Evolution and Genetic Dynamics

When things add up: environmental structure and microbial interactions drive antibiotic resistance plasmid evolution

This study shows how environmental structure and microbial interactions influence antibiotic resistance plasmid evolution in E. coli, with community contexts leading to higher tolerance and structured environments allowing prolonged resistance evolution.

Flagellotropic bacteriophage selects for evolutionary remodeling of cell motility and chemotaxis in Escherichia coli

This study shows that phage resistance in E. coli leads to diverse single-cell motility outcomes and signaling pathway changes, revealing trade-offs and trade-ups in motility and chemotaxis.

Experimental evolution of promiscuous kin recognition from a homotypic specific cell surface receptor

The paper evolves promiscuous kin recognition in Myxococcus xanthus by modifying TraA receptor specificity through experimental evolution and identifies key residues that influence recognition.

Local adaptation in a metapopulation - a multi-habitat perspective

This paper extends local adaptation models to multi-habitat scenarios, showing how polymorphism persistence depends on migration, selection pressure, and habitat symmetry.

Emergent epistasis mediates the role of negative frequency-dependent selection in bacterial strain structure

This study shows that negative frequency-dependent selection shapes bacterial strain structure through emergent epistasis, using models and genomic analysis of Streptococcus pneumoniae.

Evolutionary Sequence and Structural Basis for the Epistatic Origins of Drug Resistance in HIV

This study identifies the structural and sequence basis of epistatic interactions driving drug resistance in HIV by combining sequence models and molecular dynamics simulations.

Genomics of experimental adaptive radiation in the cryptic coloration of feather lice

This study tracks genomic changes in feather lice adapting to different host color backgrounds over four years, finding distinct genetic responses to similar environmental pressures.

How the Structure of Signaling Regulation Evolves: Insights from an Evolutionary Model

This paper develops an evolutionary model of immune signaling to show that downstream negative feedback loops evolve more robustly than upstream ones due to stronger selective pressures.

Evolution of the meiotic recombination pathway in vertebrates

The paper examines the molecular evolution of meiotic recombination genes across birds and teleost fish, finding similar selective pressures but distinct patterns of positive selection in birds.

Mixed outcomes in recombination rates after domestication: Revisiting theory and data

The paper examines recombination rate changes in domesticated species compared to their wild ancestors, finding mixed results across chicken, sheep, and goats.

PATHOGEN GROWTH AND VIRULENCE DYNAMICS DRIVE THE HOST EVOLUTION AGAINST COINFECTIONS

This study shows that host evolution against coinfections is influenced by the growth and virulence dynamics of individual pathogens, with fast-acting pathogens hindering adaptive success.

Random and non-random variation in flower color along an urban-rural gradient in the introduced mustard Hesperis matronalis

The paper examines flower color variation in Hesperis matronalis along an urban-rural gradient, finding increased diversity in urban areas and systematic shifts in morph frequencies linked to predation and historical fitness differences.

Starvation drives co-existence in cross-feeding bacterial populations

The paper shows that repeated moderate starvation promotes co-existence of bacterial ecotypes in cross-feeding populations, supporting cooperation and diversity maintenance.

Isolating selective from non-selective forces using site frequency ratios

The paper introduces a new method to estimate mutation fitness effects by analyzing site frequency ratios, showing weak selection on synonymous sites in Drosophila populations.

Computer Simulations and Analyses of Coupling Among Reproductive Barriers in Late-Stage Sympatric Speciation

This study uses computer simulations to show how reproductive barriers couple during late-stage sympatric speciation, leading to strong and irreversible reproductive isolation.

Theoretical origins of extreme cell differentiation irreversibility: a dynamic model of organismal size effects

The paper develops a dynamic model showing that extreme cell differentiation irreversibility evolves most robustly in intermediately sized multicellular organisms, revealing a non-monotonic relationship between organismal size and cell fate determinism.

Mapping DHPS Evolvability: Identification of Novel Evolutionarily Critical Sub-Structure through Evolutionary and Structural Analyses of DHPS

The paper identifies a critical substructure in DHPS through evolutionary and structural analyses, suggesting it as a target to constrain evolvability and disrupt antibiotic resistance.

A single episode of sexual reproduction can prevent population extinction under multiple stressors

The paper shows that a single sexual reproduction event in a green alga generates enough genetic variation to allow population growth under environmental stress.

Long-term laboratory Drosophila populations prefer ancestral nutritional cues from the environment

The paper tests if long-term lab populations of Drosophila subobscura show plasticity in response to different fruit hosts and finds higher fecundity and reproductive success in fruit media compared to control conditions.

Strain-specific structural variant landscapes shape mutation retention following mutagenesis in Caenorhabditis elegans

The paper examines mutation retention in C. elegans strains after mutagenesis, finding strain-specific differences in structural variant accumulation and mutation retention.

The evolution of robustness and fragility during long-term bacterial adaptation

This study shows that during long-term bacterial adaptation, fitness effects of mutations become less severe, but pleiotropic effects in new environments become more severe, indicating trade-offs between robustness and fragility.

Laboratory evolution of the bacterial genome structure through insertion sequence activation

This study accelerates bacterial genome evolution by introducing multiple insertion sequences into E. coli, resulting in significant genome rearrangements and size changes.

Resource presentation dictates genetic and phenotypic adaptation in yeast.

This study shows that subtle environmental changes in sugar presentation alter genetic and phenotypic adaptation in yeast, with predictable pleiotropic effects.

Pleiotropy increases parallel selection signatures during adaptation from standing genetic variation

The paper examines how pleiotropy influences parallel gene expression evolution in Drosophila simulans adapted to a new temperature regime, finding both direct and indirect effects of pleiotropy on parallelism.

The composition of biophysical constraints generates complex, rugged regions of protein fitness landscapes

The paper introduces a graph-based measure of protein fitness landscape ruggedness and shows it concentrates at regions where dominant constraints change.

Evolutionary dynamics under demographic fluctuations: beyond the effective population size

The paper analyzes evolutionary dynamics under fluctuating population sizes, showing that an effective population size cannot always exist and presents exact results for fixation probabilities and times in a stochastic switching model.

Evaluating the Roles of Drift and Selection in Trait Loss along an Elevational Gradient

The paper investigates the roles of genetic drift and selection in the loss of short stamens in Arabidopsis thaliana along an elevational gradient and identifies different genetic loci associated with this trait variation.

Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism

This study shows that evolutionary rescue in a bacterial mutualism occurs when one strain reverts to metabolic autonomy, allowing the community to survive lethal stresses despite the other strain's sensitivity.

Epistasis-mediated compensatory evolution in a fitness landscape with adaptational tradeoffs

The paper models compensatory evolution in a fitness landscape with adaptational tradeoffs, showing that resistance mutations can be replaced by lower-cost variants without losing resistance.

Pleiotropy accelerates tooth phenotypic and genomic evolution - An in silico study under the lens of development

This paper uses in silico evolution to study how pleiotropy affects genetic and phenotypic evolution, finding that it accelerates genetic divergence and promotes fitness improvements.