Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.

Area of Science:

• Paleogenomics
• Archaeological Science
• Molecular Ecology

Background:

• Ancient DNA (aDNA) analysis of sediments (sedaDNA) is crucial for understanding past human and mammalian populations and ecosystems.
• Screening numerous sediment samples is currently time-consuming and expensive, especially for detecting hominin DNA.

Purpose of the Study:

• To develop a novel, high-throughput method for the fast and efficient analysis of sediment samples for aDNA.
• To reduce the cost and laboratory workload associated with sedaDNA screening.

Main Methods:

• Implemented a pooled testing approach, combining multiple sediment extracts for early parallelization of laboratory procedures.
• Developed a workflow where pooled samples with detectable aDNA signals proceed to detailed analysis, while negative pools are discarded.
• Tested the method on diverse Paleolithic sites across Europe, Asia, and Africa.

Main Results:

• Ancient DNA signals remain detectable even when aDNA extracts are pooled with up to four negative samples.
• Reducing extract input for double-stranded library preparation significantly increases DNA yield, potentially mitigating inhibition effects.
• The method was successfully applied to multiple archaeological sediment samples.

Conclusions:

• The novel pooled testing method enables efficient and cost-effective screening of large numbers of sediment samples for aDNA preservation.
• This approach can reduce costs by up to 70% and decrease hands-on laboratory time by 80%.
• Facilitates broader application of sedaDNA analysis in paleoenvironmental and paleoanthropological research.