Evaluating Rapid Extraction Methods for Recovering Ancient DNA From Archaeological Sediments
5 affiliations
- 1The Gray Faculty of Medical & Health Sciences Tel Aviv University Tel Aviv Israel
- 2Institute of Archaeology, Nicolaus Copernicus University Toruń Poland
- 3Institute of Geological Sciences, Polish Academy of Sciences Warszawa Poland
- 4Área de Prehistoria, Departamento de Prehistoria, Arqueología, Antropología Social y Ciencias y Técnicas Historiográficas University of Valladolid Valladolid Spain
- 5Faculty of Exact Sciences, School of Mathematical Sciences Tel Aviv University Tel Aviv Israel
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.
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BibTeX
@article{dagtas2026evaluating,
title = {{Evaluating Rapid Extraction Methods for Recovering Ancient DNA From Archaeological Sediments}},
author = {Nihan Dilşad Dağtaş and Azhar Jabareen and Krzysztof Cyrek and Maciej T. Krajcarz and Magdalena Krajcarz and Manuel Ángel Rojo‐Guerra and Policarpo Sánchez‐Yustos and Magdalena Sudoł‐Procyk and Shmuel Safra and Viviane Slon},
journal = {Environmental DNA},
year = {2026},
month = sep,
doi = {10.1002/edn3.70356},
url = {https://doi.org/10.1002/edn3.70356},
note = {CC BY},
}
RIS
TY - JOUR
TI - Evaluating Rapid Extraction Methods for Recovering Ancient DNA From Archaeological Sediments
AU - Nihan Dilşad Dağtaş
AU - Azhar Jabareen
AU - Krzysztof Cyrek
AU - Maciej T. Krajcarz
AU - Magdalena Krajcarz
AU - Manuel Ángel Rojo‐Guerra
AU - Policarpo Sánchez‐Yustos
AU - Magdalena Sudoł‐Procyk
AU - Shmuel Safra
AU - Viviane Slon
PY - 2026
DA - 2026/09/01
JO - Environmental DNA
DO - 10.1002/edn3.70356
UR - https://doi.org/10.1002/edn3.70356
AB - 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.
SN - 2637-4943
ER -