Literature DB >> 23267075

Predictability of evolution depends nonmonotonically on population size.

Ivan G Szendro1, Jasper Franke, J Arjan G M de Visser, Joachim Krug.   

Abstract

To gauge the relative importance of contingency and determinism in evolution is a fundamental problem that continues to motivate much theoretical and empirical research. In recent evolution experiments with microbes, this question has been explored by monitoring the repeatability of adaptive changes in replicate populations. Here, we present the results of an extensive computational study of evolutionary predictability based on an experimentally measured eight-locus fitness landscape for the filamentous fungus Aspergillus niger. To quantify predictability, we define entropy measures on observed mutational trajectories and endpoints. In contrast to the common expectation of increasingly deterministic evolution in large populations, we find that these entropies display an initial decrease and a subsequent increase with population size N, governed, respectively, by the scales Nμ and Nμ(2), corresponding to the supply rates of single and double mutations, where μ denotes the mutation rate. The amplitude of this pattern is determined by μ. We show that these observations are generic by comparing our findings for the experimental fitness landscape to simulations on simple model landscapes.

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Year:  2012        PMID: 23267075      PMCID: PMC3545761          DOI: 10.1073/pnas.1213613110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  43 in total

1.  Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: application to prolyl endopeptidase and thermolysin.

Authors:  T Aita; H Uchiyama; T Inaoka; M Nakajima; T Kokubo; Y Husimi
Journal:  Biopolymers       Date:  2000-07       Impact factor: 2.505

2.  A minimum on the mean number of steps taken in adaptive walks.

Authors:  H Allen Orr
Journal:  J Theor Biol       Date:  2003-01-21       Impact factor: 2.691

3.  The evolutionary origin of complex features.

Authors:  Richard E Lenski; Charles Ofria; Robert T Pennock; Christoph Adami
Journal:  Nature       Date:  2003-05-08       Impact factor: 49.962

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

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

5.  Fitness effects of fixed beneficial mutations in microbial populations.

Authors:  Daniel E Rozen; J Arjan G M de Visser; Philip J Gerrish
Journal:  Curr Biol       Date:  2002-06-25       Impact factor: 10.834

6.  The speed of adaptation in large asexual populations.

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

7.  A simple stochastic gene substitution model.

Authors:  J H Gillespie
Journal:  Theor Popul Biol       Date:  1983-04       Impact factor: 1.570

8.  Stochastic tunnels in evolutionary dynamics.

Authors:  Yoh Iwasa; Franziska Michor; Martin A Nowak
Journal:  Genetics       Date:  2004-03       Impact factor: 4.562

9.  Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli.

Authors:  Tim F Cooper; Daniel E Rozen; Richard E Lenski
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-21       Impact factor: 11.205

10.  Quantifying the adaptive potential of an antibiotic resistance enzyme.

Authors:  Martijn F Schenk; Ivan G Szendro; Joachim Krug; J Arjan G M de Visser
Journal:  PLoS Genet       Date:  2012-06-28       Impact factor: 5.917

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  47 in total

1.  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

2.  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

3.  Repeatability of adaptation in experimental populations of different sizes.

Authors:  Josianne Lachapelle; Joshua Reid; Nick Colegrave
Journal:  Proc Biol Sci       Date:  2015-04-22       Impact factor: 5.349

4.  The effect of population structure on the rate of evolution.

Authors:  Marcus Frean; Paul B Rainey; Arne Traulsen
Journal:  Proc Biol Sci       Date:  2013-05-15       Impact factor: 5.349

5.  Adaptation in tunably rugged fitness landscapes: the rough Mount Fuji model.

Authors:  Johannes Neidhart; Ivan G Szendro; Joachim Krug
Journal:  Genetics       Date:  2014-08-13       Impact factor: 4.562

Review 6.  Empirical fitness landscapes and the predictability of evolution.

Authors:  J Arjan G M de Visser; Joachim Krug
Journal:  Nat Rev Genet       Date:  2014-06-10       Impact factor: 53.242

7.  Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

Authors:  Florien A Gorter; Mark G M Aarts; Bas J Zwaan; J Arjan G M de Visser
Journal:  Genetics       Date:  2017-11-15       Impact factor: 4.562

8.  Larger bacterial populations evolve heavier fitness trade-offs and undergo greater ecological specialization.

Authors:  Yashraj Chavhan; Sarthak Malusare; Sutirth Dey
Journal:  Heredity (Edinb)       Date:  2020-03-18       Impact factor: 3.821

9.  Adaptive benefits from small mutation supplies in an antibiotic resistance enzyme.

Authors:  Merijn L M Salverda; Jeroen Koomen; Bertha Koopmanschap; Mark P Zwart; J Arjan G M de Visser
Journal:  Proc Natl Acad Sci U S A       Date:  2017-11-13       Impact factor: 11.205

Review 10.  Modeling Tumor Clonal Evolution for Drug Combinations Design.

Authors:  Boyang Zhao; Michael T Hemann; Douglas A Lauffenburger
Journal:  Trends Cancer       Date:  2016-03
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