Evolution and Genetic Dynamics

When will hybridization bring long-term benefits?

This study investigates the long-term benefits of hybridization by modeling genetic variation and heterosis, finding that outcomes depend on epistasis variance rather than heterosis itself.

Rising temperatures favour parasite virulence and parallel molecular evolution following a host jump

This study shows that rising temperatures increase parasite virulence and drive parallel molecular evolution during host jumps.

Integrated model of the protein molecular clock across mammalian species

The paper investigates the generation time effect on protein substitution rates across mammals and develops an integrated model of protein evolution.

The population genetics of biological noise

This paper develops a theoretical framework to study the evolution of heritable biological noise, showing how natural selection shapes the amount of noise in organisms.

Super compensatory substitutions restore protein function and confer mutational robustness

The paper identifies super compensatory substitutions that restore protein function and confer mutational robustness across diverse genetic backgrounds.

Entrenchment and contingency in neutral protein evolution with epistasis

The paper shows that protein evolution with epistasis and purifying selection does not lead to entrenchment, and that rate variation is due to epistasis, not historical contingency.

Multiplicity of Type 6 Secretion System toxins limits the evolution of resistance

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

Emergence of multiple foraging strategies under competition

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

Tie that binds - Hill-Robertson Interference can produce signals of sexual antagonism even in the absence of sexually antagonistic selection

This paper shows that negative estimates of rmf,W do not necessarily indicate intralocus sexual conflict, as Hill-Robertson Interference can produce such signals under sex-limited selection.

Robustness of Selection and Timing Inference under Model Variation in Population Genetics

This paper analyzes how model mismatches affect the inference of selection coefficients and mutation timing in population genetics, showing that time of onset is sensitive to assumptions about reproductive variance and generations.

Niche construction: the case of industrial vinegar production

The paper examines niche construction in industrial vinegar production, showing how acetic acid bacteria evolve increased acidity tolerance through directional selection.

Waning immunity drives respiratory virus evolution and reinfection

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

Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy

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.

Selection can favor a recombination landscape that limits polygenic adaptation

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

Transient evolutionary epidemiology of viral adaptation and lethal mutagenesis

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.

Within-host competition sparks pathogen molecular evolution and perpetual microbiota dysbiosis.

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

Immune Pressure is Key to Understanding Observed Patterns of Respiratory Virus Evolution in Prolonged Infections

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

Genome sizes of animal RNA viruses reflect phylogenetic constraints

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.

Direct measurement of the mutation rate and its evolutionary consequences in a critically endangered mollusk

The paper estimates the germline mutation rate in the white abalone and uses it to infer population history and evolutionary patterns in the Haliotis genus.

Models of microbiome evolution incorporating host resource provisioning

This study extends an agent-based model of host-microbiome evolution by incorporating resource provisioning, showing that host resource allocation depends on microbiome composition and environmental interactions.

Similarity-weighted entropy for quantifying genetic diversity in viral quasispecies

This paper introduces similarity-weighted entropy measures to better quantify genetic diversity in viral quasispecies by accounting for sequence similarities, showing improved accuracy over traditional entropy metrics.

Shared selection and genetic architecture drive strikingly repeatable evolution in long-term experimental hybrid populations

The study shows that shared selection and genetic architecture lead to repeatable evolution in hybrid sunflower populations over 14 years.

Population Models with Phenotypic Diversity and Fluctuating Environment Illustrate Parameter Regimes of Adaptation vs. Extinction

The paper uses population dynamics models to analyze parameter regimes for adaptation versus extinction under environmental fluctuations and phenotypic diversity strategies.

Inference with Viral Quasispecies. Methods for Individual Samples Comparative Analysis.

The paper develops and compares variance estimation methods for quasispecies indicators in viral samples, finding that some metrics show consistent variance estimates while others diverge significantly.

GnT motifs: short nucleotide tracts of >=8bp that can increase T:A->G:C mutation rates >1000-fold in bacteria

The paper identifies GnT motifs, short nucleotide tracts that significantly increase T:A->G:C mutation rates in bacteria through experimental and bioinformatic analysis.

Inverted topographies in sequential fitness landscapes enable evolutionary control

This paper introduces a new metric, edge flip fraction, to compare fitness landscapes and shows it predicts evolutionary trajectories and drug sequence optimality.

CLUES2 Companion: Computational pipelines to estimate, visualize, and date selection on multi-locus sites

CLUES2 Companion provides pipelines to estimate selection coefficients and date selective sweeps using genomic data from multiple populations.

Evolution of genetic variance and its consequences oneco-evolutionary response in complex mutualistic networks

This study shows that evolving genetic variance and network architecture enhance resilience of plant-pollinator networks to temperature shifts by promoting faster adaptation and reducing trait lag.

Balancing selection and the functional effects of shared polymorphism in cryptic Daphnia species

This study examines shared polymorphisms in Daphnia species, finding that balancing selection and convergent evolution explain their distribution, with functional effects on behavior and fitness.

Genetic basis of resistance in hosts facing alternative infection strategies by a virulent bacterial pathogen

This study identifies distinct genetic resistance loci in Daphnia magna for two infection routes of the parasite Pasteuria ramosa, showing foregut and hindgut infections are controlled by separate loci, G and D, with epistatic interactions.