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Open Access Short Report

Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

Sergi Vives12, M Thomas Gilbert3, Conchita Arenas1, Elena Gigli4, Oscar Lao5 and Carles Lalueza-Fox4*

Author Affiliations

1 Departament d'Estadística, Facultat de Biologia, Universitat de Barcelona, Avda. Diagonal 645, 08028 Barcelona, Spain

2 Statistics Department, Columbia University, 1255 Amsterdam Avenue, New York, NY 10027, USA

3 Department of Biology, Center for Ancient Genetics, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark

4 Institut de Biologia Evolutiva (CSIC-UPF), Dr. Aiguader 88, 08003 Barcelona, Spain

5 Department of Forensic Molecular Biology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands

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BMC Research Notes 2008, 1:40  doi:10.1186/1756-0500-1-40

Published: 10 July 2008

Abstract

Background

We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was restricted to C→T and G→A miscoding lesions (the predominant manifestation of post mortem damage) that are seen at a frequency of more than one clone among sequences from a single PCR, but do not represent the true endogenous sequence.

Findings

The data indicates an extreme bias towards C→T over G→A miscoding lesions (observed ratio of 67:2 compared to an expected ratio of 7:2), implying that the mtDNA Light strand molecule suffers proportionally more damage-derived miscoding lesions than the Heavy strand.

Conclusion

The clustering of Cs in the Light strand as opposed to the singleton pattern of Cs in the Heavy strand could explain the observed bias, a phenomenon that could be further tested with non-PCR based approaches. The characterization of the HVS1 hotspots will be of use to future Neandertal mtDNA studies, with specific regards to assessing the authenticity of new positions previously unknown to be polymorphic.