Fold or die: experimental evolution in vitro

We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form structures that self-prime under defined conditions. Selection acts on the phenotype of self-priming, after which differences in fitness are amplified and quantified using qPCR. We outline the methodological and bioinformatics tools for the Oli system here, and demonstrate that it can be used as a conventional experimental evolution model system by test-driving it in an experiment investigating adaptive evolution under different rates of environmental change. 3 A central goal of evolutionary biology is to explain adaptation seamlessly from gene to ecosystem – to identify genetic changes within a population, quantify the action of natural selection on genetic variation, link this genetic variation to phenotypic variation and to variation in fitness, and finally, to relate organismal changes to adaptation to some aspect of the environment. To do this comprehensively in a real population in a real ecosystem requires persistence and luck. The handful of successes study traits with a simple genetic basis underlying a phenotype with a clear and easily measured adaptive value, or involve research lifetimes devoted to the careful study of a single natural system (Abzhanov et al. 2006; Schluter et al. 2010). One alternative to such luck and devotion is to bring evolution into the lab, where biologists can carefully control environmental conditions and use genetically-tractable model organisms to study traits that have clear links to fitness particular environmental drivers. This approach has been successful with systems such as Pseudomonas, where adaptive radiation can be reliably induced under laboratory conditions (Spiers et al. 2002; McDonald et al. 2009). However, we are still unable to predict or interpret most of the genetic variation that occurs during lab selection experiments, even in our best-studied model organisms evolved in monocultures in simple environments, and many of our insights stem from case studies of exceptions rather than systematic surveys (Barrick et al. 2009). Although high-throughput sequencing can give us a comprehensive picture of genetic changes, it cannot help us link these genetic changes to changes in phenotype or to particular environmental drivers. In short, published studies have provided us with a sample of what can happen in adapting populations, but have left open the question of what, on …