Evolution and Genetic Dynamics

Epidemic size and host-parasite (co)-evolution: a meta-analysis

This paper meta-analyzes 11 studies to assess how epidemic size influences host-parasite evolution, finding mixed results across different taxa and suggesting the need for more diverse studies.

A diffusion model of viral evolution predicts mutation fitness and evolutionary trajectories

VES predicts viral mutation fitness and evolutionary trajectories using a diffusion model trained on protein sequences, outperforming existing models in mutation fitting and forecasting future mutations.

Closed-loop steering locates an evolutionary barrier to multidrug resistance in Escherichia coli

The paper uses a closed-loop system to steer Escherichia coli toward multidrug resistance and identifies an evolutionary barrier linked to mutations in the efflux pump gene.

Species-specific metabolic networks shape evolutionary routes to functional rescue

This study shows species-specific metabolic networks influence evolutionary routes to functional rescue in Bacillus subtilis under different selection pressures.

Unicellular and Multicellular Modes of Selection Impose Distinct Constraints on Cellular Phenotype Evolution

This study uses a geometric model to show that selection on cellular phenotypes in unicellular and multicellular organisms imposes different constraints on the evolution of differentiation from a shared genome.

Standing genetic variation drives polygenic adaptation to different environmental shifts

This study uses simulations to show how environmental shifts affect genetic adaptation, highlighting the role of standing genetic variation and using a CNN to predict environmental changes and mutation effects.

Epistasis and the changing fitness landscapes of SARS-CoV-2

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.

Rapid speciation in small populations challenges the dominance of ecological speciation

This study shows that larger populations take longer to speciate, challenging the idea that ecological speciation drives much of species diversity.

Cyclic parthenogenesis helps populations cross fitness valleys

This study shows cyclic parthenogens outperform obligate sexuals in crossing fitness valleys due to more efficient establishment of escape genotypes.

Dynamics of mutators of arbitrary dominance in humans

The paper develops a population genetic model to analyze mutator alleles in humans, showing that most known mutators are consistent with purifying selection, but one variant remains unexplained.

Plague-driven selection enriched familial Mediterranean fever mutations in Armenia

The paper identifies recent positive selection of MEFV mutations in Armenians linked to the first Yersinia pestis plague pandemic, suggesting resistance to plague as the selective agent.

An eco-evolutionary theory of host-associated microbiomes

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 probability of evolutionary rescue with competition: scaling-up from a single species to a community

This study examines how competition affects evolutionary rescue in ecological communities, showing that survival interference reduces rescued species but weakens with diversity.

CRISPR herd immunity against a transducing phage underlies adaptive homologous recombination in resting bacteria

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.

Selectively Advantageous Instability and Information Theory in Sex-specific Aging

The paper models selectively advantageous instability as a mechanism for adaptive state space exploration in aging, showing how it can be favored despite long-term costs.

Hantavirus mutagenesis is impacted by mutagens and host antiviral proteins

This study identifies mutagens and host antiviral proteins as major contributors to hantavirus mutagenesis, influencing mutation patterns and genetic diversity.

The hidden diversity: Replication-strand asymmetry shapes short-term nucleotide and structural variation in an RNA virus

The paper characterizes replication dynamics and short-term evolutionary patterns of OrV, revealing strand asymmetry, mutational filtering, and non-standard genomes.

Growth rate and yield are not constrained by a trade-off in microbes

The paper challenges the traditional r-K trade-off theory by showing a positive correlation between growth rate and carrying capacity in microbes, with implications for community assembly and species coexistence.

Sex-specific dominance maintains multilocus polymorphism and can resolve sexual conflict

This study shows that sex-specific dominance can maintain genetic polymorphism across multiple loci and reduce within-sex phenotypic variance, resolving sexual conflict.

Sign epistasis extends the effects of balancing selection on genetic diversity

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.

The effects of supergene evolution on the structure and stability of the G-matrix

This study investigates how supergene evolution affects the structure and temporal stability of the G-matrix through mathematical analysis and simulations.

Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity

This paper uses causal inference to show that background selection and mutation rate variation jointly shape human genetic diversity, with mutation rate variation having comparable impact in some chromosomes.

No passive sidekick: mitochondrial compensatory evolution during adaptation of ETC mutant lines in Caenorhabditis elegans

This study shows mtDNA can rapidly adapt to nuclear ETC mutations in C. elegans, with compensatory mutations in nd-1 significantly improving fitness.

Untangling the effects of within-host and between-host natural selection in viruses with applications to evolution of HIV-1 co-receptor usage

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.

Co-adapting but not static predators facilitate prey adaptation to a fluctuating environment

This study shows that prey adaptation to a fluctuating environment depends on whether predators co-adapt or remain static, challenging predator removal as a conservation strategy.

EWF 2.0: Exact sampling of allele trajectories using the Wright--Fisher diffusion with time-varying demography

EWF 2.0 is an exact simulation algorithm for Wright-Fisher diffusions with time-varying demography, validated through distributional tests and maintaining computational efficiency.

Sexual selection purges mutation load, but not overall genetic diversity in populations, decreasing vulnerability to extinction

This study shows that strong sexual selection reduces deleterious mutations and extinction risk in beetle populations without decreasing genetic diversity.

Cell division timing shapes the morphology and size of nascent multicellular organisms

The paper identifies cell division timing as a key factor influencing multicellular morphology and size in snowflake yeast, showing that asynchronous division leads to smaller clusters due to increased mechanical stress.

High levels of mitotic gene conversion are needed to effectively purge deleterious mutations in asexual organisms

This study investigates how mitotic gene conversion can purge deleterious mutations in asexual organisms and compares its effectiveness to self-fertilisation.

Predicting barrier architecture and the genomic landscape of differentiation under polygenic divergent selection

The paper develops a method to predict genetic barriers and coalescence times under polygenic divergent selection using a mainland-island model and validates it with simulations.