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| Pàgina inicial > Articles > Articles publicats > Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics |
(Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (Institut Català de Paleontologia Miquel Crusafont) (Institut Català de Paleontologia Miquel Crusafont) (University of Salford. School of Science, Engineering and Environment) (University of Copenhagen. Globe Institute) (Institut Català de Paleontologia Miquel Crusafont) (University of Pittsburgh. Department of Biological Sciences) (University of California Santa Cruz. Ecology and Evolutionary Biology) (Illumina Artificial Intelligence Laboratory, San Diego) (Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (University of California Santa Cruz. Ecology and Evolutionary Biology) (Illumina Artificial Intelligence Laboratory, San Diego) (University of Utah. Department of Human Genetics) (Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (University of Copenhagen. Globe Institute) (Universitat Pompeu Fabra. Departament de Medicina i Ciències de la Vida) (Institut Català de Paleontologia Miquel Crusafont) (Institut Català de Paleontologia Miquel Crusafont)
| Data: | 2025 |
| Resum: | 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 1-2 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. |
| Ajuts: | European Commission 861389 European Commission 864203 Agencia Estatal de Investigación PID2021-126004NB-I00 Agència de Gestió d'Ajuts Universitaris i de Recerca 2021/SGR-00177 Agencia Estatal de Investigación PID2020-116908GB-I00 Agencia Estatal de Investigación PID2020-117289GB-I00 Agència de Gestió d'Ajuts Universitaris i de Recerca 2001/SGR-00620 "la Caixa" Foundation 100010434 European Commission 847648 Agencia Estatal de Investigación JDC2022-048590-I |
| Nota: | Altres ajuts: CERCA Programme/Generalitat de Catalunya |
| Drets: | Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.  |
| Llengua: | Anglès |
| Document: | Article ; recerca ; Versió publicada |
| Matèria: | Ancient biomolecules ; Primate evolution ; Dental enamel ; Paleoproteomics ; Phylogenetic analysis |
| Publicat a: | Genome biology and evolution, Vol. 17, Issue 2 (February 2025) , art. evaf007, ISSN 1759-6653 |
