Nuclear copies of mitochondrial genes: another problem for ancient DNA
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The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.
KeywordsNumt aDNA Sundasciurus Mitochondria Universal primers
Samples were kindly provided by the National Museum of Natural History ‘Naturalis’ (formerly Rijksmuseum van Natuurlijke Historie), Leiden, The Netherlands; the Natural History Museum, London; and the United States National Museum of Natural History, Smithsonian Institution. This project was funded by the Smithsonian Restricted Endowment Walcott Fund and the Swedish Research Council. Logistical support was provided by the Center for Conservation and Evolutionary Genetics, National Zoological Park, Smithsonian Institution, USA.
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