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PXD011008

PXD011008 is an original dataset announced via ProteomeXchange.

Dataset Summary

  • Title: Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny
  • 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‚Äôs 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.
  • HostingRepository: PRIDE
  • AnnounceDate: 2019-09-11
  • AnnouncementXML: Submission_2019-09-11_05:13:12.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original dataset
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Meaghan Mackie
  • SpeciesList: scientific name: Stephanorhinus; NCBI TaxID: 2003758; scientific name: Equus sp.; NCBI TaxID: 46122; scientific name: Bison; NCBI TaxID: 9900;
  • ModificationList: phosphorylated residue; monohydroxylated residue; deamidated residue
  • Instrument: Q Exactive HF; Q Exactive; Q Exactive Plus

Dataset History

RevisionDatetimeStatusChangeLog Entry
02018-09-05 05:21:08ID requested
12019-09-11 05:13:13announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. submitter keyword: Palaeoproteomics, Stephanorhinus, enamel, bone, dentine, Dmanisi, LC-MS/MS

Contact List

    Enrico Cappellini
    • contact affiliation: Lundbeck Foundation GeoGenetics Centre, Natural History Museum of Denmark, University of Copenhagen, Denmark
    • contact email: ecappellini@snm.ku.dk
    • lab head:
    Meaghan Mackie
    • contact affiliation: University of Copenhagen
    • contact email: meaghan@palaeome.org
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
Repository Record List
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