phylogenetics / evolution

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.

Gene tree conflict between genomic and functional partitions impacts phylogenetic inference in Zygophylloideae

This study investigates gene tree conflicts in Zygophylloideae by analyzing chloroplast and nuclear ribosomal data to understand challenges in phylogenetic inference.

Cave-dwelling Planariidae in Croatia exhibit differing levels of cave trait evolution

This study examines cave-dwelling planariids in Croatia, revealing multiple genera, increased diversity, and independent cave colonization events, highlighting convergent evolution of cave traits.

Phylogenomics of Cypriniformes, the most diverse order of freshwater fishes: consensus, challenges and limitations

This study presents the first comprehensive phylogenomic analysis of Cypriniformes, establishing a robust backbone topology and identifying unresolved conflicts in evolutionary relationships.

Insights into goatpox virus and sheeppox virus genomes from pangenome graphs

This study compares the genomic diversity and evolution of goatpox and sheeppox viruses using pangenome graphs, revealing structural variation at inverted terminal repeats as a key driver of diversity.

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.

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

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.

Genomic Diversity, Host Associations, and Tissue Tropism of Hydrangea Ringspot Virus: A Global and Regional Perspective

This study characterizes the genomic diversity, host associations, and tissue tropism of Hydrangea ringspot virus (HdRSV) using transcriptomic data from multiple Hydrangea species and cultivars.

Posterior simulation-based calibration tests of phylogenetic dating methods

This study uses posterior simulation-based calibration to assess phylogenetic dating methods in BEAST 2, finding good calibration but limited precision in node age estimates.

Placing very long branch taxa in the plant tree of life: a case study with Dioscoreales mycoheterotrophs

This study examines how very long branch taxa affect phylogenetic inference in Dioscoreales, finding that they reduce branch support and challenge current classifications.

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.

Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA

Whole-genome SNVs from Nigerian schistosomes show cox1/ITS genotyping wrongly flags human-derived parasites as recent hybrids or zoonotic infections; they are S. haematobium with low livestock introgression.

kamino: fast proteome-wide variant calling for amino acid phylogenomics

Proteome-wide variant calling builds amino acid phylogenomic alignments orders of magnitude faster than a BUSCO marker pipeline, with similar tree signal in three of four test taxa.

Trait evolution with incomplete lineage sorting and gene flow: the Gaussian Coalescent model

The paper introduces the Gaussian Coalescent model to account for incomplete lineage sorting and gene flow in trait evolution, showing improved accuracy over standard models.

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives

The paper examines the evolutionary patterns of AMF-related genes in aquatic and terrestrial plants, finding gene losses or divergence in aquatic lineages but retention in some seagrass species.

Molecular epidemiology of the globally spreading genetic lineage IV of peste des petits ruminants virus

This study analyzes the evolutionary history of peste des petits ruminants virus lineage IV using genome sequences from historical and recent isolates, identifying genetic changes potentially linked to its recent spread in West Africa.

Comparison of the Distribution of Fitness Effects Across Primates

Across 38 catarrhine subspecies, the population-scaled distribution of fitness effects (DFE) tracks effective population size while the unscaled deleterious DFE appears conserved, with no detectable epistasis.

Universal single-copy genes and 16S rDNA present incongruent evolutionary histories in Vibrio

The paper compares the evolutionary histories of universal single-copy genes (USCGs) and 16S rDNA in Vibrio, finding that USCGs produce more resolved and congruent phylogenies than rDNA.

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.

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.

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.

A Refined Phylochronology of the Second Plague Pandemic in Western Eurasia

This paper uses genomic and historical data to refine the timeline and origin of the Second Plague Pandemic in Western Eurasia.

Molecular characterization of chikungunya viruses associated with outbreaks in Kenya from 2017 to 2020

This study characterizes CHIKV outbreaks in Kenya from 2017 to 2020, identifying molecular features and clinical symptoms associated with the virus.

A divergent betacoronavirus with a functional furin cleavage site in South American bats

The paper reports a new bat betacoronavirus from Brazil with a functional furin cleavage site in its spike protein, highlighting its phylogenetic distinctiveness and potential zoonotic risk.

ntSynt-viz: Visualizing synteny patterns across multiple genomes

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

Microsynteny Analysis Clarifies the Early Diversification of Cypriniform Fishes

This paper uses microsynteny analysis to resolve deep phylogenetic relationships in Cypriniform fishes, showing it outperforms sequence-based methods in resolving contentious nodes.

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys)

This study uses phylotranscriptomics to distinguish between gene flow and incomplete lineage sorting in Ophrys orchids, revealing ancient adaptive gene flow events.