Neandertal and Denisovan DNA from Pleistocene sediments

TLDR

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. The study demonstrates that targeted enrichment of mitochondrial DNA reveals hominin traces in cave sediments, even where no fossils are present. The authors employed targeted mitochondrial DNA enrichment and automated screening of numerous sediment samples to detect Neandertal DNA in eight layers across four Eurasian caves. The study recovered Denisovan DNA from a deep Middle Pleistocene layer in Denisova Cave and shows that hominin presence can be inferred from sediment DNA even without skeletal remains.

Abstract

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.