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
Enzyme promiscuity shapes adaptation to novel growth substrates
Gabriela I. Guzman,Troy E. Sandberg,Ryan A. LaCroix,Ákos Nyerges,Henrietta Papp,Markus de Raad,Zachary A. King,Ying Hefner,Trent R. Northen,Richard A. Notebaart,Csaba Pál,Bernhard O. Palsson,Bernhard O. Palsson,Balázs Papp,Adam M. Feist,Adam M. Feist +15 more
TL;DR: A computational model of underground metabolism and laboratory evolution experiments are employed to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non‐native substrates in Escherichia coli K‐12 MG1655 and altered promiscuous activities were shown to be directly involved in establishing high‐efficiency pathways.
Journal ArticleDOI
Clonal cooperativity in heterogenous cancers.
TL;DR: It is proposed that disruption of clonal cooperation by targeting key factors (such as Wnt and Hedgehog, amongst others) can be an alternative approach to improving clinical outcomes.
Journal ArticleDOI
Predicting mutational routes to new adaptive phenotypes
TL;DR: The model bacterium Pseudomonas fluorescens is used in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known and mathematical descriptions of three necessary regulatory pathways are presented to predict both the rate at which each mutational route is used and the expected mutational targets.
Journal ArticleDOI
Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.
TL;DR: In this paper, the non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptive evolution, which ultimately is fuelled by mutations generating novel genetic variation.
Journal ArticleDOI
Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies
TL;DR: This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes.
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.