Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis

Abstract

DNA sequencing has revolutionised our understanding of archaic humans during the Middle and Upper Palaeolithic. Unfortunately, while many Palaeolithic sites contain large numbers of bones, the majority of these lack the diagnostic features necessary for traditional morphological identification. As a result the recovery of Pleistocene-age human remains is extremely rare. To circumvent this problem we have applied a method of collagen fingerprinting to more than 2000 fragmented bones from the site of Denisova Cave, Russia, in order to facilitate the discovery of human remains. As a result of our analysis a single hominin bone (Denisova 11) was identified, supported through in-depth peptide sequencing analysis, and found to carry mitochondrial DNA of the Neandertal type. Subsequent radiocarbon dating revealed the bone to be >50,000 years old. Here we demonstrate the huge potential collagen fingerprinting has for identifying hominin remains in highly fragmentary archaeological assemblages, improving the resources available for wider studies into human evolution.

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

“…S1 and S2 and Table S1). Together with other studies, this confirms the suitability of ZooMS as a screening technique to identify hominin specimens among unidentified fragmentary bone specimens (17,22). We confirmed these identifications for samples AR-7, AR-16, and AR-30 by analyzing the same extracts using shotgun proteomics and spectra assignment against our COL1 sequence database (SI Appendix, Fig.…”

“…It has been demonstrated previously that palaeoproteomics allows the identification of additional hominin specimens among unidentified Pleistocene faunal remains [zooarchaeology by mass spectrometry, or ZooMS (15)(16)(17)], although here the value of doing so has enabled the direct dating and unambiguous identification of the Neandertal association with the Châtelperronian. We successfully apply this to the Grotte du Renne Châtelperronian.…”

“…We obtain a direct hominin radiocarbon date at the site, thereby directly addressing the chronostratigraphic context of this specimen in relation to the hypothesis regarding movement of the hominin specimens from the underlying Mousterian into the Châtelperronian layers and provide biomolecular data (palaeoproteomics, aDNA) on the genetic ancestry of the Grotte du Renne Châtelperronian hominins. Although proteomic data on Pleistocene hominin bone specimens has been presented before (17,18), the phylogenetic and physiological implications of such datasets has, so far, not been fully explored.…”

Russia–UK Collaboration in Paleontology: Past, Present, and Future

“…Brown et al 2016;Douka et al 2015). However, there is still room to develop a large-scale interdisciplinary approach to understanding human occupation in northern Asia.…”

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response

“…Phylogenetic analysis based on collagen protein sequences was also used in a study involving fossilized bone material from ancient extinct giant ground sloths [28]. In-depth analysis of collagen sequences has also been used to identify hominin bones in the context of highly fragmentary archaeological assemblages [29]. A somewhat different paradigm was employed in a study involving analysis of tissue samples from well-preserved Andean mummies [19].…”