Evolution and Genetic Dynamics

Origins of the Fittest: Clonal Interference in Heterogeneous Networks.

This study shows how network structure influences the spread of beneficial mutations in asexual populations, revealing distinct evolutionary regimes based on mutation rates and topology.

Emergence of population-level feedback control by transposon-plasmid coevolution

This study shows how transposon-plasmid coevolution enables Escherichia coli to dynamically respond to antibiotics through population-level feedback control.

Strong promoters are mutationally robust

This study shows that strong prokaryotic promoters are more mutationally robust, with robustness influenced by box spacing and sequence flexibility.

Endosymbiosis: metabolic trade-offs drive reproductive synchronization

The paper examines the fitness consequences of reproductive synchronization in endosymbiotic relationships, finding it costly for hosts but beneficial for guests, with synchronization increasing overall fitness when new endosymbioses are rare.

Virion aggregation shapes infection dynamics and evolutionary potential

This study investigates how viral aggregation affects infection dynamics and genetic diversity in mammalian orthoreovirus, finding that it reduces replicative potential but increases evolutionary potential through reassortment.

Experimental rewilding of stickleback drives phenotypic shifts that oppose long-term evolutionary trajectories in Daphnia in Alaskan lakes

The paper examines how rewilding with stickleback affects phenotypic changes in Daphnia over three years, showing opposing trends between experimental and natural lakes.

A Trade-off Between Developmental Speed and Replication Fidelity Governs the Spontaneous Mutation Rate

This study shows that mutation rates in midges are influenced by a trade-off between developmental speed and replication fidelity, with shorter generation times leading to higher daily mutation rates.

Modeling the Tangled Bank: A Users Guide to Gillespie Eco-evolutionary Models using the Julia Programming Language

This paper introduces an optimized Julia framework for Gillespie Eco-evolutionary Models (GEMs) to simulate eco-evolutionary dynamics with improved computational efficiency.

Mutation-selection-drift balance models of complex diseases

The paper develops a mutation-selection-drift balance model for complex diseases, finding that directional selection has little role in common variation but may affect rare variants, and suggests heritability estimates may be biased.

Adaptive evolution can overwrite initial natural fitness variation only in highest-fitness yeast isolates

This study shows that high initial fitness is necessary but not sufficient for long-term success in yeast, as adaptive mutations can override small fitness differences.

Reproduction emerges from ecological interactions at the onset of multicellularity

This study shows multicellular reproduction emerges from ecological interactions in a computational model of evolving cells.

Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus)

This study quantifies selection pressures in common marmosets, finding increased purifying selection and balancing selection in immune-related genes.

Opposing copy number variation dynamics accompany adaptation to glucose and galactose in diploid yeast.

This study shows that copy number variations (CNVs) dominate genome evolution in yeast adapting to glucose or galactose, with opposing CNV dynamics in each environment.

The effect of population size on adaptation to fluctuating temperatures

This study examines how population size affects adaptation to fluctuating temperatures in fission yeast, finding no significant impact on adaptation or trade-offs.

Investigating the consequences of the mating system for drug resistance evolution in C. elegans

This study uses a population genetic model to show that androdioecious C. elegans populations adapt rapidly to drug selection and exhibit high genetic diversity.

Bounding phenotype transition probabilities via conditional complexity

This study evaluates an upper bound on phenotype transition probabilities using conditional complexity across various genotype-phenotype maps and finds it provides meaningful estimates.

Gene expression evolution is predicted by stronger indirect selection at more pleiotropic genes.

The paper shows that stronger indirect selection drives evolutionary changes in gene expression, particularly at more pleiotropic genes in red flour beetles under stress.

Genomic bases of short-term evolution in the wild revealed by long-term monitoring and population-scale sequencing

The paper uses long-term genomic data from Swiss barn owls to show that selection on few loci drives rapid phenotypic evolution in response to environmental change.

Elevated viral recombination in short-lived hosts

The paper shows that viruses in short-lived hosts recombine more frequently due to higher population density and co-infection rates, supported by avian influenza data.

Bridging energy and ribosomal allocation models to predict the cost of traits in different environments

The paper develops a model that integrates energy and ribosomal allocation to predict trait costs under varying environmental conditions and genetic backgrounds.

Maternal effects regulate population genetic structure by altering intraspecific competitive relationships

This study shows maternal effects influence population genetic structure by altering competitive dynamics among offspring clones, with temperature affecting the duration of these effects.

Genomic and Epigenetic Interplay Drives Adaptive Fusion via Reproduction Trade-Off

The paper shows how epigenetic silencing and genetic changes enable Prm1-independent fusion in yeast, but at the cost of mitotic growth, while synthetic mutations avoid this trade-off.

Quantifying feedback among traits in coevolutionary models

This paper develops a framework to quantify feedback between traits and selection gradients in coevolutionary models, demonstrating its application across different theoretical approaches.

Linked selection of insertions and deletions in coding regions of the great tit genome

The paper identifies and analyzes insertions and deletions (indels) in the great tit genome, finding they show signs of natural selection and are linked to adaptive traits.

Simulated climate change magnifies genetic vulnerabilities from mutation load and maladaptation

The paper shows that genetic makeup affects survival under simulated climate change, with deleterious mutations and maladaptive alleles reducing fitness in stressful climates.

Evolutionary rescue accelerates competitive exclusion in a parasite community

This study shows evolutionary rescue prevents parasite extinction but can destabilize communities by promoting competitive exclusion in a viral parasite system under thermal stress.

Accessible, realistic genome simulation with selection using stdpopsim

The paper extends the stdpopsim simulation framework to include realistic selection models, enabling studies of selection's impact on genetic variation across species.

Forecasting protein evolution by integrating birth-death population models with structurally constrained substitution models

This paper forecasts protein evolution by integrating birth-death population models with structurally constrained substitution models, showing acceptable errors in folding stability predictions but larger errors in sequence predictions.

Survival of thermostable {varphi}6 genotypes in acidic, basic, and UV environments

The paper tests how mutations increasing thermostability affect viral survival in acidic, basic, and UV environments, finding that the least thermostable genotype had the highest survival.

Robust detection of specific epistasis using rank statistics

This paper introduces a method to detect specific epistasis by analyzing rank statistics in mutagenesis experiments, achieving accuracy comparable to more complex methods.