☆ 4.8 Review

Epistasis and evolution: recent advances and an outlook for prediction

BMC BIOLOGY (2023)

相关参考文献

注意：仅列出部分参考文献，下载原文获取全部文献信息。

Review Biology

Global epistasis on fitness landscapes

Juan Diaz-Colunga et al.

Summary: Epistatic interactions between mutations can complicate predictions of evolution, but global epistasis patterns can actually aid in reconstructing fitness landscapes and inferring adaptive trajectories. Microscopic interactions and nonlinearity in the fitness landscape contribute to the emergence of global epistasis patterns. This review provides an overview of recent work on global epistasis, explaining why different mutations exhibit varying patterns, and highlights unanswered questions and future research directions.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2023)

添加到收藏夹

Article Biology

The landscape of antibody binding affinity in SARS-CoV-2 Omicron BA.1 evolution

Alief Moulana et al.

Summary: The Omicron BA.1 variant of SARS-CoV-2 can evade convalescent sera and monoclonal antibodies that are effective against earlier strains of the virus. This is due to mutations in the receptor binding domain (RBD) of BA.1, which is the major target for antibodies. By systematically measuring the binding affinity between 15 RBD mutations and 4 monoclonal antibodies, researchers found that BA.1 can reduce affinity to diverse antibodies by acquiring large-effect mutations or small-effect mutations. They also discovered alternative pathways for antibody escape that do not involve every large-effect mutation. Epistatic interactions were shown to have a limited impact on the affinity landscapes of most antibodies. These findings contribute to our understanding of how the virus can escape antibody neutralization and have implications for vaccine development.

ELIFE (2023)

添加到收藏夹

Article Multidisciplinary Sciences

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

Tyler N. Starr et al.

Summary: Two different sarbecoviruses have caused major human outbreaks in the past two decades. This study traced the evolutionary history of ACE2 binding in different sarbecoviruses using high-throughput assays. ACE2 binding was found to be an ancestral trait of sarbecovirus receptor-binding domains, but has been lost in some clades. Bat sarbecoviruses from outside Asia were also found to be able to bind to ACE2. The results highlight the deep ancestral origin and evolutionary plasticity of ACE2 binding in sarbecoviruses.

NATURE (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Epistatic drift causes gradual decay of predictability in protein evolution

Yeonwoo Park et al.

Summary: Epistatic interactions can cause mutations to become decorrelated from their initial effects and their windows of evolutionary accessibility to open and close transiently. This drift process is a neutral process caused by many weak epistatic interactions, and the rate of change is largely constant over time.

SCIENCE (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

Alief Moulana et al.

Summary: The Omicron BA.1 variant of SARS-CoV-2 has multiple mutations that contribute to its ability to escape antibodies. Despite individual decreases in ACE2 affinity, these mutations are compensated by interactions with other mutations that enhance affinity, allowing BA.1 to evade immunity while maintaining ACE2 binding. Compensatory epistasis plays a key role in driving substantial evolutionary change for SARS-CoV-2.

NATURE COMMUNICATIONS (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Interpretable modeling of genotype-phenotype landscapes with state-of-the-art predictive power

Peter D. Tonner et al.

Summary: LANTERN is a hierarchical Bayesian model that translates genotype-phenotype landscape measurements into a low-dimensional feature space, providing interpretability. It outperforms other methods in benchmark tests on large-scale datasets and extracts useful insights from the landscape.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

添加到收藏夹

Article Biology

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

Milo S. Johnson et al.

Summary: The distribution of fitness effects in a population can change during evolution, affecting the rate of adaptation and accumulation of deleterious mutations. This study directly measures changes in the fitness landscape neighborhood during laboratory adaptation and finds differences in the distribution due to variations in patterns of epistasis at the level of individual mutations.

ELIFE (2022)

添加到收藏夹

Article Multidisciplinary Sciences

Higher-order epistasis and phenotypic prediction

Juannan Zhou et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

添加到收藏夹

Article Genetics & Heredity

Adaptation of the yeast gene knockout collection is near-perfectly predicted by fitness and diminishing return epistasis

Karl Persson et al.

Summary: This study utilized a high-throughput method to track the adaptive evolution of cell populations and found that the preadaptation fitness of gene knockouts accurately predicts their adaptation to selection pressures, indicating a limited role for dedicated evolvability gene functions. Additionally, global epistasis was identified as a factor influencing adaptation.

G3-GENES GENOMES GENETICS (2022)

添加到收藏夹

Article Microbiology

Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes

Erol S. Kavvas et al.

