Evolutionary paleoproteomics and human origins

A PhD position for the 2021 programme in the lab of Pontus Skoglund.

Project background and description

Ancient genome sequencing has revolutionized our understanding of the evolutionary history of modern humans and close relatives such as Neandertals (Skoglund and Mathieson 2018). However, while DNA preservation in ideal cases may allow genome retrieval upwards of a million years ago, in most environments DNA retrieval may only extend up to a few thousand years ago (Skoglund et al. 2017). An emerging horizon that promises to extend our understanding of human evolution to currently unknown episodes of the past is the fact that proteins degrade more slowly than DNA, and may thus allow evolutionary informative data to be obtained from deeper time and new regions (Cappellini et al. 2019; Welker et al. 2016). However, the number of evolutionarily informative variants is much lower in paleoproteomic data, and bioinformatic methods for paleoproteome reconstruction are in their infancy (Hendy et al. 2018).

This PhD-studentship will join Pontus Skoglund and the Crick Ancient Genomics laboratory in reaching back into the deep past to gain insights into the evolution of humans and other species of the Ice Age and beyond.

Candidate background

The ideal candidate will have:

  • skills in bioinformatics and computational data science, with a strong interest in programming
  • experience or strong interest in population genetics and phylogenetics
  • a strong interest in paleoscience and the evolutionary history of hominins and other mammals

The work will include improving and developing methods for bioinformatic retrieval, authentication, and reconstruction of ancient protein sequences from extinct populations in collaboration with proteomics experts at the Francis Crick Institute and international collaborators, adapting population genetic and phylogenetic approaches, and applying the methods to data from fossil material supported by the ancient DNA facility.

References

1.         Skoglund, P. and Mathieson, I. (2018)

            Ancient genomics of modern humans: The first decade.

            Annual Review of Genomics and Human Genetics 19: 381-404. PubMed abstract

2.         Skoglund, P., Thompson, J.C., Prendergast, M.E., Mittnik, A., Sirak, K., Hajdinjak, M., . . . Reich, D. (2017)

            Reconstructing prehistoric African population structure.

            Cell 171: 59-71 e21. PubMed abstract

3.         Cappellini, E., Welker, F., Pandolfi, L., Ramos-Madrigal, J., Samodova, D., Rüther, P.L., . . . Willerslev, E. (2019)

            Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

            Nature 574: 103-107. PubMed abstract

4.         Welker, F., Hajdinjak, M., Talamo, S., Jaouen, K., Dannemann, M., David, F., . . . Hublin, J.-J. (2016)

            Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne.

            Proceedings of the National Academy of Sciences of the United States of America 113: 11162-11167. PubMed abstract

5.         Hendy, J., Welker, F., Demarchi, B., Speller, C., Warinner, C. and Collins, M.J. (2018)

            A guide to ancient protein studies.

            Nature Ecology & Evolution 2: 791-799. PubMed abstract