A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

LC-MS/MS extends on the MALDI-TOF ZooMS approach by providing fragmentation spectra for each peptide. However, ancient bone samples generate sparse datasets containing only a few collagen proteins, rendering target-decoy strategies unusable and increasing uncertainty in peptide annotation. ClassiCOL embraces and even extends this ambiguity using a novel isoBLAST approach. The exhaustive set of potential peptide candidates created in this way is then used to retain or reject different potential paths at each taxonomic branching point down to the taxonomic level attainable with the sample information, always allowing for potential mixtures in the process. As an end point, all considered ambiguity is graphically represented with a clear prioritization of the species in the sample. Using public as well as in-house data, we demonstrate the performance of this universal postprocessing approach on different instruments and explore the possibility of identifying genetic as well as sample mixtures. Diet reconstruction from 40,000 year old cave hyena coprolites illustrates the exciting potential of this approach.

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On the Mkv Model with Among-Character Rate Variation

Capobianco,

Höhna

2024

Preprint

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Models used in likelihood-based morphological phylogenetics often adapt molecular phylogenetics models to the specificities of morphological data. Such is the case for the widely used Mkv model---which introduces an acquisition bias correction for sampling only characters that are observed to be variable---and for models of among-character rate variation (ACRV), routinely applied by researchers to relax the equal-rates assumption of Mkv. However, the interaction between variable character acquisition bias and ACRV has never been explored before. We demonstrate that there are two distinct approaches to condition the likelihood on variable characters when there is ACRV, and we call them joint and marginal acquisition bias. Far from being just a trivial mathematical detail, we show that the way in which the variable character conditional likelihood is calculated results in different assumptions about how rate variation is distributed in morphological datasets. Simulations demonstrate that tree length and amount of ACRV in the data are systematically biased when conditioning on variable characters differently from how the data was simulated. Moreover, an empirical case study with extant and extinct taxa reveals a potential impact not only on the estimation of branch lengths, but also of phylogenetic relationships. We recommend the use of the marginal acquisition bias approach for morphological datasets modeled with ACRV. Finally, we urge developers of phylogenetic software to clarify which acquisition bias correction is implemented for both estimation and simulation, and we discuss the implications of our findings on modeling variable characters for the future of morphological phylogenetics.

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A 20+ Ma old enamel proteome from Canada’s High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

Cited by 3 publications

References 80 publications

Paleoproteomics sheds light on million-year-old fossils

Paleoproteomics sheds light on million-year-old fossils

ClassiCOL: LC-MS/MS analysis for ancient species Classification via Collagen peptide ambiguation

On the Mkv Model with Among-Character Rate Variation

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