Summary: This study characterizes the genotype-fitness maps of E.coli strains during adaptive laboratory evolution, providing insights into the mechanisms of microbial adaptation. The results show convergence in overall phenotypic measures across different strains, with the exception of divergence in NADPH production mechanisms. Transcriptomic adaptations involve increased expression of growth promoting genes and decreased expression of stress response and structural components. The study also identifies trade-offs in the regulatory network and correlates between causal mutations and systems-level adaptations.

MSYSTEMS (2022)

添加到收藏夹

Article Biotechnology & Applied Microbiology

MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect

Ammar Tareen et al.

Summary: Multiplex assays of variant effect (MAVEs) are a family of methods used to study the effects of mutations on proteins and gene regulatory sequences. Researchers have developed a neural-network-based Python package called MAVE-NN, which can learn genotype-phenotype maps from MAVE datasets, including biophysically interpretable models. It can effectively deconvolve mutational effects from experimental nonlinearities and noise.

GENOME BIOLOGY (2022)

添加到收藏夹

Article Biology

Emergence and propagation of epistasis in metabolic networks

Sergey Kryazhimskiy

Summary: The study revealed rules of epistasis between genes, indicating that weak epistasis between mutations at a lower level may become distorted as it propagates to higher levels. Computational analyses showed that in more realistic models, epistasis follows similar but more complex patterns.

ELIFE (2021)

添加到收藏夹

Article Genetics & Heredity

Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress

Marco Fumasoni et al.

Summary: The study explores how genomic features influence the evolutionary adaptation to DNA replication stress in budding yeast. Despite differences in selected genes among strains, adaptation targets three common functional modules: DNA replication, the DNA damage checkpoint, and chromosome cohesion. This suggests a conserved evolutionary response to genetic perturbations across different genomic features.

PLOS GENETICS (2021)

添加到收藏夹

Article Biology

Global epistasis emerges from a generic model of a complex trait

Gautam Reddy et al.

Summary: Recent research shows that consistent patterns of fitness increase in microbial evolution experiments are mainly driven by diminishing-returns and increasing-costs epistasis. Although the origin of this global epistasis remains unknown, it is found to emerge as a consequence of widespread microscopic epistasis. The specific quantitative relationship between the magnitude of global epistasis and the stochastic effects of microscopic epistasis predicts a universal form of fitness effects distribution when epistasis is prevalent.

ELIFE (2021)

添加到收藏夹

Article Multidisciplinary Sciences

Changes in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation

Dimitra Aggeli et al.

Summary: Diminishing returns are observed in the fitness gains during the second step of adaptation compared to the first step, due to a compressed distribution of fitness effects. The beneficial mutational spectra for the second adaptive step are contingent on the first step, with both shared and diverging adaptive strategies. Loss-of-function mutations are less common in the second step of adaptation, suggesting that adaptive potential decreases over time.

NATURE COMMUNICATIONS (2021)

添加到收藏夹

Article Biology

The evolutionary Plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress

Marco Fumasoni et al.

ELIFE (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis

Yu-Ying Phoebe Hsieh et al.

PLOS BIOLOGY (2020)

添加到收藏夹

Article Biochemistry & Molecular Biology

Physical Constraints on Epistasis

Kabir Husain et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

添加到收藏夹

Review Microbiology

Reconstructing organisms in silico: genome-scale models and their emerging applications

Xin Fang et al.

NATURE REVIEWS MICROBIOLOGY (2020)

添加到收藏夹

Article Ecology

Idiosyncratic epistasis creates universals in mutational effects and evolutionary trajectories

Daniel M. Lyons et al.

NATURE ECOLOGY & EVOLUTION (2020)

添加到收藏夹

Article Biology

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

Grant Kinsler et al.

ELIFE (2020)

添加到收藏夹

Article Genetics & Heredity

Modular epistasis and the compensatory evolution of gene deletion mutants

Jose I. Rojas Echenique et al.

PLOS GENETICS (2019)

添加到收藏夹

Review Evolutionary Biology

Recent insights into the genotype-phenotype relationship from massively parallel genetic assays

Harry Kemble et al.

EVOLUTIONARY APPLICATIONS (2019)

添加到收藏夹

Article Ecology

Environment changes epistasis to alter trade-offs along alternative evolutionary paths

Anne E. Hall et al.

EVOLUTION (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Higher-fitness yeast genotypes are less robust to deleterious mutations

Milo S. Johnson et al.

SCIENCE (2019)

添加到收藏夹

Article Multidisciplinary Sciences

Learning the pattern of epistasis linking genotype and phenotype in a protein

Frank J. Poelwijk et al.

NATURE COMMUNICATIONS (2019)

添加到收藏夹

Article Genetics & Heredity

Additive Phenotypes Underlie Epistasis of Fitness Effects

Andrew M. Sackman et al.

