Maximizing efficiency in sedimentary ancient DNA analysis : a novel extract pooling approach
Oberreiter, Victoria (University of Vienna)
Gelabert, Pere (Universitat Autònoma de Barcelona. Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia)
Brück, Florian (University of Vienna)
Franz, Stefan (University of Vienna)
Zelger, Evelyn (University of Vienna)
Szedlacsek, Sophie (University of Vienna)
Cheronet, Olivia (University of Vienna)
Cano, Fernanda Tenorio (University of Vienna)
Exler, Florian (University of Vienna)
Zagorc, Brina (University of Vienna)
Karavanić, Ivor (University of Zagreb)
Banda, Marko (University of Zagreb)
Gasparyan, Boris (National Academy of Sciences of the Republic of Armenia)
Straus, Lawrence Guy (EvoAdapta Group Universidad de Cantabria)
Gonzalez Morales, Manuel R. (Universidad de Cantabria)
Kappelman, John (The University of Texas)
Stahlschmidt, Mareike (University of Vienna)
Rattei, Thomas (University of Vienna)
Kraemer, Stephan M. (University of Vienna)
Sawyer, Susanna (University of Vienna)
Pinhasi, Ron (University of Vienna)

Data:	2024
Resum:	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.
Ajuts:	European Commission 101042570
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, i la comunicació pública de l'obra, sempre que no sigui amb finalitats comercials, i sempre que es reconegui l'autoria de l'obra original. No es permet la creació d'obres derivades.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Archaeology ; Biological anthropology
Publicat a:	Scientific reports, Vol. 14 (August 2024) , art. 19388, ISSN 2045-2322

DOI: 10.1038/s41598-024-69741-5
PMID: 39169089

12 p, 1.9 MB

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