Evolution and Genetic Dynamics

The paper examines the relationship between plasmid copy numbers and size, arguing for two evolutionary strategies rather than a single scaling law.

The paper shows that phenotypic heterogeneity in yeast populations is an evolutionarily stable strategy that maximizes long-term fitness under environmental changes.

This paper develops a data-validated theory of natural selection after catastrophe, showing mean fitness relaxes inversely with time and follows Levenberg-Marquardt optimization in E. coli.

The paper uses an eco-evolutionary model to show how mutualism and antagonism interact to influence diversification in ecological networks, finding that trait correlation affects diversification rates across guilds.

This study detects pervasive cryptic negative selection in human noncoding regions using a statistical test, finding that at least 7% of the genome is under negative selection, surpassing previous estimates from conservation-based methods.

The paper proposes the Gene Version Iteration Hypothesis, suggesting mutant genes may cycle through chromosomes via the Y and X chromosomes, enabling version selection and evolutionary dynamics.

The paper shows how a duplicated tRNA synthetase evolved into a novel toxin by losing its ancestral function and acquiring a new role in targeting Aurora kinase A.

The paper analyzes selection pressures on mammalian extracellular matrix proteins across species and develops an open-access browser to visualize evolutionary dynamics.

This study shows mutation-biased adaptation can intensify in large bacterial populations and lead to unpredictable collateral sensitivity to antibiotics.

The paper reviews patterns and theories on how natural selection shapes mutation rates in animal germline and somatic cells across species.

The paper tests whether prokaryotic accessory genes are adaptive by analyzing the ratio of non-synonymous to synonymous diversity in two bacterial species.

The paper introduces an additivity index [A]g to quantify local fitness landscape curvature and identifies additive channels where linear genetic predictions are effective for short-term evolutionary response.

This paper shows that accounting for global synonymous selection improves the accuracy of detecting episodic positive selection in protein evolution.

This study tests how pesticide deployment regimes affect resistance evolution in C. elegans, finding that compound mixtures with refuge most effectively constrain resistance.

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

This study evolves a minimal genome bacterium to grow at a lower temperature, revealing genetic and non-genetic adaptation mechanisms.

The paper quantifies viral genome expression and replication complexity using a propagation index and finds it correlates with viral diversification across multiple taxonomic levels.

The paper identifies epistatic constraints on adaptive evolution in Drosophila Trio protein by reconstructing evolutionary intermediates and showing reduced viability and locomotor defects.

The paper analyzes evolutionary rates of 100 meiotic recombination proteins across 400 placental mammals, finding that rapid evolution is driven by reduced purifying selection and linked to chromosome pairing proteins in long-lived species.

The paper shows that engineered synonymous mutations disrupting RNA structural elements increase de novo mutations in a virus, suggesting structural perturbations affect genomic stability.

The paper examines the evolutionary tradeoff between horizontal and vertical gene transfer in plasmids, finding mixed evidence and proposing that HGT relaxes constraints by introducing plasmids into novel hosts.

The paper shows that temperature-induced evolutionary responses in microbial populations depend on both intraspecific and interspecific ecological interactions.

The paper uses simulations to show that deleterious mutations reduce inversion fixation probabilities, but lucky inversions can still fix and influence macroevolution.

The paper compares the effects of mutational drought and meltdown on extinction risk in small populations, finding mutational drought is more significant in stable and changing environments.

This study tests if interspecific competition during range expansion leads to pushed wave dynamics and alters evolutionary patterns in duckweed species.

This study develops a mathematical model to understand selection for horizontal plasmid transfer and shows that modifying lab protocols can tip selection towards horizontal gene transfer.

The paper analyzes factors influencing mutation rates across species and suggests evolutionary mechanisms for reducing mutation rates to mitigate cancer risk.

The paper shows that plasmid-dependent phages can help high-cost plasmids persist by reducing their abundance and neutralizing their costs in host populations.

This study shows condition-dependent selfing generates within-population variation in selfing rates and contributes to mating-system diversity.

The paper shows a trade-off between competitive ability and host colonization in Pseudomonas populations has persisted for centuries.