PXD011008-1

PXD011008 is an original dataset announced via ProteomeXchange.

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’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.
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

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-05 05:21:08	ID requested
⏵ 1	2019-09-11 05:13:13	announced
2	2019-09-25 01:55:56	announced	2019-09-25: Updated publication reference for PubMed record(s): 31511700.

Dataset with its publication pending

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

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

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PRIDE project URI

• PRIDE
  1. PXD011008
     1. Label: PRIDE project
     2. Name: Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny