Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel

Taurozzi, Alberto J.; Rüther, Patrick L.; Patramanis, Ioannis; Koenig, Claire; Sinclair Paterson, Ryan; Madupe, Palesa P.; Harking, Florian Simon; Welker, Frido; Mackie, Meaghan; Ramos-Madrigal, Jazmín; Olsen, Jesper V.; Cappellini, Enrico

doi:10.1038/s41596-024-00975-3

Cited by 4 publications

(4 citation statements)

References 76 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The laboratory workflow for the CMNF-59632 teeth and the Fontana Ranuccio Stephanorhinus tooth (for comparison) generally follows that of Cappellini et al (2019) and Taurozzi et al (2024) 9,48 . Using a sterilised drill, flakes of enamel were removed from the fragmentary teeth, with care taken to avoid sampling the dentine.…”

Section: Methodsmentioning

confidence: 95%

“…Due to its thin enamel, only limited peptides were recovered from this tusk fragment, and the sample is thus excluded from further analysis and discussion. 9,48 . Using a sterilised drill, flakes of enamel were removed from the fragmentary teeth, with care taken to avoid sampling the dentine.…”

Section: Site and Specimenmentioning

confidence: 99%

“…(which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It isProteomic extraction and LC-MS/MSThe laboratory workflow for the CMNF-59632 teeth and the Fontana RanuccioStephanorhinus tooth (for comparison) generally follows that ofCappellini et al (2019) andTaurozzi et al (2024) …”

mentioning

confidence: 99%

See 2 more Smart Citations

A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Paterson,

Mackie,

Capobianco

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

In the past decade, ancient protein sequences have emerged as a valuable source of data for deep-time phylogenetic inference. Still, the recovery of protein sequences providing novel phylogenetic insights does not exceed 3.7 Ma (Pliocene). Here, we push this boundary back to 21-24 Ma (early Miocene), by retrieving enamel protein sequences of an early-diverging rhinocerotid (Epiaceratheriumsp. - CMNF-59632) from the Canadian High Arctic. We recover partial sequences of seven enamel proteins (AHSG, ALB, AMBN, AMELX, AMTN, ENAM, MMP20) and over 1000 peptide-spectrum matches, spanning over at least 251 amino acids. Authentic endogeneity of these sequences is supported by indicators of protein damage, including several spontaneous and irreversible post-translational modifications accumulated during prolonged diagenesis and reaching near-complete occupancy at many sites. Bayesian tip-dating, across 15 extant and extinct perissodactyl taxa, places the divergence time of CMNF-59632 in the middle Eocene-Oligocene, and identifies a later divergence time for Elasmotheriinae in the Oligocene. The finding weakens alternative models suggesting a deep basal split between Elasmotheriinae and Rhinocerotinae. This divergence time of CMNF-59632 coincides with a phase of high diversification of rhinocerotids, and supports a Eurasian origin of this clade in the late Eocene or Oligocene. The findings are consistent with previous hypotheses on the origin of the enigmatic fauna of the Haughton crater, which, in spite of their considerable degree of endemism, also display similarity to distant Eurasian faunas. Our findings demonstrate the potential of palaeoproteomics in obtaining phylogenetic information from a specimen that is ten times older than any sample from which endogenous DNA has been obtained.

show abstract

Section: Methodsmentioning

confidence: 95%

Section: Site and Specimenmentioning

confidence: 99%

See 1 more Smart Citation

A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Paterson,

Mackie,

Capobianco

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…All these methods provide answers to various questions, such as taxonomic identification, the proteome of bone, teeth, etc. , the metaproteome, phylogeny, and post-translational modifications (PTMs). ,− However, the destructive nature of these methods is undesirable when analyzing archeological materials, such as bone remains or rare artifacts made from bone. Several important considerations must be taken into account before destructive sampling of an artifact is carried out, such as the probability of successful analysis, the choice of sampling technique to minimize traces on the object, the amount of material to be sampled, and the effects of current sampling on future research and artifact conservation …”

Section: Introductionmentioning

confidence: 99%

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Fabrizi,

Flament,

Delhon

et al. 2024

J. Proteome Res.

View full text Add to dashboard Cite

Collagen from paleontological bones is an important organic material for isotopic measurement, radiocarbon analysis, and paleoproteomic analysis to provide information on diet, dating, taxonomy, and phylogeny. Current paleoproteomic methods are destructive and require from a few milligrams to several tens of milligrams of bone for analysis. In many cultures, bones are raw materials for artifacts that are conserved in museums, which hampers damage to these precious objects during sampling. Here, we describe a low-invasive sampling method that identifies collagen, taxonomy, and post-translational modifications from Holocene and Upper Pleistocene bones dated to 130,000 and 150 BC using dermatological skin tape discs for sampling. The sampled bone micropowders were digested following our highly optimized enhanced filter-aided sample preparation protocol and then analyzed by MALDI FTICR MS and LC-MS/MS for identifying the genus taxa of the bones. We show that this low-invasive sampling does not deteriorate the bones and achieves results similar to those obtained by more destructive sampling. Moreover, this sampling method can be carried out at archeological sites or in museums.

show abstract

Immune proteins recovered in tooth enamel as a biochemical record of health in past populations: Paleoproteomic analysis of Mission Period Native Californians

Buonasera,

Eerkens,

Malarchik

et al. 2024

Journal of Archaeological Science

View full text Add to dashboard Cite

Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel

Cited by 4 publications

References 76 publications

A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Low-Invasive Sampling Method with Tape-Disc Sampling for the Taxonomic Identification of Archeological and Paleontological Bones by Proteomics

Immune proteins recovered in tooth enamel as a biochemical record of health in past populations: Paleoproteomic analysis of Mission Period Native Californians

Contact Info

Product

Resources

About