comparative / phylogenetic analysis

A Y-specific translocated gsdf copy is a candidate master sex-determining gene in common dab (Limanda limanda)

The paper identifies a Y-specific translocated gsdf copy as the master sex-determining gene in common dab through genome sequencing and comparative analysis.

The tiger shark, Galeocerdo cuvier (Peron & Lesueur, 1822), genome reveals genomic and epigenomic signatures of shark evolution and demographic history

The paper generates the first chromosome-scale genome and methylome for the tiger shark, revealing genomic and epigenomic features of shark evolution and population decline.

Evolutionary dynamics of the pan-centromere architecture in oaks

The paper analyzes centromere evolution in oaks, showing lineage-specific expansion of QuCEN146 satellite drives turnover, while LTR-rich centromeres show low polymorphism due to suppressed recombination.

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

Parallel and lineage-dependent mitonuclear evolution in threespine stickleback

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

Ancient U/V sex chromosomes reveal slow expansion of recombination suppression in Polytrichaceae mosses.

This study analyzes ancient U/V sex chromosomes in Polytrichaceae mosses, showing that recombination suppression has limited SDR expansion and functional degeneration despite their 124 million-year-old origin.

Enzymes can activate and mobilize the cytoplasmic environment across scales

This study shows that enzymes in biomolecular condensates enhance catalytic activity through crowding-induced conformational changes and enable increased mobility despite environmental viscosity.

Convergent genome evolution reveals shared routes to salt tolerance in flowering plants

The paper identifies convergent genomic signatures of salt tolerance in flowering plants by analyzing gene expression and evolutionary patterns across multiple species.

A streamlined and abundant Nitrosopumilus population retains vitamin biosynthesis under high purifying selection in the Baltic Sea

Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses

This study identifies germline-restricted chromosomes in birds as reservoirs for active retroviruses, showing their role in promoting transposition and speciation.

The modular origin and evolutionary expansion of the enigmatic DGF-1 protein family in trypanosomatids

The paper re-annotates and characterizes the DGF-1 gene family in T. cruzi, revealing its modular structure and evolutionary history across trypanosomatids.

Ancient MAX Effector Variants of a Fungal Pathogen Evade Apoplastic Immunity in Apple

This study identifies AvrRvi6 as a fungal effector that evades Rvi6-mediated immunity in apple, revealing ancient virulence diversity in wild Malus species.

Regulatory Subfunctionalization drives OXPHOS evolution in teleosts

The paper investigates how regulatory subfunctionalization of OXPHOS paralogs contributes to ontogenetic plasticity in teleosts following whole genome duplication events.

Quantitative reanalysis of classic pigeon homing experiments rejects a liver-based magnetic compass based on superparamagnetism

This paper reanalyzes classic pigeon homing experiments and rejects a liver-based magnetic compass hypothesis, supporting instead a head-based magnetite-based system.

Widespread male-female expression imbalance of X-linked genes across phrynosomatid lizards

This study finds widespread male-female expression imbalance of X-linked genes in phrynosomatid lizards, with female-biased expression in ancestral X regions and male underexpression in neo-X regions.

Ecological and evolutionary drivers of thermal performance curves across the tree of life

The paper analyzes thermal performance curves across species to identify ecological and evolutionary drivers of thermal adaptation.

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.

A Generic Numbering Scheme for TMEM16 Scramblases

This paper introduces a generic numbering scheme for TMEM16 scramblases to enable comparative analysis across paralogs with different sequence numbering systems.

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.

Molecular arms race in WHO elements, a category of homing genetic elements distinct from inteins and introns

The paper identifies an evolutionary arms race between WHO endonucleases and their target site in the FBA1 gene in Torulaspora yeast, showing rapid sequence diversification to evade cleavage.

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.

From Neuropeptides to Toxins: Illuminating the Origins of Venom Complexity in Cone Snails

The paper identifies how neuropeptide genes in cone snails evolved into toxins through mechanisms like exon shuffling and transposable element-driven recombination, revealing dynamic genome-molecular innovation interactions.

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.

Genomic and eco-geographic features of locally adapted inversions in wild sunflowers

This study identifies locally adaptive chromosomal inversions in wild sunflowers and finds they are more common in sympatric populations and have distinct genomic features.

Comparative transcriptomic analysis of cassava genotypes under extended photoperiodism across flowering stages

The paper compares transcriptomic responses of cassava genotypes under different photoperiod conditions across flowering stages to identify gene expression patterns linked to flowering behavior.