Evolution and Genetic Dynamics

Interactions between mechanisms of reproductive isolation

The paper models interactions between reproductive isolation mechanisms and finds local adaptation is the most effective barrier, with other mechanisms evolving depending on migration rates.

Bayesian analysis of longitudinal RB-TnSeq resolves the fitness seascape in fluctuating environments

The paper develops a Bayesian framework for longitudinal RB-TnSeq to analyze fitness dynamics in fluctuating environments and identifies a 'fitness seascape' model that predicts mutational targets.

Epigenetic variation can promote adaptation by smoothing rugged fitness landscapes

This paper shows epigenetic changes can improve adaptation in asexual populations by smoothing rugged fitness landscapes through epigenetic quasispecies formation.

Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics

This study compares three simulation schemes for modeling protein evolution, finding that population genetics dynamics best capture phylogenetic correlations and selective sweeps without requiring additional data.

From constraint to opportunity: Relaxing sexual antagonism reveals adaptive potential maintained by balancing selection

This study shows that sexually antagonistic trade-offs can limit adaptive responses under selection but also maintain genetic variation subject to balancing selection.

A graphical approach of the interplay of eco-evolutionary dynamics and coexistence

The paper introduces a graphical approach to analyze eco-evolutionary dynamics and their impact on species coexistence, showing evolution can sometimes reduce coexistence stability.

Generation time is not a universal constraint on adaptive evolution

This study challenges the idea that long-lived organisms adapt more slowly, showing that generation time's effect on adaptive evolution depends on the type of selection acting on fitness components.

Determinants of mutation load in birds

This study estimates deleterious mutation load in 19 bird species, finding higher load in small populations and effects of recombination and GC-biased gene conversion.

Limits to the evolution of metabolic dependence in spatially structured microbial communities

The paper investigates how auxotrophic mutants in E. coli populations grow in spatially structured communities, finding that growth is constrained by amino acid leakage and clustering.

Gene sharing during enzyme recruitment reveals distinct adaptive strategies including massive, sustained duplication without divergence

This study investigates enzyme recruitment during adaptive evolution in E. coli, showing two mechanisms of gene amplification without divergence that maintain original function while enabling new metabolic capabilities.

Genomic signatures of asymmetric selection on membrane and cytoplasmic proteins.

The paper examines genomic variation in membrane and cytoplasmic proteins across E. coli and S. cerevisiae, finding higher non-synonymous variation and lower synonymous variation in membrane proteins.

Evolutionary rescue of freshwater copepods during historical lake acidification

This study shows that freshwater copepods evolved tolerance to acidification and then lost it after pH recovery, demonstrating evolutionary rescue in natural populations.

Context-Dependent Adaptation in Structured Environments

The paper shows that adaptive mutations in Pseudomonas fluorescens require ecological facilitation from ancestral types to successfully colonize a niche.

The genetic architecture of local adaptation is historically contingent

This study uses simulations to show how ecological and genetic factors shape the genetic architecture of local adaptation, highlighting the role of demographic history and allele age in genotype-environmental associations.

Evolutionary responses to increased opportunity for sexual selection in yeast

This study shows that increased sexual selection in yeast leads to rapid evolutionary changes in mating traits and sexual differentiation.

Comparing the evolvability of an ancestrally reconstructed and modern adenylate kinase

This study compares the evolvability of an ancestrally reconstructed and modern adenylate kinase, finding that the ancestral enzyme tolerates more mutations and generates more viable variants.

The Age of Selection-Duality Mutation under Fluctuating Selection among Individuals (FSI)

This paper studies the allele-age problem under selection-duality by analyzing mutation age profiles at different neutrality bounds in population genetics.

Predicting the topography of fitness landscapes from the structure of genotype-phenotype maps

The paper predicts fitness landscape ruggedness and navigability using genotype-phenotype map properties like neutral component sizes and evolvability.

Plastic germination, temporal niche partitioning, and emergent assortative mating in annual plants

The paper uses mathematical modeling and simulations to show that adaptive plasticity in germination timing promotes genetic divergence and ecological speciation in annual plants under temporal environmental fluctuations.

Pollution-Driven Selection in Riparian Ecosystems: Genome-Wide Responses to Bacillus thuringiensis israelensis and Copper in a Non-biting Midge

The paper uses whole-genome sequencing to analyze genomic responses to Bti and copper exposure in Chironomus riparius, revealing distinct adaptive mechanisms despite limited phenotypic adaptation.

The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability

The paper analyzes mutation dynamics in Daphnia obtusa using whole-genome sequencing of mutation accumulation lines, revealing mutation rates, spectra, and selection pressures affecting genome stability.

Direct selection under resource allocation trade-offs enables the evolution of obligate and facultative sexuality

This study shows that resource allocation trade-offs between sexual and asexual reproduction can enable direct selection for obligate or facultative sexuality, depending on fertility returns and initial allocations.

The evolution of tandem repeat sequences under partial selfing and different modes of selection

This study models how partial selfing affects tandem repeat evolution under different selection pressures, finding that selfing increases homozygosity and enhances selection against TR expansions.

Sign epistasis can be absent in multi-peaked landscapes with neutral mutations

This study shows that sign epistasis may be absent in multi-peaked fitness landscapes when neutral mutations are included, challenging previous assumptions about reciprocal sign epistasis.

Weakest link epistasis and the geometry of genetic load

The paper introduces weakest-link epistasis as a framework to analyze genetic load and shows how increasing phenotypic dimensionality affects fitness, comparing it to Fisher's geometric model.

Local Adaptation to the Sex Environment: Reciprocal Sex-Limited Selection in Different Thermal Regimes

This study shows that local adaptation to sex-specific environments differs between thermal regimes in Drosophila melanogaster.

Elevated mutation in haploid yeast driven by translesion synthesis

The paper investigates mutation rate differences between haploid and diploid yeast by examining the role of REV1 in translesion synthesis, finding higher mutation rates in haploids and convergence after REV1 deletion.

FSI (Fluctuating Selection among Individuals) Reduces the Mean Fixation Time (Generations) of a Mutation

This paper theoretically analyzes the fixation time of mutations under fluctuating selection among individuals and finds it is significantly shorter than strict neutrality.

Directed evolution for cell separation in natural isolates of budding yeast reveals selection to deactivate AMN1 and the Rim101 pathway in haploids and selection in favor of Hawthorne's deletion in diploids

The paper evolves natural yeast isolates to select for cell separation, identifying AMN1 deactivation and Rim101 pathway mutations in haploids, and Hawthorne's deletion in diploids as key adaptations.

Levels of additive genetic variation vary substantially between species

The paper examines interspecific variation in evolvability and heritability across species using phylogenetic models and finds substantial evolvability differences, particularly between plants and animals.