Evolution and Genetic Dynamics

Enhancing Detection of Polygenic Adaptation: A Comparative Study of Machine Learning and Statistical Approaches Using Simulated Evolve-and-Resequence Data

This study compares machine learning and statistical methods for detecting polygenic adaptation using simulated evolve-and-resequence data, finding that the OCSVM-FET approach performs best.

Revisiting the evolution of population stability due to selection for rapid development and early reproduction in Drosophila: the role of generation length

This study re-evaluates population stability in Drosophila by testing how generation length affects stability in populations selected for rapid development and early reproduction.

Natural selection on synonymous genetic variation in the major histocompatibility complex

This study identifies natural selection on synonymous variation in MHC-I genes, showing purifying selection in most codon sites but spikes of variation in some sites linked to potential pathogen-driven selection.

Coverage Geometry and Heuristic Discovery Times in Protein Sequence Space

The paper introduces a geometric framework to analyze protein sequence space coverage and connects it to heuristic discovery times using a stochastic exploration model.

Genomic response to sex-separated gene pools

The paper uses experimental evolution in Drosophila to separate male and female gene pools, finding diverged genes show elevated intersexual genetic correlation and enrichment for male-biased splicing-related SNPs.

Drosophila pseudoobscura third chromosome inversion arrangements have temperature-dependent and sex-specific effects on life history traits

This study examines the effects of chromosomal inversion arrangements in Drosophila pseudoobscura on life history traits, finding support for the coadaptation hypothesis over pleiotropy.

Disentangling unique site-specific and shared habitat-level adaptation in a classic system of repeated evolution

The paper transplants stickleback populations across habitats to separate shared and site-specific adaptation, finding site-specific adaptation explains most fitness variation.

Rapid evolution can select for fitness tradeoffs in fluctuating environments

This study develops a theory to predict how rapidly adapting populations select for fitness tradeoffs in fluctuating environments, showing that mutations with larger tradeoffs can be favored despite lower geometric mean fitness.

Dissecting contributions of directional and balancing selection to trajectories of mitochondrial haplotype evolution in Drosophila melanogaster.

This study investigates how directional and balancing selection influence mitochondrial haplotype evolution in Drosophila melanogaster under different thermal environments and genetic backgrounds.

Seasonal fluctuations in fitness result in severe reductions in effective population size

The paper simulates seasonally fluctuating selection in Drosophila populations and shows it reduces genome-wide effective population size by ~50%.

Response to divergent selection on meiotic recombination in Saccharomyces cerevisiae

The paper uses experimental evolution in yeast to study how recombination rates change under divergent selection, finding increased and decreased rates in selected lineages.

Sequence-free landscape inference for directed evolution

This paper introduces SLIDE, a method to estimate landscape ruggedness in directed evolution using population-level phenotypic data and mutation rate, improving selection strategies for protein design.

Host-initiated microbial association leads to stable ectosymbiosis in an ecological model

This paper uses a mathematical model to show that reduced inhibition and strong metabolic activity can stabilize ectosymbiosis between microbes, supporting the idea that syntrophy can lead to physical integration.

Dissecting fluctuating selection: A unified population and quantitative genetics

This study develops a modeling framework to investigate how fluctuating selection affects allele frequency oscillations by integrating quantitative and population genetics with simulations and spectral analysis.

Environmental stress and phenotypic tradeoff modulate the adaptive potential of novel coding sequences for de novo gene birth

The paper shows that environmental stress influences the phenotypic impact of de novo ORFs, with tradeoffs and stress-dependent growth effects observed in yeast.

Local trade-offs shape flower size evolution across Arabidopsis thaliana distribution.

The paper examines geographic variation in flower size in Arabidopsis thaliana, finding polygenic control and environmental influences on evolutionary direction.

Hierarchical Value of Information in Microbial Predator-Prey Interactions

The paper develops a value-of-information framework for microbial predator-prey interactions, showing how sensory information can disproportionately enhance survival benefits during encounters.

Ineffectual Genomic Error Correction Under Environmental Perturbation Dynamically Regulates Mutational Supply and Robustness

The paper shows that environmental changes alter proofreading enzyme rates, causing mutation supply fluctuations and evolutionary dynamics, with coding length and population size determining adaptation success.

Evolutionary rescue from antagonistic invaders: Birth-limiting competition among residents can aid rescue

The paper derives an analytical model showing how resident birth rates and invader specificity influence evolutionary rescue from antagonistic invaders.

Genome mutations and environmental perturbations reshape the epigenomic topology to drive functional collapse in digital cells

The paper shows environmental stress more often causes loss of function than mutations, by reorganizing epigenomic topology rather than causing direct sequence damage.

Fitness effects of new mutations are small and heavily confounded with non-genetic sources of variation in Escherichia coli

This study estimates the fitness effects of new mutations in E. coli and finds they are small and heavily confounded with non-genetic variation.

Gene-level complexity explains genome-wide variation in the distribution of fitness effects

The paper investigates how gene-level complexity influences genome-wide variation in the distribution of fitness effects across species.

Fitness effects of copper selection in a wild-derived population of Drosophila melanogaster

This study shows copper-selected Drosophila melanogaster exhibit increased longevity and fecundity, with no difference in egg quality but higher developmental viability under copper stress.

A metabolic model to investigate the evolution of chemodiversity

The paper develops a metabolic model to compare hypotheses about the evolution of chemodiversity, finding support for the interaction diversity hypothesis over the screening hypothesis.

Self-fertilization reverses the direction of selection on recombination

This study shows that self-fertilization changes the evolutionary pressure on a recombination modifier in C. elegans, reversing selection from positive to negative.

Experimental evolution of collective β-lactam resistance in Escherichia coli via activation of a dormant outermembrane porin

This study shows that increased collective β-lactam resistance in E. coli arises from activation of a dormant porin, NmpC, through an insertion sequence excision, enhancing drug permeability and filamentation.

Temporal resource variation promotes growth equalization through alternative plasticity strategies

The paper shows that temporal resource variation leads to growth equalization in bacteria through distinct metabolic strategies, reducing performance variance across conditions.

Mutation bias influences the emergence and effects of antibiotic resistance

This study shows that specific mutation rates, not overall mutation rates, better predict antibiotic resistance emergence in E. coli mutators.

Eco-evolutionary dynamics in competitive systems: Rescue and murder

The paper simulates eco-evolutionary dynamics in one- and two-species systems, showing evolution can enable rescue in single-species systems but lead to evolutionary murder in multi-species systems.

Genomic Landscapes of Natural Selection in Great Apes

The paper analyzes genomic diversity in great apes to identify loci under natural selection and characterizes the distribution of fitness effects across species.