Evolution and Genetic Dynamics

This study examines how different fitness statistics in high-throughput microbial experiments affect interpretations of mutant fitness and evolutionary dynamics.

The paper introduces kGain, a metric quantifying k-mer frequency shifts due to mutations, and shows it predicts adaptive potential across species and experimental systems.

The paper uses Neanderthal ancestry patterns to identify genomic regions enriched with recessive deleterious mutations using a machine learning classifier.

This study investigates how intergenomic epistasis affects endpoint repeatability in coevolving species, finding high repeatability within landscapes but varying fitness outcomes across landscapes.

The paper tracks parallel evolution of full-length genomes in bacteriophage populations over 412 generations, showing non-neutral evolutionary dynamics and biases in phylodynamic analysis.

The paper infers a multi-host fitness landscape of endive necrotic mosaic virus using cross-inoculation experiments and a Bayesian model linked to Fisher's geometrical model.

The paper introduces a numerical method to accurately model random genetic drift with or without natural selection and mutation, showing improved accuracy over standard methods.

The paper quantifies the fitness gain of DGR diversification compared to standard mutagenesis and identifies when DGR activation is evolutionarily favored.

The paper models introgression of a small genomic block with weakly selected loci into a population, showing survival depends on selection strength relative to recombination.

The paper experiments with Snowball Earth viscosity to show that it drove the evolution of motile multicellularity in unicellular algae.

This paper introduces a matrix framework to estimate genotypic selection at multiallelic loci from time-series data, demonstrating its application to yeast evolution experiments.

The paper analyzes the navigability of random fitness landscapes, showing that adaptive basins are large and increase with fitness rank.

The paper tests a new theory for faster-X adaptation by examining whether large-effect mutations are more positively selected on the X chromosome in three species, but finds no support for this hypothesis.

This study shows that constitutive sporulation in wild fission yeast enhances survival by resisting digestion by fruit flies, despite being disadvantageous under nutrient-rich conditions.

The paper extends DMI models with a network approach to study how gene interaction network structure influences the evolution of hybrid incompatibilities, finding that network density and topology significantly affect incompatibility accumulation and clustering.

The paper tracks lineage evolution and transmission of Bacteroides thetaiotaomicron across hosts and ecological scales using genomic barcoding and whole-genome sequencing.

This paper reports the parallel evolution of chimeric genes in Escherichia coli through genomic deletions, suggesting they are more common and potentially adaptive than previously thought.

This paper provides a conceptual synthesis and mathematical framework for understanding internal evolutionary conflicts across diverse biological phenomena.

This study evaluates epistasis inference methods using temporal genetic data across different evolutionary regimes, finding that accuracy depends on selection, recombination, and genetic drift.

The paper uses single-cell RNAseq and population genomic data to show that immune cell types have faster evolutionary divergence in their characteristic genes compared to non-immune cell types.

The paper shows that mutation accumulation studies in microbes may have selection bias due to reporting practices and provides a model to estimate selection and mutation spectrum.

The paper distinguishes mutational robustness from replicative robustness, showing they can be selected in opposite directions and highlighting the importance of replication event dynamics in evolutionary robustness.

This paper introduces a method to detect meiotic drivers in D. melanogaster by analyzing embryonic marker transmission.

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

The paper shows that mean fitness under stabilizing selection is maximized in small populations when mutation rates exceed a threshold determined by selection strength and environmental variance.

The paper analyzes SARS-CoV-2 genomic data to show how mutational fitness costs change over time and introduces a model of pairwise epistasis to explain these changes.

This paper develops an eco-evolutionary theory explaining how host-specific microbiomes evolve through environmental fluctuations and vertical transmission, showing their heritability and specificity despite external influences.

The paper shows that CRISPR-mediated herd immunity in E. coli promotes frequent homologous recombination by maintaining genetic diversity and enabling gene flow, enhancing adaptation rates.

The paper models how balancing selection can extend its diversity-promoting effects to loci with sign epistasis, showing dominance and recombination rate are key factors.

This paper develops a method to estimate multi-level selection coefficients for pathogens, applying it to HIV-1 co-receptor usage and finding a strong trade-off between within-host and between-host fitness.