Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals. The dozen hominin remains recovered from the deposits also include Neanderthals and the child of a Neanderthal and a Denisovan, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides 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 at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.
Main
Denisova Cave consists of three chambers (designated Main, East and South Chambers) that contain deposits with stratigraphic sequences extending from the Middle Pleistocene to the Holocene epoch. The Pleistocene deposits have chronologies that have been constructed from the radiocarbon dating of bone, tooth and charcoal5 (to around 50 thousand years ago (ka)) and optical dating of sediments8 (to more than 300 ka). Optical ages for Main and East Chambers (Fig. 1a–c) can be aligned on a common time scale (Extended Data Fig. 1) but excavations are ongoing in South Chamber, where layers are only tentatively recognized. Mitochondrial DNA and nuclear DNA have been recovered from eight hominin fossils, enabling four to be assigned to Denisovans (Denisova 2, Denisova 3, Denisova 4 and Denisova 8), three to Neanderthals (Denisova 5, Denisova 9 and Denisova 15), and one to the child of a Neanderthal and a Denisovan (Denisova 11). However, there are too few fossils to enable the detailed reconstruction of the timing and sequence of hominin occupation, and the association of the early Middle Palaeolithic, middle Middle Palaeolithic and Initial Upper Palaeolithic assemblages identified at the site with specific hominin groups. Moreover, two Denisovan fossils (Denisova 3 and Denisova 4)—but no modern human remains—have been recovered from the Initial Upper Palaeolithic layers, so it is debated whether archaic hominins or modern humans created the associated ornaments and bone tools.
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