Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

Abstract

Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.

Keywords: NGS; PCR; ancient DNA; methodological advances.

Figure 1

The relative proportion of studies discussed in this review (126 papers from 1988 to May 2017) targeting various alternative substrates for the recovery of ancient DNA. NHC: natural history collections.

Figure 2

Area chart displaying the proportion of studies utilizing various methods in the analysis of neglected substrates, demonstrating the rise of whole genome and metagenomic approaches following the emergence of NGS technologies (includes studies reviewed in this paper, from 1996 to May 2017). WGS: whole genome sequencing; PCR: polymerase chain reaction.