Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the
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ORIGINAL PAPER
Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland Julia Elsner & Jörg Schibler & Michael Hofreiter & Angela Schlumbaum
Received: 13 November 2013 / Accepted: 22 September 2014 # The Author(s) 2014. This article is published with open access at Springerlink.com
Abstract Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the— inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact
Electronic supplementary material The online version of this article (doi:10.1007/s12520-014-0213-4) contains supplementary material, which is available to authorized users. J. Elsner (*) : J. Schibler : A. Schlumbaum Integrative Prehistory and Archaeological Science, University of Basel, Spalenring 145, 4055 Basel, Switzerland e-mail: [email protected] M. Hofreiter Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions. Keywords Ancient DNA . DNA preservation . Horse . Cave . Switzerland
Introduction The analysis of ancient DNA from archaeological specimens provides the unique opportunity to study genetic diversity at different time intervals of the past. Because of this, it is coveted not only in archaeology but also in other disciplines such as evolutionary, population and conservation genetics. However, progressive post mortem degradation limits the access to genetic information from sub-fossil material. The mechanisms of DNA decay, resulting in small amounts of highly fragmented and chemically modified molecules, have been intensively studied (e.g. Pääbo 1989; Lindahl 1993; Höss 1995; Hofreiter
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