Evolution and Genetic Dynamics

Sequential evolution of antidote and toxin links genetic incompatibility with immune responses

The paper discovers a novel toxin-antidote gene pair in C. nigoni, showing the antidote evolved before the toxin and supports a microbial origin for the toxin.

Heterozygote advantage cannot explain MHC diversity, but MHC diversity can explain heterozygote advantage

The paper argues that heterozygote advantage cannot explain MHC diversity and that MHC diversity may instead explain heterozygote advantage.

Macro evolutionary patterns do not predict micro evolutionary trajectories

The paper develops a modeling framework to explore phytoplankton evolutionary trajectories under climate change, showing it captures evolved phenotypes not predicted by traditional models.

Evolutionary trade-offs between antimicrobial resistance and virulence in Pseudomonas aeruginosa

This study investigates how resistance to different antibiotics affects virulence in Pseudomonas aeruginosa, finding antibiotic-specific trade-offs between resistance and virulence.

Integrating Bottleneck Size into Selection Tests for Biological Diversity Data

This study introduces a method that integrates bottleneck size into selection tests for biological diversity data, improving the detection of selection signatures by accounting for sequencing errors and sampling biases.

Apparent stabilizing selection explains micro and macroevolution of Drosophila wings

The paper investigates stabilizing selection on Drosophila wing shape and shows it constrains macroevolutionary change despite genetic variance.

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator

This study shows that exposure to a ciliate predator reshapes evolutionary dynamics in Pseudomonas aeruginosa by maintaining genetic diversity and altering mutation frequency distributions, without consistently increasing virulence.

The evolution of a condition-dependent mutation rate enhances evolvability

This paper uses simulations to show that condition-dependent mutation rates evolve in changing environments, enhancing evolvability and adaptation.

Protein fitness landscapes are simpler under evolutionary distributions

The paper shows that protein fitness landscapes appear simpler when analyzed using an evolution-aware framework that accounts for the non-uniform distribution of sequences in nature.

Evolutionary trade-offs between intergenerational and transgenerational fitness effects

The paper shows that beneficial intergenerational fitness effects in C. elegans can lead to detrimental transgenerational effects, demonstrating evolutionary trade-offs across generations.

Chromosome, Plasmid, or Both: Short-Term Dynamics and Long-Term Outcomes of Plasmid Cost Compensation under Trade-Offs

The paper models how plasmid and chromosomal compensation affect the spread of antimicrobial resistance, finding short-term plasmid-borne compensation dominates but long-term chromosomal or combined compensation leads to multidrug resistance.

Protein language models learn the underlying accessibility of mutations alongside protein fitness landscapes

This study evaluates how protein language models capture mutational processes and fitness landscapes, finding that explicit mutational accessibility improves predictions while historical biases degrade performance.

Mutational bias shapes protein evolution across RNA viruses

The paper quantifies how mutational biases shape protein evolution in RNA viruses by analyzing SARS-CoV-2 and 34 other species, showing that mutational spectra predict amino acid composition changes and deviations indicate selection pressures.

Effect of cellular nutrient economy on the evolution of genome size in phytoplankton

This study develops a theoretical framework linking cellular nutrient economy to genome size evolution in phytoplankton, showing that 1-bp indels can be counterselected under minimal nutrient conditions.

Environment-dependent and often antagonistic effects of dominance and epistasis on heterosis in crosses between natural populations

The paper assesses how genomic regions influence heterosis in Arabidopsis thaliana crosses, finding environment- and background-dependent non-additive effects and epistasis.

The causes of signed linkage disequilibrium within genomic datasets

The paper investigates the causes of positive signed linkage disequilibrium in genomic datasets, showing it may arise from technical artifacts and frequency-based biases.

Nemo2.4: fast and accurate quantitative genetics forward-time simulations

Nemo 2.4 simulates eco-evolutionary dynamics and quantitative traits with flexible genetic models and efficient computation.

A resurrection experiment reveals reduced adaptive potential in a common agricultural weed

This study uses a resurrection experiment to show that genetic constraints on flowering phenology in Ipomoea purpurea have increased, reducing adaptive potential despite strong selection pressures.

Insecticide resistance evolution and assisted gene flow interact to shape the evolution of plasticity

The paper investigates how insecticide resistance evolution and assisted gene flow affect phenotypic plasticity in Drosophila melanogaster, finding interactions that influence trait and plasticity evolution.

Fitness flux in SARS-CoV-2 and influenza H3N2

This paper directly measures viral fitness flux in SARS-CoV-2 and influenza H3N2 by tracking variant frequency dynamics and finds it correlates with fitness variance, matching Fisher's fundamental theorem.

Experimental evolution reveals bifunctional genetic solutions to loss of trpF in Salmonella enterica

This study shows that point mutations in multiple genes can restore tryptophan biosynthesis in Salmonella enterica lacking trpF, demonstrating bifunctional genetic solutions without gene duplication.

Ecological genomics of a novel host-parasitoid arms-race in nature

The paper studies genomic signatures of coevolution between a parasitoid fly and its cricket host, revealing arms-race dynamics and selective sweeps driven by host adaptations.

DEX: an amino acid exchangeability measure for codon substitution modelling and selection inference

This paper evaluates 30 amino acid distance measures, including a new one based on deep mutational scanning, to identify the best for modeling codon substitutions and inferring natural selection across diverse lineages.

Evolution of quantitative traits: exploring the ecological, social and genetic bases of adaptive polymorphism

The paper analyzes conditions for the emergence of adaptive polymorphism under long-term evolution, identifying negative trait-dependent selection as a unifying mechanism across ecological, social, and genetic interactions.

Ultra-accurate sequencing reveals an extreme transmission bottleneck in a deep-sea clam symbiosis

The paper estimates an extreme transmission bottleneck in a deep-sea clam symbiosis using ultra-accurate sequencing, finding an effective bottleneck size of about eight symbionts per host generation.

Evolution of mutation rates in digital genomes: the roles of genetic drift, mutational supply, and genome size

This study uses a digital genomics simulation to show that mutation rates decrease over time due to genetic drift and limited supply of fidelity-improving mutations, while genome size increases as a trade-off.

Context-dependent calibration of Evo2 likelihood with bacterial fitness: a quantitative characterization across five E. coli datasets

This paper quantifies how Evo2 likelihood scores calibrate with fitness across five E. coli datasets, showing context-dependent calibration that varies by selection regime and sequence divergence.

Model-free inference of evolution from allele frequency timeseries using permutation tests

This paper introduces permutation tests to detect evolutionary features from allele frequency timeseries without assuming a model of evolutionary change.

Inferring viral proteins that act as public goods during coinfection

The paper infers viral proteins acting as public goods during coinfection in bacteriophage MS2 using experimental evolution data and Bayesian inference.

Meiotic cohesin Rec8 imposes fitness costs on fission yeast gametesfavoring the evolution of parental bias in gene expression

The paper shows that meiotic cohesin Rec8 in fission yeast gametes creates a fitness trade-off, leading to parental bias in gene expression.