Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

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• dc.contributor.author Fong Zazueta, Ricardo
• dc.contributor.author Krueger, Johanna
• dc.contributor.author Carrillo-Martin, Guillermo
• dc.contributor.author Ferrández Peral, Luis, 1991-
• dc.contributor.author Juan, David
• dc.contributor.author Orkin, Joseph D.
• dc.contributor.author Pawar, Harvinder
• dc.contributor.author Marquès i Bonet, Tomàs, 1975-
• dc.contributor.author Lizano González, Esther, 1974-
• dc.date.accessioned 2025-05-06T06:16:00Z
• dc.date.available 2025-05-06T06:16:00Z
• dc.date.issued 2025
• dc.description.abstract Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil taxa. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation in vivo and post mortem. This raises the question as to whether the enamelome alone provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments for each protein and estimated the evolutionary rate for each site. We examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1 to 2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We tested phylogenetic analysis on combinations of different enamel proteins and found that the composition of the proteome can influence deep splits in the phylogeny. With our methods, we provide guidance for researchers on how to evaluate the potential of paleoproteomics for phylogenetic studies before sampling valuable ancient specimens.
• dc.format.mimetype application/pdf
• dc.identifier.citation Fong-Zazueta R, Krueger J, Alba DM, Aymerich X, Beck RMD, Cappellini E, et al. Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics. Genome Biol Evol. 2025 Feb 3;17(2):evaf007. DOI: 10.1093/gbe/evaf007
• dc.identifier.doi http://dx.doi.org/10.1093/gbe/evaf007
• dc.identifier.issn 1759-6653
• dc.identifier.uri http://hdl.handle.net/10230/70305
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Genome Biol Evol. 2025 Feb 3;17(2):evaf007
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/861389
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/864203
• dc.rights © The Author(s) 2025. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Ancient biomolecules
• dc.subject.keyword Dental enamel
• dc.subject.keyword Paleoproteomics
• dc.subject.keyword Phylogenetic analysis
• dc.subject.keyword Primate evolution
• dc.subject.keyword info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
• dc.subject.keyword info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00
• dc.subject.keyword info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00
• dc.subject.keyword info:eu-repo/grantAgreement/EC/H2020/847648
• dc.title Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion