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MBE Advance Access published online on July 24, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn163
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

The effect of ancient DNA damage on inferences of demographic histories.

Erik Axelsson1, Eske Willerslev1, M. Thomas P. Gilbert1 and Rasmus Nielsen1,2

1 Department of Biology, Evolutionary Biology, Copenhagen University Universitetsparken 15,DK-2100 Copenhagen Ø, Denmark
2 Departments of Biology and Statistics, UC-Berkeley, VLSB 4161, Berkeley 94720, CA, USA

Corresponding author: Erik Axelsson, Mailing address: Department of Biology, Evolutionary Biology, Copenhagen University Universitetsparken 15,DK-2100 Copenhagen Ø, Denmark. Telephone number: 004535321338; Fax number: 004535321300, Email address: EAxelsson{at}bio.ku.dk

Received for publication May 9, 2008. Revision received June 19, 2008. Accepted for publication July 21, 2008.

The field of ancient DNA is casting new light on many evolutionary questions. However, problems associated with the post mortem instability of DNA may complicate the interpretation of ancient DNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include post mortem damage, and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We re-analyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus), and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of ancient DNA sequences, that do not accurately account for damage, should be interpreted with great caution.

Key Words: aDNA • genealogy • coalescent process • DNA damage • demography


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