Abstract
Many rare and valuable ancient specimens now carry the scars of ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for ancient DNA from bone.
Highlights
Ancient DNA studies are conducted upon an evergrowing number of species (Paabo et al 2004) and, increasingly, the move is away from phylogenetic studies that require few specimens and towards population genetics and phylogeographic research, which require tens to hundreds of specimens (e.g. Hofreiter et al 2004; Shapiro et al 2004)
Amino acid analysis fulfils the first condition as it requires less than 10 mg of bone, and in a pioneering investigation it was shown that DNA survival could be predicted by measuring the extent of aspartic acid racemization (AAR; Poinar et al 1996)
To resolve the question of the utility of D/L Asx as a screening tool for ancient DNA survival, we examined 91 bones for which both amino acid and DNA preservation were assessed via HPLC and PCR analyses, respectively
Summary
Ancient DNA studies are conducted upon an evergrowing number of species (Paabo et al 2004) and, increasingly, the move is away from phylogenetic studies that require few specimens and towards population genetics and phylogeographic research, which require tens to hundreds of specimens (e.g. Hofreiter et al 2004; Shapiro et al 2004). Such work often results in considerable physical damage to the ancient samples Set in this context, a screening method that does minimal damage to the samples and offers reasonable prediction of DNA survival—or, better still, amplification success—would be very valuable. Amino acid analysis fulfils the first condition as it requires less than 10 mg of bone, and in a pioneering investigation it was shown that DNA survival could be predicted by measuring the extent of aspartic acid racemization (AAR; Poinar et al 1996). We take advantage of two large ancient DNA datasets (Hofreiter et al 2004; Shapiro et al 2004) and assess the extent of racemization in animal bones in comparison with DNA amplification success.
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