comparative / phylogenetic analysis

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism that supports co-existence of diverse lineages

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

Human monogamy in mammalian context

The paper compares sibling type distributions across human societies and nonhuman mammals to assess monogamy's role in human mating systems.

Coexistence of two divergent TprA/PhrA cell-cell communication systems in Streptococcus mitis coordinate bacteriocin production, competence, oxidative stress responses, and interspecies competition with S. pneumoniae

Distinctive viral genome signatures are linked to repeated mammalian spillovers of H5N1 in North America

The paper identifies distinctive H5N1 viral genome signatures linked to repeated spillovers into U.S. dairy cattle, highlighting genetic diversity and geographic origins.

Centromeres in budding yeasts are conserved in chromosomal location but not in structure.

The paper examines centromere structure and location across nine yeast species, finding conserved chromosomal positions but diverse structures, suggesting in situ structural changes.

Evolution of Insulin, Insulin-like Growth Factor, and Their Cognate Receptors in Vertebrates, Invertebrates, and Viruses

This study analyzes the evolutionary origins and molecular diversification of insulin, IGFs, and their receptors across vertebrates, invertebrates, and viruses, revealing lineage-specific adaptations and conserved features.

Phase Separation Contributes to Pathogenicity for Nonsense Mediated Decay-Escaping Variant Alleles

This study identifies NMD-escape variants as a distinct class of disease-causing mutations, showing that altered C-terminal regions drive pathogenicity through phase separation.

No evidence that proteome composition is associated with realised thermal limit and dietary niche breadth in butterflies

The paper analyzes proteome composition in 35 butterfly species to test if it correlates with thermal limits and diet breadth, finding no such association.

Cross-species interactome analysis uncovers a conserved selective autophagy mechanism for protein quality control in plants

The paper identifies a conserved selective autophagy receptor, CESAR, critical for proteostasis under heat stress in plants through cross-species interactome analysis.

Distinct intraspecific diversification dynamics in Neotropical montane versus lowland birds revealed by whole-genome comparative phylogeography

This study compares phylogeographic dynamics between Neotropical montane and lowland birds, finding greater population structuring and genetic diversity differences in the Andes.

Expanding Ventilago to incorporate Smythea: new combinations in Ventilagineae (Rhamnaceae) based on novel sequence data and phylogenetic analysis

This paper proposes merging Smythea into Ventilago based on phylogenetic analysis showing Ventilago is paraphyletic.

Rooting the deep divergence of land plants

The paper tests bryophyte monophyly using a large genome dataset and shows it is supported despite phylogenetic disputes and outgroup effects.

Eukaryotic recombinases duplicated after divergence from known asgardarchaeal RadA: implications for the evolution of sex during eukaryogenesis

The paper uses comparative genomics and phylogenetic analysis to show eukaryotic Rad51 and DMC1 proteins diverge from asgardarchaeal RadA, supporting a model of eukaryogenesis involving mitochondrial acquisition and sex evolution.

Candidatus Peptacetobacter felis sp. nov., a novel bile acid-converting bacterial species isolated from the feces of healthy cats in the United States

The paper isolates and characterizes a novel bile acid-converting bacterial species from healthy cats, proposing a new species name and highlighting its potential for probiotic development.

G protein-coupled receptor diversity and evolution in the closest living relatives of Metazoa

The paper catalogs GPCRs, G proteins, and regulators in choanoflagellates, revealing expanded diversity and conserved families, with implications for metazoan GPCR evolution.

Topological adaptation of heliorhodopsins enables exogenous second-antenna acquisition in monoderm phototrophs

The paper identifies a conserved carotenoid-binding site in heliorhodopsins, revealing their role in light harvesting through exogenous xanthophyll recruitment due to inverted membrane topology.

Centromeres evolve progressively through selection at the kinetochore interface

The paper investigates how new centromeres evolve and become fixed in budding yeast by analyzing 138 species and 2,500 isolates, showing that kinetochore interface constraints influence centromere evolution.

Ancient gene clusters govern the initiation of monoterpenoid indole alkaloid biosynthesis and C3 stereochemistry inversion

This study identifies and characterizes a conserved oxidase-reductase pair responsible for C3 stereochemistry inversion in monoterpenoid indole alkaloids and traces the evolutionary origin of the gene clusters involved.

From duplication to divergence: single-cell insights into transcriptional and cis-regulatory landscapes

This study uses single-cell genomics to analyze transcriptional and cis-regulatory divergence in duplicated genes of soybean, revealing how chromatin accessibility and duplication mechanisms shape expression patterns.

Coordinated shifts in gene expression and regulation during mole-rat evolution

The paper identifies accelerated gene expression and regulatory evolution in mole-rats by integrating transcriptomics and cis-regulatory analysis across species.

Nonspecific interactions can lead to liquid-liquid phase separation in coiled-coil proteins models

The paper shows that nonspecific interactions in coiled-coil proteins can lead to liquid-liquid phase separation, and that linker segments can enhance this process without altering interaction specificity.

The patchy distribution of the photosynthetic gene cluster in Erythrobacteraceae

This study investigates the distribution of the photosynthetic gene cluster in Erythrobacteraceae using genomic and phylogenetic analysis, finding horizontal operon transfer as the best explanation for its patchy distribution.

Discarded diversity: Novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills

The paper identifies novel viruses, auxiliary metabolic genes, and CRISPR-Cas systems in landfill viromes, highlighting unique virus-host interactions and genetic features.

Phylum-wide propionate degradation and its potential connection to poly- γ-glutamate biosynthesis in Candidatus Cloacimonadota

This study identifies an alternative methylmalonyl-CoA pathway in Cloacimonadota, linking propionate degradation to poly-γ-glutamate biosynthesis and syntrophic interactions with methanogens.

Shortcomings of shortcuts: common species cannot fully explain multiscale patterns of species richness

This study evaluates whether focusing on common species can explain species richness patterns, finding that common species alone are insufficient and rare species are more critical for conservation.

Genomic innovation through fragmentation and gene transfer underlies adaptation in pyrophilous bacteria

This study investigates genomic adaptations in pyrophilous bacteria after wildfires, finding gene fragmentation, horizontal gene transfer, and plasmid-mediated operon expansion enhance their ability to degrade PyOM and acquire nutrients.

Impact of Slow Wave Abnormalities and Impaired Coordination of Pyloric Closure and Antral Contraction on Gastric Emptying: A Compartmental Modeling Study

This paper develops a computationally efficient gastric compartmental model to simulate diseased stomach function, showing that slow wave abnormalities and impaired coordination delay gastric emptying and reduce mixing efficiency.

Comparative genomics and pathogenicity of Pantoea stewartii subsp. stewartii reveal multiple introductions and limited distribution in Europe

This study uses whole-genome sequencing to analyze Pantoea stewartii subsp. stewartii diversity and introduction routes in Europe, revealing multiple introductions and limited distribution.

Optimizing Coarse-Grained Models for Large-Scale Membrane Protein Simulation

This paper optimizes a coarse-grained lipid model for large-scale membrane protein simulations and demonstrates its application to study PIEZO-induced membrane deformation.

Hypoxia adaptation shapes genomic architecture and vertical niche transitions in copepods

This study investigates how hypoxia adaptation shaped genomic architecture and niche transitions in copepods using phylogenetic and transcriptomic analyses.