Date of Award
Doctor of Philosophy
R. Alexander Bentley
David G. Anderson, Bridget Algee-Hewitt, Dawnie Wolfe Steadman, Benjamin Auerbach, James Fordyce
In forensic and archaeological applications, degraded DNA presents challenges during extraction, amplification, and analysis. Many of these issues can be addressed through the application of next-generation sequencing (NGS) techniques, including maximizing yields of fragmented DNA and identifying contaminant DNA. NGS is prompting a convergence between ancient and forensic genetic methods along several avenues, including DNA extraction. This dissertation discusses the convergence of extraction techniques contextualized within validation studies of ancient and modern DNA research.Two validation studies are presented. The first study validates and explores the impact of a non-destructive DNA extraction technique developed by Bolnick and colleagues (2012). The “non-destructive” (Bolnick) DNA extraction technique yields both mitochondrial and nuclear DNA. While the teeth tested remained macroscopically intact, there was loss of tooth microstructure in the tooth root and enamel, shown through treated vs. untreated weights and histological analysis. Scanning electron microscopy (SEM) results showed minimal staining of the tooth. There were no significant carbon or oxygen isotopic difference between treated and untreated teeth. The damage characterized shows that the protocol is minimally destructive but may still be of interest to stakeholders desiring maintenance of macroscopic, but not microscopic, integrity.The second study focuses on the quantity and quality of DNA extracted from post-mortem blood samples stored on untreated blood cards. Short-tandem repeats (STRs) typed from the cards are used for ancestry-based analysis. The study validated two different hypotheses: 1) cadaveric blood stored on untreated blood cards yields enough DNA for typing of STRs and 2) STRs typed from blood cards yield geographic ancestry information. Results of the second case study indicate that post-mortem interval impacts the DNA quality of samples extracted from untreated blood cards. Tri-hybrid ancestry and admixture analysis indicate that the original thirteen CODIS loci have utility in estimating geographic ancestry.These validation studies show the complications of working with degraded DNA in both ancient and forensic contexts. NGS approaches provide an opportunity in both fields to move beyond traditional markers to type expansive regions of the genome for both subfields and provides a way of addressing many issues of degraded DNA facing ancient and forensic researchers.
West, Frankie Lane, "From Ancient DNA to Forensic Genetics: Validation Studies in Degraded DNA. " PhD diss., University of Tennessee, 2019.