Literature DB >> 23036916

The peaks and geometry of fitness landscapes.

Kristina Crona1, Devin Greene, Miriam Barlow.   

Abstract

Fitness landscapes are central in the theory of adaptation. Recent work compares global and local properties of fitness landscapes. It has been shown that multi-peaked fitness landscapes have a local property called reciprocal sign epistasis interactions. The converse is not true. We show that no condition phrased in terms of reciprocal sign epistasis interactions only, implies multiple peaks. We give a sufficient condition for multiple peaks phrased in terms of two-way interactions. This result is surprising since it has been claimed that no sufficient local condition for multiple peaks exist. We show that our result cannot be generalized to sufficient conditions for three or more peaks. Our proof depends on fitness graphs, where nodes represent genotypes and where arrows point toward more fit genotypes. We also use fitness graphs in order to give a new brief proof of the equivalent characterizations of fitness landscapes lacking genetic constraints on accessible mutational trajectories. We compare a recent geometric classification of fitness landscape based on triangulations of polytopes with qualitative aspects of gene interactions. One observation is that fitness graphs provide information that are not contained in the geometric classification. We argue that a qualitative perspective may help relating theory of fitness landscapes and empirical observations.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 23036916      PMCID: PMC3529755          DOI: 10.1016/j.jtbi.2012.09.028

Source DB:  PubMed          Journal:  J Theor Biol        ISSN: 0022-5193            Impact factor:   2.691


  25 in total

Review 1.  Resolving the paradox of sex and recombination.

Authors:  Sarah P Otto; Thomas Lenormand
Journal:  Nat Rev Genet       Date:  2002-04       Impact factor: 53.242

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.  Relating HIV-1 sequence variation to replication capacity via trees and forests.

Authors:  Mark R Segal; Jason D Barbour; Robert M Grant
Journal:  Stat Appl Genet Mol Biol       Date:  2004-02-12

4.  The population genetics of adaptation on correlated fitness landscapes: the block model.

Authors:  H Allen Orr
Journal:  Evolution       Date:  2006-06       Impact factor: 3.694

5.  Aggregation of variables and system decomposition: Applications to fitness landscape analysis.

Authors:  Max Shpak; Peter Stadler; Gunter P Wagner; Joachim Hermisson
Journal:  Theory Biosci       Date:  2004-06       Impact factor: 1.919

Review 6.  Colloquium papers: Adaptive landscapes and protein evolution.

Authors:  Maurício Carneiro; Daniel L Hartl
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-30       Impact factor: 11.205

7.  Natural selection and the concept of a protein space.

Authors:  J M Smith
Journal:  Nature       Date:  1970-02-07       Impact factor: 49.962

8.  Evidence for positive epistasis in HIV-1.

Authors:  Sebastian Bonhoeffer; Colombe Chappey; Neil T Parkin; Jeanette M Whitcomb; Christos J Petropoulos
Journal:  Science       Date:  2004-11-26       Impact factor: 47.728

9.  The molecular clock may be an episodic clock.

Authors:  J H Gillespie
Journal:  Proc Natl Acad Sci U S A       Date:  1984-12       Impact factor: 11.205

10.  Analysis of epistatic interactions and fitness landscapes using a new geometric approach.

Authors:  Niko Beerenwinkel; Lior Pachter; Bernd Sturmfels; Santiago F Elena; Richard E Lenski
Journal:  BMC Evol Biol       Date:  2007-04-13       Impact factor: 3.260

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  22 in total

1.  Computational Complexity as an Ultimate Constraint on Evolution.

Authors:  Artem Kaznatcheev
Journal:  Genetics       Date:  2019-03-04       Impact factor: 4.562

2.  Genotypic Complexity of Fisher's Geometric Model.

Authors:  Sungmin Hwang; Su-Chan Park; Joachim Krug
Journal:  Genetics       Date:  2017-04-26       Impact factor: 4.562

Review 3.  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

4.  A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory.

Authors:  David Seifert; Francesca Di Giallonardo; Karin J Metzner; Huldrych F Günthard; Niko Beerenwinkel
Journal:  Genetics       Date:  2014-11-17       Impact factor: 4.562

5.  Rank orders and signed interactions in evolutionary biology.

Authors:  Kristina Crona
Journal:  Elife       Date:  2020-01-14       Impact factor: 8.140

6.  Selection Limits to Adaptive Walks on Correlated Landscapes.

Authors:  Jorge Pérez Heredia; Barbora Trubenová; Dirk Sudholt; Tiago Paixão
Journal:  Genetics       Date:  2016-11-23       Impact factor: 4.562

7.  Recombination and peak jumping.

Authors:  Kristina Crona
Journal:  PLoS One       Date:  2018-03-01       Impact factor: 3.240

Review 8.  What can we learn from fitness landscapes?

Authors:  Daniel L Hartl
Journal:  Curr Opin Microbiol       Date:  2014-10-13       Impact factor: 7.934

9.  A model of substitution trajectories in sequence space and long-term protein evolution.

Authors:  Dinara R Usmanova; Luca Ferretti; Inna S Povolotskaya; Peter K Vlasov; Fyodor A Kondrashov
Journal:  Mol Biol Evol       Date:  2014-11-17       Impact factor: 16.240

10.  Designing antibiotic cycling strategies by determining and understanding local adaptive landscapes.

Authors:  Christiane P Goulart; Mentar Mahmudi; Kristina A Crona; Stephen D Jacobs; Marcelo Kallmann; Barry G Hall; Devin C Greene; Miriam Barlow
Journal:  PLoS One       Date:  2013-02-13       Impact factor: 3.240

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