Evolution and Genetic Dynamics

The paper tests if amino acid properties affect substitution rates, finding that larger physicochemical differences between amino acids correlate with lower substitution rates across multiple datasets.

This study investigates how incomplete purifying selection affects viral phylogenies and phylodynamic inference, finding little bias in key epidemiological estimates despite mutation distribution shifts.

The paper assesses mutation fitness effects in two Arabidopsis thaliana ecotypes under natural conditions and finds beneficial mutations accumulate, with the poorly adapted ecotype showing higher mutation variance.

The paper shows that mutations in protein binding domains, combined with regulatory divergence, determine the fate of gene duplicates in a protein interaction network.

The paper examines how spatial population structure and migration affect adaptation in rugged fitness landscapes, finding that suppression of selection can enhance early adaptation but reduce long-term fitness.

The paper shows that pre-exposure to stress increases community and genetic diversity resilience in bacterial communities under severe acidification.

This study finds a female mutation bias in aye-ayes, contrasting the typical male mutation bias in mammals, and identifies potential genetic causes.

The paper examines phylogenetic correlations in susceptibility to multiple viruses across Drosophilidae hosts and finds positive correlations, with stronger links within viral species and families.

This study shows that yeast populations in predictable environments lose adaptive potential, with adaptation to stress driven by de novo mutations rather than pre-existing cryptic variations.

This study analyzes how plasmid-mediated heterozygosity can enable bacterial populations to adapt to stressors through evolutionary rescue, showing that higher plasmid copy numbers lower the fitness threshold needed for rescue.

The paper examines the evolutionary dynamics of diploid and hemizygous Z chromosome regions in Schistosoma japonicum, finding reduced efficacy of selection and relaxed purifying selection in diploid Z regions.

The paper shows that smaller habitats increase extinction risk in bacterium-virus coevolution, with viruses more likely to go extinct and surviving viruses showing reduced infectivity.

The paper identifies a mutational hotspot in nlpD linked to transcriptional induction of rpoS in Pseudomonas fluorescens SBW25, showing a 5,700-fold elevated mutation rate at this site.

This study shows ancestral plasticity to salt helped Silene uniflora adapt to zinc in mine-waste environments, demonstrating past-cue plasticity's role in rapid adaptation to novel habitats.

This study extends the fitness-class coalescent model to account for arbitrary levels of purifying selection, revealing biases in demographic inference caused by selection.

This study uses mathematical models to show that repeated exposure to abiotic stress can lead to adaptive transitions between unicellularity and differentiated multicellularity, with complexity increasing or decreasing depending on mutation order and fitness effects.

This paper investigates hybridization effects on microbiota in a successful hybrid lizard, finding transgressive segregation of host-associated microbiota traits linked to ecological success.

This study shows that dispersal within the respiratory tract affects viral genetic diversity and evolutionary potential, with nasal and tracheal regions maintaining diversity while lung regions show genetic distinctness.

The paper infers demographic histories and distribution of fitness effects of gut commensal microbes in North Americans compared to African rural populations, revealing population size changes and varying selective pressures across species.

The paper examines gene expression changes in yeast strains with adaptive copy-number variants, finding correlations between CNVs and transcript abundance, but reduced proteomic effects due to post-transcriptional compensation.

The paper investigates evolved and plastic gene expression differences in adaptation to a novel niche using peacock flies, finding ecotype-specific gene expression changes and an inversion linked to differential expression.

This study shows that multiple toxins in T6SS limit resistance evolution in bacteria, similar to combination therapies in medicine.

The paper models how competition drives the evolution of multiple foraging strategies by balancing metabolic costs and foraging efficiency in a coevolutionary framework.

The paper explains how waning immunity drives antigenic evolution in respiratory viruses through repeated emergence and replacement of immune escape variants.

The paper compares the fitness effects of chromosomal and plasmid genes in Rhizobium leguminosarum, finding that plasmids are depleted in beneficial genes, especially ancient ones, suggesting evolutionary pressure drives beneficial genes to the chromosome.

The paper shows that recombination modifiers can influence adaptation by altering local recombination rates, even if they reduce genome-wide polygenic adaptation.

The paper examines how mutation rates affect viral adaptation and lethal mutagenesis, finding that high mutation rates can hinder adaptation but may enable lethal mutagenesis.

The paper shows that within-host competition between pathogens and microbiota drives molecular evolution and microbiota dysbiosis in C. elegans hosts.

This study uses simulations to show that immune pressure, not just replicative fitness, explains observed viral evolution patterns in prolonged infections.

This study examines genome size variation in animal RNA viruses and finds that phylogenetic constraints, not host type or genome segmentation, primarily influence genome size across viral orders.