Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Extinct species identification from late Middle Pleistocene and earlier Upper Pleistocene bone fragments and tools not recognizable from their osteomorphological study by an enhanced proteomics protocol

ABSTRACT: Ancient preserved molecules offer the opportunity of gaining a deeper knowledge on their biological past. However, the development of a proteomic workflow remains a challenge. The analysis of fossils must involve a low quantity of material to avoid damaging the samples. In this study an enhanced proteomic protocol was applied to 5-milligram samples of about 130,000-year-old mammalian bones ranging from the end of the Middle Pleistocene up to the earlier Upper Pleistocene, excavated from Scladina Cave (Sclayn, Belgium). Using sequence homology with modern sequences, a biological classification was successfully achieved and the associated taxonomic ranks to each bone were identified consistently with the information gained from osteomorphological studies and palaeoenvironmental and palaeodietary data. Amino acid substitutions on collagens were identified, thus providing new information on extinct species sequences and helping in taxonomy-based clustering. Considering samples with no osteomorphological information, such as two bone retouchers, proteomics successfully identified the families providing paleontologists new information on these objects. Combining osteomorphology studies and amino acid variations identified by proteomics, one of the retouchers was potentially identified as belonging to the Ursus spelaeus species.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Mammalia

TISSUE(S): Bone

SUBMITTER: BRAY FABRICE

LAB HEAD: Fabrice Bray

PROVIDER: PXD031386 | Pride | 2022-06-29

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Robust high throughput proteomics identification and deami-dation quantitation of extinct species up to Pleistocene with Ultrahigh Resolution MALDI-FTICR Mass Spectrometry

Project description:Peptide mass fingerprinting (PMF) using MALDI-TOF mass spectrometry allows the identification of bone species based on their type I collagen sequence. In archaeological or paleontological field, PMF is known as ZooMS and is widely implement-ed to find markers for most species, including the extinct ones. In addition to the identification of bone species, ZooMS enables dating estimation by measuring the deamidation value of specific peptides. Herein, we report several enhancements to the classical ZooMS technique, which reduces to ten-fold the required bone sample amount (down to milligram scale) and achieves robust deamidation value calculation in a high throughput manner. These improvements rely on a 96-well plates samples preparation, a careful optimization of collagen extraction and digestion to avoid spurious posttranslational modifi-cations production and peptide mass fingerprinting at high resolution using MALDI-FTICR (Matrix Assisted Desorption Ionization Fourier Transform Ion Cyclotron Resonance) analysis. This method was applied to the identification of a hun-dred bones of herbivores from the Middle Paleolithic site of Caours (Somme, Northern France) well dated from the Eemian Last Interglacial climatic optimum. The method gave reliable species identification to bones already identified by their oste-omorphology, as well as to more challenging bone samples consisting of small or burnt bone fragments. The obtained de-amidation values of bones originating from the same geological layers have a low standard deviation. The method can be applied to archaeological bone remains and offers a robust capacity to identify traditionally unidentifiable bone fragments, thus increasing the number of identified specimens and providing invaluable information in specific contexts.

2023-04-28 | PXD038283 | Pride

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

Project description:The project aimed to characterize the protein composition from 3 Pleistocene bone specimens (AR-7, AR-16, AR-30). Analysed extracts concern standard ZooMS tryptic digests (AR-7, AR-16, AR-30) and additional palaeoproteomic extracts (AR-30A and AR-30B). The latter concern two biological duplicates. All extractions were performed at the Department of Human Evolution, MPI-EVA (Germany) under sterile conditions. Analyses took place on a Q-Exactive Hybrid Quadrupole-Orbitrap MS.

2016-09-27 | PXD003208 | Pride

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

Project description:Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa. Outside the permafrost, however, irreversible aDNA post-mortem degradation has so far limited aDNA recovery to the past ~0.5 million years (Ma). Contrarily, multiple analyses suggested the presence of protein residues in Cretaceous fossil remains. Similarly, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1), though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus). Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and requires systematic revision. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

2019-09-11 | PXD011008 | Pride

Palaeoproteomic analysis of Pleistocene cave hyenas from east Asia

Project description:Spotted hyena (Crocuta crocuta) is the only extant species of the genus Crocuta, which once occupied a much wider range during the Pliocene and Pleistocene. However, its origin and evolutionary history is somewhat contentious due to discordances being found between morphological, nuclear, and mitochondrial data. Due to the limited molecular data from east Asian Crocuta, and the difficulty of extracting ancient DNA from this area, here we present proteomic analysis of cave hyenas from three locations in northern China. This marks the first proteomic data generated from cave hyenas, adding new molecular data to the east Asian populations. Phylogenetic analysis based on these protein sequences reveals two different groups of cave hyenas in east Asia, one of which could not be distinguished from modern spotted hyenas from northern Africa, tentatively the result of previously suggested gene flow between these lineages. With developments of instrumentation and analytical methods, proteomics holds promising potential for the phylogenetic reconstruction of ancient fauna previously thought to be unreachable using ancient DNA.

