phylogenetics / evolution

Identification of a novel and divergent reptarenavirus in an Amazon coral snake (Micrurus spixii )

The paper identifies a novel reptarenavirus, ACSV-1, from Amazon coral snake RNA-seq data, showing high divergence from known reptarenaviruses.

Surveillance and molecular characterization of banana viruses and their association with Musa germplasm in Malawi.

The paper surveys banana viruses in Malawi, identifies BBTV, BanMMV, and BSV species, and links their prevalence to specific Musa germplasm groups.

Multiple Protein Structure Alignment at Scale with FoldMason

FoldMason uses Foldseek's 3Di+AA alphabet for progressive multiple structure alignment, beating structure aligners' LDDT on AlphaFold DB clusters at near sequence-aligner speed, scaling to 100,000 structures.

GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomics

GLADE infers gene gains, losses, and duplications across species and reconstructs ancestral genomes, showing higher accuracy than existing methods in mammalian datasets.

Phylogeographic clustering of Salmonella enterica serovar Mississippi in the Southeastern United States indicates regional transmission pathways

This study identifies phylogeographic clustering of Salmonella enterica serovar Mississippi in the Southeastern USA, revealing regional transmission patterns through genomic and geographic analysis.

Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data

This paper develops a method to analyze hybrid and polyploid evolutionary relationships using phylogenetic placement of paralogs from target enrichment data, showing its ability to detect hybridization and polyploidization events.

Global phylogeography of Amrasca biguttula (Hemiptera: Cicadellidae) across eight countries reveals a single-haplotype incursion into the United States beyond its putative native range

The paper analyzes genetic diversity of Amrasca biguttula across multiple regions to determine its native and invaded ranges and identify introduction patterns.

Structural and Evolutionary Divergence of the RAG1/1L N-Terminal Zinc-Finger Domain

The paper determines the structure of the RAG1 N-terminal zinc-finger domain using NMR spectroscopy and identifies its evolutionary relationship with Chapaev transposases.

Exploring the Space of Tumor Phylogenies Consistent with Single-Cell Whole-Genome Sequencing Data

SCOPE explores the space of tumor phylogenies consistent with scWGS data, showing multiple phylogenies are possible and highlighting how data quality and evolutionary constraints affect uncertainty.

Detection of a novel parahenipavirus from northern short-tailed shrews (Blarina brevicauda )

This study identifies a novel parahenipavirus, BbV, from northern short-tailed shrews using RNA-seq data and demonstrates its kidney tropism.

How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics

The paper uses phylogenomic analysis to study reticulate evolution in the Malvatheca clade, finding evidence of ancient hybridization and polyploidy affecting subfamilial classification.

Phylogenomics and biogeography of the parrot genus Pyrrhura with implications for systematics and conservation

This study uses whole-genome and mitogenome data from Pyrrhura parrots to reconstruct phylogenies, revealing mito-nuclear discordance, captive lineages, and historical colonization events.

Comparative genomics and phylogenomics of the Mustelinae lineage (Mustelidae, Carnivora)

This study presents the first comprehensive comparative and phylogenomic analysis of the Mustelinae lineage, revealing genome size variation, chromosomal evolution, and demographic responses to climate cycles across ten species.

LoFi drafts to map to: 4 haplotype-resolved Cannabis genomes enable characterization of large structural variants

The paper presents four haplotype-resolved Cannabis genomes using Oxford Nanopore reads and Hi-C scaffolding, showing comparable contiguity to HiFi assemblies and enabling phylogenetic and pan-NLRome analysis.

Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

This study presents a gap-free, phased genome assembly of tobacco, revealing subgenomic diversification of centromeres after allopolyploidization.

FastSpeciesTree: Fast and Scalable Species tree Inference

FastSpeciesTree rapidly and accurately infers species trees from large genomic datasets, outperforming existing methods in speed and scalability.

Genomic Characterization of a Severe West Nile Virus Transmission Season using a Single Reaction Amplicon Sequencing Approach

The paper validates a single reaction amplicon sequencing approach for generating high-quality WNV genomes and characterizes transmission dynamics during a 2023 outbreak in Nebraska.

Population genomics reveals an ancient origin of heartworms in canids

Whole-genome sequencing of 127 adult Dirofilaria immitis from four continents reveals continental population structure predating dog domestication, an Asian source for Australian worms, and recent Europe-Central America spread.

Mitochondrial DNA variation of the striped hyena (Hyaena hyaena) in Algeria and further insights into the species' evolutionary history

The paper analyzes mitochondrial DNA variation in Algerian striped hyenas and other regions to infer the species' evolutionary history and demographic patterns.

High gene flow in Atlantic vent shrimp species with multiple ridge colonizations by ecotypic lineages with contrasting symbioses

This study uses ddRAD sequencing to analyze genetic differentiation in Atlantic Rimicaris shrimp species, revealing recent population separation and secondary contacts, and synonymizing two species as one due to morphological plasticity.

Set to its place: first DNA data on freshwater tardigrades of Sakhalin (Far East Russia) shed light on the phylogenetic position of Mixibius (Eutardigrada: Hypsibioidea)

The paper presents the first DNA data on freshwater tardigrades from Sakhalin, revealing the phylogenetic position of Mixibius and transferring two species to a new genus.

Strategies for resolving cellular phylogenies from sequential lineage tracing data

This paper models a sequentially-edited lineage tracing system and identifies parameter regimes where distance-based methods can accurately reconstruct cellular phylogenies.

Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences: a case study of Niphargus amphipods

The paper presents mitogenome sequences of Niphargus amphipods using nanopore sequencing combined with Illumina polishing, achieving high accuracy and resolving phylogenetic relationships.

Systems acclimation to osmotic stress in zygnematophyte cells

Multi-omic profiling of unicellular Mesotaenium and filamentous Zygnema under osmotic and salt stress reveals a conserved protein and cell-wall remodeling chassis driving acclimation in land plants' closest algal relatives.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Rehabilitating the benefits of gene tree correction in the presence of incomplete lineage sorting

The paper challenges the claim that gene tree correction methods cause overfitting and shows they can still provide benefits despite incomplete lineage sorting.

Polymerase mutations underlie early adaptation of H5N1 influenza virus to dairy cattle and other mammals.

Cattle B3.13 H5N1 polymerase gained PB2 M631L and PA K497R, boosting replication in bovine and human cells via better bovine ANP32A use; later PB2 E627K and D740N add activity.

Late Cretaceous origins for major nightshade lineages from total evidence timetree analysis

This study estimates the origin of nightshade lineages using a total evidence timetree analysis, finding the family originated around 98 Mya, with major splits three times older than previous estimates.

Evolutionary origin and demographic trajectory of tomato spotted wilt virus (Orthotospovirus tomatomaculae)

This study uses Bayesian analysis of TSWV genome sequences to estimate its evolutionary origin, divergence date, and demographic history, finding it originated in South Korea around 1768 CE and expanded with agricultural development.

Dominant contribution of Asgard archaea to eukaryogenesis

Constrained-tree hypothesis testing on 4,290 core eukaryotic protein clusters attributes 50% of likelihood weight to Asgard archaea; Alphaproteobacterial ancestry is largely confined to oxidative phosphorylation and iron-sulfur cluster biogenesis.