Evolution and Genetic Dynamics

The paper models dN/dS dynamics in recombining bacterial populations, showing recombination explains most of the decline in dN/dS and reveals weak selection at many coding sites.

The paper introduces an agent-based model to study holobiont dynamics, showing that multiple microbial generations per host generation can buffer environmental changes and reduce fitness trade-offs between hosts and microbes.

The paper shows that partner fidelity enhances mutualistic benefits but is not required for their evolution in yeast.

The paper tests a birth-death-mutation model's ability to predict antibiotic resistance evolution in experiments, finding it partially successful with model modifications improving predictions.

This study shows genetic rescue sustains fitness benefits over 20 generations despite introduced genetic load and thermal stress in a male-dimorphic mite.

The study evaluates evolutionary responses to historic drought in scarlet monkeyflower populations across their range using a resurrection experiment and common gardens.

This paper detects epistatic interactions in viral evolution using synthetic data and applies the method to SARS-CoV-2 sequences, finding evidence of fitness valleys connecting viral variants.

This study shows that resource variation in Drosophila melanogaster affects phenotypic and genomic evolution but is secondary to seasonal selective pressures, with adaptation to resource environments being trait-specific.

The paper shows that ancestral larval development rate predicts long-term population success after evolutionary rescue in flour beetles, despite parallel rescue dynamics across populations.

This study uses meta-analysis to examine the tempo of evolutionary parallelism in clinal divergence between native and introduced plant ranges, finding increased parallelism over time.

The paper shows that spatial structure amplifies mutation load, reducing the effectiveness of natural selection and promoting the proliferation of less-fit types in structured populations.

This study investigates whether local adaptation of life-history traits can occur in a seasonal environment through mathematical modeling of population dynamics under different seasonal perturbations.

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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

This study examines how immigration and coevolution shape specialist-generalist community structures, finding that coevolution promotes diversification and local optima, while immigration increases species richness and specialization.

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

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

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