The persistence, degradation, and application of human DNA recovered from soil
- WCU Author/Contributor (non-WCU co-authors, if there are any, appear on document)
- Hannah Lynn Noel (Creator)
- Institution
- Western Carolina University (WCU )
- Web Site: http://library.wcu.edu/
- Advisor
- Frankie West
Abstract: The dynamics of the persistence of human DNA in soil are poorly understood, though increasingly crucial to genomics. Human DNA recovered from soil and sediments can be used in identifying the presence of human burial and decomposition sites as well as in paleoanthropological contexts to support phylogenetic research. To date, studies on human DNA persistence in soil have focused on the recovery and quantity of DNA in soil rather than the taphonomic processes underlying its persistence. Given these gaps in knowledge on how environmental factors influence the persistence of human DNA in soil, this experiment aims to discover trends between extrinsic factors (e.g., temperature, precipitation, body moisture) and the quantity and quality of DNA recoverable from soil following the surface-level decomposition of three body donors for eleven weeks. Nuclear DNA (nuDNA) was quantified via Quantifiler™ Trio DNA Quantification Kit while mitochondrial DNA (mtDNA) was quantified using the Kavlick triplex qPCR protocol to determine the duration of DNA persistence in soil, determine quality through degradation indices, and to determine if environmental factors had an effect on the quantity of DNA within the soil. This experiment also explores the potential application of soil-derived in human identification work by using next-generation sequencing (NGS) to analyze concordance between sample and donor reference profiles. nuDNA was sequenced using the ForenSeq™ DNA Signature Prep Kit and the mitochondrial genome was sequenced using the ForenSeq™ mtDNA Whole Genome Kit, which were both ran on the MiSeq FGx™ Sequencing System and compared to donor reference profiles. Current results suggest that human nuDNA can persist in small quantities within the soil for up to six weeks, while mtDNA is able to persist for the entire eleven-week period. mtDNA was also a more viable route for human identification via soil extracts, as haplogroup determinations coincide with donor reference haplogroups for at least three weeks into the decomposition period. Time into the decomposition period, temperature, and total body score all have a significant effect on the quantity of DNA within the soil, though some results suggest moisture may play a role in DNA persistence and degradation. However, further research needs to be done at multiple locations across various seasons to grasp the nuance behind the role of environmental factors in the mechanisms driving DNA persistence within soil. The results of this aim to encourage future works involving the persistence of DNA in soil and its utility in forensic and anthropological contexts.
The persistence, degradation, and application of human DNA recovered from soil
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Created on 7/1/2023
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Additional Information
- Publication
- Thesis
- Language: English
- Date: 2023
- Keywords
- DNA persistence, forensic genomics, soil taphonomy
- Subjects
- DNA
- Genomics
- Forensic genetics
- Taphonomy
- Soils