Improving access to endogenous DNA in ancient bones and teeth.

Area of Science:

• Paleogenomics
• Molecular Biology
• Archaeological Science

Background:

• Ancient DNA (aDNA) research is limited by poor DNA preservation in archaeological samples.
• Endogenous DNA is often a minor fraction of total DNA in extracts, hindering efficient sequencing.
• Shotgun sequencing of ancient samples is inefficient due to low endogenous DNA content.

Purpose of the Study:

• To improve the yield of endogenous DNA from ancient bones and teeth.
• To enhance the efficiency of ancient genomic research.
• To establish new standard protocols for aDNA extraction.

Main Methods:

• Enzymatic pre-digestion of powdered ancient bone samples using EDTA.
• Optimization of pre-digestion time (30 minutes to 6 hours).
• Targeted extraction of DNA from the outer layer of ancient tooth roots.

Main Results:

• A 2.7-fold average increase in endogenous DNA was observed after a 1-hour pre-digestion.
• Brief pre-digestion (15-30 minutes) improved DNA yield in 16 out of 21 samples.
• Targeting tooth roots yielded up to 14 times more endogenous DNA compared to inner dentine.

Conclusions:

• A brief enzymatic pre-digestion step should be implemented as a standard procedure in aDNA extraction.
• Targeting specific parts of teeth, like the outer roots, can maximize endogenous DNA recovery.
• These methods increase the number of ancient samples suitable for genome-scale characterization.