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PXD011008 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEarly Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny
DescriptionAncient 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMeaghan Mackie
SpeciesList scientific name: Stephanorhinus; NCBI TaxID: 2003758; scientific name: Equus sp.; NCBI TaxID: 46122; scientific name: Bison; NCBI TaxID: 9900;
ModificationListphosphorylated residue; monohydroxylated residue; deamidated residue
InstrumentQ Exactive HF; Q Exactive; Q Exactive Plus
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-09-05 05:21:08ID requested
12019-09-11 05:13:13announced
22019-09-25 01:55:56announced2019-09-25: Updated publication reference for PubMed record(s): 31511700.
Publication List
Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SKSS, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MTP, Olsen JV, Lordkipanidze D, Willerslev E, Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny. Nature, 574(7776):103-107(2019) [pubmed]
Keyword List
submitter keyword: Palaeoproteomics, Stephanorhinus, enamel, bone, dentine, Dmanisi, LC-MS/MS
Contact List
Enrico Cappellini
contact affiliationLundbeck Foundation GeoGenetics Centre, Natural History Museum of Denmark, University of Copenhagen, Denmark
contact emailecappellini@snm.ku.dk
lab head
Meaghan Mackie
contact affiliationUniversity of Copenhagen
contact emailmeaghan@palaeome.org
dataset submitter
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