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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Journal ArticleDOI
An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape.
Victoria O. Pokusaeva,Dinara R. Usmanova,Ekaterina V. Putintseva,Lorena Espinar,Karen S. Sarkisyan,Karen S. Sarkisyan,Alexander S. Mishin,Natalya S. Bogatyreva,Natalya S. Bogatyreva,Dmitry N. Ivankov,Dmitry N. Ivankov,Arseniy Akopyan,Sergey Avvakumov,Inna S. Povolotskaya,Guillaume J. Filion,Lucas B. Carey,Lucas B. Carey,Fyodor A. Kondrashov +17 more
TL;DR: The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.
Journal ArticleDOI
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment
Tobias Großkopf,Jessika Consuegra,Jessika Consuegra,Joël Gaffé,Joël Gaffé,John C. Willison,John C. Willison,John C. Willison,Richard E. Lenski,Orkun S. Soyer,Dominique Schneider,Dominique Schneider +11 more
TL;DR: The evoFBA framework represents a promising new way to model biochemical evolution, one that can generate testable predictions about evolutionary and ecosystem-level outcomes.
Journal ArticleDOI
Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.
TL;DR: The recent advances in theory, computer simulations, and experiments that advance the understanding of the links between various physical scales in biology are summarized.
Journal ArticleDOI
Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa.
TL;DR: The results confirm that the regulatory interconnections between public goods traits can significantly modulate the course of evolution, yet also suggest how to start to predict the impacts such complexities will have on phenotypic divergence and community stability.
Journal ArticleDOI
Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model
TL;DR: A simple fitness landscape model with tunable ruggedness based on the rough Mount Fuji (RMF) model originally introduced by Aita et al. in the context of protein evolution is proposed and compared to the known behavior in the MLM model.
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.