comparative / phylogenetic analysis

The paper compares genome fractionation patterns in maize and its wild relatives, finding distinct subgenome retention and gene loss trends between species.

This study investigates how retinal specializations in mammals evolve in response to ecological factors and morphological constraints, finding support for associations between horizontal streaks and habitat type, and between orbit convergence and retinal acuity regions.

The paper examines how immunoglobulin codon optimality interacts with mutability and hypermutation in antibody evolution, finding that codon deoptimization correlates with expression loss and is constrained by selective pressures.

This study investigates the expansion of the MutS gene family in plants, identifying origins through gene duplication, endosymbiotic gene transfer, and horizontal gene transfer, and highlights their roles in organelle genetics.

The paper identifies genes under relaxed selection in cassava due to clonal propagation, highlighting pollen-related genes and their implications for breeding.

This study compares β-catenin sequences and function across nonbilaterian metazoans and Xenopus embryos, revealing conserved structural and functional properties of β-catenin complexes.

The paper examines X chromosome evolution in treehoppers, finding long-term conservation with one exception of an X-autosome fusion in a species.

MEGA12 adds filtered substitution-model selection, matching full-search choices in all 240 simulated nucleotide alignments, and adaptive bootstrapping with an 81% average speed-up, accelerating maximum-likelihood phylogenetics.

This study sequenced the transcriptome of Pseudotrichomonas keilini, a free-living parabasalid, and compared its genome to parasitic relatives to understand evolutionary adaptations to anaerobic lifestyles.

The paper uses single-cell RNA sequencing to compare embryonic development in two sea urchin species, identifying evolutionary changes in cell fate specification and signaling.

The paper identifies 38 cases of enzymes with different structures but identical functions, analyzing their sequence, structure, and mechanism to support convergent evolution.

This study identifies molecular genotypes and key residues that determine receptor tropism in alphacoronaviruses, revealing generalist and specialist host ranges and potential spillover routes.

This study investigates the genomic basis of lifespan extension in bees lacking prepupal diapause, finding convergent selection on longevity-related genes and changes in selection pressures on the IIS/TOR pathway.

This study investigates how histone modifications and transposable elements influence dosage regulation in gene duplicates across D. discoideum and humans.

This study identifies two subspecies of Xenorhabdus griffiniae and shows that prophages drive intraspecies genomic variation.

The paper identifies 4,804 sap peptide precursor genes in Populus trichocarpa, revealing their conservation across angiosperms and active expression in xylem during growth transitions.

This study investigates the evolutionary distribution and functional diversification of g-type lysozymes across metazoans, revealing lateral gene transfer and specialized roles in immunity and digestion.

The paper presents the genome sequence of Tropaeolum majus and identifies genes involved in flavonoid biosynthesis, including those required for flavonol glycoside production.

This study identifies widespread linear molecular mimicry across the human virome, linking it to autoimmunity, particularly in multiple sclerosis, and suggests therapeutic strategies targeting viral infections.

The paper identifies BEAN and HABAS domains in bacterial RNA polymerase subunits, showing their evolutionary divergence and phylogenetic distribution.

This study examines hemoglobin gene evolution in teleost and cichlid fishes, showing gene duplications and rearrangements drive diversity in oxygen transport systems.

This study expands the Legionellaceae family by identifying new species and highlights the need for taxonomic restructuring based on genomic and clinical data.

The paper uses a computational model to study how archaeal membrane lipids balance stability and flexibility, finding that adding bilayer lipids to bolalipid membranes achieves both.

This study examines the evolutionary history of pro-inflammatory caspases in primates and rodents, revealing differences in gene retention, pseudogenization, and positive selection across species.

This study sequenced 166 Macadamia genotypes to analyze genetic diversity and phylogenetic relationships, revealing extensive reticulate evolution and chloroplast capture events.

This study identifies covalent small molecules that bind FOXA1, altering its chromatin remodeling activity in prostate cancer cells.

The paper examines postmating reproductive trait evolution in Drosophila species, finding strong coevolution between male and female traits but no link between remating rate and trait evolution.

The paper investigates the evolutionary origins of extracellular matrix polysaccharides in brown algae using genomic data and comparative analysis.

This paper identifies and characterizes RA-0002034, a covalent inhibitor of CHIKV nsP2 protease, showing potent inhibition and selectivity against alphaviruses.

This study defines sporopollenin (SP) as specific to embryophytes by showing all five polyketide pathway enzymes are present in embryophytes but absent in green algae.