Evolution and Genetic Dynamics

This paper shows that higher-order interactions in microbial communities are undetectable due to noise and statistical constraints, not because they are biologically insignificant.

The paper constructs a genotype-phenotype map for influenza hemagglutinin using predicted secondary structure, revealing local neutrality and limited structural evolvability.

This paper revisits the mutation-selection balance model by incorporating fluctuating stabilizing selection, showing that heritability predictions are more consistent with observations under environmental change.

TurboPRANCE enables large-scale, multi-objective continuous evolution by integrating robotic systems with phage-assisted evolution, generating high-resolution evolutionary data across diverse selection regimes.

The paper uses phylogenetic analysis to examine natural selection in zoonotic viruses, finding no evidence of pre-zoonotic adaptation for human transmission but detecting selection changes in the 1977 H1N1 reemergence.

The paper develops an eco-evolutionary model to study community assembly mechanisms and identifies how interaction types influence biodiversity and community structure.

This study shows environmental fluctuations can both hinder and promote evolutionary rescue in algae, depending on their amplitude and interaction with long-term environmental trends.

The paper tests whether genomic 'firmware' --- conserved compatibility layers --- emerges from sexual reproduction by analyzing synonymous-site conservation in mammals and Drosophila.

The paper develops a theoretical framework to detect genetic signatures of rapid adaptation to extreme environmental changes using population genetics models.

This study uses artificial selection in Drosophila to examine copper resistance and its off-target effects on other traits, finding increased resistance to copper and non-essential metals with associated costs.

This study uses genomic data from Drosophila melanogaster to show how fitness trade-offs manifest under fluctuating selection, identifying genomic regions linked to reproduction and stress tolerance.

The paper tests the nearly-neutral theory across 144 placental mammal genomes, showing correlations between genetic diversity, life-history traits, and selection efficacy at both micro- and macro-evolutionary scales.

This paper introduces BASIL, a Bayesian method to estimate fitness effects of beneficial mutations from BLT data, showing it is more accurate and robust than existing methods.

The paper models SARS-CoV-2 evolution during the pandemic, finding that immune escape became more important than infectivity as variants evolved.

This study shows how intermittent treatment pulses reshape resource landscapes and spatial growth zones, enabling resistant mutants to escape confinement and drive therapy failure.

This study investigates the genetic basis of industrial melanism in peppered moths, showing that multiple alleles at the ivory locus, including structural variants, contribute to the trait in different regions.

This study uses a mechanistic immunological model to show how immunodeficiencies shape viral evolution during primary infections, with varying effects on mutation frequency and speed depending on the type of infection and immune deficiency.

This study shows that T. thermophila adapts quickly to road salt exposure but faces fitness tradeoffs in low-salt environments.

This paper introduces an improved orthogonal replication system in E. coli that enables rapid gene evolution with high mutation rates and demonstrates its application in evolving ethanol assimilation pathways.

The paper extends the Reduction Principle by showing that stochastic mutation rate fluctuations can reverse the direction of modifier evolution compared to deterministic models.

This study shows that combining DNA-damaging agents with antibiotics can reduce resistance evolution in specific hypermutator bacterial genotypes but not others.

The paper simulates evolution in diploid and autotetraploid populations to show that pseudo-overdominance is more common in polyploids due to reduced recombination and increased masking of deleterious mutations.

The paper investigates how environmental changes affect genetic gain in plant breeding by simulating germplasm structure and selection strategies.

This study introduces a consumer-resource model to analyze higher-order interactions in auxotroph communities and shows how these interactions enhance resilience to resource fluctuations.

This study analyzes antibiotic resistance emergence in Pseudomonas aeruginosa during treatment, finding that pre-existing resistance and ecological dynamics drive resistance development.

This study estimates de novo mutation rates in barn owls, showing paternal age effects and sex-specific mutation patterns.

The paper shows that evolution on degenerate fitness landscapes is not neutral, as curvature induces directional drift toward flat regions.

The paper tracks mutation accumulation in natural C. elegans populations over time, finding a substitution rate and spatio-temporal dispersal patterns.

This study shows that compensatory mutations in yeast rewiring gene fitness across cellular processes, not just individual genes, highlighting the role of functional overlap and network interconnectedness.

The paper examines how adaptation to temperature changes affects gene expression and plasticity in the fungus Zymoseptoria tritici, finding convergent changes and unexpected pleiotropy in adaptive mutations.