Evolution and Genetic Dynamics

Growth rate structures the dynamics of bacterial trait evolution

This study shows growth rate is a major organizing axis shaping bacterial trait evolution across timescales, with distinct slow- and fast-growing regimes and varying coupling with other traits.

Scalable phylodynamic inference of mutational and epistatic fitness effects with multi-feature birth-death models

This paper develops a Bayesian framework for inferring mutational and epistatic fitness effects in microbial evolution using multi-feature birth-death models and applies it to Escherichia coli phylogenies.

Evolutionary rescue in toxic combinations of metal is dependent on metal interactions

This study shows that evolutionary rescue in toxic metal combinations depends on metal interactions, with antagonistic combinations leading to broader fitness benefits than synergistic ones.

A Vast Navigable Protein Sequence Subspace

The paper maps the genome packaging landscape of AAV2 capsid protein using high-throughput synthesis and machine learning, revealing navigable subspaces of functionally viable sequences.

The role of chromosomal inversions in local adaptation and ecotype formation across a variable landscape in an intertidal snail

This study identifies 18 chromosomal inversions in Littorina saxatilis that respond to environmental variation and influence phenotypic traits, explaining 15% of phenotypic variation.

Evidence from the field that multiple processes maintain hidden adaptive capacity to a novel environment in a wild daisy

The paper shows that genetic variation for adapting to novel environments is maintained in wild daisies through inefficient selection and dominance, with heritable effects on plasticity and fitness.

Sequential accumulation of adaptive alleles forms an inversion supergene in deer mice

The paper identifies two genes within a chromosomal inversion supergene in deer mice that contribute to forest adaptation traits and shows the supergene evolved through sequential allele accumulation.

Introgression under linear selection on continuous genomes

The paper models introgression of a small genomic block with weakly selected loci into a population, showing survival depends on selection strength relative to recombination.

Pareto fronts reveal constraints on the evolution of ecological niches

The paper uses Pareto fronts to detect evolutionary constraints on niche-determining traits in phytoplankton, showing that trade-offs persist across scales despite differing evolutionary outcomes.

Triangulating evidence to detect signatures of stabilizing selection acting on protein levels in humans

The paper detects stabilizing selection on human plasma proteins by integrating genetic and fitness-related evidence across multiple approaches.

Hybrid Drosophila genomes rapidly purge minority ancestry but repeatedly retain selected regions

The paper tracks genome-wide evolutionary dynamics in hybrid Drosophila populations, showing rapid purging of minority ancestry and repeated retention of selected regions through adaptive introgression.

Repair-Mediated Path Filtering of Mutation Load in Multilocus Homeostatic Populations

The paper analyzes a mutation--selection--repair system in asexual populations, showing how repair mechanisms suppress mutation load and alter locus associations.

Spatial structure drives the evolution of parasites into host defense systems

The paper shows that spatial structure in host populations drives the evolution of parasites into host defense systems through the emergence of hyperparasites.

Experimental speciation: selection against hybridization strengthens reproductive barriers and limits introgression

This study shows that selection against hybridization increases reproductive isolation between Drosophila populations while allowing gene flow, with intermediate selection producing the strongest isolation.

When should a pathogen strike? Navigating the landscape of birth pulses and mating season

The paper models how pathogens evolve transmission timing in relation to host life stages and phenology, finding that synchronized germination and flowering maximizes disease prevalence.

Microbiomes change the rules of host evolution

This study shows microbiomes alter host evolutionary dynamics by changing effective population size and selection coefficients, leading to different evolutionary outcomes than classical predictions.

A DNA-barcoded Luria-Delbrück assay resolves mechanisms of adaptation

This paper introduces HiDenSeq, a DNA-barcoded Luria-Delbrück assay that uses deep sequencing to analyze adaptation mechanisms by resolving the Luria-Delbrück distribution over four orders of magnitude.

Complex-trait dissection with Evolve-and-Resequence: Selection for improved flight performance in laboratory fruit fly populations

This study uses Evolve-and-Resequence to improve flight performance in Drosophila melanogaster, identifying genomic changes and phenotypic traits associated with the adaptation.

Microbially Assisted Rescue of Host Populations

This paper develops a population-genetics model to study how host-associated microbes can assist in population rescue during environmental change, identifying two microbial contributions that shape rescue outcomes.

A Variational Modeling Framework for Population Genetic Dynamics

The paper develops a variational framework for modeling population genetic dynamics, incorporating mutation, recombination, and selection, and validates it against simulations.

Fixation Probabilities of Mutant Alleles in an Ecological Context

The paper shows that ecological interactions can significantly alter fixation probabilities of mutant alleles even in effectively neutral conditions.

Viral dispersal drives changes in population composition

The paper investigates how spatial expansion and dispersal modulators affect viral population structure and genetic diversity during infection.

Intragenic epistasis in couch potato shapes life history traits and climatic adaptation in Drosophila melanogaster

The paper shows non-additive interactions among three intronic SNPs in the cpo gene affect life history traits and climatic adaptation in Drosophila melanogaster.

Comparison of intracellular and encapsidated viral RNA reveals selective constraints on reovirus recombination

The paper compares recombination rates in intracellular and encapsidated reovirus RNA, finding higher recombination in intracellular RNA and suggesting recombination occurs more frequently during plus-strand synthesis.

Contrasting relationships between evolved consumer diversity and productivity for essential vs. substitutable resources

This study models how resource type and trade-offs affect consumer diversity and productivity in metacommunities, finding that essential resources reduce productivity despite high diversity.

Ethanol stress induces siRNA-mediated epimutations and phenotypic variability in fission yeast

This study shows ethanol stress increases siRNA-mediated epimutations in fission yeast, leading to transposon expression changes and phenotypic variability.

Unstable Heteroresistance as a Stepping Stone to Stable Resistance via Compensatory Mutations

This study shows that antibiotic heteroresistance can transition to stable resistance via compensatory mutations, leaving no genetic trace in surviving isolates.

Assortative mating may have facilitated rapid evolution of locally adaptive phenologies during a biological invasion

The paper investigates how assortative mating influenced the rapid evolution of flowering phenology in Lythrum salicaria during its invasion of eastern North America.

Weak selection of phenotypic memory in periodic environments

The paper shows that small mutations creating phenotypic memory have no first-order selective advantage, while maternal effects conditioned on the environment are under first-order selection.

Strong correlations between mutation rates and selective constraint in the human genome?

The paper investigates the relationship between mutation rates and selective constraint in the human genome, finding higher mutation rates in protein-coding genes compared to non-coding regions.