T. Dagan

The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages

The paper shows that antibiotic resistance islands in MDR plasmids are biased towards specific plasmid lineages and evolve rapidly within these lineages.

Pseudogenes in plasmid genomes reveal past transitions in plasmid mobility

The paper analyzes pseudogenes in plasmid genomes to show higher pseudogene density compared to chromosomes and links non-functionalization to loss of plasmid mobility.

T6SS-mediated competitive exclusion among Pantoea agglomerans associated with plants

The paper investigates T6SS-mediated competition among closely related Pantoea agglomerans strains, showing that competition strength depends on effector and immunity gene repertoires rather than phylogenetic relatedness.

Closely related Bacteroides of the murine intestinal microbiota affect each other's growth positively or negatively

The paper tests growth interactions between closely related Bacteroides strains from mice and finds both positive and negative effects, with growth promotion more common than inhibition.

Phylogenomic Testing of Root Hypotheses

The paper tests root hypotheses in phylogenomic analysis using statistical hypothesis testing and shows agreement with known opisthokonta LCA and new insights into proteobacteria LCA.

Segregational drift hinders the evolution of antibiotic resistance on polyploid replicons

This study shows that polyploid replicons hinder the evolution of antibiotic resistance due to segregational drift, affecting allele establishment probabilities.

Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)

The paper reconstructs the colonization history of eelgrass using genomic data, showing trans-Pacific currents drove its spread and Atlantic populations arrived more recently with lower genetic diversity.

Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids

This study develops a population genetics model for polyploid prokaryotes, showing that beneficial mutations can fix phenotypically before genotypically, creating a heterozygosity window.

Denitrification in foraminifera has ancient origin and is complemented by associated bacteria

The paper shows denitrification genes are conserved in foraminifera and their microbiome complements the pathway, revealing an ancient origin of this trait in these organisms.

Pangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance

This study examines pangenome evolution in symbionts of deep-sea mussels, finding that vertical inheritance, not horizontal gene transfer, drives genetic diversity in environmentally acquired bacterial symbionts.

The order of trait emergence in the evolution of cyanobacterial multicellularity

This paper examines the evolution of cyanobacterial multicellularity, finding nitrogen fixation as the primary driver that enabled the transition from unicellular to multicellular forms through metabolic specialization and division of labor.

Natural competence in Chlorogloeopsis fritschii PCC 6912 and other ramified cyanobacteria

This study demonstrates natural competence in ramified cyanobacteria, showing they can acquire DNA via transformation and highlighting its evolutionary significance.

Two novel heteropolymer-forming proteins maintain multicellular shape of the cyanobacterium Anabaena sp. PCC 7120

This study identifies two novel heteropolymer-forming proteins in Anabaena that maintain multicellular shape by interacting with other proteins involved in cell structure.

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.

This study identifies that insertions and deletions (indels) contribute to antibiotic resistance evolution in Mycobacterium tuberculosis during an outbreak, with indels showing a slower evolutionary rate than substitutions.

Somatic genetic drift and multi-level selection in modular species

The paper investigates somatic genetic variation in modular species, finding that clonal growth leads to genetically differentiated modules with varying levels of selection.

Identification and characterization of novel filament-forming proteins in cyanobacteria

The paper identifies and characterizes two novel filament-forming proteins in cyanobacteria, showing their roles in cell morphology, motility, cytokinesis, and colony integrity.

The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

This study shows that temperature has a stronger effect on genetic diversity and fitness in bacteria than population bottleneck size following bottlenecks.

Higher stochasticity of microbiota composition in seedlings of domesticated wheat compared to wild wheat

This study compares microbial diversity in domesticated and wild wheat, finding reduced diversity and increased variability in domesticated wheat seedlings.

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

This study shows that horizontally transmitted symbionts in deep-sea mussels form genetically isolated populations due to restricted bacterial uptake and serial founder effects during host life-cycle.

Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

Segregational drift and the interplay between plasmid copy number and evolvability

This study shows that segregational drift in multicopy plasmids reduces their evolvability by increasing mutation loss and fixation time, despite higher mutational supply.