GENETICS (2018)

添加到收藏夹

Article Genetics & Heredity

Additive Phenotypes Underlie Epistasis of Fitness Effects

Andrew M. Sackman et al.

GENETICS (2018)

添加到收藏夹

Article Multidisciplinary Sciences

Inferring the shape of global epistasis

Jakub Otwinowski et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

添加到收藏夹

Article Biology

Genetic variation in adaptability and pleiotropy in budding yeast

Elizabeth R. Jerison et al.

ELIFE (2017)

添加到收藏夹

Article Ecology

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory

Andrea Wunsche et al.

NATURE ECOLOGY & EVOLUTION (2017)

添加到收藏夹

Article Multidisciplinary Sciences

Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness

Yinhua Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

添加到收藏夹

Review Biochemistry & Molecular Biology

Epistasis in protein evolution

Tyler N. Starr et al.

PROTEIN SCIENCE (2016)

添加到收藏夹

Article Ecology

Evolution of Fitness Trade-Offs in Locally Adapted Populations of Pseudomonas fluorescens

Alana Schick et al.

AMERICAN NATURALIST (2015)

添加到收藏夹

Article Genetics & Heredity

The rule of declining adaptability in microbial evolution experiments

Alejandro Couce et al.

FRONTIERS IN GENETICS (2015)

添加到收藏夹

Article Genetics & Heredity

The Impact of Macroscopic Epistasis on Long-Term Evolutionary Dynamics

Benjamin H. Good et al.

GENETICS (2015)

添加到收藏夹

Article Ecology

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

L. Perfeito et al.

EVOLUTION (2014)

添加到收藏夹

Article Genetics & Heredity

Deleterious Passengers in Adapting Populations

Benjamin H. Good et al.

GENETICS (2014)

添加到收藏夹

Article Biochemical Research Methods

Deep mutational scanning: a new style of protein science

Douglas M. Fowler et al.

NATURE METHODS (2014)

添加到收藏夹

Article Multidisciplinary Sciences

Global epistasis makes adaptation predictable despite sequence-level stochasticity

Sergey Kryazhimskiy et al.

SCIENCE (2014)

添加到收藏夹

Article Multidisciplinary Sciences

Long-Term Dynamics of Adaptation in Asexual Populations

Michael J. Wiser et al.

SCIENCE (2013)

添加到收藏夹

Article Genetics & Heredity

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

Kenneth M. Flynn et al.

PLOS GENETICS (2013)

添加到收藏夹

Article Multidisciplinary Sciences

Genomic analysis of a key innovation in an experimental Escherichia coli population

Zachary D. Blount et al.

NATURE (2012)

添加到收藏夹

Article Multidisciplinary Sciences

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

Benjamin H. Good et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

添加到收藏夹

Article Multidisciplinary Sciences

The noisy edge of traveling waves

Oskar Hallatschek

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

添加到收藏夹

Article Multidisciplinary Sciences

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

Aisha I. Khan et al.

SCIENCE (2011)

添加到收藏夹

Article Multidisciplinary Sciences

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

Hsin-Hung Chou et al.

SCIENCE (2011)

添加到收藏夹

Review Genetics & Heredity

Molecular mechanisms of epistasis within and between genes

Ben Lehner

TRENDS IN GENETICS (2011)

添加到收藏夹

Article Genetics & Heredity

Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa

R. C. MacLean et al.

GENETICS (2010)

添加到收藏夹

Article Ecology

Predicting epistasis: an experimental test of metabolic control theory with bacterial transcription and translation

R. C. MacLean

JOURNAL OF EVOLUTIONARY BIOLOGY (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

Jeffrey E. Barrick et al.

MOLECULAR BIOLOGY AND EVOLUTION (2010)

添加到收藏夹

Article Multidisciplinary Sciences

The Genetic Landscape of a Cell

Michael Costanzo et al.

SCIENCE (2010)

添加到收藏夹

Article Biochemistry & Molecular Biology

The Genetics of Adaptation for Eight Microvirid Bacteriophages

Darin R. Rokyta et al.

JOURNAL OF MOLECULAR EVOLUTION (2009)

添加到收藏夹

Article Genetics & Heredity

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation

Hsin-Hung Chou et al.

PLOS GENETICS (2009)

添加到收藏夹

Article Genetics & Heredity

Epistasis and the adaptability of an RNA virus

R Sanjuán et al.

GENETICS (2005)

添加到收藏夹

Article Biology

Pervasive compensatory adaptation in Escherichia coli

FBG Moore et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2000)

添加到收藏夹

© Peeref 2019-2024. All rights reserved.