Academic journal article Genetics

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia Coli

Academic journal article Genetics

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia Coli

Article excerpt

THE long-term evolution experiment (LTEE) spans . 25 years and 60,000 generations of bacterial evolution. In this experiment, 12 replicate populations of Escherichia coli have been propagated in a simple environment, and samples of each population have been frozen at 500-generation intervals. This experiment originally focused on whether and to what extent the populations would diverge in their mean fitness and other phenotypic properties as they adapted to identical environments (Lenski et al. 1991; Lenski and Travisano 1994). Over time, this experiment has become a model for exploring many other aspects of evolution, including the emergence of new functions (Blount et al. 2008), the evolution of mutation rates (Sniegowski et al. 1997), the maintenance of genetic diversity (Elena and Lenski 1997; Rozen and Lenski 2000; Le Gac et al. 2012), and the structure of the fitness landscape (Khan et al. 2011; Woods et al. 2011; Wiser et al. 2013). The ability to examine these and other issues has grown tremendously as data that were difficult or impossible to obtain when the LTEE began have yielded to new technologies, particularly genome sequencing (Barrick and Lenski 2009, 2013; Barrick et al. 2009; Blount et al. 2012; Wielgoss et al. 2013).

The LTEE has also inspired theoretical work, especially on the dynamics of adaptation in large asexual populations (Gerrish and Lenski 1998; Hegreness et al. 2006; Desai and Fisher 2007; Schiffels et al. 2011; Park and Krug 2013; Wiser et al. 2013). The LTEE populations are subject to clonal interference, a phenomenon that limits the rate of adaptation by natural selection in large asexual populations. In the absence of recombination, two or more beneficial mutations that appear in different lineages in the same population cannot recombine into a single background; instead, the lineages that possess alternative beneficial mutations compete with one another. As a consequence, each beneficial mutation will interfere with the progress of other contending beneficial mutations toward fixation, though the mean fitness of the population will nonetheless rise as the beneficial alleles collectively displace their progenitors. Although some early theory on clonal interference was developed with the LTEE in mind (Gerrish and Lenski 1998), other evolution experiments using bacteria and yeast have provided compelling demonstrations of this phenomenon by combining dense temporal sampling with intensive discrimination using genetic markers (de Visser and Rozen 2006; Hegreness et al. 2006; Woods et al. 2011; Barroso-Batista et al. 2014; Levy et al. 2015), in-depth analysis of genes under positive selection (Lee and Marx 2013), or wholegenome sequencing (Lang et al. 2011, 2013).

Without clonal interference, the classic model of periodic selection in asexual populations involves selective sweeps of beneficial mutations that arise singly and fix sequentially. Neutral and nearly neutral mutations that would otherwise accumulate in an evolving population are swept out (or occasionally to fixation) as each successive beneficial mutation goes to fixation (Atwood et al. 1951). As a consequence, within-population genetic diversity rises and falls in conjunction with the successive sweeps, and no specific polymorphism is maintained indefinitely. Clonal interference can increase genetic diversity in three ways. First, the multiple beneficial mutations, all rising to moderate frequencies, increase diversity relative to a single allele rising to high frequency. Second, the beneficial alleles remain at intermediate frequencies longer than would a single beneficial mutation of comparable effect size during a classic sweep. Third, while the beneficial mutations remain at intermediate frequencies, their associated lineages can accumulate neutral and nearly neutral polymorphisms that also persist longer than they would in the face of selective sweeps that progress to fixation. Nonetheless, the diversity-promoting effects of clonal interference are only transient because eventually one lineage or another will prevail, either because the beneficial mutation it carries is superior to the others (even though all lineages are more fit than their predecessors) or because one lineage acquires additional beneficial mutations that eventually break the logjam. …

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