Evolution and Genetic Dynamics

Estimation of demography and mutation rates from one million haploid genomes

This paper introduces DR EVIL, a method to estimate mutation rates and demographic history from large haploid genome datasets, revealing mutation-rate heterogeneity and the impact of multiple mutation events on rare variants.

Unique genetic bases of repeated life-history divergence associated with high altitude adaptation in Mimulus perennials

The paper investigates genetic repeatability in high altitude adaptation of Mimulus plants, finding that while phenotypic modules are repeated, genetic architecture is largely non-repeatable.

An Eco-Evolutionary Framework to Predict Long-term Strain Diversity and Turnover in Infectious Diseases

The paper introduces MultiSEED, a framework predicting pathogen strain diversity and turnover by distinguishing transient and established strains across diseases.

Cobalt and nickel ion synergy promotes gene duplication amplification and enables stable metal resistance in Shewanella oneidensis

This paper shows that cobalt and nickel ions induce gene duplication amplification in Shewanella oneidensis, enabling stable metal resistance without fitness cost.

The Role of Environmental Stress in Promoting Mutators Through Evolutionary Rescue: Quantitative Predictions

This study quantitatively predicts how environmental stress can promote mutator lineages through evolutionary rescue, showing their effectiveness depends on wildtype mutation rates and environmental change speed.

The evolution of irreversible cell differentiation under cell death effect

This study investigates how cell death influences the evolution of irreversible cell differentiation in multicellular organisms, showing that linear death rate differences between cell types promote irreversible differentiation.

Pleiotropy increases with gene age in six model multicellular eukaryotes

The paper examines pleiotropy across gene age in six model organisms and finds that middle-aged and ancient genes are more pleiotropic than young genes.

Evolutionary rescue in a consumer-resource system depends on the affected ecological traits and the population's resident life-history

This study examines how evolutionary rescue in a consumer-resource system depends on ecological traits and population life-history, showing that intrinsic growth rates alone are insufficient for predicting rescue probabilities.

Beyond Recombination: Exploring the Impact of Meiotic Frequency on Genome-wide Genetic Diversity

This study examines how meiotic frequency and sexual strategies affect genetic diversity in facultatively sexual species like yeast, showing that low meiotic frequency can reduce genome-wide diversity during selective sweeps.

Remote-control meiotic drive of sex chromosomes

The paper models a remote-control meiotic drive mechanism where an autosomal gene causes a sex chromosome to drive without itself driving, showing potential applications in pest management.

Multicellular group formation as a resource competition strategy for marine bacteria

This study shows multicellular bacterial groups out-compete single cells in resource competition due to a trade-off between resource encounter consistency and quantity, driven by physical constraints.

The Diverse Phenotypic and Mutational Landscape Induced by Fluoroquinolone Treatment

This study examines how fluoroquinolone treatment induces diverse phenotypic and mutational changes in E. coli, showing that tolerance and resistance can evolve independently with varied fitness effects.

Identification of multivariate phenotypes most influenced by mutation: Drosophila serrata wings as a case study

The paper identifies multivariate phenotypes most influenced by mutation using Drosophila serrata wing data, showing robust mutational variance across samples.

Transposons and accessory genes drive adaptation in a clonally evolving fungal pathogen

This study shows that transposable elements and accessory genes drive rapid adaptation in the fungal pathogen Fusarium oxysporum through serial passaging under selection.

Unpacking fitness differences between two invaders in a multispecies context

The paper develops a framework to quantify fitness differences between two co-invading strains using the replicator equation and applies it to antibiotic-resistant E. coli in the gut microbiota.

The structure of an ancient genotype-phenotype map shaped the functional evolution of a protein family

The paper reconstructs ancestral transcription factors to study how ancient genotype-phenotype maps influenced the evolution of protein function.

Detecting epidemic-driven selection: a simulation-based tool to optimize sampling design and analysis strategies

This paper introduces a simulation framework to detect epidemic-driven selection by optimizing sampling design and analysis strategies.

Purifying Selection Shapes the Dynamics of P-element Invasion in Drosophila simulans Populations

The paper uses experimental evolution to study purifying selection on P-element invasion in Drosophila simulans, finding 73% of new insertions are under purifying selection with a mean selection coefficient of -0.056.

Testing for the genomic footprint of conflict between life stages in an angiosperm and moss species

The paper examines genomic signals of selection across life stages in plants, finding stronger purifying selection on unbiased genes and synergistic pleiotropy rather than antagonistic pleiotropy.

The fitness landscape of the E.coli lac operator is highly rugged in two different environments

The paper maps the fitness landscape of E. coli lac operator variants in two environments, finding highly rugged landscapes with few shared fitness peaks.

Noncovarying storage effect: balancing and positive directional selection on mutant alleles that amplify random fitness and demographic fluctuations

This study identifies a novel evolutionary force, the noncovarying storage effect, that maintains genetic variation and amplifies population size fluctuations through interactions between demography and selection.

Copy number variation facilitates rapid toggling between ecological strategies

The paper shows CNVs act as reversible toggles between ecological strategies in yeast, with imbalanced ratios defining specialists and balanced ratios defining generalists.

The fitness consequences of coinfection and reassortment for segmented viruses depend upon viral genetic structure

This study models the fitness effects of coinfection and reassortment in segmented viruses, finding that increased genetic divergence and inter-strain mixing generally reduce viral fitness.

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate

The paper shows plasmid mutation rates increase logarithmically with copy number, outpacing segregational drift, enhancing bacterial evolvability.

Accessibility of Modified NK Fitness Landscapes

This paper introduces two modified NK fitness landscape models, theta NK and HNK, and shows that increasing parameters like theta or H improves landscape accessibility despite ruggedness.

Intracellular replication dynamics of influenza A virus impose strong bottleneck effects

This study uses stochastic modeling to show that intracellular replication of influenza A virus creates strong bottleneck effects, reducing genetic diversity and increasing genetic drift.

Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness

The paper identifies 58 loci in budding yeast that interact with fitness, showing global epistasis where genetic perturbations have greater effects in more fit individuals.

Complex genetic determinism of male-fertility restoration in the gynodioecious snail Physa acuta

The paper investigates male-fertility restoration in Physa acuta snails, finding that genetic determinism varies between naive and non-naive populations.

Triggered and Spontaneous Dormancy in Bacteria During Feast-Famine Cycles with Stochastic Antibiotic Application

The paper shows that spontaneous dormancy in bacteria is advantageous only when antibiotic application and feast periods are decoupled, and combining both dormancy types is optimal with stochastic antibiotic timing.

Deleterious mutations and selection for sex in spatially structured, diploid populations

The paper examines how population structure and selection influence the evolution of sex in diploid organisms with deleterious mutations, finding that intermediate sex rates are generally favored.