We assess the degree to which adaptation to a uniform environment among independently evolving asexual populations is associated with increasing divergence of those populations. In addition, we are concerned with the pattern of adaptation itself, particularly whether the rate of increase in mean fitness tends to decline with the number of generations of selection in a constant environment. The correspondence between the rate of increase in mean fitness and the within-population genetic variance of fitness, as expected from Fisher's fundamental theorem, is also addressed. Twelve Escherichlia coli populations were founded from a single clonal ancestor and allowed to evolve for 2,000 generations. Mean fitness increased by about 37%. However, the rate of increase in mean fitness was slower in later generations. There was no statistically significant within-population genetic variance of fitness, but there was significant between-population variance. Although the estimated genetic variation in fitness within populations was not statistically significant, it was consistent in magnitude with theoretical expectations. Similarly, the variance of mean fitness between populations was consistent with a model that incorporated stochastic variation in the timing and order of substitutions at a finite number of nonepistatic loci, coupled with substitutional delays and interference between substitutions arising from clonality. These results, taken as a whole, are consistent with theoretical expectations that do not invoke divergence due to multiple fitness peaks in a Wrightian evolutionary landscape.
Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.
The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.
The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. Here, we analyze the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at 500-generation intervals through 60,000 generations. Despite a declining rate of fitness gain, molecular evolution continues to be characterized by signatures of rapid adaptation, with multiple beneficial variants simultaneously competing for dominance in each population. Interactions between ecological and evolutionary processes play an important role, as long-term quasi-stable coexistence arises spontaneously in most populations, and evolution continues within each clade. We also present new evidence that the targets of natural selection change over time, as epistasis and historical contingency alter the strength of selection on different genes. Together, these results show that long-term adaptation to a constant environment can be a more complex and dynamic process than is often assumed.
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