How can we understand how bacterial pathogens evolve? Current sequencing techniques allow us to receive high-quality genomes from samples within and between hosts. Typically, the pathogens will amass their genomic changes within the host. Thus, to understand pathogen evolution, we need to understand within-host evolution. However, present-day inference tools for evolutionary parameters (selection, demography) are often designed for other species (for instance humans) and work on large evolutionary timescales (many generations) and thus are not automatically suited for analysing within-host samples, as these are operating on relatively short(er) timescales. Your task will be to simulate various evolutionary scenarios of within-host evolution of bacterial pathogens, understand what drives changes in genetic diversity of within-host populations, assess whether current methods allow to infer population genetic parameters and, if not, design your own inference methods using a machine-learning approach – as well as observing the limits what we can infer from a sample of a given size. Now equipped with a suitable approach to inference, you will assess the within-host evolution of several (previously sequenced and available) within-host data sets from Heliobacter pylori and Streptococcus pneumoniae.    Sounds interesting as your PhD thesis? Want to come to Leicester (UK) for this? Then, have a look at the full description here: https://le.ac.uk/study/research-degrees/funded-opportunities/bbsrc-mibtp , which also shows other very interesting projects of my colleagues in Leicester you can apply for. The studentship is part of the BBSRC Midlands Integrative Biosciences Training Partnership, whose 4-year studentships are open to UK and international applicants and come with tuition and a project budget. Please see https://warwick.ac.uk/fac/cross_fac/mibtp/phd/ for more information (and even more interesting projects at other Midlands universities). Deadline for application is January 16th 2025. Any more questions? Feel free to send me an email: ff95@leicester.ac.uk. Fabian Freund, Lecturer for Population Genomics Department of Genetics and Genome Biology, University of Leicester, UK ff95@leicester.ac.uk (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)