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

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 o...

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Autores: Fong Zazueta, Ricardo, Krueger, Johanna, Carrillo-Martin, Guillermo, Ferrández Peral, Luis, 1991-, Juan, David, Orkin, Joseph D., Pawar, Harvinder, Marquès i Bonet, Tomàs, 1975-, Lizano González, Esther, 1974-
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/70305
Acceso en línea:http://hdl.handle.net/10230/70305
http://dx.doi.org/10.1093/gbe/evaf007
Access Level:acceso abierto
Palabra clave:Ancient biomolecules
Dental enamel
Paleoproteomics
Phylogenetic analysis
Primate evolution
info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00
info:eu-repo/grantAgreement/EC/H2020/847648
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spelling Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomicsFong Zazueta, RicardoKrueger, JohannaCarrillo-Martin, GuillermoFerrández Peral, Luis, 1991-Juan, DavidOrkin, Joseph D.Pawar, HarvinderMarquès i Bonet, Tomàs, 1975-Lizano González, Esther, 1974-Ancient biomoleculesDental enamelPaleoproteomicsPhylogenetic analysisPrimate evolutioninfo:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00info:eu-repo/grantAgreement/EC/H2020/847648Ancient 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.Oxford University Press202520252025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/70305http://dx.doi.org/10.1093/gbe/evaf007http://hdl.handle.net/10230/70305reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGenome Biol Evol. 2025 Feb 3;17(2):evaf007info:eu-repo/grantAgreement/EC/H2020/861389info:eu-repo/grantAgreement/EC/H2020/864203© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/703052026-05-29T05:05:01Z
dc.title.none.fl_str_mv Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
title Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
spellingShingle Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
Fong Zazueta, Ricardo
Ancient biomolecules
Dental enamel
Paleoproteomics
Phylogenetic analysis
Primate evolution
info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00
info:eu-repo/grantAgreement/EC/H2020/847648
title_short Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
title_full Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
title_fullStr Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
title_full_unstemmed Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
title_sort Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
dc.creator.none.fl_str_mv Fong Zazueta, Ricardo
Krueger, Johanna
Carrillo-Martin, Guillermo
Ferrández Peral, Luis, 1991-
Juan, David
Orkin, Joseph D.
Pawar, Harvinder
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author Fong Zazueta, Ricardo
author_facet Fong Zazueta, Ricardo
Krueger, Johanna
Carrillo-Martin, Guillermo
Ferrández Peral, Luis, 1991-
Juan, David
Orkin, Joseph D.
Pawar, Harvinder
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author_role author
author2 Krueger, Johanna
Carrillo-Martin, Guillermo
Ferrández Peral, Luis, 1991-
Juan, David
Orkin, Joseph D.
Pawar, Harvinder
Marquès i Bonet, Tomàs, 1975-
Lizano González, Esther, 1974-
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ancient biomolecules
Dental enamel
Paleoproteomics
Phylogenetic analysis
Primate evolution
info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00
info:eu-repo/grantAgreement/EC/H2020/847648
topic Ancient biomolecules
Dental enamel
Paleoproteomics
Phylogenetic analysis
Primate evolution
info:eu-repo/grantAgreement/ES/3PE/PID2021-126004NB-100
info:eu-repo/grantAgreement/ES/2PE/PID2020-116908GB-I00
info:eu-repo/grantAgreement/ES/2PE/PID2020-117289GB-I00
info:eu-repo/grantAgreement/EC/H2020/847648
description 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.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025
2025
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/70305
http://dx.doi.org/10.1093/gbe/evaf007
http://hdl.handle.net/10230/70305
url http://hdl.handle.net/10230/70305
http://dx.doi.org/10.1093/gbe/evaf007
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Genome Biol Evol. 2025 Feb 3;17(2):evaf007
info:eu-repo/grantAgreement/EC/H2020/861389
info:eu-repo/grantAgreement/EC/H2020/864203
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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