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Experimental evolution reveals hidden diversityin evolutionary pathways

  1. Peter A Lind  Is a corresponding author
  2. Andrew D Farr
  3. Paul B Rainey
  1. Uppsala University, Sweden
  2. Massey University, New Zealand
Research Article
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Cite this article as: eLife 2015;4:e07074 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.

Article and author information

Author details

  1. Peter A Lind

    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
  2. Andrew D Farr

    New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.
  3. Paul B Rainey

    New Zealand Intitute for Advanced Study, Massey University, Auckland, New Zealand
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. Wenying Shou, Fred Hutchinson Cancer Research Center, United States

Publication history

  1. Received: February 17, 2015
  2. Accepted: March 24, 2015
  3. Accepted Manuscript published: March 25, 2015 (version 1)
  4. Accepted Manuscript updated: March 30, 2015 (version 2)
  5. Version of Record published: April 14, 2015 (version 3)


© 2015, Lind et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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