Biochemistry & Proteomics Computational & Systems Biology Ecology, Evolution & Ethology Genetics & Genomics Infectious Disease
A 2023 Crick PhD project with Pontus Skoglund
Project background and description
This PhD-student will join the Crick ancient genomics laboratory and Group Leader Pontus Skoglund to study evolution and history in the human past. We use ancient protein and DNA retrieval together with computational biology and evolutionary genetics to address questions about human evolution and ancestry. The overarching goal is to understand central episodes in the human past, and their impact on human societies and health.
Questions that the laboratory studies include:
• Computational ancient proteomics and human evolution. Developing computational methods in the incipient field of ancient proteomics to increase the proteomic complexity recovered, understand and exclude contamination, and eliminate biases in downstream population genetic analyses. The ultimate goal is to solve outstanding questions about the origin of Homo sapiens and other hominin species. This project requires a background in proteomics or computational biology, and an interest in evolutionary genetics and paleoanthropology.
• Ancient pathogen genomics and metagenomics. Studying ancient pathogen genome evolution using metagenomic analysis of ancient genome sequence data. The goal is to understand the functional genomics and evolution of strains in human prehistory and history. The project includes using metagenomic approaches to search for viral and bacterial pathogen DNA in large ancient DNA data sets in the lab and the literature, and follow up potential positives with targeted sequencing, phylogenetic-, and functional genomic analysis. This project would benefit from a background in pathogen genomics, computational biology, paleopathology, ancient DNA and/or evolutionary genetics.
• Origins and evolution of domestic dogs. Using ancient canid material collected in the lab to understand where the first dogs came from, how dog populations continued to track human groups, and evolution of traits in response to new environments. This project is focused on computational population genetics, with possibilities to also participate in collection, sampling and molecular retrieval of ancient DNA.
These are examples of the sorts of projects that may be available. Only one studentship is available with this group and the precise project will be decided in consultation with the supervisor.
We are looking for driven, disciplined, and collegial candidates with a humble can-do learn-it-all attitude and documented ability to acquire quantitative and computational skills. The ideal candidate will have a strong academic track record and research project experience in one or more relevant fields such as: proteomics, metagenomics, population genetics, ancient DNA, computational biology, palaeoanthropology, and archaeological science.
1. Swali, P., Schulting, R., Gilardet, A., Kelly, M., Anastasiadou, K., Glocke, I., . . . Skoglund, P. (2022)
Preprint: Yersinia pestis genomes reveal plague in Britain 4,000 years ago.
Available at: BioRxiv. https://www.biorxiv.org/content/biorxiv/early/2022/01/26/2022.01.26.477195.full.pdf
2. Bergström, A., Stanton, D.W.G., Taron, U.H., Frantz, L., Sinding, M.H.S., Ersmark, E., . . . Skoglund, P. (2022)
Grey wolf genomic history reveals a dual ancestry of dogs.
Nature 607: 313-320. PubMed abstract
3. Hajdinjak, M., Mafessoni, F., Skov, L., Vernot, B., Hübner, A., Fu, Q., . . . Pääbo, S. (2021)
Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.
Nature 592: 253-257. PubMed abstract
4. Bergström, A., Stringer, C., Hajdinjak, M., Scerri, E.M.L. and Skoglund, P. (2021)
Origins of modern human ancestry.
Nature 590: 229-237. PubMed abstract
5. Bergström, A., Frantz, L., Schmidt, R., Ersmark, E., Lebrasseur, O., Girdland-Flink, L., . . . Skoglund, P. (2020)
Origins and genetic legacy of prehistoric dogs.
Science 370: 557-564. PubMed abstract