Dataset Information

Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive Plus, Q Exactive HF, Q Exactive

ORGANISM(S): Equus Sp. Stephanorhinus Bison

TISSUE(S): Dentin, Bone, Tooth Enamel

SUBMITTER: Meaghan Mackie

LAB HEAD: Enrico Cappellini

PROVIDER: PXD011008 | Pride | 2019-09-11

REPOSITORIES: Pride

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Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Cappellini Enrico E Welker Frido F Pandolfi Luca L Ramos-Madrigal Jazmín J Samodova Diana D Rüther Patrick L PL Fotakis Anna K AK Lyon David D Moreno-Mayar J Víctor JV Bukhsianidze Maia M Rakownikow Jersie-Christensen Rosa R Mackie Meaghan M Ginolhac Aurélien A Ferring Reid R Tappen Martha M Palkopoulou Eleftheria E Dickinson Marc R MR Stafford Thomas W TW Chan Yvonne L YL Götherström Anders A Nathan Senthilvel K S S SKSS Heintzman Peter D PD Kapp Joshua D JD Kirillova Irina I Moodley Yoshan Y Agusti Jordi J Kahlke Ralf-Dietrich RD Kiladze Gocha G Martínez-Navarro Bienvenido B Liu Shanlin S Sandoval Velasco Marcela M Sinding Mikkel-Holger S MS Kelstrup Christian D CD Allentoft Morten E ME Orlando Ludovic L Penkman Kirsty K Shapiro Beth B Rook Lorenzo L Dalén Love L Gilbert M Thomas P MTP Olsen Jesper V JV Lordkipanidze David D Willerslev Eske E

Nature 20190911 7776

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the ...[more]

PMID: 31511700

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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.

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