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
Novelty and Innovation in the History of Life.
TL;DR: The history of life as documented by the fossil record encompasses evolutionary diversifications at scales ranging from the Ediacaran-Cambrian explosion of animal life and the invasion of land by vascular plants, insects and vertebrates to the diversification of flowering plants over the past 100 million years and the radiation of horses.
Journal ArticleDOI
On the (un)predictability of a large intragenic fitness landscape
TL;DR: A uniquely large multiallelic fitness landscape comprising 640 engineered mutants that represent all possible combinations of 13 amino acid-changing mutations at 6 sites in the heat-shock protein Hsp90 in Saccharomyces cerevisiae under elevated salinity is presented.
Journal ArticleDOI
Environmental changes bridge evolutionary valleys.
TL;DR: This work comprehensively examined possible evolutionary pathways leading to one high-fitness allele and found that an initially deleterious mutation is key to the allele’s evolutionary history.
Journal ArticleDOI
Negative Epistasis and Evolvability in TEM-1 β-Lactamase--The Thin Line between an Enzyme's Conformational Freedom and Disorder.
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 +7 more
TL;DR: The structural basis of sign epistasis between G238S and R164S, two adaptive mutations in TEM-1 β-lactamase, an enzyme that endows antibiotics resistance is described, which underlines the reshaping potential of protein's structures and functions but also limits protein evolvability because of the fragility of the interactions networks that maintain protein structures.
Journal ArticleDOI
The complete local genotype–phenotype landscape for the alternative splicing of a human exon
Philippe Julien,Belén Miñana,Pablo Baeza-Centurion,Pablo Baeza-Centurion,Juan Valcárcel,Juan Valcárcel,Ben Lehner,Ben Lehner,Ben Lehner +8 more
TL;DR: The landscape provides important mechanistic insights, revealing that regulatory information is dispersed throughout nearly every nucleotide in an exon, that the exon is more robust to the effects of mutations than its immediate neighbours in genotype space, and that high mutation sensitivity will drive the rapid divergence of alternative splicing between species unless it is constrained by selection.
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.