Changing fitness effects of mutations through long-term bacterial evolution

The distribution of fitness effects of new mutations shapes evolution, but it is challenging to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 generations of evolution, we quantify the fitness effects of insertion mutations in every gene. Macroscopically, the fraction of deleterious mutations changed little over time whereas the beneficial tail declined sharply, approaching an exponential distribution. Microscopically, changes in individual gene essentiality and deleterious effects often occurred in parallel; altered essentiality is only partly explained by structural variation. The identity and effect sizes of beneficial mutations changed rapidly over time, but many targets of selection remained predictable because of the importance of loss-of-function mutations. Taken together, these results reveal the dynamic—but statistically predictable—nature of mutational fitness effects. Editor’s summary The benefits and costs of mutations that undergo natural selection can change depending on genetic interactions with subsequent mutations. In an enduring experiment, 12 lineages of Escherichia coli have been maintained for more than 75,000 generations, with each generation sampled and preserved. Couce et al. made transposon insertion libraries in ancestral and evolved strains taken at the 50,000 generation point and measured fitness in competition experiments using these samples. The numbers of beneficial mutations rapidly tailed off during long-term passage, with parallel changes in fitness cost and gene essentiality occurring across the lineages. The authors found nonessential genes that became essential and essential genes that became nonessential in all lineages. Predictability stemmed from the importance of loss-of-function mutations that scale with the length of the target genes. —Caroline Ash Predictable and parallel changes occur in the fitness effects of mutations in Escherichia coli over 50,000 generations. INTRODUCTION Evolution is constrained by the mutations accessible to natural selection. The benefits and costs of these mutations are described by the distribution of fitness effects (DFE). The DFE governs the tempo and mode of adaptation by capturing the fitness landscape of the local mutational neighborhood and reflects the mutational robustness of genotypes. However, the DFE need not remain static over evolution; with every accumulating mutation, the effects and accessibility of subsequent mutations may change through genetic interactions. Understanding how the DFE changes is important for models that seek to explain the speed of adaptation, maintenance of genetic diversity, and pace of the molecular clock. RATIONALE We quantified the effects of hundreds of thousands of insertion mutations in 12 populations of Escherichia coli through 50,000 generations of experimental evolution. We generated high-coverage transposon insertion libraries in the ancestral and evolved strains and measured the fitness effects of these mutations in bulk competitions. We characterized both the statistical properties of the DFEs and the effects of mutations in specific genes. RESULTS We saw no systematic change in the deleterious tail of the DFE. By contrast, the fraction of beneficial mutations declined rapidly, with its form approaching an exponentially distributed tail. At the gene level, we saw frequent changes in the fitness effects of insertion mutations in specific genes. Both the genetic identity and effect sizes of beneficial mutations changed over time. In the deleterious tail, there were frequent changes in the costs of specific mutations and even in gene essentiality. These changes often evolved in parallel across lineages and the changes in essentiality were only partially explained by structural variation. Despite pervasive changes in the fitness effects of particular mutations over time, many targets of selection could still be predicted by combining gene length with the ancestral DFE, owing to the benefit conferred by loss-of-function mutations during early adaptation. CONCLUSION Overall, the high-level features of the fitness landscape were largely unchanged over this multi-decade evolution experiment, except for truncation of the beneficial tail of the DFE. Over the short term, the drivers of adaptation were often predictable from the gene-level details of the DFE, especially combined with the length of genes available for beneficial mutations. As the populations accumulated more mutations over longer timescales, pervasive epistasis led to changes in the magnitude and even the sign of the fitness effects of many mutations, making some previously advantageous mutations deleterious and vice versa. Consequently, some evolutionary paths that were inaccessible to the ancestor became accessible to the evolving populations, while others were closed off. Moreover, many of the changes in the fitness effects of particular mutations, both beneficial and deleterious, occurred in parallel across the replicate populations. Thus, some features of the DFEs changed repeatedly and predictably over time, even as the overall form of the fitness landscape was largely unchanged. Taken together, our results demonstrate the dynamic—but often statistically predictable—nature of mutational fitness effects. Changing distribution of fitness effects over evolution. Transposon mutagenesis of E. coli strains from a long-term evolution experiment and bulk fitness assays enable characterization of genome-wide and gene-level distribution of fitness effects (DFE). The overall shape of the DFE is conserved, except for a declining beneficial tail, while the effects of specific mutations and gene essentiality often evolve in parallel across populations. The ancestral DFE, combined with gene length, predicts drivers of adaptation.