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

Abstract

59 Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides 60 that persist for long periods of time. In particular, peptides from the enamel proteome 61 (enamelome) have been used to reconstruct the phylogenetic relationships of fossil 62 specimens and to estimate divergence times. However, the enamelome is based on only 63 about 10 genes, whose protein products undergo fragmentation post mortem. Moreover, 64 some of the enamelome genes are paralogous or may coevolve. This raises the question as 65 to whether the enamelome provides enough information for reliable phylogenetic inference. 66 We address these considerations on a selection of enamel-associated proteins that has 67 been computationally predicted from genomic data from 232 primate species. We created 68 multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate 69 for each site and examined which sites overlap with the parts of the protein sequences that 70 are typically isolated from fossils. Based on this, we simulated ancient data with different 71 degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these 72 trees to a reference species tree. Up to a degree of fragmentation that is similar to that of 73 fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at 74 family level are consistent with the reference species tree. We found that the composition of 75 the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of 76 molecular phylogenies based on paleoproteomic data, we recommend characterizing the 3 bioRxiv preprint doi: https://doi.org/10.1101/2024.02.28.580462; this version posted February 29, 2024. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 77 evolution of the proteomes from the closest extant relatives to maximize the reliability of 78 phylogenetic inference. 79