Evolution and Genetic Dynamics

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

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.

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

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.

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

The paper shows that essential amino acids are more costly to synthesize than non-essential ones, leading to their outsourcing in animals due to selective pressures under high respiratory conditions.

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.

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.

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

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

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.

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.

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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

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 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.

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.