Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Significance Bacterial genomes are extremely diverse in size and composition. Biologists have long sought to explain such variability based on present-day selective and mutational forces. However, mutation rates can change dramatically over time, and experiments with hypermutable bacteria show that their genomes rapidly decay when propagated under the near absence of selection. Whether selection can prevent this decay is unclear. Here, we document the rapid genome decay of hypermutable bacteria even during tens of thousands of generations of sustained adaptation to a laboratory environment. These findings suggest the need to reexamine current ideas about the evolution of bacterial genomes, and they have implications for other hypermutable systems such as viruses and cancer cells. Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak selection, casting doubt on their general relevance. Here, we circumvent this limitation by analyzing genomes from mutator populations that arose during a long-term experiment with Escherichia coli, in which populations have been adaptively evolving for >50,000 generations. We develop an analytical framework to quantify the relative contributions of mutation and selection in shaping genomic characteristics, and we validate it using genomes evolved under regimes of high mutation rates with weak selection (mutation accumulation experiments) and low mutation rates with strong selection (natural isolates). Our results show that, despite sustained adaptive evolution in the long-term experiment, the signature of selection is much weaker than that of mutational biases in mutator genomes. This finding suggests that relatively brief periods of hypermutability can play an outsized role in shaping extant bacterial genomes. Overall, these results highlight the importance of genomic draft, in which strong linkage limits the ability of selection to purge deleterious mutations. These insights are also relevant to other biological systems evolving under strong linkage and high mutation rates, including viruses and cancer cells.