Literature DB >> 25449178

The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment.

Kami E Chiotti1, Daniel J Kvitek2, Karen H Schmidt1, Gregory Koniges1, Katja Schwartz2, Elizabeth A Donckels2, Frank Rosenzweig3, Gavin Sherlock4.   

Abstract

The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However, empirical data as to the topography of fitness landscapes are limited, owing to difficulties in measuring fitness for large numbers of genotypes under any condition. We previously reported a case of reciprocal sign epistasis (RSE), where two mutations individually increased yeast fitness in a glucose-limited environment, but reduced fitness when combined, suggesting the existence of two peaks on the fitness landscape. We sought to determine whether a ridge connected these peaks so that populations founded by one mutant could reach the peak created by the other, avoiding the low-fitness "Valley-of-Death" between them. Sequencing clones after 250 generations of further evolution provided no evidence for such a ridge, but did reveal many presumptive beneficial mutations, adding to a growing body of evidence that clonal interference pervades evolving microbial populations.
Copyright © 2014 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Epistasis; Evolution; Genomics; Yeast

Mesh:

Substances:

Year:  2014        PMID: 25449178      PMCID: PMC4454348          DOI: 10.1016/j.ygeno.2014.10.011

Source DB:  PubMed          Journal:  Genomics        ISSN: 0888-7543            Impact factor:   5.736


  56 in total

1.  Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes.

Authors:  Frank J Poelwijk; Sorin Tănase-Nicola; Daniel J Kiviet; Sander J Tans
Journal:  J Theor Biol       Date:  2010-12-16       Impact factor: 2.691

2.  Crystal structure of an ancient protein: evolution by conformational epistasis.

Authors:  Eric A Ortlund; Jamie T Bridgham; Matthew R Redinbo; Joseph W Thornton
Journal:  Science       Date:  2007-08-16       Impact factor: 47.728

3.  The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.

Authors:  S J Gould; R C Lewontin
Journal:  Proc R Soc Lond B Biol Sci       Date:  1979-09-21

4.  Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment.

Authors:  C J Brown; K M Todd; R F Rosenzweig
Journal:  Mol Biol Evol       Date:  1998-08       Impact factor: 16.240

Review 5.  Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems.

Authors:  Patrick C Phillips
Journal:  Nat Rev Genet       Date:  2008-11       Impact factor: 53.242

6.  The rate at which asexual populations cross fitness valleys.

Authors:  Daniel B Weissman; Michael M Desai; Daniel S Fisher; Marcus W Feldman
Journal:  Theor Popul Biol       Date:  2009-03-13       Impact factor: 1.570

7.  Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C.

Authors:  F Winston; C Dollard; S L Ricupero-Hovasse
Journal:  Yeast       Date:  1995-01       Impact factor: 3.239

8.  Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape.

Authors:  Daniel J Kvitek; Gavin Sherlock
Journal:  PLoS Genet       Date:  2011-04-28       Impact factor: 5.917

9.  Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.

Authors:  Jared W Wenger; Jeffrey Piotrowski; Saisubramanian Nagarajan; Kami Chiotti; Gavin Sherlock; Frank Rosenzweig
Journal:  PLoS Genet       Date:  2011-08-04       Impact factor: 5.917

10.  Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data.

Authors:  Frank J Poelwijk; Daniel J Kiviet; Sander J Tans
Journal:  PLoS Comput Biol       Date:  2006-05-26       Impact factor: 4.475

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  8 in total

1.  Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.

Authors:  Diamantis Sellis; Daniel J Kvitek; Barbara Dunn; Gavin Sherlock; Dmitri A Petrov
Journal:  Genetics       Date:  2016-05-18       Impact factor: 4.562

2.  Adaptive Roles of SSY1 and SIR3 During Cycles of Growth and Starvation in Saccharomyces cerevisiae Populations Enriched for Quiescent or Nonquiescent Cells.

Authors:  Dominika M Wloch-Salamon; Katarzyna Tomala; Dimitra Aggeli; Barbara Dunn
Journal:  G3 (Bethesda)       Date:  2017-06-07       Impact factor: 3.154

3.  Cancer progression models and fitness landscapes: a many-to-many relationship.

Authors:  Ramon Diaz-Uriarte
Journal:  Bioinformatics       Date:  2018-03-01       Impact factor: 6.937

4.  Ensemble epistasis: thermodynamic origins of nonadditivity between mutations.

Authors:  Anneliese J Morrison; Daria R Wonderlick; Michael J Harms
Journal:  Genetics       Date:  2021-08-26       Impact factor: 4.402

Review 5.  Elucidating the molecular architecture of adaptation via evolve and resequence experiments.

Authors:  Anthony Long; Gianni Liti; Andrej Luptak; Olivier Tenaillon
Journal:  Nat Rev Genet       Date:  2015-09-08       Impact factor: 53.242

6.  Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

Authors:  Aditi Gupta; Christoph Adami
Journal:  PLoS Genet       Date:  2016-03-30       Impact factor: 5.917

7.  Evolutionary rescue by compensatory mutations is constrained by genomic and environmental backgrounds.

Authors:  Marie Filteau; Véronique Hamel; Marie-Christine Pouliot; Isabelle Gagnon-Arsenault; Alexandre K Dubé; Christian R Landry
Journal:  Mol Syst Biol       Date:  2015-10-12       Impact factor: 11.429

8.  Every which way? On predicting tumor evolution using cancer progression models.

Authors:  Ramon Diaz-Uriarte; Claudia Vasallo
Journal:  PLoS Comput Biol       Date:  2019-08-02       Impact factor: 4.475

  8 in total

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