Evolution and Genetic Dynamics

Emergence of mutants in bacterial populations: a simulation-based approach for parameter inference in extended Luria & Delbru&x0308;ck scenarios

This paper introduces a simulation-based method to infer mutation rates and fitness effects in bacterial populations, accounting for ecological complexities not handled by traditional models.

Parallel evolution of chimeric genes in microbial evolution experiments

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.

Internal evolutionary conflicts: a conceptual synthesis and mathematical primer

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

Interpreting GC content differences across populations at polymorphic sites

This study shows that GC content differences at polymorphic sites across populations are shaped by demographic history, mutation bias, and GC-biased gene conversion, not by ongoing divergence or mutation pattern shifts.

A model for within- and between-host evolution in pathogens

This paper models within- and between-host evolution in pathogens, showing that bottlenecks reduce within-host variation and skew site frequency spectra, suggesting biases in population genetic inference.

Adaptive excursions across the drift barrier

The paper examines whether genetic drift limits adaptation in finite populations and finds that directional selection can often overcome drift constraints in natural populations.

Mitigating biases of rescaling in forward-in-time population genetic simulations

This study shows that biases in rescaling forward-in-time population genetic simulations can be reduced by using a different simulation algorithm.

Phenotypic plasticity affects species packing in seasonally fluctuating environments

This study shows how phenotypic plasticity and competition shape ecological responses to environmental variability by affecting species coexistence and community productivity.

Evolutionary regimes determine the accuracy of epistasis inference from temporal genetic data

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

Rates of evolution differ between cell types identified by single-cell RNAseq in threespine stickleback

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.

Selection mode changes the fate of nearly neutral deleterious mutations

This study shows that competitive soft selection can purge recessive deleterious mutations that are nearly neutral under hard selection, reducing genetic load and inbreeding depression.

Selection bias in microbial mutation accumulation studies and the impact of colony growth

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.

Phenotypic diversity acts as a higher-order functional trait of populations

The paper tests if phenotypic and genetic diversity among genotypes predicts non-additive population growth in Spirodela polyrhiza, finding that specific phenotypic traits and genetic loci influence synergistic growth.

Who are my Neighbours? Selection Targets Robustness to Full Replication Events, Not to Individual Mutations

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.

Somatic differentiation evolves rapidly and repeatedly through the modification of developmental plasticity

This study shows that somatic differentiation can evolve rapidly through environmental stress by modifying developmental plasticity in Eudorina algae.

Selection history alters fitness across ecological interactions in a fly-parasitoid system

This study shows that evolutionary history under one ecological interaction affects fitness in other interactions in a fly-parasitoid system.

Estimates of the rate of adaptive evolution in four wild populations of Nemophila menziesii

The study estimates adaptive evolution rates in four wild populations of Nemophila menziesii by comparing parental and offspring fitness under natural conditions.

The effect of a reduction in population size on mean fitness and inbreeding depression

The paper develops a theoretical framework to predict how population bottlenecks affect mean fitness and inbreeding depression, showing that recovery depends on selection strength and mutation recessivity.

Recombination accelerates adaptation across genetic architectures and demographic histories

This study shows that higher recombination rates modestly speed up adaptation in populations, primarily by reducing Hill-Robertson interference, with effects varying by demographic history.

Abiotic and biotic ecological factors affect the genomic consequences of plant-butterfly coevolution

The paper examines how abiotic and biotic factors influence genomic divergence in plants coevolving with butterflies and bumblebees across different temperature environments.

Maintenance of quantitative genetic variation in regions of restricted recombination via associative overdominance

The paper shows that weakly selected QTLs linked to regions with associative overdominance can increase additive genetic variance, but recessive deleterious alleles may reduce fitness when exposed by selection.

Accelerated Evolution of Context-Dependent Gene Expression in Primate Immune Cells

The paper examines gene expression evolution in primate immune cells under different conditions, finding that perturbation-responsive genes evolve faster than baseline genes.

Lineage-specific positive selection on stress-response genes in wild wheat relatives

The paper detects lineage-specific positive selection on stress-response genes in wild wheat relatives using transcriptome data and molecular evolution models.

A method to screen for meiotic drive using embryonic markers

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

Environmental history can counteract nutrient quality in shaping the evolution of bacterial growth rates

This study shows that environmental history influences bacterial growth rates through proteome allocation, often opposing expectations based on nutrient quality.

Forging an evolutionary individual from separate replicators

The paper demonstrates how plasmid communities in yeast cells can become units of selection through packaging and segregation, leading to reliable heredity and an evolutionary transition in individuality.

Positive selection tends to act on exposed extracellular regions and delineate interaction modules targeted by pathogens

The paper identifies positive selection in human proteins, showing PSRs are enriched in extracellular regions and interaction interfaces, and links them to pathogen targeting and drug targets.

Comparison of the Distribution of Fitness Effects Across Primates

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.

Experimental evolution of root-associated microbial communities

This study uses experimental evolution to show that complex microbial communities can adapt to new plant hosts through genomic changes, improving colonization fitness without destabilizing the microbiota.

Mean fitness is maximized in small populations under stabilizing selection on highly polygenic traits

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.