Evolution and Genetic Dynamics

The paper introduces a theoretical framework to analyze homoplasy caused by recombination, showing how it depends on mutation rates, selection, drift, and allele frequencies.

The study compares adaptation to soil type and climate in two Arabidopsis thaliana populations, finding that soil adaptation contributes little to overall adaptive differentiation.

The paper demonstrates that an epigenetic switch in Salmonella allows bistability in fluctuating environments but not in stable ones, supporting bet-hedging as an evolutionary strategy.

The paper investigates how promoter variability affects the evolution of essential genes in E. coli, finding that promoters of essential genes show biased mutational variability toward lower activity, constraining future expression level evolution.

This study shows that experimental evolution of Drosophila melanogaster under post-infection survival selection leads to increased disease resistance but not disease tolerance.

The paper tracks ecological and evolutionary changes in a bacterial community under copper stress, finding that siderophore production converges at intermediate levels through both species sorting and evolution.

This study shows that autonomous genotypes can evolve from cooperative microbial specialists in fluctuating environments through horizontal gene transfer.

This paper derives an expression for effective migration rate under polygenic local adaptation and shows how dominance and genetic architecture affect barriers to gene flow.

This paper develops a Bayesian method to infer host-pathogen interaction matrices from genome-wide polymorphism data and applies it to HCV-infected humans to identify new resistance genes and GxG interactions.

This study evolves an engineered microbial community to show how metabolic interactions increase, leading to interdependence and indirect selection for mutualism.

The paper identifies cis-regulatory evolution in translation genes in stem cells of M. m. castaneus compared to sister taxa using expression and population-genomic data.

The paper investigates the molecular mechanisms of asexual reproduction emergence in brown algae, finding convergent gene expression changes and a key autosomal locus associated with the loss of sex.

The paper duplicates and evolves an homodimeric enzyme to show that compensatory mutations can lead to functional heteromers through subfunctionalization.

The paper tracks adaptive genetic changes in Drosophila melanogaster under fluctuating selection pressures, revealing rapid, parallel genomic responses and predictable selection targets over time.

This study infers the distribution of fitness effects of mutations in C. elegans using recombinant inbred lines, finding that positive effects are common but LD can skew results.

popDMS infers mutation effects from DMS data by applying population genetics theory, showing consistency across replicates and outperforming existing methods.

The paper investigates how genomic architecture influences the formation and fitness of adaptive copy number variants (CNVs) in yeast, finding that template switching during DNA replication is a common mechanism for CNV generation.

The paper investigates how traits developed under ecological scaffolding can persist after scaffolding conditions are removed, using mathematical models to identify conditions for endogenisation.

The paper analyzes the asymptotic behavior of latent mutations in a genetic locus under selection and mutation, showing that under certain conditions, the distribution of mutations matches the Ewens sampling formula.

This study evaluates combination antibiotic therapy to limit resistance evolution by analyzing drug interactions and optimal dosing strategies using a stochastic pharmacodynamic model.

The paper shows that adaptive reversion explains dN/dS decay in microbiomes, challenging the classical interpretation of purifying selection.

This paper conducts a meta-analysis of viral mutation fitness effects across hosts, finding positive pleiotropy is common and fitness effects are positively correlated between hosts.

This study examines mitonuclear interactions in Drosophila populations, finding that natural disruptions affect mitochondrial function and fitness traits like reproduction and survival.

The paper develops a computational method to correct barcode processing biases in bulk fitness assays, improving fitness estimates in yeast variant libraries.

The paper develops a neutral speciation model with realistic dispersal for butterflies, showing speciation occurs under realistic conditions and exhibits scaling behavior.

PEMPS simulates metabolic pathway evolution using mutation-selection models and phylogenetics to infer selection and ancestral states.

This paper identifies a 39.8kb flavi-like virus without an exonuclease that overcomes the RNA virus error threshold by using bacterial nucleic acid metabolism domains.

The paper tracks yeast lineages in static and fluctuating environments, finding fitness deviations and environmental memory effects due to prior conditions.

The paper maps mutation tolerability across a viral proteome, revealing structural and functional correlates and implications for drug target selection.

This study identifies hydrogen peroxide detoxification as the mechanism behind density-dependent mutation rate plasticity in microbial populations.