Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples.

Area of Science:

• Paleogenomics
• Molecular Biology
• Archaeological Science

Background:

• Ancient DNA (aDNA) studies frequently use degraded skeletal remains.
• DNA extraction protocols predominantly target bone and teeth, neglecting skin and hair.
• Degraded soft tissues like skin and fur yield fragmented DNA with low endogenous content.

Purpose of the Study:

• To evaluate and compare DNA extraction efficiencies from ancient skin and hair samples.
• To assess the performance of commercial and custom laboratory ancient DNA (aDNA) extraction methods.
• To identify optimal methods for recovering DNA from historical and archaeological soft tissues.

Main Methods:

• Comparison of two DNA extraction protocols: a commercial kit and a custom laboratory method.
• Application of protocols to hair and skin samples from museum specimens and Iron Age archaeological material.
• Analysis of DNA yield and quality, focusing on endogenous DNA content.

Main Results:

• Skin samples generally yielded more endogenous DNA than hair samples across both protocols.
• Both methods successfully recovered DNA from ancient soft tissues.
• The custom laboratory method demonstrated superior performance in DNA yield and quality compared to the commercial kit, attributed to the commercial binding buffer's limitations.

Conclusions:

• Skin is a viable source of ancient DNA (aDNA), often yielding more endogenous DNA than hair.
• Custom laboratory protocols may be more effective than commercial kits for extracting aDNA from degraded soft tissues.
• Further development of extraction methods is crucial for maximizing DNA recovery from challenging ancient samples.