The Dynamics of Fitness and Metagenomic Trajectories in a Long-Term Evolution Experiment with E. coli
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During evolution in a constant environment, large asexual populations undergo an initial phase of rapid fitness increase, followed by an indefinitely long period of slower adaptation. While the initial phase has been extensively examined, the mechanisms underlying long-term adaptation remain poorly understood. In this study, we construct and analyze the long-term fitness trajectory ofAra+2, a population from the Lenski E. coli Long-Term Evolution Experiment (LTEE), over later generations when adaptation is slow. We find that Ara+2 increased in mean fitness by ~8% between 36,000 and 66,000 generations, with its steadily rising fitness punctuated by step-like gains. Using a model that reflects mutational frequencies from metagenomic sequencing, we show that each step corresponds to a selective sweep of beneficial and hitchhiking mutations. Indeed, the metagenomic model predicts fitness changes in Ara+2 better than any traditional curvilinear model. Understanding such genotype-phenotype relationships is necessary to build a more comprehensive understanding of fitness landscapes and a more predictive theory of bacterial evolution. By studying the coupling of metagenomic and fitness trajectories in the LTEE, we take an important step towards this goal.