Literature DB >> 24913663

Empirical fitness landscapes and the predictability of evolution.

J Arjan G M de Visser1, Joachim Krug2.   

Abstract

The genotype-fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.

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Year:  2014        PMID: 24913663     DOI: 10.1038/nrg3744

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  93 in total

1.  Interaction between directional epistasis and average mutational effects.

Authors:  C O Wilke; C Adami
Journal:  Proc Biol Sci       Date:  2001-07-22       Impact factor: 5.349

2.  A comparison of genotype-phenotype maps for RNA and proteins.

Authors:  Evandro Ferrada; Andreas Wagner
Journal:  Biophys J       Date:  2012-04-18       Impact factor: 4.033

3.  Microbial experiments on adaptive landscapes.

Authors:  Nick Colegrave; Angus Buckling
Journal:  Bioessays       Date:  2005-11       Impact factor: 4.345

4.  Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape.

Authors:  David Heckmann; Stefanie Schulze; Alisandra Denton; Udo Gowik; Peter Westhoff; Andreas P M Weber; Martin J Lercher
Journal:  Cell       Date:  2013-06-20       Impact factor: 41.582

5.  A biophysical protein folding model accounts for most mutational fitness effects in viruses.

Authors:  C Scott Wylie; Eugene I Shakhnovich
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-24       Impact factor: 11.205

6.  Second-order selection for evolvability in a large Escherichia coli population.

Authors:  Robert J Woods; Jeffrey E Barrick; Tim F Cooper; Utpala Shrestha; Mark R Kauth; Richard E Lenski
Journal:  Science       Date:  2011-03-18       Impact factor: 47.728

Review 7.  Genotype to phenotype: lessons from model organisms for human genetics.

Authors:  Ben Lehner
Journal:  Nat Rev Genet       Date:  2013-01-29       Impact factor: 53.242

8.  Stepwise acquisition of pyrimethamine resistance in the malaria parasite.

Authors:  Elena R Lozovsky; Thanat Chookajorn; Kyle M Brown; Mallika Imwong; Philip J Shaw; Sumalee Kamchonwongpaisan; Daniel E Neafsey; Daniel M Weinreich; Daniel L Hartl
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-08       Impact factor: 11.205

9.  Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases.

Authors:  Paul E O'Maille; Arthur Malone; Nikki Dellas; B Andes Hess; Lidia Smentek; Iseult Sheehan; Bryan T Greenhagen; Joe Chappell; Gerard Manning; Joseph P Noel
Journal:  Nat Chem Biol       Date:  2008-09-07       Impact factor: 15.040

10.  Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations.

Authors:  Gregory I Lang; Daniel P Rice; Mark J Hickman; Erica Sodergren; George M Weinstock; David Botstein; Michael M Desai
Journal:  Nature       Date:  2013-07-21       Impact factor: 49.962

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  225 in total

Review 1.  Changing preferences: deformation of single position amino acid fitness landscapes and evolution of proteins.

Authors:  Georgii A Bazykin
Journal:  Biol Lett       Date:  2015-10       Impact factor: 3.703

2.  Breaking evolutionary constraint with a tradeoff ratchet.

Authors:  Marjon G J de Vos; Alexandre Dawid; Vanda Sunderlikova; Sander J Tans
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-13       Impact factor: 11.205

3.  How mutational epistasis impairs predictability in protein evolution and design.

Authors:  Charlotte M Miton; Nobuhiko Tokuriki
Journal:  Protein Sci       Date:  2016-01-22       Impact factor: 6.725

4.  Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.

Authors:  Eynat Dellus-Gur; Mikael Elias; Emilia Caselli; Fabio Prati; Merijn L M Salverda; J Arjan G M de Visser; James S Fraser; Dan S Tawfik
Journal:  J Mol Biol       Date:  2015-05-22       Impact factor: 5.469

5.  Contingency and entrenchment in protein evolution under purifying selection.

Authors:  Premal Shah; David M McCandlish; Joshua B Plotkin
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-08       Impact factor: 11.205

6.  The impact of macroscopic epistasis on long-term evolutionary dynamics.

Authors:  Benjamin H Good; Michael M Desai
Journal:  Genetics       Date:  2014-11-12       Impact factor: 4.562

7.  Minimum epistasis interpolation for sequence-function relationships.

Authors:  Juannan Zhou; David M McCandlish
Journal:  Nat Commun       Date:  2020-04-14       Impact factor: 14.919

Review 8.  Modeling Tumor Clonal Evolution for Drug Combinations Design.

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

9.  Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution.

Authors:  Weronika Jasinska; Michael Manhart; Jesse Lerner; Louis Gauthier; Adrian W R Serohijos; Shimon Bershtein
Journal:  Nat Ecol Evol       Date:  2020-02-24       Impact factor: 15.460

10.  The emergence of latent infection in the early evolution of Mycobacterium tuberculosis.

Authors:  Rebecca H Chisholm; Mark M Tanaka
Journal:  Proc Biol Sci       Date:  2016-05-25       Impact factor: 5.349

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