Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing

Abstract

Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.

Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting

“…Kirby et al (12) also used destructive sampling techniques to analyze a Koran and other objects. Teasdale et al (13) have recently reported genomic data from postmedieval parchment using, on average, 50 mg of parchment. In addition to the destructive nature of sampling, a further hidden cost of molecular analysis is adequate storage of extracted samples.…”

“…A notable proponent of follicle pattern analysis was Ryder (10), who used the technique to identify animal species; however, not all parchments had discernible follicle patterns, not every pattern could be identified, and paleographers have often been overconfident in their ability to discern species origin from such patterns. Protein (11,12) and DNA-based methods (13)(14)(15)(16)(17) potentially offer absolute determination of species but, until now, have had other limitations. Toniolo et al (11) analyzed 5 mg of parchment from the 13th-century "Marco Polo Bible" at the Biblioteca Medicea Laurenziana, and used peptide sequences to identify a single leaf as calfskin, although if more leaves had been analyzed the results may have revealed different species as was the case with the family's archival documents (Table S1).…”

Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material

“…The results presented in this article and the research described in literature (Burger et al, 2000;Teasdale et al, 2014) suggest that DNA present in historical parchments can be a good source of information about cultural heritage objects.…”

“…This could be attributed to the greater number of copies of mtDNA compared to that of nuclear DNA (nuDNA), as well as shorter product fragments that could facilitate further analyses (Bollongino et al, 2006;Vuissoz et al, 2007;Scheu et al, 2008;Stock et al, 2009;Rizzi et al, 2012). However, it must be emphasized that analyses based on ancient mitochondrial DNA may be more vulnerable to contamination than those involving genomic DNA (Teasdale et al, 2014). The cytochrome b sequence is often used with great success in aDNA analyses (Poulakakis et al, 2007;Campana et al, 2010;Pangallo et al, 2010).…”

“…In this study, we have analyzed the recovery of aDNA from parchment, one of the first surfaces for writing, which was developed and used by people throughout the centuries, and which determined cultural, artistic, and technological progress. At present, advanced research techniques, including aDNA testing, have rendered parchments as rich sources of data on the development of historical communities Pangallo et al, 2010;Teasdale et al, 2014). It must be emphasized, however, that the acquisition of functional DNA from parchment can be particularly difficult because of its considerable degradation caused by the animal skin preparation and parchment production processes (Poulakakis et al, 2007;Bower et al, 2010;Campana et al, 2010).…”