Literature DB >> 28450460

Genotypic Complexity of Fisher's Geometric Model.

Sungmin Hwang1, Su-Chan Park2, Joachim Krug1.   

Abstract

Fisher's geometric model was originally introduced to argue that complex adaptations must occur in small steps because of pleiotropic constraints. When supplemented with the assumption of additivity of mutational effects on phenotypic traits, it provides a simple mechanism for the emergence of genotypic epistasis from the nonlinear mapping of phenotypes to fitness. Of particular interest is the occurrence of reciprocal sign epistasis, which is a necessary condition for multipeaked genotypic fitness landscapes. Here we compute the probability that a pair of randomly chosen mutations interacts sign epistatically, which is found to decrease with increasing phenotypic dimension n, and varies nonmonotonically with the distance from the phenotypic optimum. We then derive expressions for the mean number of fitness maxima in genotypic landscapes comprised of all combinations of L random mutations. This number increases exponentially with L, and the corresponding growth rate is used as a measure of the complexity of the landscape. The dependence of the complexity on the model parameters is found to be surprisingly rich, and three distinct phases characterized by different landscape structures are identified. Our analysis shows that the phenotypic dimension, which is often referred to as phenotypic complexity, does not generally correlate with the complexity of fitness landscapes and that even organisms with a single phenotypic trait can have complex landscapes. Our results further inform the interpretation of experiments where the parameters of Fisher's model have been inferred from data, and help to elucidate which features of empirical fitness landscapes can be described by this model.
Copyright © 2017 by the Genetics Society of America.

Entities:  

Keywords:  adaptation; epistasis; fitness landscape; fitness peaks; genotype–phenotype map

Mesh:

Year:  2017        PMID: 28450460      PMCID: PMC5499163          DOI: 10.1534/genetics.116.199497

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


  47 in total

1.  Fisher's model and the genomics of adaptation: restricted pleiotropy, heterogenous mutation, and parallel evolution.

Authors:  Luis-Miguel Chevin; Guillaume Martin; Thomas Lenormand
Journal:  Evolution       Date:  2010-11       Impact factor: 3.694

2.  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

3.  Fisher's microscope and Haldane's ellipse.

Authors:  D Waxman; J J Welch
Journal:  Am Nat       Date:  2005-08-05       Impact factor: 3.926

4.  Distributions of epistasis in microbes fit predictions from a fitness landscape model.

Authors:  Guillaume Martin; Santiago F Elena; Thomas Lenormand
Journal:  Nat Genet       Date:  2007-03-18       Impact factor: 38.330

5.  Local properties of Kauffman's N-k model: A tunably rugged energy landscape.

Authors: 
Journal:  Phys Rev A       Date:  1991-11-15       Impact factor: 3.140

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.  Properties of selected mutations and genotypic landscapes under Fisher's geometric model.

Authors:  François Blanquart; Guillaume Achaz; Thomas Bataillon; Olivier Tenaillon
Journal:  Evolution       Date:  2014-11-17       Impact factor: 3.694

8.  Experimental rugged fitness landscape in protein sequence space.

Authors:  Yuuki Hayashi; Takuyo Aita; Hitoshi Toyota; Yuzuru Husimi; Itaru Urabe; Tetsuya Yomo
Journal:  PLoS One       Date:  2006-12-20       Impact factor: 3.240

9.  A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments.

Authors:  Claudia Bank; Ryan T Hietpas; Alex Wong; Daniel N Bolon; Jeffrey D Jensen
Journal:  Genetics       Date:  2014-01-07       Impact factor: 4.562

10.  Not just a theory--the utility of mathematical models in evolutionary biology.

Authors:  Maria R Servedio; Yaniv Brandvain; Sumit Dhole; Courtney L Fitzpatrick; Emma E Goldberg; Caitlin A Stern; Jeremy Van Cleve; D Justin Yeh
Journal:  PLoS Biol       Date:  2014-12-09       Impact factor: 8.029

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  9 in total

1.  Inferring the shape of global epistasis.

Authors:  Jakub Otwinowski; David M McCandlish; Joshua B Plotkin
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-23       Impact factor: 11.205

2.  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

3.  Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation.

Authors:  Austin H Patton; Emilie J Richards; Katelyn J Gould; Logan K Buie; Christopher H Martin
Journal:  Elife       Date:  2022-05-26       Impact factor: 8.713

4.  The utility of fitness landscapes and big data for predicting evolution.

Authors:  J Arjan G M de Visser; Santiago F Elena; Inês Fragata; Sebastian Matuszewski
Journal:  Heredity (Edinb)       Date:  2018-08-20       Impact factor: 3.821

5.  Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.

Authors:  Ke Chen; Amitesh Anand; Connor Olson; Troy E Sandberg; Ye Gao; Nathan Mih; Bernhard O Palsson
Journal:  PLoS Comput Biol       Date:  2021-01-19       Impact factor: 4.475

6.  Interpretable modeling of genotype-phenotype landscapes with state-of-the-art predictive power.

Authors:  Peter D Tonner; Abe Pressman; David Ross
Journal:  Proc Natl Acad Sci U S A       Date:  2022-06-21       Impact factor: 12.779

7.  On the incongruence of genotype-phenotype and fitness landscapes.

Authors:  Malvika Srivastava; Joshua L Payne
Journal:  PLoS Comput Biol       Date:  2022-09-19       Impact factor: 4.779

8.  Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns.

Authors:  Alexis Simon; Nicolas Bierne; John J Welch
Journal:  Evol Lett       Date:  2018-08-14

9.  Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase.

Authors:  Mark P Zwart; Martijn F Schenk; Sungmin Hwang; Bertha Koopmanschap; Niek de Lange; Lion van de Pol; Tran Thi Thuy Nga; Ivan G Szendro; Joachim Krug; J Arjan G M de Visser
Journal:  Heredity (Edinb)       Date:  2018-07-02       Impact factor: 3.821

  9 in total

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