Evolution and Genetic Dynamics

Metabolite toxicity as a driver of bacterial metabolite externalization

The paper investigates whether metabolite externalization by bacteria is driven by toxicity to the producer or reciprocal benefit, finding that adenine externalization by Rhodopseudomonas palustris is likely a physiological response to its toxicity.

Synaptation - a missing concept in the science of evolved complexity

This paper introduces the concept of synaptation to explain evolutionary origins of selected effects in systems lacking shared inheritance, extending multilevel selection theory to non-reproducing collectives.

Strategies for resolving cellular phylogenies from sequential lineage tracing data

This paper models a sequentially-edited lineage tracing system and identifies parameter regimes where distance-based methods can accurately reconstruct cellular phylogenies.

Dynamics of fixation probability in a population with fluctuating size

The paper studies how population size fluctuations affect mutant fixation probability over time in a conditional Wright-Fisher process.

Learning the Shape of Evolutionary Landscapes: Geometric Deep Learning Reveals Hidden Structure in Phenotype-to-Fitness Maps

This paper introduces a geometric deep learning method to model phenotype-to-fitness maps, showing it outperforms linear methods in capturing nonlinear structure and predicting fitness landscapes.

Beyond acute toxicity: evolutionary response by rapid polygenic adaptation to a complex environmental stressor in Chironomus riparius

This study investigates how multigenerational exposure to urban runoff sediment affects fitness and genomic adaptation in Chironomus riparius, revealing polygenic adaptation and fitness trade-offs.

How and why to quantify pairwise pleiotropy and genotype-by-environment interactions

The paper introduces a method to quantify pleiotropy and genotype-by-environment interactions and provides an R package for implementation.

Viral Simulation Reveals Overestimation Bias in Within-Host Phylodynamic Migration Rate Estimates Under Selection

This study shows that phylodynamic migration rate estimates for HIV-1 within hosts are overestimated under selection using common models like BEAST2.

Directed evolution of multimeric proteins is enabled by dual-compensatory gene duplication

This paper introduces a directed evolution strategy for multimeric proteins using gene duplication to enable the selection of diverse high-performing variants.

Mutation rate variability in viral populations: implications for lethal mutagenesis

This paper shows that mutation rate variability in influenza A virus affects lethal mutagenesis models, suggesting gamma-Poisson distributions are more accurate than Poisson models for predicting viral extinction.

SIMPLICITY: an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution.

SIMPLICITY models SARS-CoV-2 intra- and between-host evolution, showing that immune waning and infection history drive realistic evolutionary dynamics.

Weak pervasive incompatibilities and compensatory adaptation drive hybrid genome evolution in yeast

This study shows that weak genetic incompatibilities, rather than strong pairwise ones, drive adaptation in hybrid yeast genomes through background-dependent interactions and mutational targeting.

Consequences of benzalkonium chloride tolerance for selection dynamics and de novo resistance evolution driven by antibiotics

This study shows that BAC tolerance in E. coli affects antibiotic resistance evolution, with BAC-tolerant strains outcompeting sensitive ones under low ciprofloxacin concentrations but being less likely to develop resistance to other antibiotics.

Multidimensional plasticity of gene expression underlying higher macrolide tolerance in saline and warm environments

This study examines how gene expression changes in E. coli under different salinity and temperature conditions when exposed to azithromycin, revealing interactions that influence antibiotic tolerance.

Genomic basis of adaptation to constant and fluctuating environments in a global pest of cereals

This study identifies genomic mechanisms underlying adaptation to constant and fluctuating environments in the cereal pest Aceria tosichella, revealing a polygenic basis involving stress response and detoxification pathways.

Within-host adaptive evolution is limited by genetic drift in experimental human influenza A virus infections

This study examines within-host evolutionary dynamics of influenza A virus in humans and ferrets, finding that genetic drift limits selection efficiency in humans but not in ferrets.

Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing

This study estimates the reduction in genetic diversity from background selection in populations with non-equilibrium demography and partial selfing, finding weak effects in outcrossers and stronger effects in selfers.

Sex-allocation trade-offs and their genetic architecture revealed by experimental evolution

This study uses experimental evolution to show a genetic trade-off in sex allocation in hermaphroditic plants, supporting the fundamental assumption of sex-allocation theory.

Novel genes arise from genomic deletions across the bacterial tree of life

The paper identifies deletion-born gene fusions as a mechanism for novel gene emergence in bacteria, demonstrating their prevalence across the bacterial tree of life.

Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations

This study shows that inducing lysogen populations of Pseudomonas aeruginosa increases adaptive mutation diversity compared to non-lysogens under antibiotic stress.

Phylodynamics of Somatic Evolution: A Likelihood-Based Approach for Cellular Reproduction

This paper introduces a likelihood-based framework for modeling somatic evolution by linking mutations to discrete cell division events, demonstrating its application on simulated and hematopoietic stem cell data.

EZ-DMS - A Simple and Accessible Protocol and Software Package for Deep Mutational Scanning of Virus Proteins

EZ-DMS provides a simple, cost-effective protocol and software for deep mutational scanning of HIV-1 Env protein variants, enabling analysis of amino acid fitness without bioinformatics expertise.

Density dependence during evolutionary rescue increases extinction risk but does not prevent adaptation

A glyphosate-based herbicide selects for genetic changes while retaining within-species diversity in a freshwater bacterioplankton community

This study shows that glyphosate-based herbicide affects bacterial community diversity but not within-species genetic diversity, identifying gene targets of selection in freshwater bacterioplankton.

Linkage-aware inference of fitness from short-read time-series genomic data

This paper introduces a method to infer fitness effects from short-read time-series genomic data while accounting for genetic linkage, validated on HIV and SARS-CoV-2 datasets.

Substantial Deceleration of Adaptation of HIV-1 Within 1,500 Generations in an Experimental Evolution: A Genomic Perspective

This study tracks HIV-1 adaptation over 1,500 generations in human T-cell lines, finding a substantial deceleration in adaptive mutation fixation rates and fitness gains.

Mutations in filamentous bacteriophages spark eco-evolutionary feedbacks in Pseudomonas aeruginosa

This study shows that filamentous phage mutations drive eco-evolutionary feedbacks in Pseudomonas aeruginosa by promoting phage resistance and altering key traits.

Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation

The paper shows antibiotic history shapes microbial response through eco-evolutionary and environmental feedbacks, creating a trade-off between resistance and recovery.

Chronic infections can generate SARS-CoV-2-like bursts of viral evolution without epistasis

This study shows chronic infections can generate SARS-CoV-2-like mutation bursts without epistasis, increasing global evolutionary rates.

wavess 1.2: Presenting an HLA-aware within-host virus sequence simulation framework

wavess 1.2 simulates within-host virus sequences with an HLA-aware CTL response and variable recombination rate to improve accuracy in immune-dominated regions.