comparative / phylogenetic analysis

Tracing the Evolutionary Histories of Human Cholinergic Proteins Across Eukaryotes: A Comparative Phylogenomic Study

This study traces the evolutionary histories of human cholinergic proteins across eukaryotes using phylogenomic analysis, revealing heterogeneous patterns and phylogenetic relationships.

Genomic characterization and evolutionary path of human satellite 1B in primates highlight a dynamic relationship with transposable elements

This study characterizes HSat1B across primates, showing its evolutionary origin linked to transposable elements and lineage-specific expansion in Homininae.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

Genome evolution and glycosyltransferase diversification shape asperosaponin biosynthesis in Dipsacus asperoides

The paper reconstructs the asperosaponin biosynthesis pathway in Dipsacus asperoides by integrating genomics, transcriptomics, and biochemical analyses, revealing gene family diversification and glycosylation order.

1D model simulations suggest biofilms can suppress cathodic H2 bubble formation

The paper uses computational modeling to show cathodic biofilms can reduce H2 loss and suppress bubble formation in microbial electrosynthesis systems.

Parallel and lineage-dependent mitonuclear evolution in threespine stickleback

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

A Deep Phylogenetic Split Between Short- and Long-Wavelength-Tuned Visual Systems in Surgeonfishes (Acanthuridae)

This study investigates visual plasticity in surgeonfishes by analyzing opsin gene expression across 22 species, revealing a deep phylogenetic split in visual systems that predates ecological diversification.

Ancient U/V sex chromosomes reveal slow expansion of recombination suppression in Polytrichaceae mosses.

This study analyzes ancient U/V sex chromosomes in Polytrichaceae mosses, showing that recombination suppression has limited SDR expansion and functional degeneration despite their 124 million-year-old origin.

Evolution Shapes Cortical Interneuron Migration

This study compares cortical interneuron migration across species, finding that human interneurons migrate slower and more dispersedly due to CCP1-dependent changes in microtubule dynamics.

Comparative genomics of canonical antifungal dsRNA target genes across fungal plant pathogens: conserved siRNA-length windows define the scope for broad-spectrum spray-induced gene silencing

This study evaluates the conservation of antifungal dsRNA target genes across fungal plant pathogens at siRNA-length resolution, finding limited conservation beyond closely related species.

Enzymes can activate and mobilize the cytoplasmic environment across scales

This study shows that enzymes in biomolecular condensates enhance catalytic activity through crowding-induced conformational changes and enable increased mobility despite environmental viscosity.

Genetic and environmental sources of behavioral individuality: a test of the standard model

The paper tests the standard model of behavioral individuality by comparing among-individual variation in inbred and outbred crickets, finding greater variance in outbred lines.

Hemodynamic Analysis of a Repaired Ascending Aorta with Preserved Aortic Root

The paper evaluates the hemodynamic impact of a novel STJ reconstruction in ATAA repair using computational modeling, showing restored sinus vortices post-surgery.

Comparative genomics reveals modular virulence repertoires and extensive horizontal gene transfer in Vibrio species associated with white syndrome of Porites cylindrica

The paper compares Vibrio genomes associated with coral white syndrome to identify virulence modules and horizontal gene transfer patterns.

Diversification and coexistence amid widespread and persistent gene flow in Andean trees

The paper investigates gene flow and species boundaries in Andean Prunus, finding extensive ancient introgression and recent admixture despite Miocene divergence.

Convergent genome evolution reveals shared routes to salt tolerance in flowering plants

The paper identifies convergent genomic signatures of salt tolerance in flowering plants by analyzing gene expression and evolutionary patterns across multiple species.

A conserved NLR activation switch governs global transcriptional control of antibiotic biosynthesis in Streptomyces

This study identifies a conserved NLR activation switch in bacterial AfsR that regulates antibiotic biosynthesis and reveals its evolutionary conservation across Actinomycetota.

SpiE is a distinct gut microbial 4-cholesten-3-one 5β-reductase that acts with SpiR to convert cholesterol to coprostanol

The paper identifies SpiE as a gut microbial enzyme that, along with SpiR, converts cholesterol to coprostanol, and shows its correlation with stool coprostanol levels and antibiotic impact.

Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus

This study identifies novel antiviral defense systems in Streptococcus thermophilus by analyzing genomic islands, revealing previously uncharacterized systems and highlighting their role as reservoirs of bacterial immunity.

A streamlined and abundant Nitrosopumilus population retains vitamin biosynthesis under high purifying selection in the Baltic Sea

A dichotomous family of Cache domain proteins evolved through c-type heme acquisition

Cache sensor domains of DUF3365/Tll0287 family bind covalent c-type heme through a CXXCH insertion; a signaling member behaves like an NO sensor, a stand-alone one like a redox protein.

Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses

This study identifies germline-restricted chromosomes in birds as reservoirs for active retroviruses, showing their role in promoting transposition and speciation.

NLR immune receptors can exhibit tissue-specific expression patterns across legume species

This study identifies tissue-specific NLR expression patterns across legume species using phylogenomics and transcriptomics.

The modular origin and evolutionary expansion of the enigmatic DGF-1 protein family in trypanosomatids

The paper re-annotates and characterizes the DGF-1 gene family in T. cruzi, revealing its modular structure and evolutionary history across trypanosomatids.

Nomenclature updates to the hemagglutinin gene clade designations resulting from the continued evolution of high pathogenicity avian influenza A(H5) virus clades 2.3.2.1c and 2.3.4.4

The paper updates clade designations for H5N1 avian influenza viruses based on phylogenetic analysis of HA gene sequences from multiple regions.

Comparative analysis of adhesin-like proteins from Methanobacteriales species

The paper analyzes adhesin-like proteins (ALPs) in Methanobacteriales species to understand their role in gut microbiota interactions and species-specific adaptations.

Unearthing a fungal giant: Dianjunaceae fam. nov., a novel Paleocene lineage of Xylariales harbouring Dianjunus rex gen. et sp. nov.

The paper describes a new fungal family and species, Dianjunaceae and Dianjunus rex, discovered in Yunnan, China, with large stromata and a Paleocene origin.

PgaR is a positive regulator of the pgaABCD biosynthetic operon in Klebsiella pneumoniae

This paper identifies PgaR as a positive regulator of the pgaABCD operon in Klebsiella pneumoniae, showing that genetic variation in this region leads to loss or hyper-production of PNAG, with distinct fitness consequences.

Comparative genomics of Sympodiorosea identifies genome evolution mediated through selective pressure on the metabolic gene repertoire

This study uses comparative genomics to analyze Sympodiorosea fungi, revealing that selective pressures on metabolic genes drive genome evolution and functional diversification in ant-associated fungi.