Phylogenetic Signal in Primate Tooth Enamel Proteins and its Relevance for Paleoproteomics

作者：Ricardo Fong-Zazueta, Johanna Krueger, David M. Alba, Xènia Aymerich, Robin M. D. Beck, Enrico Cappellini, Guillermo Carrillo-Martin, Omar Cirilli, Nathan L Clark, Omar E. Cornejo, Kyle Kai‐How Farh, Luis Ferrández-Peral, David Juan, Joanna L. Kelley, Lukas F. K. Kuderna, Jordan Little, Joseph D. Orkin, Ryan Paterson, Harvinder Pawar, Tomàs Marquès‐Bonet, Esther Lizano · 发表于：Genome Biology and Evolution · 年份：2025 · DOI：10.1093/gbe/evaf007 · 被引用次数：8 · 研究领域：Bone and Dental Protein Studies、Forensic Anthropology and Bioarchaeology Studies、dental development and anomalies

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 ...