Optimized DNA sampling of ancient bones using Computed Tomography scans.

Area of Science:

• Ancient DNA research
• Palaeogenomics
• Biomolecular archaeology

Background:

• Ancient bone samples are often >99% contaminant microbial DNA, limiting palaeogenomic studies.
• Previous methods to reduce contaminant DNA have shown variable success.
• Identifying optimal sampling locations within ancient bones is crucial for maximizing endogenous DNA recovery.

Purpose of the Study:

• To develop a simple, highly effective method for increasing the proportion of endogenous DNA from ancient bone samples.
• To leverage computed tomography (CT) scanning for identifying optimal bone sampling sites.
• To improve the efficiency and reduce the cost of palaeogenomic analyses.

Main Methods:

• Computed tomography (CT) scanning was employed to identify the densest bone regions.
• Targeted sampling focused on these dense regions, particularly the outermost layer of long bones.
• Compared endogenous DNA content from targeted dense regions versus softer, trabecular bone.

Main Results:

• CT scanning accurately identified dense regions in petrous and long bones suitable for sampling.
• Targeted sampling of the outermost dense layer of long bones yielded up to a 50-fold increase in endogenous DNA proportion.
• Increased endogenous DNA proportion did not reduce absolute endogenous molecule recovery and is applicable across various bone types, ages, and species.

Conclusions:

• Computed tomography (CT) guided targeted bone sampling is a highly effective method to enrich for endogenous DNA in palaeogenomic studies.
• This technique significantly reduces contaminant DNA, thereby lowering sequencing costs and improving data quality.
• The method's consistency and broad applicability are expected to greatly advance the study of ancient populations and species.