Evaluating Rapid Extraction Methods for Recovering Ancient DNA From Archaeological Sediments

Abstract

Sedimentary ancient DNA provides a powerful means to reconstruct past environments and populations. However, sedimentary ancient DNA research is hindered by low success rates due to poor DNA preservation, the largely opportunistic nature of field sampling, and long delays between sampling and results—meaning that substantial time and effort are often spent on samples that eventually yield little or no ancient DNA. Field‐compatible rapid DNA extraction methods could help accelerate the assessment of ancient DNA preservation, which could be particularly valuable when site access is temporary (e.g., seasonal excavations or salvage operations), where delays or poor preservation can mean missed opportunities to recover optimal samples. Here, we compared three rapid DNA extraction protocols—an Amicon ultrafiltration method, an alkaline lysis approach, and a paper‐binding method—across three sediment types (clay, sand, and soil), benchmarking them against a silica‐based protocol optimized for ancient sediments but designed for laboratory rather than field conditions. The Amicon‐based method, originally validated for ancient bones and coprolites, was modified here to improve the recovery of very short DNA fragments. We found that this modified protocol outperformed the other rapid extraction protocols, recovering from sediments both short synthetic DNA and modern DNA sheared to mimic the fragment size distribution of ancient DNA. When applied to Pleistocene and Holocene sediments, this method successfully recovered amplifiable ancient DNA within approximately 3 h. Although not a replacement for laboratory extractions, this rapid, portable, non‐hazardous approach adds a practical tool to the sedimentary ancient DNA research toolkit, establishing a premise for more informed sampling in time‐sensitive or logistically constrained excavations.