Collagen of ancient bones gives an indication of endogenous DNA preservation based on next-generation sequencing technology

Abstract

Ancient genome analysis has become an indispensable tool in studies of human population history and evolution since the breakthrough of whole-genome sequencing technology. The problem remains, however, that ancient genomes cannot be analyzed without crushing non-small pieces of precious specimens; moreover, in many cases, there is insufficient DNA remaining in the pieces of sample to obtain whole-genome sequences. In previous studies, therefore, a couple of indicators (e.g. racemization ratios) have been proposed to estimate the endogenous DNA in ancient samples. However, these studies have used polymerase chain reaction (PCR) to test whether endogenous DNA remains, but this has proved inadequate because the success or failure of PCR amplification does not necessarily reflect the DNA remaining. To assess the amount of endogenous DNA, we use the ratios of reads generated by next-generation sequencing (NGS) mapped to the human reference genome sequence. We investigated 40 human remains excavated from three shell-mound sites of the late to final Jomon culture. The associations between the environmental/molecular factors and the mapping ratios (MRs) were examined. There were no significant associations between the environmental factors and MRs, or between the collagen residual ratios (CRRs) and the MRs. However, we found a significant association between CRRs in rib bones and MRs. The weight of bone required to measure residual collagen is much less than that required to obtain the DNA necessary for NGS analysis, and the process of measuring CRRs is always involved in dating. Hence, we propose the collagen in the ribs as a good indicator for successful ancient genome analyses.