Sequencing of mtDNA captures of sediments from the Pleistocene layers of Denisova Cave.

Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group related to Neanderthals. The dozen hominin remains recovered from the deposits also include Neanderthals and the child of a Neanderthal and a Denisovan7, suggesting that Denisova Cave was a contact zone between these archaic hominins. Uncertainties persist, however, about the order in which they appeared at the site, the timing and environmental context of hominin occupation, and their association with lithic assemblages. Here we report the analysis of DNA from 728 sediment samples, collected in a grid-like manner from the Pleistocene layers. Ancient faunal and hominin mitochondrial (mt) DNA was retrieved from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, associated with early Middle Palaeolithic stone tools deposited approximately 250,000 to 170,000 years ago, whereas Neanderthal mtDNA first appeared towards the end of this period. We detect a turnover in the mtDNA of Denisovans, coinciding with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic, when modern human mtDNA is first recorded in the sediments.