Whole-population whole-genome sequencing of virus fX174 during a 426-generation evolution experiment
The study of evolution in organisms with high mutation rates requires detailed data on the genomic composition of the population. Here we report on an innovative use of high-throughput sequencing technology combined with robotics that allowed us to follow the evolutionary dynamics of four independent bacteriophage populations for 426 generations in unprecedented detail. Tracing over 80'000 bacteriophage genomes, of which 884 are unique, we find multiple instances of parallel evolution on the level of full-length genomes, not just on the level of mutations at single sites. Computer simulations that recapitulate our experiments in great detail show that this extreme form of paralellism is inconsistent with neutral evolution. Our approach is applicable to many other viruses and opens the door to a new level of population genetic investigations, especially those that aim to shed light on phenomena that relate to genetic linkage.