Mutation-Driven Parallel Evolution during Viral Adaptation

Elevating fitness after a horizontal gene exchange in bacteriophage φX174

(2017) Sarah M. Doore et al.   VIROLOGY

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Predictable convergence in hemoglobin function has unpredictable molecular underpinnings

(2016) Chandrasekhar Natarajan et al.   SCIENCE

Love the one you’re with: replicate viral adaptations converge on the same phenotypic change

(2016) Craig R. Miller et al.   PeerJ

Synergistic Pleiotropy Overrides the Costs of Complexity in Viral Adaptation

(2015) L. W. McGee et al.   GENETICS

The Kinetic and Thermodynamic Aftermath of Horizontal Gene Transfer Governs Evolutionary Recovery

(2015) Sarah M. Doore et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the Causes of Evolutionary Transition:Transversion Bias

(2015) Arlin Stoltzfus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

(2015) Spencer C. Galen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread convergence in toxin resistance by predictable molecular evolution

(2015) Beata Ujvari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bypass of genetic constraints during mutator evolution to antibiotic resistance

(2015) A. Couce et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages

(2015) Andrew M. Sackman et al.   PeerJ

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

(2014) C. Bank et al.   GENETICS

Adaptation in Tunably Rugged Fitness Landscapes: The Rough Mount Fuji Model

(2014) J. Neidhart et al.   GENETICS

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Payoffs, Not Tradeoffs, in the Adaptation of a Virus to Ostensibly Conflicting Selective Pressures

(2014) Lindsey W. McGee et al.   PLoS Genetics

Influenza Virus Drug Resistance: A Time-Sampled Population Genetics Perspective

(2014) Matthieu Foll et al.   PLoS Genetics

Environment Determines Epistatic Patterns for a ssDNA Virus

(2013) S. Brian Caudle et al.   GENETICS

The Adaptive Potential of Hybridization Demonstrated with Bacteriophages

(2013) Andrew M. Sackman et al.   JOURNAL OF MOLECULAR EVOLUTION

The Consistency of Beneficial Fitness Effects of Mutations across Diverse Genetic Backgrounds

(2012) Victoria M. Pearson et al.   PLoS One

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme

(2012) Martijn F. Schenk et al.   PLoS Genetics

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Cost of Adaptation and Fitness Effects of Beneficial Mutations inPseudomonas fluorescens

(2011) Thomas Bataillon et al.   GENETICS

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

(2011) Darin R. Rokyta et al.   PLoS Genetics

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

POPULATION GENETICS, PLEIOTROPY, AND THE PREFERENTIAL FIXATION OF MUTATIONS DURING ADAPTIVE EVOLUTION

(2010) Matthew A. Streisfeld et al.   EVOLUTION

FISHER'S MODEL AND THE GENOMICS OF ADAPTATION: RESTRICTED PLEIOTROPY, HETEROGENOUS MUTATION, AND PARALLEL EVOLUTION

(2010) Luis-Miguel Chevin et al.   EVOLUTION

The Genetics of Adaptation for Eight Microvirid Bacteriophages

(2009) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION

Genic Incompatibilities in Two Hybrid Bacteriophages

(2009) D. R. Rokyta et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa

(2009) R. Craig MacLean et al.   PLoS Genetics

The Distribution of Beneficial and Fixed Mutation Fitness Effects Close to an Optimum

(2008) Guillaume Martin et al.   GENETICS

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence

(2008) J. P. Bollback et al.   GENETICS

A General Extreme Value Theory Model for the Adaptation of DNA Sequences Under Strong Selection and Weak Mutation

(2008) Paul Joyce et al.   GENETICS

Genomic evolution in a virus under specific selection for host recognition

(2008) Kim M. Pepin et al.   INFECTION GENETICS AND EVOLUTION

Beneficial Fitness Effects Are Not Exponential for Two Viruses

(2008) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION