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Experimental evolution reveals hidden diversity in evolutionary pathways

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 path...

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Detalles Bibliográficos
Autores principales: Lind, Peter A, Farr, Andrew D, Rainey, Paul B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395868/
https://www.ncbi.nlm.nih.gov/pubmed/25806684
http://dx.doi.org/10.7554/eLife.07074
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author Lind, Peter A
Farr, Andrew D
Rainey, Paul B
author_facet Lind, Peter A
Farr, Andrew D
Rainey, Paul B
author_sort Lind, Peter A
collection PubMed
description 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. DOI: http://dx.doi.org/10.7554/eLife.07074.001
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spelling pubmed-43958682015-04-14 Experimental evolution reveals hidden diversity in evolutionary pathways Lind, Peter A Farr, Andrew D Rainey, Paul B eLife Genomics and Evolutionary Biology 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. DOI: http://dx.doi.org/10.7554/eLife.07074.001 eLife Sciences Publications, Ltd 2015-03-25 /pmc/articles/PMC4395868/ /pubmed/25806684 http://dx.doi.org/10.7554/eLife.07074 Text en © 2015, Lind et al http://creativecommons.org/licenses/by/4.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Genomics and Evolutionary Biology
Lind, Peter A
Farr, Andrew D
Rainey, Paul B
Experimental evolution reveals hidden diversity in evolutionary pathways
title Experimental evolution reveals hidden diversity in evolutionary pathways
title_full Experimental evolution reveals hidden diversity in evolutionary pathways
title_fullStr Experimental evolution reveals hidden diversity in evolutionary pathways
title_full_unstemmed Experimental evolution reveals hidden diversity in evolutionary pathways
title_short Experimental evolution reveals hidden diversity in evolutionary pathways
title_sort experimental evolution reveals hidden diversity in evolutionary pathways
topic Genomics and Evolutionary Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395868/
https://www.ncbi.nlm.nih.gov/pubmed/25806684
http://dx.doi.org/10.7554/eLife.07074
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