PXD040213-1

PXD040213 is an original dataset announced via ProteomeXchange.

Title	Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo
Description	Pleistocene Pongo teeth show substantial variation in size and morphology, fueling taxonomic debates about the paleodiversity of the genus. We investigated prominent features of the enamel-dentine-junction junction (EDJ) – phylogenetically informative internal structures – of 71 fossil Pongo lower molars from various sites by applying geometric morphometrics and conducted paleoproteomic analyses from enamel proteins to attempt to identify extinct orangutan species. Forty-three orangutan lower molars representing Pongo pygmaeus and Pongo abelii were included for comparison. The shape of the EDJ was analyzed by placing five landmarks on the tip of the main dentine horns, and 142 semilandmarks along the marginal ridges connecting the dentine horns. Paleoproteomic analyses were conducted on 15 teeth of Late Pleistocene Pongo using high-resolution tandem mass spectrometry. The geometric morphometric results show variations in EDJ shape regarding aspects of the height and position of the dentine horns and connecting ridges. Despite the issue of molar position and sample size, modern molars are distinguished from fossil counterparts by their elongated tooth outline and narrowly positioned dentine horns. Proteomic results show that neither a distinction of P. pygmaeus and P. abelii, nor a consistent allocation of fossil specimens to extant species is feasible. Based on the EDJ shape, the (late) Middle to Late Pleistocene Pongo samples from Vietnam share the same morphospace, supporting the previous allocation to P. devosi, although substantial overlap with Chinese fossils could also indicate close affinities with P. weidenreichi. The hypothesis that both species represent one chronospecies cannot be ruled out. Two fossil specimens, one from Tam Hay Marklot (Laos, Late Pleistocene), and another from Sangiran (Java, Early to Middle Pleistocene), along with some specimens within the Punung sample (Java), exhibit affinities with Pongo abelii. The Punung fossils might represent a mix of early Late Pleistocene and later specimens (terminal Pleistocene to Holocene) related to modern Pongo. The taxonomy and phylogeny of the complete Punung sample needs to be further investigated.
HostingRepository	PRIDE
AnnounceDate	2023-09-06
AnnouncementXML	Submission_2023-09-05_17:16:07.291.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	JulideKubat
SpeciesList	scientific name: Pongo sp.; NCBI TaxID: 9603;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-16 14:57:55	ID requested
⏵ 1	2023-09-05 17:16:07	announced

Dataset with its publication pending

submitter keyword: LC-MS, Paleoproteomics,Pongo

EnricoCappellini
contact affiliation	Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
contact email	ecappellini@sund.ku.dk
lab head
JulideKubat
contact affiliation	Université Paris Cité
contact email	juelide.kubat@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040213
     1. Label: PRIDE project
     2. Name: Geometric morphometrics and paleoproteomics enlighten the paleodiversity of Pongo