Mutation bias shapes the spectrum of adaptive substitutions

2022/02/10 by Alejandro V. Cano, Hana Rozhoňová, Arlin Stoltzfus +2 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms

paper · pdf · doi:10.1073/pnas.2119720119

openalex publication_date 2022/02/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

Using species-specific mutation spectra based on prior knowledge, we find that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species. Indeed, we find that by inferring the mutation rates that best explain the spectrum of adaptive substitutions, we can accurately recover the species-specific mutation spectra. However, we also find that the predictive power of the model differs substantially between the three species. To better understand these differences, we use population simulations to explore the factors that influence how closely the spectrum of adaptive substitutions mirrors the mutation spectrum. The results show that the influence of the mutation spectrum decreases with increasing mutational supply ([Formula: see text]) and that predictive power is strongly affected by the number and diversity of beneficial mutations.

Citations

• Widespread convergence in toxin resistance by predictable molecular evolution
• Precise estimates of mutation rate and spectrum in yeast
• An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus
• Bias in the introduction of variation as an orienting factor in evolution
• Developmental Constraints and Evolution: A Perspective from the Mountain Lake Conference on Development and Evolution
• Evidence That Mutation Is Universally Biased towards AT in Bacteria
• Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa
• Modeling Evolution Using the Probability of Fixation: History and Implications
• Antimicrobial Resistance in Mycobacterium tuberculosis : The Odd One Out
• Constraint-Based Reasoning for Search and Explanation: Strategies for Understanding Variation and Patterns in Biology
• What drives parallel evolution?
• Mutation-Driven Parallel Evolution during Viral Adaptation
• The dynamics of molecular evolution over 60,000 generations
• Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis
• The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
• The Role of Mutation Bias in Adaptive Evolution
• Mutation bias interacts with composition bias to influence adaptive evolution
• Mutation bias can shape adaptation in large asexual populations experiencing clonal interference
• Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses
• Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes
• The fate of competing beneficial mutations in an asexual population

Cited by

• Bias in the introduction of variation [wikipedia]