Fold or die: experimental evolution in vitro

TL;DR

The paper presents a novel in vitro experimental evolution system using DNA hairpins in qPCR, allowing detailed study of genetic, phenotypic, and fitness changes during adaptation.

Contribution

It introduces the Oli system, a new method for experimental evolution that is tractable at multiple biological levels and adaptable for various evolutionary studies.

Findings

Oli system successfully models adaptive evolution under different environmental change rates.

The system provides detailed genetic, phenotypic, and fitness data.

Methodological and bioinformatics tools are developed for the Oli system.

Abstract

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.