Adaptation by natural selection depends on the rates, effects, and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. We analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to mutation-accumulation lines evolved under a bottlenecking regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long-term populations, further supporting the inference that most mutations that reached high frequency were favoured by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.

*These authors contributed equally to this work.Adaptation depends on the rates, effects, and interactions of many mutations. We analyzed 264 genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The trajectories for genome evolution in populations that retained the ancestral mutation rate fit a model where most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and neutral mutations accumulate at a constant rate. We also compared these populations to lines evolved under a mutation--accumulation regime that minimizes selection. Nonsynonymous mutations, intergenic mutations, insertions, and deletions are overrepresented in the long--term populations, supporting the inference that most fixed mutations are favored by selection. These results illuminate the shifting balance of forces that govern genome evolution in populations adapting to a new environment.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Mutations are the ultimate source of heritable variation for evolution. Understanding how mutation rates themselves evolve is thus essential for quantitatively understanding many evolutionary processes. According to theory, mutation rates should be minimized for well-adapted populations living in stable environments, whereas hypermutators may evolve if conditions change. However, the long-term fate of hypermutators is unknown. Using a phylogenomic approach, we found that an adapting Escherichia coli population that first evolved a mutT hypermutator phenotype was later invaded by two independent lineages with mutY mutations that reduced genome-wide mutation rates. Applying neutral theory to synonymous substitutions, we dated the emergence of these mutations and inferred that the mutT mutation increased the point-mutation rate by ∼150-fold, whereas the mutY mutations reduced the rate by ∼40-60%, with a corresponding decrease in the genetic load. Thus, the long-term fate of the hypermutators was governed by the selective advantage arising from a reduced mutation rate as the potential for further adaptation declined. experimental evolution | genomics | mutators | phylogenomics M utations are the ultimate source of heritable variation for evolution. Therefore, understanding how selection can change mutation rates is crucial for quantitatively describing evolutionary processes (1). More mutations are deleterious than beneficial (2), and organisms from bacteria to eukaryotes encode proofreading and repair enzymes that reduce mutation rates (3). If selection for beneficial mutations is weak relative to selection against deleterious mutations, then the rate of adaptation in asexual populations is maximized at some intermediate mutation rate (4). However, when populations encounter new environments, selection for beneficial mutations can be strong (5), and much higher mutation rates may evolve. Indeed, surveys of laboratory populations of microbes (6-10), clinical isolates of bacterial pathogens (11,12), and some types of eukaryotic tumors (13) have revealed a surprisingly high proportion of lineages that have evolved genetic defects in repair pathways. These hypermutators often have 10-to 100-fold increased mutation rates, and such elevated mutation rates can accelerate the progression of chronic diseases and the evolution of resistance to therapeutic agents.Hypermutable mutants can become established in asexual populations while they adapt to changed environments owing to their higher per capita probability of discovering rare beneficial mutations compared with nonmutators (14-18). Although hypermutable genotypes should produce beneficial mutations at a higher rate than their less mutable counterparts, they do not necessarily increase the rate of adaptation to a corresponding, or even measurable, degree. In large asexual populations, the waiting time for new beneficial mutations to occur may be short relative to the time required for a mutant to increase from one individual to fixation in the population, assuming the be...

The quantification of spontaneous mutation rates is crucial for a mechanistic understanding of the evolutionary process. In bacteria, traditional estimates using experimental or comparative genetic methods are prone to statistical uncertainty and consequently estimates vary by over one order of magnitude. With the advent of next-generation sequencing, more accurate estimates are now possible. We sequenced 19 Escherichia coli genomes from a 40,000-generation evolution experiment and directly inferred the point-mutation rate based on the accumulation of synonymous substitutions. The resulting estimate was 8.9 × 10−11 per base-pair per generation, and there was a significant bias toward increased AT-content. We also compared our results with published genome sequence datasets for other bacterial evolution experiments. Given the power of our approach, our estimate represents the most accurate measure of bacterial base-substitution rates available to date.