comparative / phylogenetic analysis

This study uses a comprehensive fossil dataset to show that Cenozoic climate changes influenced skeletal diversification in carnivorans, with major transitions occurring during key climatic events.

The paper investigates the rapid evolution of self/non-self recognition genes in Dictyostelium by analyzing genome sequences and identifying a hypermutable hotspot in the tgrBC locus.

This study identifies MpSABATH2 in liverwort Marchantia polymorpha as essential for development, linking it to gibberellin metabolism and showing convergent evolution of SABATH functions in land plants.

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.

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

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

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

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.

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.

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

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

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

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

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

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.

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.

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

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.

This study identifies the timing of gene evolution related to multicellularity in cyanobacteria leading up to the Great Oxidation Event.

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.

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.

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.

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

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.

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.

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

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

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.

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.