Dataset Information

A Pleistocene hominin enamel proteome from Homo antecessor

ABSTRACT: Hominin relationships and their dispersal throughout Eurasia during the Early and Middle Pleistocene are highly debated. The relationships between Early and Middle Pleistocene hominins, like Homo antecessor and Homo erectus, and hominin species that dominate the Late Pleistocene fossil record, like Homo sapiens, Neanderthals and Denisovans, are unclear. Here, we obtain enamel proteomes from Homo antecessor (Atapuerca, Spain) and Homo erectus (Dmanisi, Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal, and divergence. We recover endogenous ancient proteomes from the Atapuerca and Dmanisi hominins. In addition, our proteomic data indicates that the sampled Homo antecessor molar derives from a male hominin through amelogenin protein sexing. Our data includes preserved in vivo phosphorylation and enamel proteome proteolytic digestion.

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive HF-X, Q Exactive HF

ORGANISM(S): Homo

TISSUE(S): Dentin, Tooth, Tooth Enamel

SUBMITTER: Frido Welker

LAB HEAD: Enrico Cappellini

PROVIDER: PXD014342 | Pride | 2020-04-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Atapuerca_Blank_161213_S_ASES_02_01_atapuerca_blank1070.raw	Raw
	Atapuerca_Blank_20161004_QE5_nLC11_MEM_COLLAB_GeoG_1070_01.raw	Raw
	Atapuerca_Blank_20161109_QE5_nLC5_MEM_COLLAB_GeoG_1070_02.raw	Raw
	Atapuerca_Enamel_161213_S_ASES_01_01_atapuerca_sample1069.raw	Raw
	Atapuerca_Enamel_20161004_QE5_nLC11_MEM_COLLAB_GeoG_1069_02.raw	Raw

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Publications

The dental proteome of Homo antecessor.

Welker Frido F Ramos-Madrigal Jazmín J Gutenbrunner Petra P Mackie Meaghan M Tiwary Shivani S Rakownikow Jersie-Christensen Rosa R Chiva Cristina C Dickinson Marc R MR Kuhlwilm Martin M de Manuel Marc M Gelabert Pere P Martinón-Torres María M Margvelashvili Ann A Arsuaga Juan Luis JL Carbonell Eudald E Marques-Bonet Tomas T Penkman Kirsty K Sabidó Eduard E Cox Jürgen J Olsen Jesper V JV Lordkipanidze David D Racimo Fernando F Lalueza-Fox Carles C Bermúdez de Castro José María JM Willerslev Eske E Cappellini Enrico E

Nature 20200401 7802

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated<sup>1-5</sup>. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge<sup>6-8</sup>. Her ...[more]

PMID: 32269345

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Project 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.