Evolution and Genetic Dynamics

Molecular adaptation reflects taxon-specific mutational biases

The paper quantifies how taxon-specific mutational biases influence adaptive amino acid substitutions across 14 species.

The Product neutrality function defining genetic interactions emerges from mechanistic models of cell growth

The paper confirms the Product neutrality function accurately predicts double mutant fitness in budding yeast and shows it emerges from mechanistic models of cell growth.

Modeling the Relationship between the Capsid Spike Protein Stability and Fitness in {varphi}X174 Bacteriophage

This study models how protein stability affects fitness in {phi}X174 bacteriophage using deep mutational scanning and a multistage binomial model, finding that large destabilizing mutations predict inviability but smaller ones do not reliably predict survival.

Genome-wide screening using TraDIS accelerates identification of key adaptive mutations of longer-term evolution experiment in Escherichia coli.

The paper compares long-term evolution experiments with short-term transposon library screening to identify adaptive mutations in E. coli, finding significant overlap in gene targets.

Low mutation rate but high male-bias in the germline of a short-lived opossum

This study reports the lowest germline mutation rate in mammals and a typical male mutation bias in the gray short-tailed opossum, suggesting alternative mechanisms to cell division drive sex-specific mutation rates.

Uncovering differential tolerance to deletions versus substitutions with a protein language model

The paper uses a protein language model to analyze amino acid deletions in the human proteome, identifying sites with differential tolerance to deletions versus substitutions.

Atypical Replication Error Pattern and Limited Repair Efficiency Contribute to Elevated Mutation Rate in Phage lambda

This study measures the mutation rate of phage lambda and finds it is higher than its host E. coli but not significantly increased by MMR inactivation.

Quantitative Genetics of Microbiome Mediated Traits

The paper extends quantitative genetic theory to include host-associated microbes as factors influencing phenotypic variation and demonstrates how microbiome-mediated responses to selection can arise from various transmission modes.

Variation in inbreeding depression within and among Caenorhabditis species

The paper investigates inbreeding depression in Caenorhabditis species, finding it universal but variable, with some species showing low depression and potential as models for outcrossing systems.

Virulence evolution: thinking outside of the host

This study investigates the trade-off between virulence and transmission in microsporidia by examining parasite survival outside hosts.

MutagenesisForge: A Framework for Modeling Codon-Level Mutational Biases and Calculating dN/dS

MutagenesisForge simulates codon-level mutagenesis and calculates dN/dS ratios under user-defined conditions to test evolutionary hypotheses.

A Nonlinear Dynamics Framework for Mutation-Selection Balance Reveals Dominance-Dependent Bistability in Auto- and Allotetraploids

This paper develops a nonlinear dynamics framework to analyze mutation-selection balance in tetraploids, revealing dominance-dependent bistability and altered temporal dynamics compared to diploids.

A synoptic solution to a Wright-Fisher model with recurrent mutation, drift and selection

The paper derives an ex-Gaussian distribution for the time to fixation in a Wright-Fisher model with mutation, drift, and selection, and applies it to analyze evolutionary forces and adaptation.

Quasi epigenetic equilibrium: the implications of plasticity and variability on evolution and extinction

This paper introduces quasi-epigenetic equilibrium (QEE) to simplify population epigenetic models and shows how epigenetics affects evolutionary parameters and extinction risk.

Interplay of immigration and coevolution constrains the structure of specialist-generalist communities

This study examines how coevolution and immigration shape specialist-generalist community structures, finding that evolutionary rates and dispersal influence diversity and community composition.

The distribution of the number of mutations in the genealogy of a sample from a single population

The paper derives a new sampling formula for the number of mutations in a genealogy under different population models, improving numerical accuracy and efficiency.

Functional selection in a population of synthetic cells with a minimal metabolism

The paper demonstrates that synthetic cells with minimal metabolism can undergo Darwinian evolution by filtering functional genotypes and mapping mutations in a key enzyme.

Idiosyncratic evolvability among single-point ribosomal mutants towards multi-aminoglycoside resistance

The paper examines how single-point mutations in rpsL in E. coli affect evolvability towards multi-aminoglycoside resistance, finding some mutations block further adaptation.

Adaptation of protein stability to thermally heterogeneous environments

This study develops a mathematical framework to analyze how protein stability adapts to complex thermal environments, showing that mean temperature and thermal fluctuations have distinct effects on thermodynamic parameters.

A gene-based model of fitness and its implications for genetic variation: Genetic and inbreeding loads

The paper compares the gene model and sites model of fitness, showing the gene model leads to lower genetic load and smaller inbreeding load, suggesting overestimation of inbreeding depression.

A gene-based model of fitness and its implications for genetic variation: Linkage disequilibrium

The paper compares two models of mutation effects on fitness, showing the gene model predicts positive linkage disequilibrium where the sites model predicts zero or negative LD.

Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects

The paper shows that terrestrial aphid herbivory indirectly drives adaptive evolution in aquatic Daphnia populations by altering macrophyte and phytoplankton dynamics.

Beyond single-trait GxE: higher-order environmental interactions and clonal diversity govern trait relationships in yeast

The paper examines how temperature and salinity interact with genetic background to shape growth and flocculation in yeast, revealing context-dependent trait relationships and clonal variability.

Adaptive radiation during long-term experimental evolution of the multicellular bacterium, Streptomyces

This study tracks adaptive radiation in Streptomyces over 3000 generations, showing parallel loss of sporulation, morphological changes, and metabolic diversification under relaxed selection.

Host replacement dynamics shape virulence and genome evolution in a plant RNA virus

This study examines how host replacement dynamics influence virulence and genome evolution in a plant RNA virus, showing that sudden transitions lead to faster virulence changes and more severe symptoms.

Mathematical model of replication-mutation dynamics in coronaviruses

This paper develops a mathematical model to study replication-mutation dynamics in coronaviruses, analyzing steady states and stability under different mutation regimes and antiviral treatments.

Frequency-dependent fitness effects are ubiquitous in rapidly adapting microbial populations

The paper tests the assumption of constant fitness effects in microbial populations and finds frequency-dependent effects are common, with negative frequency dependence and non-transitive fitness outcomes.

Developmental bias explains the evolutionary trend towards simple leaf shapes

The paper shows that developmental bias, not natural selection, drives the evolutionary trend towards simpler leaf shapes in angiosperms.

Learning sequence-function relationships with scalable, interpretable Gaussian processes

The paper introduces interpretable Gaussian process models for sequence-function relationships, capturing epistasis and achieving superior predictive performance on large biological datasets.

The Polymorphism of Globin and Virus RdRP and Protein Space

The paper analyzes polymorphisms in globin and viral RdRP proteins, finding a positive correlation with residue solvent accessibility and proposing purifying selection as the main evolutionary force.