Evolution and Genetic Dynamics

The paper infers the distribution of fitness effects in aye-ayes, considering population history and mutation/recombination rate variation, finding more deleterious mutations and rapid evolution in immune and sensory genes.

This study examines the metabolic costs of meiotic drive in stalk-eyed flies, finding impaired mitochondrial function and increased metabolic rates in individuals with the drive genotype.

The paper simulates adaptive peak tracking in species over time using fossil data to infer environmental relationships and predict phenotypic changes.

The paper shows that evolution within communities reduces phytoplankton coexistence but has limited effects on total productivity.

This study examines how host changes affect viral evolution by analyzing allele frequency dynamics and finding that Taylor's power law governs mutation distribution during host replacement.

The paper identifies and quantifies compensatory evolution following deleterious gBGC episodes in rodents, showing rapid repair through standing genetic variation.

Apollo simulates within-host viral evolution and infection dynamics, validating limitations of transmission inference tools using HIV cohort data.

The paper shows dispersal evolution can only rescue a limited set of species from climate change, depending on prior environmental conditions and evolutionary rates.

The paper quantifies fluctuations in protein evolution by analyzing correlations between mutations and shows ancestral sequence properties influence evolutionary dynamics and reconstruction accuracy.

This study shows that selecting for early or late host transmission in a parasite affects virulence, host mortality, and life cycle traits, highlighting the need to consider the entire transmission cycle in parasite evolution studies.

This paper uses mathematical modeling and simulations to show how recombination suppression on sex chromosomes expands through sheltering from deleterious mutations and lower mutational load.

This study shows that host genetic variation, not microbiome evolution, primarily drives rapid adaptation to insecticide stress in Drosophila, with microbiomes playing a secondary role.

This study shows that mutation impacts on populations depend on their adaptive state, with increased mutation rates beneficial near extinction but harmful in well-adapted populations.

This study shows that genetic adaptations to DNA replication stress in yeast are robust across different nutrient conditions, with recurrent mutations improving fitness.

The paper investigates how mtDNA deletion variants (rho-) outcompete wild-type mtDNA (rho+) in yeast, finding higher copy numbers and intracellular fitness advantage contribute to biased inheritance.

This study shows that complex nutrient environments drive genetic diversification in Bacteroides thetaiotaomicron through increased SNPs and DNA inversions, leading to adaptive traits like faster glucose depletion and amylopectin degradation.

The paper investigates how fluctuating environments shape gene regulatory networks by analyzing the impact of regulation on fitness under metabolic fluctuations.

The paper analyzes sequence variation and structural features of influenza A virus PB1 protein, finding that solvent accessibility predicts polymorphism likelihood and that purifying selection maintains functional constraints.

This paper introduces a method to efficiently infer epistasis from temporal genetic data, finding strong negative epistasis between beneficial mutations in HIV-1 evolution.

This study shows that metabolically-driven fluid flows in yeast clusters enable exponential growth by overcoming nutrient transport limitations, mimicking circulatory systems without genetic adaptations.

This paper presents a stochastic model showing that intermediate phenotypic plasticity can enhance evolutionary rescue by balancing the acceleration of adaptation and the reduction of mutant fitness advantage.

The paper shows that balancing selection promotes pseudo-overdominance and recombination suppression in genomic regions.

This study uses longitudinal sequencing in Drosophila to show that genomic response to selection involves both polygenic shifts and epistatic interactions, with DEGs enriched for selected SNPs.

This study shows that innate immune memory in hosts does not increase average virulence but increases variation in virulence among pathogens evolved in primed hosts.

This study shows the tga1 allele in maize originated 41,000-49,000 years ago, predating domestication, and suggests standing genetic variation, not de novo mutation, drove maize domestication.

This study shows that GC-biased gene conversion (gBGC) evolves under weak stabilising selection and can increase population load, suggesting it may have been positively selected in humans.

The paper shows that paralog interference enhances negative selection on loss-of-function mutations, preserving genetic redundancy over longer timescales.

The paper estimates de novo mutation rates in three-spined sticklebacks using family trios and finds a mutation rate of 5.05 x 10^-9/bp/gen with a positive correlation between mutation rate and recombination rate.

The paper derives an optimality principle for gene regulatory architectures using population genetics and information theory, showing how evolutionary selection optimizes genotype-phenotype maps.

This study uses a biophysical model to show how regulatory architectures evolve to balance crosstalk and evolvability by optimizing short, weak binding sites and synergistic activation.