comparative / phylogenetic analysis

The ecology of carbon sequestration in coastal upwelling ecosystems

This paper reviews carbon sequestration mechanisms in coastal upwelling ecosystems and suggests a model to predict climate change impacts on carbon dioxide uptake.

Identification of a Highly Expressed Gene Cluster Likely Coding for Benzene Activation Enzymes in a Methanogenic Enrichment Culture

The paper identifies two gene clusters in a methanogenic enrichment culture that likely code for benzene activation enzymes, providing genetic and proteomic evidence for anaerobic benzene degradation mechanisms.

Genomic Analysis of Human-infecting Leptospira borgpetersenii isolates in Sri Lanka expanded PF07598 gene family repertoire, less overall genome reduction than bovine isolates

This paper reports the complete genomes of seven human-infecting Leptospira borgpetersenii isolates from Sri Lanka, showing less genome decay and expanded PF07598 gene family compared to bovine isolates.

Native Korean wild mice (Mus musculus): molecular phylogeny and morphometrics

The paper analyzes genetic and morphological data of Korean wild mice to determine their phylogenetic relationships and taxonomic status within the Mus musculus subspecies.

Transposons Triggered Dynamic Evolution of MKK3 Gene, a Key Regulator for Seed Dormancy in Barley

This study identifies transposon-driven evolution of the MKK3 gene in barley, revealing three independent origins of nondormant alleles and their impact on seed dormancy.

Tracing the vertebrate selenoproteome evolution reveals expansions in ray-finned fishes and convergent depletions in tetrapods

A Fragment Screen Identifies Acrylamide Covalent Inhibitors of the TEAD/YAP Protein-Protein Interaction

The paper identifies acrylamide fragments that covalently inhibit TEAD4-YAP interaction by reacting with a conserved cysteine in the TEAD palmitate pocket.

Reshaping Organellar Translation and tRNA Metabolism: The Consequences of Photosynthesis Loss and Massive Horizontal Gene Transfer

This study investigates how photosynthesis loss and horizontal gene transfer reshape organellar translation and tRNA metabolism in holoparasitic plants.

Negative allometry of egg size among 29 species of drosophilid flies

The paper examines egg size and shape evolution in 29 drosophilid species, finding negative allometry between egg size and adult body size and moderate phylogenetic signal.

Origin of Eukaryotic Plasmalogen Biosynthesis by Horizontal Gene Transfer from Myxobacteria

The paper traces the origin of eukaryotic plasmalogen biosynthesis to horizontal gene transfer from Myxobacteria, revealing evolutionary divergence in plasmalogen synthesis across eukaryotic lineages.

Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity

The paper shows plant-associated Sphingomonas use two flagellar FliC variants to balance swimming and immune evasion by partitioning motility and colonization functions.

FLASH Radiotherapy is faster than a heartbeat: A compartmental model to illustrate the interplay between tissue oxygen perfusion and ultra-high dose rate effects.

The paper develops a compartmental model to simulate oxygen perfusion and its interaction with ultra-high dose rate radiation in FLASH Radiotherapy, showing a sigmoidal dose-rate-response curve for lipid peroxidation.

Drowning in a sandy ocean: Epiarenic growth of Tillandsia in the hyperarid Atacama Desert

This study examines how Tillandsia landbeckii in the Atacama Desert interacts with sand and wind to maintain vegetation, showing that sand transport and vegetation structure are interdependent.

Integrated epidemiological and genomic analysis of some respiratory Bovine Coronavirus isolates reveals circulation of GIIb strains and ongoing viral evolution in U.S. Cattle (2020-2025)

The paper analyzes respiratory BCoV isolates from U.S. cattle 2020-2025, identifying GIIb strains and amino acid substitutions suggesting ongoing viral evolution.

Discovery of new marine species Stentor hondawara and its whole-genome reveal their unique ecology in comparison with freshwater stentors

This paper describes the discovery of a new marine Stentor species, Stentor hondawara, and reports its whole-genome analysis revealing unique ecological adaptations compared to freshwater Stentor species.

Schistosome esophageal gland factor MEG-8.2 drives host cell lysis and interacts with host immune proteins

The paper identifies MEG-8.2 as a key esophageal gland factor in schistosomes that drives host cell lysis and interacts with host immune proteins to aid immune evasion.

Revision of Archaeosporomycetes with two old and two new fungal orders: Archaeosporales, Geosiphonales, Polonosporales, and Ambisporales

This paper reclassifies the fungal class Archaeosporomycetes into four orders based on phylogenetic and morphological analyses, including the description of two new orders.

Liquid-liquid phase separation of tau regulates client binding via a conformational relay

The paper investigates how tau's liquid-liquid phase separation affects its binding to BRICHOS and tubulin, showing conformational changes regulate these interactions.

Lessons from the equator: a window on the future of vibriosis in a warming Earth

This study compares vibriosis incidence and causative species between equatorial Singapore and temperate United States, finding higher incidence in Singapore with stable rates, while US rates are rising, suggesting ecological impacts of warming oceans.

Divergent mechanics of inner ear morphogenesis are coupled to developmental tempo over vertebrate evolution

The paper examines inner ear morphogenesis across 12 vertebrate species, finding that divergent mechanical processes in tissue expansion are coordinated with developmental tempo to maintain conserved morphology.

Coding sequence clustering universally predicts fine- and coarse-scale chromatin compartment landscapes

The paper identifies coding DNA sequence density as a universal predictor of chromatin compartmentalization across species, revealing its conservation over evolutionary time.

Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors

The paper uses phylogenomic analysis to show that anthropophily in Southeast Asian Anopheles mosquitoes evolved in response to early hominin arrival in Sundaland around 1.8 million years ago.

Aneuploidy, polyploidy, and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans

This study analyzes genomic variation in serial Candida albicans isolates from patients, identifying aneuploidy, polyploidy, and loss of heterozygosity as factors driving antifungal drug tolerance.

Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds

The paper identifies convergent and lineage-specific genomic changes in sugar-feeding birds through genome and transcriptome analyses, revealing adaptive mechanisms in metabolic pathways.

Repeated evolution of supergenes on an ancient social chromosome

This paper identifies a new supergene in desert ants associated with social polymorphism, showing that social chromosomes are ancient and conserved across Hymenoptera.

Territoriality modulates the coevolution of cooperative breeding and female song in songbirds

The paper examines coevolutionary relationships between cooperative breeding, female song, and male song traits in songbirds, finding context-dependent associations influenced by territoriality.

Physical mechanisms of nanoparticle-membrane interactions: A coarse-grained study

This study uses coarse-grained simulations to investigate how nanoparticle properties affect their interaction with cell membranes, identifying regimes that influence cellular uptake.

Genetic Evidence Indicates the Evolutionary Importance of the SARS-CoV-2 ORF9b protein

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.

Genomic Islands as minimal hitchers of conjugative elements

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.

Coarse-grained Martini 3 model of chondroitin sulfate A

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.