phylogenetics / evolution

Expanding the known nucleorhabdovirus world: the final chapter in a trilogy exploring the hidden diversity of plant-associated rhabdoviruses

This study identifies 47 novel nucleorhabdoviruses from metatranscriptomics data, expanding their known host range and phylogenetic diversity.

Lower Bounds on the Sample Complexity of Species Tree Estimation when Substitution Rates Vary Across Loci

Chromosome-level genome assembly for Sichuan taimen (hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage

The paper presents the first chromosome-level genome assembly for Sichuan taimen, revealing high tandem repeat proportions and population shrinkage.

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans

This study presents chromosome-level genomes for sloths and anteaters, revealing retrocopy formation and domestication as key drivers of xenarthran genome evolution and physiological specializations.

The evolution of function in the DNA binding domain of the CRP/FNR family

The paper analyzes the evolutionary divergence of DNA binding and transcriptional activation functions in the CRP/FNR family across prokaryotic genomes.

The phylogenetic position of the Yunxian cranium elucidates the origin of Homo longi and the Denisovans

The study reconstructs the Yunxian 2 cranium and shows it belongs to the Homo longi clade, likely including Denisovans, and is closely related to the H. sapiens clade.

A haplotype-based evolutionary history of barley domestication

All five wild populations fed an early barley founder population in the Fertile Crescent during extended pre-domestication cultivation; about 91% of wild-matched haplotypes split 32 to 8 ka BP.

EMS hypothesis of Macroevolution

The paper proposes the EMS hypothesis, which unifies ecosystem organization rules with metabolic scaling to model macroevolution as a Fibonacci sequence driven by metabolic self-organization.

Construction of a reference genome for Starmerella batistae and annotation of Starmerella species reveal a close evolutionary relationship with Schizosaccharomyces pombe and suggest an alternative pathway for sophorolipid production.

The paper constructs a reference genome for Starmerella batistae and annotates 29 Starmerella species, revealing a close evolutionary relationship with Schizosaccharomyces pombe and suggesting alternative sophorolipid production pathways.

Diagnostics of dated phylogenies in microbial population genetics

The paper introduces diagnostic methods to evaluate the reliability of dated phylogenies in microbial population genetics without model comparison.

Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

The paper analyzes olfactory and gustatory receptor genes and transposable elements in aphid genomes to understand their evolutionary dynamics and role in host adaptation.

Mutation ages and population origins inferred from genomes in structured populations

The paper develops a method to estimate mutation age and population of origin in structured populations using genomic data and applies it to human skin pigmentation SNPs.

Reference genome choice compromises population genetic analyses

This study shows that using a conspecific reference genome improves variant detection and genetic diversity estimates compared to heterospecific references in gray foxes.

Insights into the patterns of molecular evolution and functional diversification of NAC gene family in land plants

This study identifies 5052 NAC genes across 46 land plants, revealing evolutionary patterns and functional divergence, particularly in maize, through phylogenetic and synteny analyses.

Tracing the evolutionary origins of human voltage-gated K+ channels: where they come from and what we lost along the way

The paper traces the evolutionary origins of human voltage-gated K+ channels, identifying which were present in common ancestors and which were lost, and functionally characterizes the missing channels from other vertebrates.

Phylogeny and gene function integration uncovers multiple convergences in multicellular and terrestrial transitions

The paper integrates phylogenomics and functional annotations to trace gene function evolution across species, revealing convergent adaptations in multicellular and terrestrial transitions.

Evolutionary history and recurrent host adaptation in ancient Salmonella enterica

This study reconstructs the evolutionary history of ancient Salmonella enterica using 53 new genomes, revealing host adaptation events and convergent evolution in pathogenic lineages.

Genome dynamics across the radiation of a mega-diverse genus

The paper analyzes genome dynamics in Begonia species to link repetitive element expansion with speciation and genetic isolation across different radiations.

Viro3D: a comprehensive database of virus protein structure predictions

Viro3D predicts and curates protein structures for 4,400 viruses, expanding structural coverage 30-fold and enabling functional and evolutionary analysis of viral proteins.

A plant-centric investigation of Class B Flavin-dependent Monooxygenase evolution and structural diversity

This study investigates the evolution and structural diversity of Class B Flavin-dependent Monooxygenases (FMOs) in plants, identifying eight families and refining conserved motifs.

Longitudinal Phylogenetic Inference of Copy Number Alterations and Single Nucleotide Variants from Single-Cell Sequencing

LoPhy reconstructs the joint evolution of SNVs and CNAs from longitudinal single-cell data, revealing their roles in AML progression and therapy resistance.

A comparison of two universal angiosperm bait sets and the phylogenomics of Alismatales

The paper compares two universal angiosperm bait sets, finding OzBaits v2 recovers more genes and provides higher phylogenetic utility than Angiosperms353 for the Alismatales order.

Chlorophyllide a oxygenase (CAO) gene duplication across the Viridiplantae

This study investigates CAO gene duplication across Viridiplantae, finding independent duplications in land plants and a conserved degron sequence in embryophytes.

The role of peripheral regions in shaping the phylogeography of the Bear s ear complex across the Alps

The paper investigates the genetic structure of the Primula auricula complex across the Alps, highlighting the role of peripheral regions in shaping its phylogeography.

Generative design of novel bacteriophages with genome language models

Fine-tuned Evo 1 and Evo 2 genome language models designed complete ΦX174-like phage genomes; 16 of 285 assembled designs were viable, and some outperformed ΦX174 in competition.

Repeated climate-driven dispersal and speciation in peripheral populations of Pleistocene mastodons

This study analyzes mitochondrial genomes of mastodons to show repeated dispersal and speciation in peripheral populations across North America during the Pleistocene.

Genome assembly and annotations of a Cyprinidae fish, Sinibrama wui

This study presents a high-quality chromosome-level genome assembly of Sinibrama wui and identifies expanded gene families related to lipid metabolism and nervous system.

Phylogenomic timetree-calibrated speciation clocks for Caenorhabditis nematodes reveal slow but disproportionate accumulation of post-zygotic reproductive isolation

The paper estimates speciation clocks in Caenorhabditis nematodes, finding post-zygotic reproductive isolation accumulates faster than pre-zygotic isolation.

Large-scale genome analyses provide insights into Hymenoptera evolution

This study uses large-scale comparative genomics to analyze 131 Hymenoptera species, revealing genomic patterns and innovations linked to key evolutionary traits.

Reciprocal exchange obscures phylogenetic patterns of introgression

The paper identifies reciprocal introgression as a hidden process that distorts phylogenetic patterns and introgression detection, showing it produces conflicting signals that obscure true introgression events.