Literature DB >> 18505866

The distribution of beneficial and fixed mutation fitness effects close to an optimum.

Guillaume Martin1, Thomas Lenormand.   

Abstract

The distribution of the selection coefficients of beneficial mutations is pivotal to the study of the adaptive process, both at the organismal level (theories of adaptation) and at the gene level (molecular evolution). A now famous result of extreme value theory states that this distribution is an exponential, at least when considering a well-adapted wild type. However, this prediction could be inaccurate under selection for an optimum (because fitness effect distributions have a finite right tail in this case). In this article, we derive the distribution of beneficial mutation effects under a general model of stabilizing selection, with arbitrary selective and mutational covariance between a finite set of traits. We assume a well-adapted wild type, thus taking advantage of the robustness of tail behaviors, as in extreme value theory. We show that, under these general conditions, both beneficial mutation effects and fixed effects (mutations escaping drift loss) are beta distributed. In both cases, the parameters have explicit biological meaning and are empirically measurable; their variation through time can also be predicted. We retrieve the classic exponential distribution as a subcase of the beta when there are a moderate to large number of weakly correlated traits under selection. In this case too, we provide an explicit biological interpretation of the parameters of the distribution. We show by simulations that these conclusions are fairly robust to a lower adaptation of the wild type and discuss the relevance of our findings in the context of adaptation theories and experimental evolution.

Mesh:

Year:  2008        PMID: 18505866      PMCID: PMC2429884          DOI: 10.1534/genetics.108.087122

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  27 in total

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2.  Adaptation and the cost of complexity.

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3.  The rhythm of microbial adaptation.

Authors:  P Gerrish
Journal:  Nature       Date:  2001-09-20       Impact factor: 49.962

4.  The distribution of fitness effects among beneficial mutations.

Authors:  H Allen Orr
Journal:  Genetics       Date:  2003-04       Impact factor: 4.562

5.  The population genetics of adaptation: the adaptation of DNA sequences.

Authors:  H Allen Orr
Journal:  Evolution       Date:  2002-07       Impact factor: 3.694

6.  Modularity and the cost of complexity.

Authors:  John J Welch; David Waxman
Journal:  Evolution       Date:  2003-08       Impact factor: 3.694

7.  The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus.

Authors:  Rafael Sanjuán; Andrés Moya; Santiago F Elena
Journal:  Proc Natl Acad Sci U S A       Date:  2004-05-24       Impact factor: 11.205

8.  The speed of adaptation in large asexual populations.

Authors:  Claus O Wilke
Journal:  Genetics       Date:  2004-08       Impact factor: 4.562

Review 9.  The genetic theory of adaptation: a brief history.

Authors:  H Allen Orr
Journal:  Nat Rev Genet       Date:  2005-02       Impact factor: 53.242

10.  A comprehensive model of mutations affecting fitness and inferences for Arabidopsis thaliana.

Authors:  Frank H Shaw; Charles J Geyer; Ruth G Shaw
Journal:  Evolution       Date:  2002-03       Impact factor: 3.694

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  41 in total

1.  The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

Authors:  Pablo Razeto-Barry; Javier Díaz; Rodrigo A Vásquez
Journal:  Genetics       Date:  2012-03-16       Impact factor: 4.562

2.  Scaling expectations for the time to establishment of complex adaptations.

Authors:  Michael Lynch
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-07       Impact factor: 11.205

3.  The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens.

Authors:  Michael J McDonald; Tim F Cooper; Hubertus J E Beaumont; Paul B Rainey
Journal:  Biol Lett       Date:  2010-07-21       Impact factor: 3.703

Review 4.  Beneficial mutations and the dynamics of adaptation in asexual populations.

Authors:  Paul D Sniegowski; Philip J Gerrish
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2010-04-27       Impact factor: 6.237

Review 5.  The population genetics of beneficial mutations.

Authors:  H Allen Orr
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2010-04-27       Impact factor: 6.237

6.  Diminishing returns from beneficial mutations and pervasive epistasis shape the fitness landscape for rifampicin resistance in Pseudomonas aeruginosa.

Authors:  R C MacLean; G G Perron; A Gardner
Journal:  Genetics       Date:  2010-09-27       Impact factor: 4.562

7.  Environment determines epistatic patterns for a ssDNA virus.

Authors:  S Brian Caudle; Craig R Miller; Darin R Rokyta
Journal:  Genetics       Date:  2013-11-08       Impact factor: 4.562

8.  A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation.

Authors:  Paul Joyce; Darin R Rokyta; Craig J Beisel; H Allen Orr
Journal:  Genetics       Date:  2008-09-14       Impact factor: 4.562

9.  The genetic basis of phenotypic adaptation II: the distribution of adaptive substitutions in the moving optimum model.

Authors:  Michael Kopp; Joachim Hermisson
Journal:  Genetics       Date:  2009-10-05       Impact factor: 4.562

10.  The distribution of fitness effects in an uncertain world.

Authors:  Tim Connallon; Andrew G Clark
Journal:  Evolution       Date:  2015-05-19       Impact factor: 3.694

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