comparative / phylogenetic analysis

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

This study investigates the evolutionary distribution of chemosensory systems in Actinomycetota, finding lineage-specific retention and expansion, with TCS playing a dominant role in regulatory networks.

Tracing the Evolutionary Histories of Human Cholinergic Proteins Across Eukaryotes: A Comparative Phylogenomic Study

This study traces the evolutionary histories of human cholinergic proteins across eukaryotes using phylogenomic analysis, revealing heterogeneous patterns and phylogenetic relationships.

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.

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.

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.

Poxvirus gene repertoires are shaped by expansion-biased birth-and-death dynamics and genome architectural constraints

This study analyzes poxvirus gene repertoires and finds that they evolve through expansion-biased birth-and-death dynamics and genome architectural constraints.

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

The paper presents a high-quality genome assembly of the sea stickleback and reveals chromosomal fusions and fissions that reshape understanding of karyotype evolution in sticklebacks.

Emended description of the genus Henriciella: morphological and phylogenetic analysis identifies two subgenera with different reproductive strategies

The paper reclassifies Henriciella into two subgenera based on reproductive strategies and phylogenetic analysis, correcting previous classifications.

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.

From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum

This study investigates the evolution of distyly and stigma-height dimorphism in Jasminum using phylogenetic analysis and morphology, finding that distyly originated in the common ancestor and SHD arose multiple times through reversion.

Life finds a way: Integrative phylogenomics resolves an overlooked bivalve order with chromosome fusion and mitochondrial translational-code evolution

This paper integrates phylogenomic, genomic, transcriptomic, proteomic, and morphological data to resolve the systematics of the APPD lineage, elevating it to a new order and identifying unique genomic and mitochondrial features.

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

This study compares TAD conservation and evolution across five cereal species, finding high conservation of TAD boundaries and their role in genome stability during evolution.

Ancestral phototrophic Rhizobiaceae evolved in association with algae, then plants

This study reveals that ancestral Rhizobiaceae bacteria evolved photosynthesis in association with algae and plants, later losing it in some lineages that became plant symbionts or pathogens.

No signal of a super-archaic origin of the Denisovan AMBN gene, a comment on the protein affinity of Homo erectus and Denisovan enamel proteins.

The paper challenges a model proposing Denisovan AMBN introgression from Homo erectus by showing no signal of super-archaic origin in late Denisovans.

Found in translation: CCA-adding enzymes reveal bacterialization of Asgard archaea prior to eukaryogenesis

The paper identifies CCA2 enzymes in Asgard archaea and Heimdallarchaeia, challenging the evolutionary separation between archaeal and eukaryotic CCA-adding enzymes and supporting bacterial gene integration prior to eukaryogenesis.

The free-living wellspring of symbiotic nitrogen fixation in Bradyrhizobium

This paper identifies free-living Bradyrhizobium as the ancestral state of nitrogen fixation, showing that symbiotic nitrogen fixation evolved multiple times independently from free-living ancestors.

338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders

From 338 beetle genomes, eight ancestral linkage groups were inferred; rearrangement rates vary widely, peaking in major radiations, and the X chromosome dates to Holometabola's ancestor.

Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera

This study presents the first plastome-scale phylogenomic analysis of the tribe Spermacoceae, clarifying generic boundaries and supporting taxonomic revisions.

Ecological axes of skull diversification in a massive 1 vertebrate radiation

The paper analyzes skull diversification in eupercarian fishes, showing habitat and trophic ecology independently shape skull shape, with rapid evolution in certain clades and convergence in freshwater lineages.

The Iberian white-oak syngameon as a legacy of introgression in southern Europe

The paper uses RAD-seq to study Iberian white oaks, revealing hybrid swarms and redefining species boundaries through introgression and phylogeography.

Peculiar Pigment Pattern and Population Profile of a Poisonous Pufferfish

This study investigates the phylogenetic origin and pigment patterns of mushifugu, finding it to be a distinct species with evidence of past hybridization with komonfugu.

Global diversity and dispersal routes of the Ostreid herpesvirus type 1 infecting Magallana gigas

This study analyzes 275 OsHV-1 genomes to investigate global diversity and dispersal routes of the virus infecting Pacific oysters.

Explaining the rapid evolution of mammalian meiotic recombination proteins

The paper analyzes evolutionary rates of 100 meiotic recombination proteins across 400 placental mammals, finding that rapid evolution is driven by reduced purifying selection and linked to chromosome pairing proteins in long-lived species.

Resolving the oak tree of life: comparing RADseq and whole genome resequencing methods for oak phylogenetics

The paper compares RADseq and whole genome resequencing methods to resolve oak phylogeny and address uncertainties in divergence times and gene tree discordance.

The Culicinae are Monophyletic and Ancient: A response to Pierce et al. 2025

This paper challenges recent claims that mosquito subfamilies are not monophyletic by presenting evidence supporting two monophyletic subfamilies and an ancient divergence.

The evolution of plant actins

This study investigates the evolutionary diversification of plant actins, finding that actin copy number increases correlate with plant complexity and that functional distinctions are maintained through specific sequence changes.

Convergent genome streamlining accompanies independent miniaturization in the world's smallest fishes

This study investigates the genomic correlates of miniaturization in Cypriniformes, finding convergent genome streamlining in progenetic miniatures but not proportioned dwarfs.

Native Korean wild mice (Mus musculus): molecular phylogeny and morphometrics

The paper analyzes genetic and morphological data of Korean wild mice to determine their phylogenetic relationships and taxonomic status within the Mus musculus subspecies.

Coding sequence clustering universally predicts fine- and coarse-scale chromatin compartment landscapes

The paper identifies coding DNA sequence density as a universal predictor of chromatin compartmentalization across species, revealing its conservation over evolutionary time.