# Assessing the Potential of Ancient Protein Sequences in the Study of Hominid Evolution

## TL;DR

This study explores how ancient protein sequences can help understand hominid evolution, showing both their potential and limitations in reconstructing evolutionary relationships.

## Contribution

The study quantifies the information content of ancient protein sequences and evaluates their effectiveness in phylogenetic reconstructions compared to DNA data.

## Key findings

- Some ancient proteins contain more evolutionary information than others due to differential sequence conservation.
- Protein data can sometimes lead to incorrect tree topologies due to information loss compared to DNA data.
- Concatenating multiple proteins improves resolution, but protein-based trees may not match genome-wide population trees, especially for closely related hominid groups.

## Abstract

Palaeoproteomic data can provide invaluable insights into hominid evolution over long timescales. Yet, the potential and limitations of ancient protein sequences to resolve evolutionary relations between species remains largely unexplored. In this study, we aim to quantify how much information about these relations can be obtained from limited ancient protein data, at the scale that is currently available or will be available in the near future. We harness sequence alignments of 12 enamel and collagen proteins that have been previously reported in fossil material that is at least 1 million years old. We utilize in silico translations of hominid DNA sequences of these proteins and highlight their differential sequence conservation, indicating some of them contain much larger amounts of information than others. We also evaluate the extent to which inferred topologies from protein data differ from inferred topologies from the more informationally dense DNA data. We show that the former may sometimes lead to inferences of the wrong tree topology due to the informational loss that comes when working with peptide data. Additionally, we determine the number of concatenated proteins necessary to confidently reconstruct the population/species tree summarizing the relations between humans, chimpanzees, and gorillas, as well as those between modern humans, Neanderthals, and Denisovans. As expected, increasing the number of proteins in a concatenation enhances resolution, but we note that trees inferred from the full set of collagen and enamel proteins do not necessarily correspond to population trees inferred from genome-wide data. We show this is especially the case in the closely related groups of our recent ancestors. We further demonstrate that while a number of proteins fall within archaic introgressed haplotypes of present day humans, ancient admixture is not the main source of the observed tree incongruence. Our study underscores the potential and limitations of utilizing palaeoproteomic data in deep time phylogenetic reconstructions, indicating that these will be aided not only by increased recovery of proteins in the future, but also by more careful modeling of evolutionary relations across the genome, beyond simply building single phylogenetic trees.