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Age estimates for hominins at Denisova Cave: genetic data

ABSTRACT: Age estimates for hominins at Denisova Cave: genetic data

PROVIDER: PRJEB29061 | ENA |

REPOSITORIES: ENA

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Denisova Cave sediment DNA

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

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Examining collagen preservation through glutamine deamidation at Denisova Cave

Project description:Samples were used for a study on the ability to use deamidation rates to assess relative chronology at Denisova Cave. The majority of the samples for the study were analyzed using peptide mass fingerprinting (data publicly available - see associated manuscript for details). 15 samples from 7 layers in Denisova Cave were chosen for LC-MS/MS analysis. Prior to analysis samples were demineralized in hydrochloric acid, gelatinized in ammonium bicarbonate, digested with trypsin, and desalted with C18 ZipTips. Data was processed using Byonic with SwissProt as the database to obtain a focused database of just the proteins present in the samples. This focused database was combined with curated collagen sequences (database presented here) and used for analysis with MaxQuant and deamiDATE. For more details see associated publication. Provided here are the raw files, peak lists for Byonic, results files for Byonic, sequence database (focused database and currated collagen sequences), metadata file with information linking the file names here to the file names of the peptide mass fingerprinting samples, and a zip file of the Max Quant and deamiDATE results.

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Project description:Denisova Genome Project

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Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Project description:Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4-6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population 'Denisovans' and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

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Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave.

Project description:Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.

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