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The earliest Denisovans and their cultural adaptation

Abstract

Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave’s sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205–192 ka at 68.2% or 217–187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.

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Fig. 1: The five new human fossils from Denisova Cave identified using ZooMS analysis.
Fig. 2: mtDNA maximum parsimony phylogenetic trees for the newly identified hominin bones.
Fig. 3: Stratigraphic and chronological relationship of the newly identified fossils from the East Chamber.
Fig. 4: Denisovan lithic tools from the lowermost archaeological layers (15 and 14) of the East Chamber.

Data availability

The mtDNA consensus sequences generated for the current study are available in NCBI GenBank under accession numbers MT576650–MT576653.

Dataset 1

Raw MALDI-TOF files from ZooMS analysis of the hominin bones DC4969 (Denisova 17), DC7277 (Denisova 18), DC8846 (Denisova 19), DC7795 (Denisova 20) and DC8591 (Denisova 21) converted to open source format. Files have been uploaded to: https://doi.org/10.17617/3.44.

Dataset 2

MicroCT scan files of the hominin bones DC4969 (Denisova 17), DC7277 (Denisova 18), DC8846 (Denisova 19) and DC7795 (Denisova 20). Files have been uploaded to: https://doi.org/10.17617/3.45.

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Acknowledgements

We thank the European Research Council, the Max Planck Society, the Oxford Radiocarbon Accelerator Unit (ORAU) and the Institute of Archeology and Ethnography, Russian Academy of Sciences Siberian Branch for their ongoing support. M. O’Reilly from the Max Planck Institute for the Science of Human History and I. Cartwright from the University of Oxford photographed the hominin fossils. We also thank in particular the volunteers who helped us sample the material (M. Jenkins, E. Gillespie, L. Bell, M. Caldarola, R. Heikkila, L. Doody, S. Amirova, G. Church, L. Koster, R. Holmes, L. Ghent, P. Ewles-Bergeron, N. Siemens, M. Sandilands and J. Zavodski); V. Slon, S. Peyrégne, E. Essel, S. Nagel and J. Richter from the Max Planck Institute for Evolutionary Anthropology for discussions and laboratory work. This work received funding from the ERC under the European Union’s Horizon 2020 Research and Innovation Programme grant agreement no. 715069 (FINDER) to K.D. and under the European Union’s Seventh Framework Programme (FP7/2007–2013) grant agreement no. 324139 (PalaeoChron) to T.H. and grant agreement no. 694707 (100 Archaic Genomes) to S.P. The archaeological field studies were funded by the Russian Foundation for Basic Research (no. 20-29-01011).

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K.D. designed the study; S.B., D.M., B.J.-S. and A.S. performed the laboratory work; S.B., D.M., A.S., M.M., J.K., S.P. and K.D. analysed the data; M.B.K., M.V.S. and A.P.D. provided samples and site-specific expertise; S.B., D.M., T.H. and K.D. wrote the paper with the assistance and input of all co-authors.

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Correspondence to Samantha Brown, Diyendo Massilani or Katerina Douka.

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Brown, S., Massilani, D., Kozlikin, M.B. et al. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 6, 28–35 (2022). https://doi.org/10.1038/s41559-021-01581-2

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