Evolution and Genetic Dynamics

Discovery and evaluation of cadmium-adapted Daphnia pulex genotypes in a region of historical mining reveals adaptation protects the germline from cadmium-induced mutations

The paper identifies cadmium-adapted Daphnia pulex genotypes and shows they have reduced germline mutations under cadmium exposure compared to nonadapted genotypes.

Prevalence, distribution, and mechanisms of genetic dominance in the yeast mating pathway

The paper quantifies dominant and recessive mutation rates in yeast mating pathway mutants and identifies genes associated with dominance.

Life history stage-dependent nuclear selection in chimeric fungi

The paper investigates nuclear selection in chimeric fungi during different life stages, finding strong selection during spore germination and mycelium establishment but not during mycelium growth.

Adaptive coupling of chromosomal inversions with multilocus ecological, mating-bias, and hybrid-incompatibility genotypes facilitates sympatric speciation

This study shows chromosomal inversions can either promote or hinder sympatric speciation by altering effective locus numbers and coupling different reproductive barriers.

Low-Dimensional Organization of Metabolic Phenotypes Underlies Recurrent Evolutionary Diversification

The paper shows that metabolic phenotypes in Escherichia coli vary along low-dimensional, recurring modules during natural and experimental evolution.

Phenotypic cliffs in the RNA genotype-phenotype map

The paper analyzes the RNA genotype-phenotype map to show that phenotypic changes from point mutations can be abrupt, with robust sites producing larger phenotypic shifts when changes occur.

Context-dependent activation and evolutionary buffering of a mating pheromone in fission yeast

The paper shows how mutations in a mating pheromone can change function based on environmental conditions and how compensatory mutations allow evolutionary adaptation.

Amino acid exchangeability and surface accessibility underpin the effects of single substitutions

The paper performs a statistical meta-analysis of single amino acid substitutions using deep mutational scans to quantify physicochemical trends and derive an empirical amino acid exchangeability matrix.

Warming and predation drive rapid evolution of ecosystem functioning but not functional traits

This study shows that warming and predation drive rapid evolution of ecosystem functioning but not functional traits in Asellus aquaticus over two years.

Adaptation to free-living drives loss of beneficial endosymbiosis through metabolic trade-offs

The paper shows that adaptation to free-living conditions in algal endosymbionts leads to loss of host benefits, driven by metabolic trade-offs, with nitrogen availability as a key factor.

Environmental and mutational modulation of collateral fitness effects informs their mechanisms

The paper measures how environmental and mutational factors influence collateral fitness effects in TEM-1 β-lactamase, finding that reducing aggregation or stabilizing the protein can mitigate deleterious effects.

Emergent frequency-dependent selection predicts mutation outcomes in complex ecological communities

The paper integrates ecological interactions into population genetics using dynamical mean-field theory to predict mutation outcomes in complex communities.

Collateral effects of drug resistance evolution: explaining repeatability and directionality patterns

This study investigates the factors driving repeatability and directionality in drug resistance evolution, showing how drug concentration, population dynamics, and genetic architecture influence collateral effects.

Dynamics of genotype frequencies in finite partially clonal populations under mutation and genetic drift

The paper develops a population genetic model to predict genotype frequency changes in partially clonal populations, showing clonality affects trajectory speed but not equilibrium.

The geometry of dominance shows broad potential for stable polymorphism under antagonistic pleiotropy

The paper challenges the notion that stable polymorphism under antagonistic pleiotropy is rare, showing that it is possible under various models without requiring dominance reversal or weak selection.

Physiological architecture and evolutionary origins of cellular adaptability

The paper shows that cellular adaptability is shaped by evolutionary history through a prioritization hierarchy of transcriptional responses to environmental cues.

Evolutionary invasion analysis for structured populations: a synthesis

This paper develops a theoretical framework to predict evolutionary dynamics in structured populations by integrating invasion determinants with a compressed ecological model.

Ancient balanced polymorphism underlies long-standing adaptation for seasonal camouflage in the least weasel

The paper identifies a mutation in the MC1R gene responsible for seasonal camouflage in least weasels and shows it was maintained by spatially varying selection.

Trapped in the web: network architectures spread coevolution and shape adaptation

The paper investigates how network architectures influence coevolutionary dynamics and adaptation in ecological communities through simulations across empirical and artificial networks.

A reassessment of positive growth effects of expressed random sequence clones in E. coli

The paper reassesses the positive growth effects of random sequence clones in E. coli, showing some clones confer genuine fitness advantages independent of vector artifacts or clone competition.

Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models

The paper integrates genotype-to-phenotype maps into ecological models to develop an ecology of metagenomes, revealing gene-level dynamics and metagenomic hitchhiking.

Divergent landscapes of positive and negative selection signatures across residue-resolved human-virus protein-protein interaction interfaces

The paper analyzes selective pressures on virus-targeted host proteins by integrating PPI data and residue contacts, revealing spatial patterns of positive and negative selection across interaction interfaces.

Generation-Establishment Tradeoffs Shape the Temporal Window of Recombinant Evolution

The paper develops a hybrid model showing that recombinant viral lineages succeed based on timing and parental population dynamics, not just fitness.

Experimental evolution of cellular miniaturization reveals a putative mechanism for cell size evolution

This study uses experimental evolution to reduce yeast cell size and identifies genetic factors contributing to cell size regulation.

Competition constrains parasite adaptation to thermal heterogeneity

This study shows that competition reduces thermal adaptation in bacteriophages under fluctuating temperatures compared to monoculture conditions.

Organism-Environment Topological Interfaces Drive the Origination of Organismal Form

This paper proposes a topological framework explaining the origin of organismal forms through interfaces with the environment, validated by cross-kingdom empirical data.

Polygenic and monogenic adaptation drive evolutionary rescue at different magnitudes of environmental change

The paper uses simulations to show that polygenic and monogenic mutations drive evolutionary rescue differently under varying environmental change magnitudes.

Genes shielded, repeats exposed: mutation bias in the midge Chironomus riparius

This study identifies genomic features that influence mutation distribution in Chironomus riparius, showing that coding regions are protected while repetitive elements and gene proximity shape mutational patterns.

The fitness costs of reproductive specialization scale inversely with organismal size

The paper shows that the fitness costs of reproductive specialization decrease with organism size, using a population genetic framework and empirical data from algae.

Module-selection balance in the evolution of modular organisms

This study investigates how modular genotype-phenotype-fitness maps constrain trait evolution, showing that modular systems reach a module-selection balance where traits improve at the same rate.