Evolution and Genetic Dynamics

Quantifying the predictability of evolution by analysis of coalescent rate variation

The paper develops coalescent models to quantify evolutionary predictability by analyzing lineage coalescence rates and applies them to microbial and viral datasets to detect selective effects.

Divergent Thermal Reaction Norms of the Spontaneous Mutation Rate Among Populations of Chironomus riparius

The study shows that mutation rates in Chironomus riparius vary with temperature differently across populations from Central Europe and the Mediterranean.

Rare variants drive high variance in human ancestral fitness at mutation-selection-drift balance

The paper estimates human genetic load variation due to rare and ultra-rare deleterious mutations, showing significant ancestral fitness differences between individuals.

Quantitative Logics for Directed Evolution of an Asexual Population

This paper introduces ten quantitative logics for directed evolution of asexual populations, showing they can accelerate evolution by tenfold with 85% accuracy in simulations.

Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance

This study shows that function-specific epistasis shapes antibiotic resistance evolution, with some genetic backgrounds leading to novel resistance trajectories and slower resistance development.

Hypermutability of integrated sequences of viral origin in a Chlorarachniophyte

The paper identifies hypermutable regions in the nuclear genome of Bigelowiella natans, showing extreme mutation rate variation and a distinctive mutational signature in virus-derived sequences.

Lichen symbiosis does not impose a uniform genomic syndrome on algae

This study examines whether lichen symbiosis imposes a uniform genomic syndrome on algae by analyzing molecular evolution signatures across four lichen-forming algal taxa and their free-living relatives.

Complete Mutagenesis of the Genome and Proteome of {Phi}X174

This paper systematically mutagenizes the genome and proteome of PhiX174, revealing that most mutations impair fitness, with protein interaction disruptions being a major cause.

Evolutionary adaptation proceeds through a small number of phenotypic modules

The paper shows that fitness variation across drug environments in yeast is organized by a low-dimensional phenotypic structure, revealing modular phenotypic modules that constrain adaptive mutations.

Beyond Fixation: Persistent Genetic Variation Under Intense Selection

This study shows that genetic variation persists under intense directional selection in Drosophila and can be rapidly redeployed when selection reverses, suggesting balancing-selection maintains this variation.

Coevolution of Codependent Hosts and Symbionts

This paper develops theory to explain how host-symbiont coevolution leads to either cooperation or exploitation, depending on population-genetic factors.

Plasticity of the mutation rate and spectrum in eukaryotic marine phytoplankton

This study measures mutation rate and spectrum plasticity in Ostreococcus tauri under different environmental conditions, finding significant variation in SNM rates and spectra.

Elevated mutation near crossovers inhibits the evolution of recombination

The paper models how recombination-associated mutation affects the evolution of recombination rates, finding that mutation near crossovers reduces the advantage of recombination.

sept-1/zina-1 is an Ancient Toxin-Antidote System in Caenorhabditis elegans

The paper identifies an ancient toxin-antidote system in C. elegans, showing that sept-1/zina-1 predates other known TA systems and has undergone functional changes across strains.

Strain-Specific Epistasis Shapes Fitness Landscapes of APOBEC3G Antagonism By HIV-1 Vif Proteins

The paper maps mutational landscapes of HIV-1 Vif proteins to understand how they antagonize APOBEC3G, revealing strain-specific epistasis and structural flexibility.

Stabilizing selection generates selection against introgressed DNA

The paper shows stabilizing selection on quantitative traits can purge introgressed DNA even when populations have similar optimal trait values and identical demographics.

Predation, evo-devo, and historical contingency: A nematode predator drives evolution of aggregative multicellularity

This study shows that nematode predation influences the evolution of aggregative multicellularity in Myxococcus xanthus, with effects mediated by the presence of shared prey.

Haplotype and diversity signatures of ultra-soft selective sweeps in HIV-1

The paper shows HIV can adapt to antibody treatment without reducing genetic diversity, challenging methods that rely on diversity and haplotype signatures to detect resistance.

Parallel and Divergent Evolution in Pseudomonas aeruginosa Under Constant and Fluctuating Predator-Mediated Selection

This study shows that constant and fluctuating protozoan predation shape evolutionary trajectories in Pseudomonas aeruginosa by altering mutation dynamics, adaptation targets, and historical contingency.

Effect of population structure and stabilizing selection on quantitative genetic variation

The paper analyzes how population structure and stabilizing selection affect genetic variation, finding that migration thresholds influence variance and GWAS portability between subpopulations.

Changing abiotic and biotic environments affect the genetics of adaptation and speciation

This paper models how different types of environmental change affect adaptation and speciation, finding that biotic conflicts can lead to divergence without reducing hybrid fitness.

The adaptive landscapes of three global Escherichia coli transcriptional regulators

This study maps in vivo adaptive landscapes for three Escherichia coli transcription factors, revealing rugged landscapes with pervasive epistasis and showing de novo gene regulation is feasible but constrained.

Direct estimation of genotype fitness from time series

The paper introduces a method to directly estimate genotype fitness from time series data without assumptions on epistasis or iterative optimization, demonstrating its effectiveness across simulations and experimental datasets.

Evolution of mutational fitness effects in island populations

The paper investigates how environmental changes on islands affect the distribution of fitness effects (DFE) in Peromyscus mice populations.

Metabolic inhibition can enable compact physical integration of microbial partners

This paper uses a mathematical model to show how metabolic self-inhibition can drive the evolution of physical integration between microbial partners.

Hybrid breakdown is temporary and not expressed in a novel environment during 50 generations of experimental evolution in Tetranychus urticae hybrids

This study tracks hybrid fitness in Tetranychus urticae over 50 generations, showing initial incompatibilities resolve and hybrids gain adaptive potential in novel environments.

Estimate of the mutation rate in the endangered Devils Hole pupfish provides equivocal support for the drift-barrier hypothesis at an outlying extreme

The study estimates mutation rates in Devils Hole pupfish, finding higher rates than expected for its small population size, contradicting the drift-barrier hypothesis.

Epistatic impacts of cis- and trans-regulatory mutations on the distribution of mutational effects for gene expression in Saccharomyces cerevisiae

The paper examines how cis- and trans-regulatory mutations affect the distribution of mutational effects on gene expression in yeast, finding changes in variance and skewness that influence mutational robustness and compensatory potential.

The effect of genome organisation on selection efficiency in two contrasted plant species

The paper investigates how mutational pleiotropy, expression level, and network connectivity affect the distribution of fitness effects of new mutations across the genome in two plant species.

Positive germline selection of mtDNA: evidence from the oocyte.

The paper analyzes mtDNA mutation dynamics in human oocytes and finds evidence of positive selection for noncoding and coding mutations, suggesting a shift from positive to purifying selection upon inheritance.