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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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			Action	DRS
	ERR2824984.fastq.gz	Fastqsanger.gz
	ERR2824984_1.fastq.gz	Fastqsanger.gz
	ERR2824984_2.fastq.gz	Fastqsanger.gz
	ERR2824985.fastq.gz	Fastqsanger.gz
	ERR2824985_1.fastq.gz	Fastqsanger.gz

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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.

2020-12-02 | MSV000086548 | MassIVE

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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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Project description:The PedBE clock estimates DNA methylation age in pediatric buccal cells [APrON]

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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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Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.

Project description:Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1-4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, 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 assemblages5,8-11. 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.

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