Evolution and Genetic Dynamics

Quantifying microbial fitness in high-throughput experiments

This study examines how different fitness statistics in high-throughput microbial experiments affect interpretations of mutant fitness and evolutionary dynamics.

Linking the fundamental and realized niches in ahypersaline consumer-resource system

The paper investigates how salinity affects algal growth, grazer survival, and interaction strength in a hypersaline system, finding that ecological responses to salinity are evolvable and influence the relationship between fundamental and realized niches.

Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations

The paper uses Neanderthal ancestry patterns to identify genomic regions enriched with recessive deleterious mutations using a machine learning classifier.

Adaptation to complex environments is associated with higher fitness costs under benign conditions

This study shows that adaptation to complex environments with multiple stressors leads to lower fitness gains and higher fitness reductions under benign conditions compared to single stressors.

Eco-evolutionary Dynamics of Colonization: When Does Source Selection Matter?

This study uses simulations to show balancing selection in source populations increases colonization success in new habitats when founder populations are small, regardless of environmental conditions.

Stochastic population growth and its implications for mutation dynamics under carrying capacity constraints

This study introduces a stochastic logistic growth model with carrying capacity to analyze mutation dynamics in microbial populations, showing that random fluctuations significantly impact population variability near carrying capacity.

The influence of drug dosing regimen on extinction and adaptation during experimental evolution in Candida albicans

This study examines how fluconazole dosing regimens affect extinction and adaptation in Candida albicans, finding that high concentrations with rapid transfers increase extinction risk.

Hydrodynamic flow in the gut hinders the fixation of beneficial mutants but accelerates their invasion

The paper shows that hydrodynamic flow in the gut reduces the fixation probability of beneficial mutants but speeds up their invasion.

Experimental evolution unveils a role for structural variants and sex-specificity in the genetic architecture of lifespan

This study uses experimental evolution in seed beetles to show that structural variants and sex-specific genetic factors influence lifespan evolution.

How many mutations does it take to evolve a new function?

The paper investigates how many mutations are needed to evolve a new function using a Boolean-network model of genotype-phenotype maps, showing a power-law scaling with network size.

Repeatability of adaptation in interacting species

This study investigates how intergenomic epistasis affects endpoint repeatability in coevolving species, finding high repeatability within landscapes but varying fitness outcomes across landscapes.

Parallel evolution of full-length genomes in a long-term evolution experiment with phage ΦX174

The paper tracks parallel evolution of full-length genomes in bacteriophage populations over 412 generations, showing non-neutral evolutionary dynamics and biases in phylodynamic analysis.

The B-value calculator: expected diversity with background selection

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Adaptive responses to antifungal selection depend on dose and drug combination in experimentally evolved yeast

This study shows that antifungal selection in yeast varies with drug dose and combination, leading to distinct genomic responses and resistance mechanisms.

Inferring the multi-host fitness landscape of endive necrotic mosaic virus from cross-inoculation experiments

The paper infers a multi-host fitness landscape of endive necrotic mosaic virus using cross-inoculation experiments and a Bayesian model linked to Fisher's geometrical model.

Sequence-structured fitness landscapes predict influenza evolution

This study develops a generative framework to infer influenza virus fitness landscapes from sequence data, revealing antigenic determinants and improving evolutionary predictions.

The Cumulative Distribution Function Based Method for Random Drift Model

The paper introduces a numerical method to accurately model random genetic drift with or without natural selection and mutation, showing improved accuracy over standard methods.

Simulating protein evolution with programmable fitness objectives derived from modern protein models

This paper simulates protein evolution using programmable fitness objectives derived from modern protein models, showing that combined objectives improve evolutionary realism and molecular plausibility.

Early bird dynamics reduce selection imposed by species interactions in boom-and-bust regimes

The paper shows that boom-and-bust growth regimes reduce selection from species interactions that affect growth rates but not from interactions that affect mortality.

Environmental gradients and the establishment of chromosomal inversions

This study derives the growth rate, establishment probability, and total establishment rate of chromosomal inversions along environmental gradients using analytical theory and stochastic simulations.

Dynamical consequences of context-dependent mutation: visualizing antibody sequence evolution during somatic hypermutation

The paper develops a framework to analyze long-term sequence dynamics from context-dependent mutation processes, applied to somatic hypermutation in antibodies, revealing mutational biases and their effects on sequence evolution.

Long-term experimental evolution of seasonal influenza A/H3N2 virus reveals diverse evolutionary potential

This study shows that A/H3N2 influenza virus evolves differently in independent human airway cultures, with limited parallelism and novel mutations, suggesting evolutionary paths are influenced by selective context rather than intrinsic constraints.

Robustness of the inference of the distribution of fitness effects to selective sweeps

This study evaluates how selective sweeps affect DFE inference using fitdadi, finding that performance declines at low recombination rates and with unfolded SFS, but remains largely unbiased with a flexible demographic model.

Conflicts and coalitions among selfish toxin-antidote elements shape the evolution of hyperdivergent haplotypes

The paper investigates genetic conflict between toxin-antidote elements in C. tropicalis, revealing their role in shaping hyperdivergent haplotypes through competition and recombination.

Evolutionary Advantage of Diversity-Generating Retroelements in Switching Environments

The paper quantifies the fitness gain of DGR diversification compared to standard mutagenesis and identifies when DGR activation is evolutionarily favored.

Obligate multicellularity circumvents population genetic barriers to collective-level adaptation

This study shows obligate multicellularity reduces population genetic barriers to collective adaptation in yeast by enabling rapid group size increases through whole genome duplication.

The distribution of fitness effects of new mutations in regulatory regions of the D. melanogaster genome

The paper estimates the distribution of fitness effects of new mutations in regulatory regions of D. melanogaster genomes and finds they contribute more deleterious and beneficial mutations than coding regions.

Rapid enhancement of antibiotic resistance and divergent remodeling of gene expression in single cells of bacteria

This study shows that antibiotic resistance in E. coli emerges rapidly in single cells under chloramphenicol exposure through phenotypic heterogeneity and gene expression remodeling.

Microdiversity drives resilience and niche partitioning in the bloom forming cyanobacteria Limnospira platensis

The study examines microdiversity in Limnospira platensis across time and space, showing resilience and niche partitioning through genetic changes and horizontal gene transfer.

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.