Experimental evolution reveals hidden diversity in evolutionary pathways

• Published in: eLife Vol. 4
• Main Authors: Lind, Peter A, Farr, Andrew D, Rainey, Paul B
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 25.03.2015; eLife Sciences Publications, Ltd
• Subjects: bacterial evolution; Bias; Biological Evolution; c-di-GMP; diguanylate cyclase; Directed Molecular Evolution; Evolution; Evolution & development; evolutionary rule; evolutionary rules; Experiments; Gene Fusion; genetic constraint; Genetic Fitness; Genomes; Genomics and Evolutionary Biology; Mutation; Mutation - genetics; parallel evolution; Phenotype; Population; Promoter Regions, Genetic - genetics; Pseudomonas fluorescens - genetics; Pseudomonas fluorescens SBW25; RNA, Messenger - genetics; RNA, Messenger - metabolism; Transcription, Genetic; diguanylate cyclase; parallel evolution; evolutionary biology; genetic constraint; bacterial evolution; genomics; Pseudomonas fluorescens; evolutionary rules
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/eLife.07074

Replicate populations of natural and experimental organisms often show evidence of parallel genetic evolution, but the causes are unclear. The wrinkly spreader morph of Pseudomonas fluorescens arises repeatedly during experimental evolution. The mutational causes reside exclusively within three pathways. By eliminating these, 13 new mutational pathways were discovered with the newly arising WS types having fitnesses similar to those arising from the commonly passaged routes. Our findings show that parallel genetic evolution is strongly biased by constraints and we reveal the genetic bases. From such knowledge, and in instances where new phenotypes arise via gene activation, we suggest a set of principles: evolution proceeds firstly via pathways subject to negative regulation, then via promoter mutations and gene fusions, and finally via activation by intragenic gain-of-function mutations. These principles inform evolutionary forecasting and have relevance to interpreting the diverse array of mutations associated with clinically identical instances of disease in humans. Different living things often develop similar strategies to adapt to the environments in which they live. Sometimes two species that share a common ancestor independently evolve the same trait by changing the exact same genes. This is called ‘parallel evolution’, and it has led some scientists to ask: are there certain traits that can only evolve in a limited number of ways? Or are there other ways to evolve the same trait that, for some reason, are not explored? Experimentally, investigating these questions is challenging, but parallel evolution occurs in the laboratory as well as in the wild. Many commonly studied organisms—such as fruit flies or bacteria—can be used in relevant studies, because they can be grown in large numbers and then exposed to identical environments. However, if this method fails to find a new way that a trait can evolve, it doesn't mean that alternative mechanisms do not exist. Lind et al. used a different approach that instead relies on removing all of the known pathways that can be mutated to produce a given trait and then seeing if that trait can still evolve via mutations elsewhere. The experiments involved a bacterium called Pseudomonas fluorescens that can evolve to grow flattened and wrinkled colonies (instead of smooth, round ones) when it has to compete for access to oxygen. Previous experiments had shown that the evolution of the so-called ‘wrinkly spreader’ form can be caused by mutations in one of three biological pathways. But P. fluorescens can survive unharmed without these pathways, which enabled Lind et al. to ask if there might be other ways that this trait could evolve. Bacteria without these three pathways were engineered and then grown under oxygen-deprived conditions. This experiment produced 91 new mutants that each had the wrinkly spreader phenotype. Further experiments revealed that together these mutants represented 13 previously unrecognized ways that the ‘wrinkly spreader’ phenotype can evolve. The new rare mutants had similar fitness as the previously known, common ones—so this cannot explain why they hadn't been seen before. Lind et al. instead suggest a set of principles to explain why these newly discovered pathways are rarely mutated and how genetic constraints can bias the outcome of evolution. Further work could investigate whether these principles can help us to predict the course of evolution in other biological contexts, such as in the evolution of antibiotic resistance.