Genomics of eco-evolutionary dynamics in coevolving predator-prey systems

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Reciprocal evolutionary changes of interacting species are major drivers for diversification and speciation and have mainly been studied in host-parasite systems and for mutualistic interactions. Although predator-prey interactions are commonplace and characterized by strong selection from both sides, predator-prey coevolution and its consequences on diversification have rarely been studied and never on the sequence level. Here we propose to combine a long-term experimental evolution study with whole genome sequencing of microbial populations over time. We allowed 7 bacterial species to evolve in replicate cultures in the absence and in the presence of the ciliate Tetrahymena thermophila (predator) for 34 months. We have already collected data on the population sizes over time and started to assay evolutionary changes in the prey and predator on the phenotype level of prey (growth and defense against ciliate) and predator (growth and offence) from preserved samples. Within the proposed project, we plan to sequence predator and prey populations from multiple time points. Based on previous work, we aim to identify adaptive allele changes, follow allele trajectories over time, compare within and between species changes in the prey, correlate changes in the prey and predator population and finally link these dynamics to the phenotypic and population size changes. These will be the first data following predator-prey coevolution on the genome level including information on the whole genome and for whole populations over time. The experimental design allows us further to compare evolutionary changes within replicates of the same species as well as across species, giving us the unique opportunity to assess the repeatability of evolutionary change in terms of mutations arsing and their trajectory as well as in terms of patterns of evolutionary change, such as the occurrence of selective sweeps, clonal interference or frequency dependent selection.