phylogenetics / evolution

Loss of replication and transcription systems accompanying transition to nucleus-dependent replication in Ariadnavirales, a proposed new order in nucleocytoviricot class Megaviricetes

The paper identifies a new viral order, Ariadnavirales, based on genomic analysis of SmDNAV, which lacks key replication and transcription genes, indicating host-dependent replication.

In genomes we trust: assessing genomic reliability within the family Nectriaceae

The paper evaluates genomic resources across the Nectriaceae family, identifying metadata gaps, assembly quality issues, and phylogenomic inconsistencies.

Why This Code? A Constrained Mapping Framework for the Evolutionary Stability of the Canonical Genetic Code

The paper evaluates the evolutionary stability of the canonical genetic code by analyzing constrained mappings and shows it ranks among the top candidates under specific objectives.

Quartet-based species tree methods enable fast and consistent tree of blobs reconstruction under network multispecies coalescent

The paper introduces TOB-QMC, a method for scalable and accurate tree of blobs reconstruction under network multispecies coalescent, improving upon TINNiK in both speed and accuracy.

FigTreeKit: A Python toolkit for programmatic FigTree styling, taxonomy-aware clade auditing, and phylogenetic tree rendering

FigTreeKit provides a Python toolkit for programmatically styling and auditing phylogenetic trees, with scalability testing on large bacterial and archaeal datasets.

Asynchronous origins of Yellow-Stripe transporters and Nicotianamine Synthase underlie the evolution of plant Strategy-II iron uptake

The paper traces the evolutionary origins of YSL transporters and NAS in plants, showing they arose asynchronously and independently, supporting the exaptation of pre-existing transport mechanisms for Strategy-II iron uptake.

Extended genomic regions flanking ultraconserved elements allow efficient species identification and intraspecific diversity assessment in coral

This paper presents a method using ultraconserved elements to identify coral species and assess intraspecific diversity efficiently.

The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

Mite Genome Miniaturization: Assembly of the biological control agent Floracarus perrepae reveals dynamic genome evolution in eriophyoid mites

The paper sequenced the genome of the mite Floracarus perrepae, revealing dynamic genome evolution and streamlining in eriophyoid mites, associated with non-genic elements.

ROADIES-XP: GPU Acceleration and Phylogenetic Update Improve Scalability of Species Tree Inference from Raw Genomic Assemblies

ROADIES-XP enables efficient incremental species tree updates from raw genomic assemblies using GPU acceleration, achieving high speedups and maintaining topological accuracy.

The Drosophila Secretome

A tiered catalogue of 5,280 Drosophila genes encoding putative secreted proteins (1,802 high-confidence) with a web portal; these genes are less conserved, more tissue-restricted and disproportionately down-regulated with age.

Evolution of transposons as controlling elements

This study shows that transposases can act as transcriptional regulators and evolved into transcription factors through loss of catalytic activity.

Genomic evidence of early-diverging domesticated lineages in Norwegian farmhouse yeast

The paper sequenced Norwegian farmhouse yeasts to study their genetic diversity and domestication history, finding they form an early diverging lineage with distinct phylogenetic and population genetic characteristics.

The Little Transib That Could -- and Could Not: Contrasting Invasion Outcomes within a Novel DDE DNA Transposon Lineage

The paper identifies and characterizes two related Transib elements in Drosophila, showing contrasting invasion patterns and genomic impacts.

Domain-combination based pan-genomic Tree of Life

This paper reconstructs a pan-genomic Tree of Life using protein domain combinations, revealing evolutionary relationships and processes across Bacteria, Archaea, and Eukaryota.

Computing coalescence rates for complex demographies and sampling configurations

The paper introduces demestats, a software library to compute coalescence rates for demographic models, showing improved accuracy in inferring recent population history from genetic data.

Repeated cases of allopatric divergence and secondary contact in cattail (Typha) speciation

This study uses genome-wide data to show that Typha species diverged allopatrically without gene flow, followed by secondary contact, with little evidence of ecological speciation driving differentiation.

Genomic Characterization of the Endangered Medicinal Polypore Agarikon (Laricifomes officinalis syn. Fomitopsis officinalis)

This study presents the first annotated nuclear and mitochondrial genomes of Agarikon, revealing biosynthetic pathways and phylogenetic placement, and provides a foundation for future research on its medicinal properties.

Differential Effects of Incomplete Lineage Sorting and Gene Tree Estimation Error on Gene Tree Distributions and Species Tree Inference

This study compares the effects of incomplete lineage sorting and gene tree estimation error on species tree inference using simulated and real datasets.

Phylogenomics supports the reinstatement of Sinia (Ochnaceae)

The paper uses phylogenomic data to reinstate Sinia as a distinct genus within Ochnaceae, resolving taxonomic uncertainty by showing its close relationship to Indosinia and distant relationship to Sauvagesia.

Peptonella octanoica gen. nov., sp. nov., a new medium-chain carboxylate-producing bacterium, and the reclassification of Eubacterium pyruvativorans as Peptonella pyruvativorans comb. nov.

The paper describes a new bacterial species, Peptonella octanoica, and reclassifies Eubacterium pyruvativorans into this genus based on phylogenetic and phenotypic analysis.

Subgenome-Level Phylogeny Reveals an Allopolyploid Origin of Chloranthales from Ancestral Monocot and Eudicot Lineages

The paper investigates the origin of Chloranthales by analyzing subgenome phylogenies and finds evidence of an ancient allopolyploidization event involving monocot and eudicot lineages.

The diverse functions of viral microproteins

A >50,000-element viral smORF library screened by growth, MHC-I, ER stress, Perturb-seq and mass spectrometry yields >2,000 active microproteins and shows EBV BNLF2b inhibits PKA by mimicry.

Modelling a rapid radiation of crown-group placentals

This paper models the rapid radiation of crown-group placentals using the Covariant Evolutionary Tempo (CET) model, showing elevated diversification and molecular evolution rates post-K-Pg boundary.

Integrative morphology and phylogenetics of Arcellidae (Amoebozoa:Arcellinida), with redescription of Arcella leidyana and Arcella artocrea and description of Galeripora purdoni sp. nov.

The paper integrates morphology and phylogenetics to redescribe and classify Arcellidae species, revealing hidden diversity and a new species.

DICAROS: Diffeomorphic Ancestral Shape Reconstruction on Phylogenies

DICAROS improves ancestral shape reconstruction by modeling shape correlations using diffeomorphic dynamics, outperforming traditional methods on non-symmetric trees.

Multidimensional host-associated diversification in natural Festuca_Epichloe festucae symbioses across the Iberian Peninsula

The paper characterizes host-associated diversification in Epichloe festucae symbioses across Iberian Festuca species, revealing host-driven genetic and chemical differentiation.

Serial acquisition of virulence determinants and aminoglycoside resistance by the emerging Streptococcus agalactiae sequence type 1010 lineage

This paper analyzes the genomic characteristics of Streptococcus agalactiae ST1010 strains, showing they share virulence genes with CC17 and have a subclade with high-level gentamicin resistance.

From life history to proteome via mutagenesis: an ecological footprint in genome evolution

The paper examines how mutational pressures from life history and ecology shape mitochondrial genome and proteome evolution by comparing long-lived termites with short-lived cockroaches.

Cytonuclear Conflict and Reticulate Evolution in the Morelloid Clade (Solanum, Solanaceae): Insights from Genome Skimming and Network Phylogenomics

The paper investigates reticulate evolution in the Morelloid clade using genome skimming and phylogenomic methods, revealing widespread chloroplast capture events.