phylogenetics / evolution

One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex

This study uses whole genome re-sequencing to reveal deep divergence within the Amphiprion clarkii species complex, identifying five lineages and challenging the taxonomic status of A. tricinctus.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Evolutionary Diversification of Nitric Oxide Signaling Components Across Metazoa: A Comparative Phylogenomic Analysis

The paper traces the evolutionary history of nitric oxide signaling components across metazoan species using phylogenomic analysis, revealing conserved and divergent patterns in gene family evolution.

Resolving Allopolyploid Origins Within the Genus Clarkia Using a Novel Read-Mapping and Modeling Approach

This paper introduces a method to determine the likely progenitor species and timing of allopolyploid origins in Clarkia using read-mapping and modeling, applied to six allotetraploid species.

An explicit birth-death-reticulation model for studying the diversification of phylogenetic networks

The paper develops a birth-death-reticulation model to analyze phylogenetic networks and applies it to study diversification in ferns, finding evidence that polyploids have lower diversification rates than diploids.

Horizontal gene transfer rivals gene duplication as a source of anti-parasitoid immune innovation in the Drosophilidae

The paper investigates anti-parasitoid immune mechanisms in Drosophilidae, finding that horizontal gene transfer of CdtB is more prevalent than melanotic encapsulation in some clades.

Atypical RanGAP drives nucleocytoplasmic transport in a parasitic Alveolate

A RabGAP-fold protein, TBC9, supplies the missing RanGAP activity in Toxoplasma; its acidic C-terminal motif promotes Ran binding and marks TBC9 orthologs across non-ciliate alveolates.

Structural and Stereochemical Elucidation of Cyanochelin C, a Siderophore Associated with Novel Class of Cyanobacterial Acyl Hydrolases

Cyanochelin C, a non-acylated peptide siderophore from Atacama Desert Myxacorys chilensis, was fully stereochemically resolved; its gene cluster carries CcsQ, a putative deacylase from a cyanobacteria-specific, siderophore-linked acylase lineage.

Establishment of the grass lignin metabolic network during monocot evolution

This study traces the evolutionary development of the grass lignin metabolic network through phylogenomics and biochemical analyses across multiple monocot species.

Karyotypic evolution in a diverse primate clade and the role of chromosomal fissions as barriers to gene flow

This study investigates chromosomal fissions in guenons, finding they may act as barriers to gene flow but with inconsistent evidence across species.

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

This study identifies centromeric repeat turnovers in Arabidopsis species, revealing evolutionary mechanisms and the role of genetic drift and centromere drive in repeat replacement.

Genomic hallmarks of parasexual reproduction in three hybrid groups of the human pathogen Cryptococcus neoformans

This study identifies three hybrid groups in Cryptococcus neoformans with genomic features indicative of parasexual reproduction, including LOH, aneuploidy, and haploid recombinants.

An exact version of Hunt's ancestor-descendant directional random walk model

The paper corrects Hunt's model by using a tridiagonal covariance matrix instead of a diagonal one, improving step size estimation in evolutionary models.

Sequence Generation and Phylogenetic Inference with Generative Flow Networks

This paper introduces AncestorGFN, a method using Generative Flow Networks for alignment-free sequence generation and phylogenetic inference, showing it can recover ancestral relationships and generate novel sequences.

Comparative Genomics of COBRA-like Genes in Theobroma and Herrania Reveals Structural Conservation and Lineage-Specific Variation

The paper performs a comparative genomic analysis of COBL genes in Theobroma and Herrania species, identifying structural conservation and lineage-specific variation.

Comparative phylogenetic analyses of limestone and non-limestone Begonias in Peninsular Malaysia

This study uses molecular phylogenetics to analyze Begonia species in Peninsular Malaysia, finding that speciation into limestone habitats occurred three times and climate, not substrate, was more important for diversification.

Persistent co-infection mediates inter-virus and host-virus gene exchange in marine protists

The paper identifies a new viral order, Skiavirales, in marine protists through long-read sequencing and shows gene exchange between viruses and host genomes.

Skeletal remains of a freshwater jalodontid chondrichthyan from the Upper Triassic Arden Sandstone Formation of Warwickshire, UK.

The paper describes the first articulated chondrichthyan skeletal remains from the Upper Triassic, including cranial and postcranial elements, and provides insights into the paleoenvironment and phylogeny of Keuperodus brodiei.

Real-time accessible phylogenetics for every highly sampled virus

The paper introduces viral_usher, a tool for scalable viral phylogenetics, and demonstrates that replication machinery explains most variance in viral mutation spectra.

Retention of a single Cenp-C gene in different syntenic locations in the montium group of Drosophila species

The paper investigates whether Cenp-C genes duplicated alongside Cid genes in the montium group of Drosophila, finding that most species retain only one Cenp-C gene despite multiple syntenic loci.

Taxonomic and biogeographic insights into Australasian fingerworts in the Lepidozia ulothrix clade

This study uses phylogenetic analysis and molecular species delimitation to refine species boundaries in the Lepidozia ulothrix clade, revealing new subspecies and uncovering overlooked diversity.

Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process

The paper corrects an overcounting issue in the unresolved FBD model for tip-dating and demonstrates its application to empirical datasets.

Genomic and ecological characterization of unclassified tetraploid Echinochloa plants distributed in northern Japan

This study characterizes unclassified tetraploid Echinochloa plants in Japan, revealing their distinct genomic composition and ecological distribution, suggesting a potential new origin for hexaploid E. crus-galli.

A robust phylogenetic framework for ophiostomatoid fungi: orders Ophiostomatales and Microascales (Sordariomycetes, Ascomycota)

This study constructs a comprehensive phylogenetic framework for ophiostomatoid fungi by integrating dense species sampling and ecological data across two orders.

RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics

RAxML-NG 2.0 introduces new features for phylogenetic inference, including automatic model selection and faster branch support metrics, with significant speed improvements.

RNA-guided transcriptional repression by TIGR-Tas systems

TIGRFinder annotated 6,685 TIGR arrays; cryo-EM structures show inactive RuvC domains, and E. coli reporter assays show CsTasR and MbTasA repress transcription in a guide-dependent manner.

Improved ancestral genome reconstruction using a learned gene-content grammar

This paper improves ancestral genome reconstruction by incorporating gene-content grammar, leading to more accurate and consistent reconstructions across different methods.

One Molecule, Multiple Histories: Comparative Phylogenomics of Glutamate Metabolism, Transport and Receptor Families Across 89 Eukaryotic Proteomes

The paper compares the evolutionary histories of glutamate metabolism, transport, and receptor families across 89 eukaryotic proteomes using phylogenomic methods.

A novel RRM activity orchestrates ribosome homeostasis

40S subunit binding to a previously unrecognised RRM in LARP1 activates its TOP-binding HEAT repeats, licensing repression of ribosomal protein mRNA translation in human cells.

When Metabolism Became Messaging: The Stepwise Evolution of the GABAergic Signaling System

This study reconstructs the evolutionary origin of the GABAergic signaling system across 53 metazoan species, revealing a stepwise assembly from metabolic components into a synaptic inhibitory system.