Evolution and Genetic Dynamics

Environmental impacts on gene expression noise and its relationship with fitness

The paper examines how environmental factors influence gene expression noise and its fitness effects in yeast, showing environment-specific relationships.

Cryptic Evolution of Heteroresistance as Adaptation to Treatment Interruptions

This study shows that heteroresistance evolves under treatment interruptions in E. coli, using phenotypic flexibility to maintain resistance with minimal fitness cost.

Optimal Control and the Dynamics of Ancestral Lineages

This paper introduces a framework to infer selection coefficients from phylogenetic trees by integrating optimal control theory with evolutionary dynamics.

Environmental stochasticity can account for patterns of within-host respiratory virus evolution

This study shows environmental stochasticity can explain within-host viral evolution patterns without needing demographic stochasticity or constant population size assumptions.

Asexual Adaptation Drives Transient and Reversible Changes in Mating Efficiency.

This study shows that asexual adaptation in yeast leads to dynamic, environment-dependent changes in mating efficiency that are often reversible and do not lead to stable reproductive isolation.

Predator adaptation to single prey species yields positive specialization and multiple forms of diversification

This study shows that adaptation of bacterial predators to a single prey species leads to increased specialization and diversification in predation profiles.

Global epistasis in ecosystems arises from resource constraints

The paper explains global epistasis in ecosystems as arising from resource constraints, showing linear relationships in single- and multi-species systems.

Simulated microgravity alters short-term evolutionary trajectories of Orsay virus in Caenorhabdidits elegans

This study examines how simulated microgravity affects the short-term evolutionary trajectories of Orsay virus in C. elegans, finding modest phenotypic changes and no significant virulence shifts.

The lack of simplicity in sequence-fitness relationships

The paper investigates sequence-fitness relationships, showing that higher order epistasis can reconcile contradictory findings and introduces signed bipyramids to detect consequential interactions.

Reciprocal cross-feeding between bacteria can limit the emergence of metabolic dependencies

This study compares mutation accumulation in bacterial monocultures and cocultures, finding that cross-feeding can limit rather than promote metabolic dependencies.

Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments

The paper compares fitness of microbial metabolic strategies in fluctuating environments, finding sequential utilizers gain an advantage in diverse communities.

From diminishing returns to entrenchment: a unifying theory of epistasis along adaptive walks revealed by Fisher's geometric model

This paper uses Fisher's geometric model to show that epistasis along adaptive walks can be classified into diminishing returns, contingency, and entrenchment based on phenotypic complexity and selection pressure.

MHC-I diversity enables rapid adaptation during viral pandemic in wild rabbit populations

The paper shows MHC-I diversity allowed wild rabbits to rapidly adapt to the myxoma virus pandemic through evolutionary shifts in allele frequencies.

Predictable adaptive evolution of a phage endolysin through substrate recognition optimization

This study shows how endolysins adapt predictably through mutations that enhance substrate recognition, despite functional trade-offs and some variability in evolutionary paths.

Natural variation in male frequency fails to predict inbreeding responses in Caenorhabditis elegans

This study tests whether male frequency predicts inbreeding responses in C. elegans by measuring fitness changes across strains with varying male frequencies.

Evolution of species' range and niche in changing environments

This study identifies an expansion threshold in species range dynamics caused by eco-evolutionary feedback, where genetic drift overwhelms selection, leading to range contraction or fragmentation.

Environment heterogeneity creates fast amplifiers of natural selection in graph-structured populations

The paper shows environment heterogeneity can amplify natural selection and speed up mutant fixation in graph-structured populations, depending on migration rates and mutant fitness advantages.

Genome-wide sweeps create fundamental ecological units in the human gut microbiome

The paper identifies genome-wide selective sweeps in the human gut microbiome, revealing ecologically distinct populations linked to age and colorectal cancer.

The crop pathogen Blumeria hordei exhibits genome-wide pervasive selective and neutral sweepstakes reproduction signatures.

This study analyzes genome-wide polymorphism data in Blumeria hordei to infer sweepstakes reproduction and quantify selective and neutral processes in its genome.

The effect of spontaneous mutations on CUP1 copy number and copper tolerance in Saccharomyces cerevisiae

The paper examines spontaneous mutations affecting CUP1 copy number and copper tolerance in yeast, finding rapid copy number loss but limited phenotypic impact.

Coevolution of Species' Range Borders: Interactions Between Interspecific Competition, Gene Flow, and Matching Habitat Choice

This paper develops a mathematical model to study how adaptive dispersal strategies affect species range borders, finding that they can lead to sharper range limits and reduced character displacement.

Genome-wide architecture of prolonged starvation adaptation in experimentally evolved Drosophila and comparative enrichment in human orthologs

This study evolves Drosophila under starvation stress, identifies genomic changes, and finds parallels in human orthologs.

The heterogeneous selection landscape of genome evolution in prokaryotes

The paper examines the relationship between genome size and selection pressure in prokaryotes, revealing heterogeneous selection patterns across bacteria and archaea.

A growth-survival trade-off quantitatively predicts microbial selection under periodic disinfection

The paper develops a mathematical framework to predict microbial selection under periodic disinfection by quantifying the growth-survival trade-off between strains.

Flower color locus resists introgression due to correlational selection with other floral traits in Ipomoea cordatotriloba

The paper shows that correlational selection on flower size and sugar concentration, rather than direct selection on flower color, reduces introgression at the color locus in Ipomoea cordatotriloba.

Inferring patterns of purifying, positive and balancing selection in the coppery titi monkey (Plecturocebus cupreus) utilizing a well-fit evolutionary baseline model

This study identifies patterns of purifying, positive, and balancing selection in the coppery titi monkey using a demographic model and genome-wide scans.

Accelerated evolution of whole gene clusters by an engineered lytic phage system in E. coli

The paper develops a phage-based system for accelerating the evolution of large gene clusters in E. coli, achieving significant improvements in tigecycline resistance and biomass production.

Population dynamics of generalist/specialist strategies in the feast-famine cycles

The paper models microbial nutrient utilization strategies, showing that growth-death trade-offs determine whether generalists or specialists dominate under fluctuating nutrient conditions.

Pervasive suppressors halt the spread of selfish Segregation Distorter in a natural population

The paper identifies suppressors that limit the spread of the selfish Segregation Distorter in Drosophila melanogaster by analyzing genetic variation across 90 strains.

Do sex differences in autosomal recombination rates facilitate divergence?

This study uses simulations to examine how sex differences in autosomal recombination rates affect divergence and adaptation, finding that their effect is typically weak and limited to specific conditions.