A NOVEL ALGORITHM FOR SELECTIVE SWEEPS DETECTION IN BACTERIA

The neutral theory posits that most regions in a given genome are neutrally evolving. Identifying the specific genomic regions that evolve by natural selection is thus an important task linking phenotypic evolution and genomics. With the availability of thousands of fully sequenced genomes, we can now search for signals of positive selection better than ever before. At the population level, one method to detect signals for positive selection is to search for selective sweep. Selective sweeps were thoroughly investigated in several eukaryote organisms. However, selective sweeps in bacteria received little to no attention. This difference stems from the expectation that selective sweeps will only be found in sexual reproducing organisms and not in asexual ones such as bacteria.

In this work I demonstrate that selective sweeps can also be detected in bacteria. More specifically, focusing on an E. coli database, I first study the performance of SweepFinder, a state of the art method for selective sweep detection in eukaryotes, over these data and I discuss its limitations. Subsequently, I develop a novel phylogeny-based method, for the detection of incomplete selective sweeps and apply it over the E. coli database. I detect several interesting cases of selective sweep events. Using simulations, I demonstrate that most of the detected cases cannot be explained by neutral evolution under a model of no selection and no recombination, suggesting there is a bona fide signal for sweeps. The results presented in this study should contribute to the effort of understanding bacterial phenotypic variation and adaptation at the genomic level.