E. V. Koonin

Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.

This study shows that environmental variation and horizontal gene transfer can stabilize microbial diversity and ecological complexity in a mathematical model of competing populations.

Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection

This study uses mathematical modeling to show that optimal strategies for balancing somatic damage repair and asymmetric allocation depend on extrinsic mortality and damage accumulation rates, linking these to the evolutionary r/K selection theory.

Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

The paper identifies 56 metagenome-assembled genomes of Bathyarchaeia viruses and describes their CRISPR system components, revealing potential counter-defense mechanisms.

DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution

The paper identifies Polinton diversity in nematode genomes, showing ancient and recent integrations and horizontal gene transfer of distinct DNA polymerases across phyla.

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

The paper identifies and characterizes CoCoNuTs, a new subclass of Type IV restriction systems that target RNA, with additional potential DNA targeting capabilities and regulatory mechanisms.

Distinct groups of RNA viruses associated with thermoacidophilic bacteria

The paper identifies two new groups of RNA viruses associated with thermoacidophilic bacteria in acidic hot springs and other environments.

Activation of programmed cell death and counter-defense functions of phage accessory genes

The paper identifies and characterizes phage accessory genes (AGs) that activate host antiviral immunity, including programmed cell death, and explores their evolutionary implications.

Widespread PRC barrel proteins play critical roles in archaeal cell division

This study identifies three PRC barrel proteins in Haloferax volcanii essential for archaeal cell division, showing their conservation and role in division across haloarchaea.

Kiwa is a bacterial membrane-embedded defence supercomplex activated by phage-induced membrane changes

The paper characterizes the Kiwa defence system as a bacterial membrane supercomplex that detects phage-induced membrane changes and inhibits phage replication.

Exaptation of inactivated host enzymes for structural roles in orthopoxviruses and novel protein folds revealed by protein structure modeling

The paper uses AlphaFold2 to predict structures of orthopoxvirus proteins, revealing exaptation of inactivated host enzymes for structural roles and novel protein folds.

Compensatory Relationship between Low Complexity Regions and Gene Paralogy in the Evolution of Prokaryotes

The paper shows an inverse correlation between low complexity regions and gene paralogy in prokaryotic evolution, suggesting compensatory relationships between short-term and long-term evolutionary mechanisms.

Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes

This paper models the coevolution of reproducers and replicators to identify conditions for the origin of genomes and symmetrical cell division.

A family of novel immune systems targets early infection of nucleus-forming jumbo phages

This study identifies a novel immune system, Juk, in Pseudomonas aeruginosa that targets jumbo phages by inhibiting early phage transcription, DNA replication, and nucleus assembly.

Synergistic anti-phage activity of bacterial defence systems

The paper investigates bacterial defence systems against phage predation, finding synergistic anti-phage activity and compatibility between systems in different bacterial taxa.

Host Age Structure Defines Interactions with Pathogens: Grandparent Effect under Collaboration and Virulent Mutualism under Competition

The paper uses mathematical modeling to show how host age structure affects pathogen interactions, finding that virulent pathogens can benefit competitive populations while harming collaborative ones.

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

The paper identifies 11,420 viroid-like circular RNAs across 5,131 metatranscriptomes and 1,344 plant transcriptomes, revealing a five-fold increase in known viroid-like agents and novel ribozyme combinations.

Varidnaviruses in the human gut: a major expansion of the order Vinavirales

This study identifies and characterizes varidnaviruses in the human gut virome, revealing their prevalence as prophages and suggesting limited active infections.

Conservation and evolution of the sporulation gene set in diverse members of the Firmicutes

The paper analyzes sporulation gene conservation across 180 Firmicutes genomes to identify lineage-specific losses and confirm the vertical inheritance of sporulation genes.

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer

The paper develops Coselens to quantify conditional selection of driver mutations in cancer, identifying 296 conditionally selected gene pairs across 16 cancer types and revealing modular epistasis networks.

Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

This study analyzes 27 human pathogenic RNA viruses to show they form multiple co-circulating lineages with low turnover rates, occupying non-competing epidemiological niches.

tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector

The paper shows that Cas13a cleaves tRNA anticodons to induce bacterial dormancy and activates toxin-antitoxin modules for mRNA and rRNA cleavage.

Towards a Theory of Evolution as Multilevel Learning

This paper develops a theory of biological evolution as multilevel learning, using neural networks and learning principles to explain replication, selection, and complexity emergence.

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

This study analyzes epistatic interactions among RBD mutations in SARS-CoV-2 variants to assess their impact on vaccine escape potential.

Viruses of Asgard archaea

This study identifies three new viral families associated with Asgard archaea in deep-sea sediments, showing they are prokaryotic-like viruses with no clear evolutionary link to eukaryotic viruses.

A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses

The paper presents a phylogenomic framework for classifying and understanding the diversity and evolution of giant viruses in the phylum Nucleocytoviricota.

Insertions in SARS-CoV-2 genome caused by template switch and duplications give rise to new variants that merit monitoring

The paper identifies 347 unique insertions in SARS-CoV-2 genomes, showing they arise from polymerase slippage and template switch, and some may affect immune evasion.

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

The paper uses a ratio-dependent Lotka-Volterra model to show that the parasite-free state in replicator-parasite coevolution is unstable, supporting the hypothesis that genetic parasites are inherent to life.

Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

The paper examines the evolutionary factors shaping the U-shaped gene commonality distribution in prokaryotic pangenomes and identifies the horizontal gene transfer barrier as a key factor.

Prediction of the virus incubation period for COVID-19 and future outbreaks

The paper predicts the upper limit of the incubation period for viruses like SARS-CoV-2 using genomic features to aid in outbreak control.

Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2

This study analyzes 300,000 SARS-CoV-2 genomes to show ongoing adaptive evolution, with positive selection in spike and nucleocapsid proteins and regional diversification over time.