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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Dissertation
Role of phenotype switching during biological evolution in static environments
TL;DR: Traditional models of evolution over genotype space fail to account for the observation that biological diversity is rife, even amongst genetically identical cells that exist in the same environment, and should consider different fitness landscapes for each of the distinct phenotypic states that exist.
Posted ContentDOI
Learning genotype-fitness landscape of SARS-CoV-2 in embedding space
TL;DR: In this paper , the authors present a Phenotype-Embedding theorem and prove that the virus fitness can be calculated under the Encoder-Decoder framework, using only the sequence data of the SARS-CoV-2 spike protein, and obtain a calculable quantitative relationship between immune escape mutations and virus fitness and plot a genotype-fitness landscape in the embedded space.
Journal ArticleDOI
Driven Disordered Systems Approach to Biological Evolution in Changing Environments
TL;DR: In this paper , a model of antibiotic resistance evolution in bacteria where the antibiotic concentration is an environmental parameter and the fitness landscapes incorporate trade-offs between adaptation to low and high antibiotic concentration was proposed.
Book ChapterDOI
The devil is in the details
Katrina M. Dlugosch,Samantha R. Anderson,Joseph E. Braasch,F. Alice Cang,Heather D. Gillette +4 more
Journal ArticleDOI
Correction to ‘Bypass of genetic constraints during mutator evolution to antibiotic resistance’
TL;DR: This work was supported by predoctoral fellowship FI05/00569 to A.C. and by Plan
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.