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HOminin Proteomes in human Evolution

Periodic Reporting for period 1 - HOPE (HOminin Proteomes in human Evolution)

Reporting period: 2018-11-01 to 2020-10-31

This project aimed to reconstruct the genetic relationships between our and extinct hominin species from sites and time periods incompatible with ancient DNA preservation through mass-spectrometry based sequencing of ancient hominin proteins. Understanding the evolutionary relationships between extinct and extant hominins is a major goal of palaeoanthropology, including insights into population dynamics and traits selected for/against in particular hominin lineages. Up to recently this was exclusively achieved through ancient DNA analysis. Ancient DNA survives for a limited amount of time, however, and is commonly degraded entirely after 0.5 or 1.0 Ma. A new biomolecular approach to this issue is the analysis of ancient proteins preserved in enamel, dentine and bone from hominin fossils, as recent studies demonstrate that ancient proteins survive for longer stretches of time than DNA. HOPE will advance these developments by applying novel methodological approaches to the extraction and characterization of hominin ancient proteins in samples beyond the survival of ancient DNA. Specific objectives were 1) to test proposed evolutionary hypotheses on hominin evolution through the characterization of ancient enamel protein sequences from a number of extinct hominin populations of significant age, 2) to increase non-collagenous protein sequence recovery, 3) to explore the population proteomic potential of hominin proteomes, and 4) to understand changes in enamel proteome composition throughout hominid evolution. These objectives were realized by analysing hominin specimens from a range of taxonomic clades present in the Early, Middle and Late Pleistocene of Africa and Eurasia.
HOPE primarily utilized protein mass spectrometry analysis on a range of fossil samples to characterize proteome and protein sequence composition. This included fauna samples, hominin samples, or a combination of both, depending on objectives and material availability. The molecular work was carried out in ancient biomolecular laboratories now housed at the Globe Institute, the University of Copenhagen (Denmark). For comparison, the project also studied a limited number of modern or near-modern dental specimens. During this period, I gained advanced insights into protein mass spectrometry, extraction method (development), and bioinformatic analysis of the resulting datasets. In return, I brought my human evolution knowledge to the hosting institute.

The main outcome of this research was that proteins are recoverable beyond the limits of ancient DNA preservation, and that proteins preserved in enamel specifically survive over extended geological time scales. These proteins remain phylogenetically informative. In other words, their amino acid sequences are variable enough from species to species to determine evolutionary relationships. Simultaneously, be either enlarging the number of proteases used, or entirely eliminating them, the project was involved in enhancing extraction methods for proteins in skeletal material generally. These new approaches either allow access to extremely ancient proteomes, or enhance proteome complexity, and thereby their evolutionary utility.

During HOPE, a 3-month secondment to the group of Dr.. Skoglund at the Crick Institute provided a training opportunity to acquire enhanced insights into population genetic methods and their potential applicability to ancient protein datasets in the future. The training was completed successfully.
HOPE provided novel interdisciplinary insights into human evolution and methodological tools of use across palaeonthropology and evolutionary biology. The main result of HOPE, that ancient proteins survive in the hominin fossil record across their Eurasian range for the past 2 million years, thereby covering the entire presence of hominins outside of Africa, has tremendous implications for our understanding of human evolution. Ultimately, this includes a better understanding of our own background as a species as well. These results have opened up new questions for even older time periods, both within and outside of Eurasia, while some of the methodological advances provided through HOPE have further applications beyond human fossils. Within the context of the latter, significant advances might therefore be possible in utilizing ancient proteins to further characterize hominin behaviour, disease, and interactions with the environment, partly based on advances made during HOPE.

The bioinformatics training achieved during the secondment have shown potential for future enhancement, and would opportunistically provide another step-change in our ability to analyze ancient protein datasets for evolutionary purposes.

The impact of this research has been noticed by global media, and resulted in the appearance in various written, radio, and TV outlets.
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