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
Corrigendum: Different Genomic Changes Underlie Adaptive Evolution in Populations of Contrasting History.
Sofia G. Seabra,Inês Fragata,M A Antunes,Gonçalo S. Faria,Marta A. Santos,Vitor C. Sousa,Pedro Simões,Margarida Gaspar de Matos +7 more
TL;DR: The importance of the historical genetic background in the outcome of evolution at the genome-wide level is studied, finding that history played a major role in genomic variation and evolution, with initially differentiated populations reaching the same adaptive outcome through different genetic routes.
Journal ArticleDOI
Computational design of hepatitis C virus immunogens from host-pathogen dynamics over empirical viral fitness landscapes.
TL;DR: A computational approach is employed to translate HCV sequence databases into empirical landscapes of viral fitness and simulate the intrahost evolution of the viral quasispecies over these landscapes and can guide and accelerate experimental vaccine design efforts.
Journal ArticleDOI
Evolutionary assembly patterns of prokaryotic genomes
TL;DR: The results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.
Journal ArticleDOI
Inverse Statistical Physics of Protein Sequences: A Key Issues Review
TL;DR: In this paper, an overview of some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them is given, as well as some open questions which are expected to be addressed over the next years.
Journal ArticleDOI
Epistasis and Adaptation on Fitness Landscapes
TL;DR: Fitness landscape theory and experiments are reviewed and their implications for the role of epistasis in adaptation are discussed and theoretical expectations in the light of empirical fitness landscapes are discussed.
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″."
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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.
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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.