comparative / phylogenetic analysis

The paper investigates how the MoeA enzyme evolved multifunctionality through evolutionary and structural analyses, showing its repurposing in both bacteria and eukaryotes for diverse roles.

The paper demonstrates that ambisense transcription allows compact circular RNA viruses to expand coding capacity by expressing additional genes, using kolmioviruses as a case study.

This study characterizes the genomic distribution and evolution of pks islands in E. coli strains associated with colorectal cancer, revealing phylogenetic patterns and horizontal gene transfer.

This study examines how temperature affects circadian clock function in two Nothofagus tree species, revealing species-specific thermal limits and impacts on growth and survival.

This study examines cell wall composition's role in photosynthesis across land plants, finding that pectin content correlates with mesophyll conductance, but crops show deviations from this pattern.

This study investigates how amino acid changes in C4-NADP-ME and nonC4-NADP-ME enzymes affect their oligomeric states and function in Poaceae species.

This study examines the evolution of the hymenopteran skeletomuscular phenome across developmental stages and anatomical hierarchies, showing that phenome-wide reorganization drives lineage diversification.

This study identifies evolutionary links between bacterial IS110 transposons and archaeal/eukaryotic RNA modification systems, suggesting RNA-guided mechanisms evolved from transposon components.

The paper identifies a new subgroup of type V-K CAST systems in cyanobacteria through phylogenetic analysis and characterizes its unique features.

This study analyzes trait evolution and diversification in the fungal order Hymenochaetales, revealing multiple adaptive periods and identifying key drivers of diversification.

The paper computationally optimizes a peptide inhibitor of the CXCL12/HMGB1 heterocomplex, resulting in a variant with significantly improved affinity and activity.

The paper identifies a provirus-encoded CRISPR-Cas system in Haloferax lucentense and shows it relies on a plasmid-encoded system for adaptation, suggesting horizontal transfer and cooperative immunity.

This study shows that the common symbiotic pathway genes are essential for arbuscular mycorrhizal symbiosis in bryophytes, indicating conservation of this pathway for 450 million years.

This study identifies convergent genomic changes in socially parasitic ants, showing gene loss, innovation, and network rewiring in parasites compared to hosts.

This paper shows chromatin reduces regulatory errors in gene expression by silencing off-target genes and enabling scalable gene regulation.

The paper compares genome fractionation patterns in maize and its wild relatives, finding distinct subgenome retention and gene loss trends between species.

This study investigates how retinal specializations in mammals evolve in response to ecological factors and morphological constraints, finding support for associations between horizontal streaks and habitat type, and between orbit convergence and retinal acuity regions.

The paper examines how immunoglobulin codon optimality interacts with mutability and hypermutation in antibody evolution, finding that codon deoptimization correlates with expression loss and is constrained by selective pressures.

This study investigates the expansion of the MutS gene family in plants, identifying origins through gene duplication, endosymbiotic gene transfer, and horizontal gene transfer, and highlights their roles in organelle genetics.

The paper identifies genes under relaxed selection in cassava due to clonal propagation, highlighting pollen-related genes and their implications for breeding.

This study compares β-catenin sequences and function across nonbilaterian metazoans and Xenopus embryos, revealing conserved structural and functional properties of β-catenin complexes.

The paper examines X chromosome evolution in treehoppers, finding long-term conservation with one exception of an X-autosome fusion in a species.

MEGA12 adds filtered substitution-model selection, matching full-search choices in all 240 simulated nucleotide alignments, and adaptive bootstrapping with an 81% average speed-up, accelerating maximum-likelihood phylogenetics.

This study sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalid, and compared its genome to parasitic relatives to understand evolutionary adaptations to anaerobic lifestyles.

The paper uses single-cell RNA sequencing to compare embryonic development in two sea urchin species, identifying evolutionary changes in cell fate specification and signaling.

The paper identifies 38 cases of enzymes with different structures but identical functions, analyzing their sequence, structure, and mechanism to support convergent evolution.

This study identifies molecular genotypes and key residues that determine receptor tropism in alphacoronaviruses, revealing generalist and specialist host ranges and potential spillover routes.

This study investigates the genomic basis of lifespan extension in bees lacking prepupal diapause, finding convergent selection on longevity-related genes and changes in selection pressures on the IIS/TOR pathway.

This study investigates how histone modifications and transposable elements influence dosage regulation in gene duplicates across D. discoideum and humans.

This study identifies two subspecies of Xenorhabdus griffiniae and shows that prophages drive intraspecies genomic variation.