Evolution and Genetic Dynamics

This paper develops an intra-host eco-evolutionary model of poliovirus under pocapavir treatment, showing that antiviral potency must balance immediate viral suppression with preserving coinfection to prevent resistance.

The paper shows that slightly deleterious mutations, rather than a few large-effect mutations, explain slow viral load changes and heritability in HIV evolution.

The paper shows that evolution in a stressful environment allows two spider mite species to coexist, but evolution of one species in isolation leads to exclusion.

The paper proposes a mathematical model showing how genome size evolution is shaped by mutation biases and robustness selection, leading to an equilibrium non-coding fraction.

This study examines the long-term thermal adaptation of four yeast species and their hybrids over 140 generations under extreme cold and warm conditions, finding hybrids show greater fitness improvements and resilience.

This study shows that mistranslation costs in E. coli are generally lower than antibiotic costs, but both can shape adaptation and have collateral effects on antibiotic resistance.

This study shows that local negative frequency-dependent selection can reduce global coexistence in fragmented populations, contradicting its role in maintaining biodiversity in continuous landscapes.

SLiM 5 extends the simulation framework to support multiple chromosomes, enabling full-genome simulations with various chromosome types.

This study identifies abundant mitochondrial mutations and widespread mitonuclear epistasis in C. elegans by analyzing genetic variation and phenotypic outcomes across diverse strains.

The paper examines how molecular interactions and activity-fitness functions determine phenotypic dominance in homomeric proteins.

The paper analyzes how slow migration, spatial structure, and environmental fluctuations affect fixation and extinction in metapopulations of bacteria under time-fluctuating conditions.

This study shows that initial mutations can constrain adaptive diversification in structured environments, highlighting the role of genotype-by-environment interactions in evolutionary outcomes.

This study measures within-cell plasmid fitness and shows that incompatible plasmids co-occur longer due to methylation-based eclipsing, with less transcriptionally active plasmids having a selective advantage.

The paper derives the distribution of the time to the most recent pairwise genetic common ancestor in a recombining population, finding a characteristic scaling with population size.

The paper compares the effectiveness of bacteriostatic and bactericidal drugs in preventing antimicrobial resistance evolution in bacterial populations under different resource conditions.

The paper investigates how interdependent protein interactions evolve by studying toxin-antidote elements, finding that toxins and antidotes can arise simultaneously through the duplication of a regulatory module.

This study shows that longevity can hinder evolutionary rescue by slowing growth but not necessarily adaptation, depending on heritability and selection dynamics.

The paper examines how stronger selection affects evolutionary rescue across different population genetic models and finds that it can only facilitate rescue if it increases the absolute fitness of the rescue homozygote.

This study quantifies how genotype-dependent gene flow affects mutation fixation in subdivided populations, finding similar fixation probabilities but different fixation times between island and stepping stone models.

This paper reviews the development of balancing selection theory over the last century and examines its biological scenarios and genetic system features.

This paper unifies optimal offspring size theory and bacterial aging models by showing that resource distribution strategies depend on the convexity of the resource-survivorship function.

This paper develops a gene-regulatory network model to study density-dependent and sex-biased dispersal evolution during range expansions and finds GRNs enable faster range expansion under mutation effects.

This study measures mutation rates and spectra in anaerobic lactic acid bacteria over 1000 generations, revealing elevated rates and transition biases, with novel mutation dynamics in specific species.

The paper introduces a fitness landscape model to predict hybrid fitness across varying ploidy and lineage complexity, validated using maize and rye hybrid data.

The study examines how community complexity affects coevolution between Pseudomonas fluorescens and Variovorax sp., finding that pairwise coevolution remains unaffected by the presence of other species.

The paper generates essential gene deletion mutants in Streptococcus sanguinis and identifies suppressor mutations through experimental evolution, revealing new gene and pathway relationships.

This study investigates how coevolutionary cycling in allele frequencies affects virulence evolution in a free-living parasite using population and quantitative genetic approaches.

This study identifies environmental factors affecting the growth fitness of antibiotic-resistant Escherichia coli mutants and their resistance prevalence.

The paper investigates environment-by-environment interactions (ExE) across genetic backgrounds (ExExG) in yeast, showing that drug combinations vary in effectiveness among mutants and introducing a new predictive framework.

This study uses population and comparative genomics to analyze how natural selection affects TF-DNA interaction motifs, finding purifying selection on TF-BDs and increased positive selection in species with large Ne.