Hominin phyloproteomics for the Pleistocene: PalaeoPROteomics of Skeletal Parts for Evolutionary Research

Project Information

PROSPER

Grant agreement ID: 948365

DOI

10.3030/948365

EC signature date 6 November 2020

Start date 1 December 2020

End date 31 December 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 995,00

EU contribution

€ 1 499 995,00

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 3 - PROSPER (Hominin phyloproteomics for the Pleistocene: PalaeoPROteomics of Skeletal Parts for Evolutionary Research)

Reporting period: 2023-12-01 to 2025-05-31

Summary of the context and overall objectives of the project

A new picture of our own ancestral past has emerged through the genomic elucidation of the complex evolutionary relationships between Neanderthals, Denisovans, and modern humans. The insight that these three hominin populations exchanged genetic material through hybridization, and that this is detectable in modern humans living today, is now a central part of both scientific and societal discourse. Understanding these evolutionary processes in detail, and how they might affect the health of people living today, has become central of our understanding of ourselves. Nevertheless, how preceding hominin populations fit into their story is currently unknown. It has become clear that Pleistocene hominin populations were highly diverse. In addition to Homo erectus and Homo antecessor, they also include recently described populations such as the Denisovans, Homo floresiensis, Homo luzonensis, and Homo naledi, and previously described but elusive, and highly discussed, populations, such as Homo heidelbergensis. These hominins were present across Africa and Eurasia, with large portions of the hominin fossil record beyond the reach of ancient DNA research. It is difficult to understand the distribution in time and space of these hominin populations, and elucidate their relation to the emergence of novel hominin behaviours evident in the archaeological record, using traditional approaches.

Palaeoproteomic analysis of skeletal proteomes has recently emerged as a potential biomolecular approach across the Pleistocene, and can provide molecular evidence on hominin evolutionary relationships on a global scale. In order to fulfil the promise of palaeoproteomics on Pleistocene material, PROSPER aims to (1) characterize the variation in proteome composition within the human skeleton, (2) develop enhanced approaches to sampling skeletal remains, and (3) acquire enhanced protein recovery and analysis methods dedicated to the analysis of ancient hominin proteomes. With these insights and methods available, PROSPER aims to gain unique insights into the evolutionary relationships between Pleistocene hominins across their African and Eurasian distribution, specifically in the last one million years, for a number of hominin specimens of particular significance. This includes the emergence and dispersal of our own species, Homo sapiens.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

PROSPER has made progress towards its overall objectives in several areas. The research team is largely assembled. In addition, PROSPER has also made it possible for three PhD students to visit the group at the University of Copenhagen, ensuring transfer of knowledge as well as the generation of some of the datasets at the core of PROSPER.

We have begun laboratory work on the characterization of skeletal proteome variation. Various technical and methodological approaches for skeletal proteome quantification and comparison have been explored. Initial results are positive in terms of the core research goals, with the bulk of proteomic data currently being generated.

We have begun our comparative research in determining optimal extraction approaches for Pleistocene skeletal proteomes, with surprising and novel insights being generated for both fauna and hominin datasets. The PROSPER team is finalizing the first round of publications on extraction method comparisons and comparative sampling approaches for a range of tissues and preservation conditions, demonstrating that significant steps can be made towards the generation of larger skeletal proteomes from Pleistocene archaeological material.

Proteomic screening to determine proteome preservation at key sites of interests, as well as to identify additional hominin remains, is in an advanced state. The collaborative team has expanded in this area, providing the potential for additional material of phyloproteomic interest to be analyzed in the future. In addition, PROSPER has been involved in the realization of a new proteomic approach for medium-throughput, medium-depth species identification approach. We plan to use this approach for subsequent proteomic screening part of PROSPER, alongside existing, traditional approaches. PROSPER has also been involved in enabling a first workshop on ZooMS and its integration with zooarchaeological research practices (2023, University of Kent). The workshop was very well attended, will result in a special issue of the journal Paleoanthropology, and hopefully results in further research network activities in the coming period.

Finally, PROSPER has begun analysis and publication of the first sets of Middle and Late Pleistocene hominin skeletal samples.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

PROSPER has provided a surprising amount of insights into proteome preservation and the complexities involved in their extraction. Furthermore, through our various approaches to fauna screening using different proteomic methods we have become increasingly interested in further collaborations with the zooarchaeological community. In the coming period, PROSPER expect to deliver the results of sampling and processing guidelines for skeletal proteomes and the completion of the phyloproteomic analysis of several Middle and Late Pleistocene hominin proteomes of relevance to understanding human evolution in this time period. We will also hire our final team member.

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