PXD069138

PXD069138 is an original dataset announced via ProteomeXchange.

Title	Palaeoproteomic insights into the deep roots of the cave bear lineage in Europe
Description	Palaeoproteomics has emerged as a powerful tool for reconstructing the evolutionary history of extinct species, particularly when ancient DNA is poorly preserved or beyond recovery. Here, we present the first large-scale enamel proteomic study focused on the cave bear, spanning specimens from the Early to Late Pleistocene. A primary objective was to determine whether the ursid population from level TD4 of Gran Dolina (Sierra de Atapuerca, Spain) belongs to the cave or the brown bear lineage, a long-standing taxonomic debate. We analyzed specimens from the Atapuerca sites, alongside comparative material from other southwestern European localities. Using LC-MS/MS and an acid demineralization protocol without enzymatic digestion, we successfully recovered enamel proteomes from all fossil samples, including the oldest specimens. Protein profiles were obtained for each extinct ursid, enabling the identification of taxonomically informative peptides across multiple individuals per taxon. Notably, two novel single amino acid polymorphisms (SAPs), found in ameloblastin (AMBN) and alpha-1 antitrypsin (SERPINA1), were restricted to Middle and Late Pleistocene cave bears and may represent new phylogenetic markers for this clade. This study provides the first molecular phylogenetic placement of Ursus dolinensis, supporting its basal position within the speloid lineage and suggesting its role as an ancestral form. Our results highlight the strong phylogenetic signal preserved in dental enamel and the exceptional biomolecular preservation at Atapuerca, providing a robust framework for reconstructing the evolutionary history of Ursidae. Moreover, the consistent recovery of systemic proteins, such as serpins, underscores the potential of enamel proteomes to capture not only evolutionary relationships but also physiological signals relevant to extinct ursids.
HostingRepository	PRIDE
AnnounceDate	2026-02-02
AnnouncementXML	Submission_2026-02-02_05:29:43.377.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD069138
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Amanda Gutierrez Carbajal
SpeciesList	scientific name: Ursus arctos (Brown bear) (Grizzly bear); NCBI TaxID: NEWT:9644;
ModificationList	phosphorylated residue; deamidated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-10-05 07:19:42	ID requested
⏵ 1	2026-02-02 05:29:43	announced

10.6019/PXD069138;

submitter keyword: None

Tomas Marques-
contact affiliation	Institut de Biologia Evolutiva (Universitat Pompeu Fabra - CSIC); Dr. Aiguader 88, ES-08003, Barcelona
contact email	tomas.marques@upf.edu
lab head
Amanda Gutierrez Carbajal
contact affiliation	Institut de Biologia Evolutiva (CSIC-UPF)
contact email	amandagc94@hotmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD069138

PRIDE project URI

• PRIDE
  1. PXD069138
     1. Label: PRIDE project
     2. Name: Palaeoproteomic insights into the deep roots of the cave bear lineage in Europe