comparative / phylogenetic analysis

The paper shows that mutations increasing ORF9b expression are common in SARS-CoV-2 variants and PCI sequences, suggesting ORF9b's role in viral evolution and immune evasion.

The paper identifies novel origins of transfer (oriTs) in Genomic Islands, revealing their role as hitchhikers on conjugative elements and their contribution to bacterial genetic adaptation.

The paper develops a coarse-grained Martini 3 model of chondroitin sulfate A to enable efficient molecular dynamics simulations of its structural and electrostatic properties.

This study examines the relationship between pigmentation pattern diversity, species richness, and geography in coral reef fishes, finding a positive correlation and evidence of rapid phenotypic diversification.

The paper generates chromosome-level genomes for two Stemona species to investigate fatty acid differentiation in elaiosomes and seeds, revealing molecular mechanisms underlying wasp seed dispersal.

This study presents a near-complete genome of Trypanosoma rangeli using hybrid sequencing, transcriptomics, and proteomics, revealing novel insights into its biology and evolution.

The paper identifies coordinated adaptations in neural progenitor cells that drive neocortical downscaling in marmosets compared to humans.

The paper identifies proto-point centromeres in Saccharomycodales yeast, showing they evolved from retrotransposon LTRs, supporting the hypothesis that point centromeres originated from ancestral retrotransposons.

Across 269 functional responses from 45 freshwater fish species, invasive species exceed non-invasive species only when sampled in their native range; introduced populations match non-invasive species.

The paper shows that counter-gradient growth and cuticle integrity maintain apical hook curvature in plants through mechanical and biochemical coordination.

This study investigates how scale insects evolved alternative sex determination systems by analyzing genomic changes across transitions from X-chromosomal sex determination to other systems.

This study shows bacterial Teneurins are accessory proteins with encapsulated toxins, suggesting they were repurposed by metazoans for neuronal communication.

This study evaluates how ancient protein sequences can inform hominid evolution, showing they provide limited resolution compared to DNA data but can still offer insights when combined with better modeling.

The paper measures wing loading in 30 Drosophila species under controlled conditions and finds it lacks phylogenetic signal, unlike body mass and wing area.

This study identifies gene clusters in Pseudomonas protegens PBL3 associated with antimicrobial activity against Burkholderia glumae using comparative genomics.

The paper investigates the evolutionary and functional roles of translation initiation factor 2 (IF2) terminal extensions across bacteria, showing their role in stress response and adaptation.

The paper presents SHE, a phylogeny of eukaryotic proteomes based on structural comparisons, revealing a bipartite model of evolution and a framework for model organism selection.

This study identifies novel Bacilli endophytes from plants with different lifestyles, revealing extensive biosynthetic potential and functional diversity.

The paper examines genomic variation in membrane and cytoplasmic proteins across E. coli and S. cerevisiae, finding higher non-synonymous variation and lower synonymous variation in membrane proteins.

This study quantifies introgression's role in phylogenetic discordance among diploid Oryza species, finding it explains most gene tree-species tree conflict.

This study compares two Exiguobacterium strains from different environments, showing their adaptability and antibiotic resistance traits.

The paper examines the relationship between gonad size, brain size, and reproductive tactics in fish, finding that energetic trade-offs are not consistent across morphs, suggesting correlated selection rather than direct resource allocation.

The paper investigates PSMB8 evolution in holosteans, identifying unique S and K types that may impact MHC class I peptide antigen processing.

This study reveals the structural and functional mechanism of Retron-Eco8, a bacterial defense system that uses a holocomplex to cleave phage DNA and inhibit infection.

The paper compares single-cell transcriptomic data from turtles, mice, and chickens to show divergence in gonadal cell types and genetic programs across sex determination systems.

The paper surveys banana viruses in Malawi, identifies BBTV, BanMMV, and BSV species, and links their prevalence to specific Musa germplasm groups.

The paper investigates the evolutionary history of delayed plumage maturation in manakins using phylogenetic analysis and developmental schedules of plumage patches, revealing multiple origins and sociosexual functions of prolonged maturation.

The paper characterizes CR1-group retrotransposons across chordates, revealing new phylogenetic relationships, older origins, and novel elements, along with horizontal transfer events.