Evolution and Genetic Dynamics

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.

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.

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.

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.

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.

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.

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

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

The paper introduces a geometric framework on the extended complex plane to quantify gene-by-gene and gene-by-environment interactions using complex transformations and buffering concepts.

This study identifies genes linked to cancer risk variation across species, showing indirect effects on body size dominate cancer suppression, while direct effects increase tumour prevalence.

This study combines theory and experiments to show how trait-resource matching constrains coexistence in microbial communities under nonequilibrium conditions.

This paper introduces a framework to infer fitness landscapes with structured epistasis and applies it to protein and RNA mutagenesis data, revealing complex genetic interactions.

This study identifies genetic variants in Arabidopsis thaliana that enable adaptation to urban environmental gradients through a city-wide colonization experiment.

The paper models influenza transmission bottlenecks using a branching-process framework to quantify diversity loss during early viral growth and host-specific filters.

The paper estimates gene-specific sweep origins in human gut microbiomes and finds that complex adaptations spread slowly due to low mutation rates and genetic constraints.

This study shows that prophage induction via SOS response limits resistance evolution to DNA-damaging antibiotics by eliminating mutants with high DNA damage.

The paper examines how host susceptibility distributions reflect pathogen geographic structure in an insect baculovirus, finding that generalist viruses show lower susceptibility heterogeneity across populations.

This study investigates the reconstructability of evolutionary intermediates using generative sequence landscapes, finding that conditional sampling better captures plausible histories than maximum-likelihood prediction.

The paper uses whole genome sequencing to study adaptation in Trinidadian guppies over two periods, finding genomic signatures of selection and inbreeding patterns.

This study examines the error landscape of hemagglutinin-encoding RNA in influenza, showing that mutations from high-frequency errors are preferentially selected during evolution.

This study shows that parasites at the front of an epidemic evolve higher infectivity and lower virulence, which accelerates epidemic spread when host dispersal is limited.

The paper investigates factors determining effective reassortment in orthohantaviruses, finding that ecological overlap and molecular compatibility are key for reassortant establishment.

The paper identifies nine putative chromosomal inversions in purple sea urchins, three showing signs of selection, suggesting structural variants contribute to adaptation in marine species with high gene flow.

The paper examines the relationship between plasmid copy numbers and size, arguing for two evolutionary strategies rather than a single scaling law.

This paper develops a data-validated theory of natural selection after catastrophe, showing mean fitness relaxes inversely with time and follows Levenberg-Marquardt optimization in E. coli.

The paper uses an eco-evolutionary model to show how mutualism and antagonism interact to influence diversification in ecological networks, finding that trait correlation affects diversification rates across guilds.

This study detects pervasive cryptic negative selection in human noncoding regions using a statistical test, finding that at least 7% of the genome is under negative selection, surpassing previous estimates from conservation-based methods.

The paper proposes the Gene Version Iteration Hypothesis, suggesting mutant genes may cycle through chromosomes via the Y and X chromosomes, enabling version selection and evolutionary dynamics.

The paper shows how a duplicated tRNA synthetase evolved into a novel toxin by losing its ancestral function and acquiring a new role in targeting Aurora kinase A.

The paper analyzes selection pressures on mammalian extracellular matrix proteins across species and develops an open-access browser to visualize evolutionary dynamics.