Journal ArticleDOI
Empirical fitness landscapes and the predictability of evolution
TLDR
This work reviews recent empirical and theoretical developments of the genotype–fitness map, identifies methodological issues and organizing principles, and discusses possibilities to develop more realistic fitness landscape models.Abstract:
A central topic in biology concerns how genotypes determine phenotypes and functions of organisms that affect their evolutionary fitness. This Review discusses recent advances in the development of empirical fitness landscapes and their contribution to theoretical analyses of the predictability of evolution. 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.read more
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Geometry of fitness landscapes: Peaks, shapes and universal positive epistasis
TL;DR: In this article, the shape approach uses triangulations (shapes) induced by fitness landscapes for a large protein fitness landscape for an immunoglobulin-binding protein expressed in Streptococcal bacteria.
Posted ContentDOI
General theory of specific binding: insights from a genetic, mechano-chemical protein model
TL;DR: In this paper , the authors present a model that combines chemistry, mechanics and genetics to explain how their interplay governs the evolution of specific protein-ligand interactions and make testable, specific predictions about the role of flexibility and shape mismatch in discrimination, and how evolution can independently tune affinity and specificity.
Journal ArticleDOI
A Two-Level, Intramutant Spectrum Haplotype Profile of Hepatitis C Virus Revealed by Self-Organized Maps.
Soledad Delgado,Celia Perales,Celia Perales,Celia Perales,Carlos García-Crespo,Carlos García-Crespo,María Eugenia Soria,María Eugenia Soria,María Eugenia Soria,Isabel Gallego,Isabel Gallego,Ana Isabel de Ávila,Ana Isabel de Ávila,Brenda Martínez-González,Brenda Martínez-González,Lucía Vázquez-Sirvent,Lucía Vázquez-Sirvent,Cecilio López-Galíndez,Federico Morán,Esteban Domingo,Esteban Domingo +20 more
TL;DR: In this article, the haplotype profiles of three amplicons of the NS5A-NS5B coding region of hepatitis C virus (HCV) were constructed for 44 related HCV populations derived from a common clonal ancestor that was passaged up to 210 times in human hepatoma Huh-7.5 cells in the absence of external selective pressures.
Posted ContentDOI
Impact of population size on early adaptation in rugged fitness landscapes
TL;DR: In this article , the authors show that the accessibility of the different fitness peaks is key to determining whether this height overall increases or decreases with population size, and that there is often a finite population size that maximizes the height of the first fitness peak encountered when starting from a random genotype.
Posted ContentDOI
The mutation effect reaction norm (MERN) highlights environmentally dependent mutation effects and genetic interactions
TL;DR: In this article, the authors formalize the notion of a mutation effect reaction norm (MERN) as an instrument through which one can analyze or depict the phenotypic consequences of interactions between mutations across environmental contexts.
References
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Journal ArticleDOI
Evolution in Mendelian Populations.
TL;DR: Page 108, last line of text, for "P/P″" read "P′/ P″."
Journal ArticleDOI
Evolution in Mendelian populations
TL;DR: The frequency of a given gene in a population may be modified by a number of conditions including recurrent mutation to and from it, migration, selection of various sorts and, far from least in importance, were chance variation.
Book
Wonderful Life: The Burgess Shale and the Nature of History
TL;DR: In this article, the authors explore what the Burgess Shale tells us about evolution and the nature of history and find that it holds the remains of an ancient sea where dozens of strange creatures lived.
Journal ArticleDOI
Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems.
TL;DR: There is a renewed appreciation both for the importance of studying gene interactions and for addressing these questions in a unified, quantitative manner with the advent of high-throughput functional genomics.