Literature DB >> 18493075

The stochastic edge in adaptive evolution.

Eric Brunet1, Igor M Rouzine, Claus O Wilke.   

Abstract

In a recent article, Desai and Fisher proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the population. Desai and Fisher perform an elaborate stochastic calculation of the mean time tau until a new class of mutants has been established and interpret 1/tau as the speed of adaptation. As they note, however, their calculations are valid only for moderate speeds. This limitation arises from their method to determine tau: Desai and Fisher back extrapolate the value of tau from the best-fit class's exponential growth at infinite time. This approach is not valid when the population adapts rapidly, because in this case the best-fit class grows nonexponentially during the relevant time interval. Here, we substantially extend Desai and Fisher's analysis of the stochastic edge. We show that we can apply Desai and Fisher's method to high speeds by either exponentially back extrapolating from finite time or using a nonexponential back extrapolation. Our results are compatible with predictions made using a different analytical approach (Rouzine et al.) and agree well with numerical simulations.

Mesh:

Year:  2008        PMID: 18493075      PMCID: PMC2390637          DOI: 10.1534/genetics.107.079319

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


  14 in total

1.  The rate of adaptation in asexuals.

Authors:  H A Orr
Journal:  Genetics       Date:  2000-06       Impact factor: 4.562

Review 2.  Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology.

Authors:  I M Rouzine; A Rodrigo; J M Coffin
Journal:  Microbiol Mol Biol Rev       Date:  2001-03       Impact factor: 11.056

3.  The solitary wave of asexual evolution.

Authors:  Igor M Rouzine; John Wakeley; John M Coffin
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-13       Impact factor: 11.205

4.  The speed of adaptation in large asexual populations.

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

5.  The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation.

Authors:  Igor M Rouzine; Eric Brunet; Claus O Wilke
Journal:  Theor Popul Biol       Date:  2007-10-22       Impact factor: 1.570

6.  Beneficial mutation selection balance and the effect of linkage on positive selection.

Authors:  Michael M Desai; Daniel S Fisher
Journal:  Genetics       Date:  2007-05-04       Impact factor: 4.562

7.  The fate of competing beneficial mutations in an asexual population.

Authors:  P J Gerrish; R E Lenski
Journal:  Genetica       Date:  1998       Impact factor: 1.082

8.  Modelling evolving populations.

Authors:  A Prügel-Bennett
Journal:  J Theor Biol       Date:  1997-03-07       Impact factor: 2.691

9.  Linkage and the limits to natural selection.

Authors:  N H Barton
Journal:  Genetics       Date:  1995-06       Impact factor: 4.562

10.  Genetic progression and the waiting time to cancer.

Authors:  Niko Beerenwinkel; Tibor Antal; David Dingli; Arne Traulsen; Kenneth W Kinzler; Victor E Velculescu; Bert Vogelstein; Martin A Nowak
Journal:  PLoS Comput Biol       Date:  2007-11       Impact factor: 4.475

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  25 in total

1.  Real time forecasting of near-future evolution.

Authors:  Philip J Gerrish; Paul D Sniegowski
Journal:  J R Soc Interface       Date:  2012-04-18       Impact factor: 4.118

2.  Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations.

Authors:  Benjamin H Good; Igor M Rouzine; Daniel J Balick; Oskar Hallatschek; Michael M Desai
Journal:  Proc Natl Acad Sci U S A       Date:  2012-02-27       Impact factor: 11.205

3.  Fast stochastic algorithm for simulating evolutionary population dynamics.

Authors:  William H Mather; Jeff Hasty; Lev S Tsimring
Journal:  Bioinformatics       Date:  2012-03-21       Impact factor: 6.937

4.  Mutational effects and population dynamics during viral adaptation challenge current models.

Authors:  Craig R Miller; Paul Joyce; Holly A Wichman
Journal:  Genetics       Date:  2010-11-01       Impact factor: 4.562

5.  The noisy edge of traveling waves.

Authors:  Oskar Hallatschek
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-27       Impact factor: 11.205

6.  The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation.

Authors:  Igor M Rouzine; Eric Brunet; Claus O Wilke
Journal:  Theor Popul Biol       Date:  2007-10-22       Impact factor: 1.570

7.  Genomic mutation rates that neutralize adaptive evolution and natural selection.

Authors:  Philip J Gerrish; Alexandre Colato; Paul D Sniegowski
Journal:  J R Soc Interface       Date:  2013-05-29       Impact factor: 4.118

8.  The dynamics of genetic draft in rapidly adapting populations.

Authors:  Katya Kosheleva; Michael M Desai
Journal:  Genetics       Date:  2013-09-03       Impact factor: 4.562

9.  Rate of adaptation in sexuals and asexuals: a solvable model of the Fisher-Muller effect.

Authors:  Su-Chan Park; Joachim Krug
Journal:  Genetics       Date:  2013-08-26       Impact factor: 4.562

10.  Impact of deleterious passenger mutations on cancer progression.

Authors:  Christopher D McFarland; Kirill S Korolev; Gregory V Kryukov; Shamil R Sunyaev; Leonid A Mirny
Journal:  Proc Natl Acad Sci U S A       Date:  2013-02-06       Impact factor: 11.205

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