phylogenetics / evolution

Integrative identification of Tetratostichococcus sp. CCAH0201 (Trebouxiophyceae, Chlorophyta) from Rhizophora leaves in the Can Gio Mangrove Forest, Vietnam

The paper identifies a microalgal strain from mangrove leaves using molecular markers and phylogenetic analysis, placing it closely related to Tetratostichococcus jenerensis.

Structural and evolutionary insights into FcαμR recognition of polymeric immunoglobulins

This study determines cryo-EM structures of FcR bound to IgM and IgA, revealing its binding mechanism and evolutionary insights into pIg receptor recognition.

Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

This paper presents the first high-quality genome assembly of a cave-dwelling remipede, revealing a repeat-rich genome with extensive gene family turnover and phylogenetic signals.

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

The paper resolves taxonomic confusion in sun corals by combining molecular phylogenetics and genome assemblies, revealing T. coccinea as the cosmopolitan species and T. tagusensis as endemic to the Galapagos.

Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

Characterization of the Preclinical in Vitro and in Vivo Pharmacokinetic Properties of the Cyclic Oligomeric Depsipeptide Ryanodine Receptor 2 Inhibitor ent-Verticilide

This study characterizes the pharmacokinetic properties of ent-verticilide, identifying limited intestinal availability and CYP-mediated metabolism as key factors affecting its oral exposure.

Genomic detection of domoic acid biosynthesis uncovers expanded toxigenic diversity across Pseudo-nitzschia diatoms

The paper identifies genomic features of domoic acid biosynthesis in Pseudo-nitzschia diatoms, revealing expanded toxigenic diversity and environmental expression patterns.

Horizontal transfer of an antimicrobial peptide across insects

The paper identifies horizontal gene transfer of the Drosomycin antimicrobial peptide gene across insect species, suggesting HGT contributes to immune system novelty and defense capabilities.

Phylogenomic screening reveals idsA2 loss conferring nitroimidazole cross-resistance in Mycobacterium tuberculosis

A length- and mutation-load-corrected homoplasy screen of 1,813 MDR-TB genomes flags idsA2; its loss raises pretomanid MIC fourfold, delamanid and ethambutol twofold, via isoprenoid flux redirection.

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

Phenotypic and genomic changes associated with the evolutionary loss of heterostyly in primroses

The paper investigates the genetic and phenotypic changes associated with the loss of heterostyly in Primula boveana, revealing a disrupted CYP gene and developmental shifts leading to autonomous selfing.

Development and pharmacological characterization of a stable HEK293 cell model for the study of human FLT3 signaling and its pharmacological modulation

The paper develops a stable HEK293 cell line expressing FLT3 for pharmacological studies and shows it effectively models FLT3 signaling and response to inhibitors.

DIMPLE: A Tree-Guided Divide-and-Conquer Framework for ILS-Aware Phylogenetic Network Inference on Large-Scale Data

DIMPLE infers phylogenetic networks from large-scale data using a divide-and-conquer approach, achieving accurate merging and improved reticulation recovery over existing methods.

Solving Paleobotany's 200-year problem with fluorescence and artificial intelligence

This paper uses fluorescence and AI to solve paleobotany's 200-year problem by revealing detailed leaf venation in fossils.

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

EZHIP, a PRC2 inhibitor, arose on the placental mammal X chromosome, evolves under positive selection in primates, and duplicated, including a testis-expressed primate paralog, EZHIP2, whose gorilla copy inhibits H3K27me3.

Evolution of multidrug-resistant IncC plasmids in the seventh pandemic Vibrio cholerae O1 El Tor lineage between 1979 and 2024

The paper analyzes IncC plasmids from Vibrio cholerae O1 El Tor isolates between 1979 and 2024, revealing their evolution and antimicrobial resistance gene diversity.

Evolution of histone mRNA 3' end processing machinery in eukaryotes

This study reconstructs the evolution of histone mRNA 3' end processing machinery across eukaryotes, revealing broader conservation of SLBP and related factors than previously thought.

Multipartite mitochondrial genomes and phylogenetic relationships of five newly characterized chewing-louse species of placental mammals (Parvorder Trichodectera)

The paper characterizes mitochondrial genomes of five new chewing-louse species, revealing recombination patterns and phylogenetic relationships among trichodecteran lice.

From promiscuity to specialization: The origin of cholinergic and monoaminergic signaling is pre-bilaterian

This study shows that cholinergic and monoaminergic signaling originated before Bilateria, using a combination of metabolomics, phylogenetics, and single-cell analysis.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Distinct mechanisms of CNV formation at the human 15q13.3 locus

The paper identifies distinct mechanisms of CNV formation at the human 15q13.3 locus, showing that non-allelic homologous recombination is the primary mechanism, influenced by inversion polymorphisms and population-specific susceptibility.

Origin and evolution of acrocentric chromosomes in human and great apes

The paper identifies evolutionary processes in acrocentric chromosomes of great apes, including repeat enrichment, inversion, and gene family amplification, with implications for human genomic instability.

The olfactory ventricle: an overlooked and evolutionarily conserved feature of the mammalian brain

The paper identifies the olfactory ventricle as an ancestral and conserved feature in mammals, showing its persistence into adulthood and conserved cellular organization across species.

Corallimorpharian genome supports the monophyly of Scleractinia and illuminates the cellular evolution of coral calcification

This study presents a corallimorpharian genome and single-cell transcriptomes to show that coral calcification evolved through a derived calicoblast cell state and genomic innovations.

Cldn18 evolution reveals pleiotropic constraints in vertebrate stomach loss

The paper analyzes the evolution of CLDN18 across vertebrates, showing gene loss, alternative splicing, and regulatory changes linked to stomach loss and pleiotropy.

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.

Evolutionary diversification of the biological screw joint in weevils

The paper examines the evolutionary diversification of screw joints in weevils, showing continuous variation and modular evolution rather than discrete types.

Reticulate Evolution and Plastome Restructuring Shape Asian Passiflora Diversification

This study investigates the evolutionary relationships and plastome evolution of Asian Passiflora species, revealing reticulate evolution, incomplete lineage sorting, and population differentiation.

The chromosome level genome of the Blueberry Stem Gall Wasp, Hemadas nubilipennis (Hymenoptera: Ormyridae) on lowbush blueberry (Vaccinium angustifolium) reveals repeat-driven expansion

The paper presents the first chromosome-level genome of the blueberry stem gall wasp, revealing repeat-driven genome expansion and insights into symbiont interactions and host adaptation.