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
Citations
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Journal ArticleDOI
Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.
TL;DR: A structure-guided approach for predicting protease substrate specificity landscapes, in which data from experiments in yeast and molecular simulations are combined using machine learning, and a possible role for residue-level energetics in shaping plateau-like functional landscapes predicted from viral quasispecies theory is suggested.
Journal ArticleDOI
Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.
Florien A. Gorter,Florien A. Gorter,Florien A. Gorter,Mark G. M. Aarts,Bas J. Zwaan,J. Arjan G. M. de Visser +5 more
TL;DR: This work reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change.
Journal ArticleDOI
Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana
Mark A. Taylor,Amity M. Wilczek,Judith L. Roe,Stephen Welch,Daniel E. Runcie,Martha D. Cooper,Johanna Schmitt +6 more
TL;DR: This work quantified the adaptive value of mutant traits, finding that certain mutations increased fitness in some environments but not in others, indicating that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions.
Journal ArticleDOI
Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase.
TL;DR: This study is the first to systematically examine pairwise epistasis throughout an entire protein performing its native function in its native host.
Journal ArticleDOI
Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences.
TL;DR: The in vitro evolution of triphosphorylating ribozymes is analyzed and their fitnesses are translated into absolute estimates of catalytic activity for hundreds of ribozyme families, consistent with a mechanism for the emergence of activity as the product of many independent contributions.
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.