Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach
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.
Authors
- Manuel R. González Morales (ORCID: https://orcid.org/0000-0001-7277-7837)
- Mareike Stahlschmidt (ORCID: https://orcid.org/0000-0002-0505-7570)
- Brina Zagorc (ORCID: https://orcid.org/0000-0002-7685-1958)
- Boris Gasparyan
- Stefan Franz
- Marko Banda (ORCID: https://orcid.org/0000-0002-1348-5241)
- Stephan M. Kraemer (ORCID: https://orcid.org/0000-0002-3378-8530)
- Ron Pinhasi (ORCID: https://orcid.org/0000-0003-1629-8131)
- John Kappelman (ORCID: https://orcid.org/0000-0002-8058-0564)
- Susanna Sawyer (ORCID: https://orcid.org/0000-0002-8477-6089)
- Lawrence Guy Straus (ORCID: https://orcid.org/0000-0003-0348-3338)
- Pere Gelabert (ORCID: https://orcid.org/0000-0003-3019-0725)
- Evelyn Zelger
- Thomas Rattei (ORCID: https://orcid.org/0000-0002-0592-7791)
- Florian Exler
- Olivia Cheronet (ORCID: https://orcid.org/0000-0001-6760-1204)
- Victoria Oberreiter (ORCID: https://orcid.org/0000-0003-0766-3782)
- Ivor Karavanić (ORCID: https://orcid.org/0000-0003-1452-8394)
- Sophie Szedlacsek
- Fernanda Tenorio Cano
- Florian Brück
Institutions
- Universitat Autònoma de Barcelona (ES)
- University of Vienna (AT)
- Universidad de Cantabria (ES)
- University of New Mexico (US)
- University of Zagreb (HR)
- Institute of Human Sciences (AT)
- Environment Agency Austria (AT)
- Banco Santander (Spain) (ES)
- Institute of Archaeology and Ethnography (AM)
- The University of Texas at Austin (US)
Publication Details
- Journal
- Scientific Reports
- Published
- 2024-08-20
- DOI
- https://doi.org/10.1038/s41598-024-69741-5
- Citations
- 3
- Primary Topic
- Environmental DNA in Biodiversity Studies
- Type
- article
- Field-Weighted Citation Impact
- 1.38
Funders
- Austrian Science Fund
- Hrvatska Zaklada za Znanost