I developed 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.
Short bits of DNA, also knows as short oligonucleotides, can be copied in the lab using a technique called PCR. I developed a system that treats these short oligonucleotides (or Olis) as individuals (much like viruses, only instead of living in a cell, they live in a few microliters of liquid in a tiny tube). These populations of small Olis can evolve in response to changing conditions in their environment. Because they are so small, and so simple genetically, their evolution is easy to follow, and they can be used as a toy system to develop and test basic theory before applying it to more complex, living, systems.
The Oli system works, and evolution can be followed at the genetic, phenotypic, or fitness level.