Ancient genomics

About the project

About the Project A 2027 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 functional evolution and history in the human past. We use approaches in computational biology, bioinformatics, population genetics and statistical genetics to address questions about human evolution and ancestry, using thousands of ancient genomes sequenced in our lab. The overarching goal is to understand central episodes in the human past, and their impact on human societies and health. In the 2027 Crick programme, we are primarily calling for students with an interest in computational genomics in four areas. Experimental functional biology of ancient adaptive variants. Using functional experiments in immunology, virology or bacteriology to follow-up on internal findings of ancient mutations that could have been important in disease and immunity in the ancient past. Ancient functional genomics: Our in-house ancient DNA data provides variants of interest, both from human- and pathogen genomes. An emerging strand in the lab is to follow-up such variants with approaches in immunology and infection biology to understand and dissect their exact function. This would rely on substantial collaboration with immunology and/or infection experimental biology at the Crick. Ancient human genomics: We are sequencing hundreds of ancient human genomes on a regular basis, and combine them with previously published genomes to understand human history in Europe and surrounding regions. This could include analysis of British and European human genomes together with the UK Biobank, to understand high-resolution human genetic history, and/or studies of natural selection, complex structural variation, and complex traits. It could also include studying other regions and other time frames. Approaches will build on high-resolution ancestry reconstruction developed in our lab [1] and approaches to study natural selection [2, 3]. Ancient pathogen genomics: We search for pathogen DNA in the metagenomes we sequence from ancient DNA. The goal is to understand the functional genomics and evolution and prevalence of pathogens in human prehistory and history [4]. 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 phylogenetic-, and functional genomic analysis. This project would benefit from a background in pathogen genomics, computational biology, paleopathology, ancient DNA and/or evolutionary genetics. Ancient archaeological or historical genomics: Our work is also intersecting heavily with questions driven by the archaeological and historical record. Applicants with interest in integrating large-scale human- and pathogen genomic data with such questions are welcome to apply. Only one studentship is available with this group and the precise project will be decided in consultation with the supervisor. Candidate background I am looking for driven, highly organised, and collegial candidates with a documented ability to acquire strong quantitative and computational skills. The ideal candidate will have a strong academic track record in one or more of relevant fields such as: immunology, infection biology, archaeology, history, population genetics, human genetics, pathogen genomics, statistical genetics, computational biology, mathematics, and/or ancient DNA. Lab-specific question Among the topics in our lab, what range of questions are you interested in? Examples include – following up on ancient discovered mutations with experimental immunology, virology or microbiological approaches, computational genomics and statistical genetics of evolution in humans, fauna, or pathogens, ancient proteomics of human evolution, studying genetic history integrating history and archaeology. See our lab page for details .

Research areas