Y. Ram

Template switching during DNA replication is a prevalent source of adaptive gene amplification

The paper investigates how genomic architecture influences the formation and fitness of adaptive copy number variants (CNVs) in yeast, finding that template switching during DNA replication is a common mechanism for CNV generation.

Phenotype switching of the mutation rate facilitates adaptive evolution

This paper shows that switching between mutator and non-mutator phenotypes enhances adaptive evolution by maintaining mutator states and increasing the likelihood of adaptive mutations.

Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation

This paper infers mutation rates and selection parameters from RNA virus haplotypes using neural posterior estimation, revealing epistasis in MS2 bacteriophage evolution.

Cultural transmission, competition for prey, and the evolution of cooperative hunting

This study models how cooperative hunting evolves through cultural transmission and competition for prey, finding that horizontal learning is essential for its spread.

Simulation-based inference of evolutionary parameters from adaptation dynamics using neural networks

The paper estimates beneficial mutation rates and fitness effects using simulation-based Bayesian inference on CNV dynamics in yeast.

Phenotype switching of the mutation rate as a strategy for crossing fitness valleys

This paper shows that intermediate mutation rate switching enhances adaptation on rugged fitness landscapes by enabling the crossing of fitness valleys and reducing deleterious mutation accumulation.

Oblique Transmission, Conformity, and Preference in the Evolution of Altruism

This study examines how oblique and vertical cultural transmission, along with genetic transmission, affect the evolution of altruism under additive and multiplicative fitness assumptions.

Non-Vertical Cultural Transmission, Assortment, and the Evolution of Cooperation

The paper studies cultural evolution of cooperation under vertical and non-vertical transmission, finding conditions for cooperation and defection fixation, coexistence, and stable polymorphism.

Generation of Variation and Mean Fitness Increase: Necessity is the Mother of Genetic Invention

The paper shows that increasing variation in low-fitness individuals under constant selection raises mean population fitness, supporting the idea that necessity drives genetic innovation.

Evolution of vertical and oblique transmission under fluctuating selection

The paper analyzes the evolution of vertical and oblique cultural transmission under different selection regimes and finds that stable polymorphism conditions depend on selection dynamics and transmission rates.

Key Issues Review: Evolution on rugged adaptive landscapes

This paper reviews theoretical and empirical studies on evolution on rugged adaptive landscapes and provides source code for simulations.