Bone Proteomics for Neanderthal and Denisovan Genotyping

Ancient biomolecules have revolutionized our understanding of human evolution. Ancient proteins, in particular, preserve longer than DNA and have the potential to provide crucial insights into the evolution and demise of archaic hominins. The emerging field of palaeoproteomics, which studies ancient proteins, has mostly focused on the analyses of dental material and complete bones. However, smaller bone fragments that are morphologically uninformative—often the most common type of excavated fossil remains— remain an untapped source of important evolutionary information. BONETAG aims to utilize these fragments using recent technological advances and a unique fossil collection, and study the proteins preserved in the bones of our closest archaic relatives: Neanderthals and Denisovans. This will involve comprehensive proteomic sequencing of bones from archaic populations, some of which are linked to high-quality genetic data. BONETAG is the first project that compares ancient DNA and protein data from the same individuals in a comprehensive way. The project will initially focus on the extraction of bone proteins using a series of protocols to enhance protein recovery. This will be followed by the development of a computational method to differentiate the proteomic sequences of Neanderthals, Denisovans, and modern humans. Finally, the two workflows will be applied to a collection of hominin bone fragments that have previously failed DNA analyses but show positive signs of protein preservation. The results, as well as the workflows developed during BONETAG will be shared with the palaeoproteomic community. This will allow researchers in regions with poor DNA preservation to utilize proteins, and achieve reliable taxonomic identifications of morphologically uninformative bone fragments. By providing such broadly applicable tools and methodologies, BONETAG will significantly advance our understanding of Human Evolution and ensure that no fossil remains unexplored.