TY - JOUR
T1 - Maximizing efficiency in sedimentary ancient DNA analysis
T2 - a novel extract pooling approach
AU - Oberreiter, Victoria
AU - Gelabert, Pere
AU - Brück, Florian
AU - Franz, Stefan
AU - Zelger, Evelyn
AU - Szedlacsek, Sophie
AU - Cheronet, Olivia
AU - Cano, Fernanda Tenorio
AU - Exler, Florian
AU - Zagorc, Brina
AU - Karavanić, Ivor
AU - Banda, Marko
AU - Gasparyan, Boris
AU - Straus, Lawrence Guy
AU - Gonzalez Morales, Manuel R
AU - Kappelman, John
AU - Stahlschmidt, Mareike
AU - Rattei, Thomas
AU - Kraemer, Stephan M
AU - Sawyer, Susanna
AU - Pinhasi, Ron
N1 - © 2024. The Author(s).
PY - 2024/8/20
Y1 - 2024/8/20
N2 - In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
AB - In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.
KW - DNA, Ancient/analysis
KW - Geologic Sediments
KW - Humans
KW - Animals
KW - Archaeology/methods
KW - Fossils
KW - High-Throughput Nucleotide Sequencing/methods
KW - Hominidae/genetics
KW - Europe
KW - Africa
UR - http://www.scopus.com/inward/record.url?scp=85201688849&partnerID=8YFLogxK
U2 - 10.1038/s41598-024-69741-5
DO - 10.1038/s41598-024-69741-5
M3 - Article
C2 - 39169089
SN - 2045-2322
VL - 14
SP - 19388
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 19388
ER -