2020-10-19 | PXD020530 | Pride

COL1 database samples for the Late Pleistocene of Western Eurasia

Project description:The project aimed to characterize the collagen type I (COL1) sequences from various modern, Holocene and Pleistocene bone, antler and skin samples for phylogenetic purposes. All extractions were performed at BioArCh, University of York (UK) or the Department of Human Evolution, MPI-EVA (Germany). Analyses took place on Q-Exactive Hybrid Quadrupole-Orbitrap MS.

2016-09-27 | PXD003190 | Pride

Multi-protease analysis of Pleistocene bone proteomes

Project description:Palaeoproteomics of skeletal tissues has the potential to provide new insights into the evolutionary relationships between globally distributed hominin fossils across the Pleistocene. The use of alternative or additional proteases has the potential to increase both proteome size and protein. However, the potential of alternative proteases beside trypsin remains unexplored systematically in palaeoproteomic studies. Here, we present a comparison of the bone proteome size and protein sequence recovery of six different proteases from four Pleistocene bone specimens. We observe that the majority of the preserved bone proteome is inaccessible to trypsin. We also note that for proteins recovered consistently across several proteases, protein sequence coverage can be increased significantly by combining peptide identifications from two or more proteases. Our results thereby demonstrate that the proteolysis of Pleistocene proteomes by several proteases has clear advantages when addressing evolutionary questions in palaeoproteomics.

2020-10-13 | PXD018264 | Pride

PALEOPROTEOMICS APPLIED TO THE WAZIERS SITE

Project description:The ancient preserved molecules in bones offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study extinct species and phylogenetic evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. This study applied a proteomic methodology to mammalian bones of 130,000 / 120,000 years old from the last Chibanian and the earlier Upper Pleistocene site of Waziers (France). The presence of lithic artefacts and the traces of butchery observed on the bones indicate the presence of Neanderthal Man on this site. Starting from 5 milligram samples, our results show that most detected peptides match collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60 %. Using sequence homology with modern sequences, a biological classification was successfully achieved. Each bone taxonomic rank by proteomics was consistent with the existing osteomorphological studies and palaeoenvironmental and palaeodietary data.

2023-04-20 | PXD039657 | Pride

A Pleistocene hominin enamel proteome from Homo antecessor

Project description:Hominin relationships and their dispersal throughout Eurasia during the Early and Middle Pleistocene are highly debated. The relationships between Early and Middle Pleistocene hominins, like Homo antecessor and Homo erectus, and hominin species that dominate the Late Pleistocene fossil record, like Homo sapiens, Neanderthals and Denisovans, are unclear. Here, we obtain enamel proteomes from Homo antecessor (Atapuerca, Spain) and Homo erectus (Dmanisi, Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal, and divergence. We recover endogenous ancient proteomes from the Atapuerca and Dmanisi hominins. In addition, our proteomic data indicates that the sampled Homo antecessor molar derives from a male hominin through amelogenin protein sexing. Our data includes preserved in vivo phosphorylation and enamel proteome proteolytic digestion.

2020-04-02 | PXD014342 | Pride

Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)

Project description:Recent improvements in the analysis ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a “multi-omics” study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified “Villabruna cluster”. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analyses of dental calculus using genomics and proteomics showed a similar oral microbiome composition as Neandertals, but distinct from later foragers and farmers, revealing also a diet based on mammals, fish and plants. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.

2022-10-27 | PXD024346 | Pride

Oxidative damage signatures in human bone collagen from Pompeii and Herculaneum.

Project description:In search of markers for protein aging, we used an extraordinary test case of human bones from the excavations sites of Pompei and Herculaneum (79 AD), analyzed by a shotgun proteomic approach using LC-MS/MS. Human bones from Scalandrone Bay (II sec AD, another volcanic area, yet not related to Vesuvius eruption were also analysed for the comparison of the PTMs provoked from a volcanic ground to an almost coeval standard burial condition. In addition, already published archaeological bones, approximately 17 centuries younger than the test case, were used as control samples. Deamidation of asparagine and glutamine was examined as a now widely considered aging molecular marker. Deamidation profile was quite robust for samples with a similar age whereas the fewer proteins were detected, the more degraded the sample were found to be. Positional investigation of deamidation in the polypeptide sequence of collagen type I revealed that some zones are more susceptible to deamidation than others. Back bone cleavage analysis confirmed that some zones apart from deamidation are more susceptible to spontaneous hydrolysis too. Analysis of post-translational modifications showed higher advanced glycation products of lysine and arginines in the samples of Pompeii and Herculaneum. Furthermore, oxidative products of methionine, histidine and the conversion of ST to glycine were also detected. Interestingly, multiple oxidation products of proline and dehydration of hydroxyproline were detected for the first time, turning the scientific interest to this amino acid (P), which is usually ignored due to its natural conversion to hydroxyproline. As a matter of fact, we can observe that collagen degradation in bones from Pompeii and Herculaneum underwent different degradation processes.

2021-07-10 | PXD020462 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data