Evolution and Genetic Dynamics

This study uses simulations to show that migration increases repeated genetic adaptation despite pleiotropy, suggesting repeatability is more common in local adaptation than global adaptation.

This paper introduces a neutrality index combining within- and between-species variation to detect diversifying selection on quantitative traits, applied to brain and body mass in mammals.

The paper tracks genetic and phenotypic evolution in a century-long barley experiment, showing natural selection reduces diversity to a single clonal lineage by generation F50.

This study shows that environmental variation and horizontal gene transfer can stabilize microbial diversity and ecological complexity in a mathematical model of competing populations.

This paper introduces PoMoBalance, a polymorphism-aware model to disentangle balancing selection and GC-biased gene conversion using genomic data from Drosophila populations.

This study evolves four bacterial species in isolation and community to examine how positive interactions influence evolution, finding weakened interactions and resource specialization.

This study measures the fitness effects of spontaneous single-nucleotide substitutions and microsatellite mutations in yeast, finding they have distinct distributions of mutational effects on growth rate.

The paper models how environmental gradients affect dispersal evolution during biological invasions, finding that gradients can reduce dispersal and increase invasion predictability.

The paper models the evolution of two meiotic drivers in a population, showing how duplication and divergence can lead to fixation and impact synthetic gene drive design.

This study examines how spontaneous mutations affect survival and reproduction in Drosophila serrata infected with Drosophila C virus, finding no directional bias in mutational effects on survival but pleiotropic effects on reproductive output.

The paper compares heteroplasmy durations in plant mitochondria and plastids, finding plastid alleles persist longer despite similar mutation rates.

The paper analyzes SFS dynamics in a Daphnia magna metapopulation to show how propagule model and immigration influence allele frequency shifts compared to classical populations.

This study shows biotic interactions enhance local adaptation to soil in Brassica rapa by promoting antagonistic pleiotropy through evolutionary history involving herbivory and pollination.

This study evolves two Orsay virus strains in C. elegans, finding slight infectivity changes, non-synonymous mutations, and non-random distribution of minor variants in polymorphic regions.

This study shows E. coli continuously adapts genetically for six years under resource exhaustion, with high parallelism and frequent historical contingency in mutation patterns.

The paper models ORF evolution as a Markov-jump process and shows that de novo ORFs are more likely to shrink than elongate in neutral evolution, supporting the idea that selection retains longer ORFs.

This paper develops a somatic genetic clock to estimate age in clonal species by analyzing fixed somatic genetic variation, demonstrating its application in Zostera marina and revealing genet ages up to 1,403 years.

The paper derives constraints on serial strain replacement in pathogens, showing that original antigenic sin limits diversity and imposes a 'speed limit' on strain evolution.

The paper develops a theoretical framework to study how molecular recognition promiscuity influences the evolution of self-incompatibility networks in plants.

The paper introduces two metrics to quantify drug-target interactions across genetic variants and drug panels, and analyzes their interactions in a beta-lactamase and beta-lactam drug system.

The paper shows that inbreeding and reproductive compensation together explain the persistence of lethal t-haplotypes in natural populations better than previous models.

This study investigates how coevolution-induced stabilizing and destabilizing selection influences species diversification in clade co-diversification, showing contrasting effects on dependent and independent clades.

The study shows that mutations in yeast are deleterious on average, regardless of the testing environment's adaptation level.

The paper models how environmental changes during Snowball Earth glaciations created selective pressures that favored multicellularity in eukaryotes but not prokaryotes.

This study examines genetic adaptation in Pseudomonas putida during prolonged resource exhaustion, showing convergent mutation patterns and mutator emergence, with some similarities to Escherichia coli.

This study uses an agent-based model to show that pleiotropy in immune signaling networks can be advantageous by reducing fitness costs from resource allocation trade-offs, especially in competitive host interactions.

The paper identifies terminal regions of genes as hotspots for low complexity regions and positive selection, showing their role in functional diversity and purifying selection across Tetrapoda clades.

The paper models the spatial evolution of multi-drug resistance in bacteria under varying drug gradients using a reaction-diffusion system and Price equation framework.

The paper shows that increased positive selection in highly recombining genes is not due to more effective selection but rather to gBGC-driven fixation of beneficial mutations.

This study shows that fly populations rapidly adapt to increased bicoid dosage by normalizing gene expression and improving survival through metabolic and developmental changes.