Evolution and Genetic Dynamics

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.

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.

This study analyzes the evolution of deleterious mutations and structural variants in tomato domestication, finding reduced genetic diversity and increased deleterious alleles, with implications for breeding.

This study shows that adaptation to similar environments leads to unpredictable adaptive responses but predictable pleiotropic effects based on ancestral fitness.

This study experimentally evolved marine copepods under global change stressors and found complementary genetic and epigenetic changes contribute to resilience, with epigenetic changes linked to stress response and gene expression.

This study reconciles two perspectives on microbial adaptation by showing how interactions between mobile genetic elements influence evolutionary dynamics and adaptation speed.

The paper develops a theoretical framework to study how conflicting selection pressures shape amino acid frequencies in plant self-incompatibility proteins, showing asymmetric effects on female and male proteins.

This paper models the evolution of mutual dependence and reproductive cohesion in endosymbioses, showing how population dynamics and asymmetries affect the transition to collective survival.

The paper tests how changing mutation bias affects the distribution of fitness effects in E. coli, finding that reversing the mutation bias increases the proportion of beneficial mutations.

This study investigates how plasmid copy number and mutation rate affect evolutionary outcomes using the OrthoRep system, finding that low copy number accelerates beneficial allele enrichment while high copy number increases robustness and hitchhiking of deleterious mutations.

This study identifies convergent genetic adaptations to serpentine soil in two Alyssum species and compares them to Arabidopsis arenosa to find shared pathways.

This study uses experimental evolution to test the necessity of chemotaxis pathway components in E. coli, finding that core components are essential but some auxiliary proteins can be compensated for.

The paper identifies cryptic genetic variants in tomato that drive phenotypic change through hierarchical epistasis in a gene regulatory network.

This study shows that ecological matching between metabolic roles and nutrient strategies stabilizes multi-species consortia during microbial metabolic evolution.

The paper estimates parameters of somatic mutation evolution in long-lived plants using cell-layer-enriched DNA sequencing data.

This study identifies a robust collateral sensitivity between tigecycline and polymyxin B in E. coli through laboratory evolution and validates it in clinical isolates.

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