo1, Janet Kelso1 and Richard E Green1

Author Affiliations

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

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Genome Biology 2010, 11:R47  doi:10.1186/gb-2010-11-5-r47

Published: 6 May 2010

Abstract

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.