Mitochondrial DNA analysis of ancient hair shafts from the Dakhleh Oasis, Egypt : challenges and recommendations

Abstract

To date, there have been no previous reports in the literature on DNA extraction or analysis of ancient human hair. The hair shaft has an extraordinarily stable structure that enables it to remain unchanged for centuries and persist in the archaeological record. Hair shafts, in theory, should provide one of the best archives of mitochondrial DNA, since hair is well protected by the cuticle layer (anhydrotic) and is not subject to postmortem DNA destroying autolytic enzymes. In this thesis, the latest extraction and purification methodologies were tested on modem human and ancient Egyptian hair shafts. In addition, closer attention was paid to the structural components of hair, particularly keratin. PGR amplification of DNA retrieved from the ancient Egyptian hair shafts was limited in success. PCR inhibitors that co-purified with DNA extracted from the ancient hair shafts contributed to PCR failure. A variety of analytical techniques were used to identify the presence of PCR inhibitors present in the DNA extracts including Gaschromatography- Mass spectrometry (GC-MS), Secondary Ion Mass Spectrometry (SIMS), Raman Spectrometry and Induced Coupled Plasma (ICP) Spectrometry. Realtime PCR proved to be pivotal in the analysis of DNA from ancient Egyptian hair shafts. The preliminary Real-time PCR results indicate that mtDNA is present in low yet analyzable levels in ancient human hair shafts from two Kellis burials (K2 124, G 10-3). The use of Real-time PCR with the Gilbert et al (2004) method holds the greatest potential for future ancient DNA research.