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

Victoria Oberreiter, Pere Gelabert (Corresponding author), Florian Brück, Stefan Franz, Evelyn Zelger, Sophie Szedlacsek, Olivia Cheronet, Fernanda Tenorio Cano, Florian Exler, Brina Zagorc, Ivor Karavanić, Marko Banda, Boris Gasparyan, Lawrence Guy Straus, Manuel R Gonzalez Morales, John Kappelman, Mareike Stahlschmidt, Thomas Rattei, Stephan M Kraemer, Susanna Sawyer (Corresponding author)Ron Pinhasi (Corresponding author)

Publications: Contribution to journalArticlePeer Reviewed

Abstract

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.

Original languageEnglish
Article number19388
Pages (from-to)19388
JournalScientific Reports
Volume14
Issue number1
DOIs
Publication statusPublished - 20 Aug 2024

Austrian Fields of Science 2012

  • 106018 Human biology

Keywords

  • DNA, Ancient/analysis
  • Geologic Sediments
  • Humans
  • Animals
  • Archaeology/methods
  • Fossils
  • High-Throughput Nucleotide Sequencing/methods
  • Hominidae/genetics
  • Europe
  • Africa

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