Periodontal disease is characterized by progressive degradation of the gingival extracellular matrix and loss of the physical confinement it imposes on resident stromal cells. In human periodontal tissue, ECM collagen integrity is inversely correlated with facultative nuclear histone acetylation in stromal cells. We hypothesized that matrix stiffness directly coordinates an epigenomic shift in stromal cells. […]

Population connectivity and adaptive gene flow in disease vectors can shape the emergence and spread of insecticide resistance, with direct implications for control strategies such as insecticide spraying or the use of bed nets for malaria control. Using whole-genome sequencing, we first resolved the geographic population structure of the major but understudied malaria vector, Anopheles […]

Deep learning DNA sequence-to-function models offer the promise of gaining mechanistic insights into genome regulation, however their performance is often limited by data scarcity in the species of interest. We present DanioDecima, a zebrafish-specific model leveraging transfer learning from human and mouse-trained models to predict tissue- and cell-type-specific gene expression during zebrafish embryogenesis. Initializing DanioDecima […]

The southern African endemic tree genus Greyia Hook. & Harv. (Francoaceae, Geraniales) comprises three species distinguished by striking variation in trichome morphology and floral architecture, yet the genomic and regulatory basis of these traits has remained largely unexplored. Here, we present chromosome-scale genome assemblies for all recognized Greyia species, namely Greyia radlkoferi, Greyia sutherlandii, and […]

This study presents a mathematical framework for investigating the dynamics of coexistence and competition among heterotrophic microbes across different time scales. Focusing on metabolic interactions, we examine how three strategies: public metabolizing, private metabolizing, and cheating, shape population behaviour. The framework integrates generalized Lotka-Volterra dynamics with evolutionary game theory to capture the effects of resource […]

Biting behavior is an important natural defense mechanism in honeybees (Apis mellifera) against Varroa destructor. Significant variation in this behavior exists across genetic lines of honeybees, with certain colonies exhibiting higher mite-biting activity than others. Selective breeding for enhanced biting behavior provides a promising strategy for sustainable mite control and colony resilience. However, successful implementation […]

OrthoFinder’s all-vs-all DIAMOND step systematically misses single-copy orthogroups (SC OGs) at deep taxonomic divergence: a marker recovered cleanly within a tightly defined cohort is dropped when the same marker is searched against phylum-broad metagenome-assembled genome (MAG) sets, because pairwise sequence similarity falls below DIAMOND’s detection threshold even when the underlying ortholog is present. The result […]

West Nile virus dynamics are shaped by hydrological conditions that influence mosquito habitat and pathogen transmission, but identifying causal relationships is difficult in managed landscapes where irrigation decouples local water conditions from precipitation, complicating climate-disease inference. We address this challenge using a 21-year panel of more than 19 million Culex tarsalis mosquitoes from California’s Central […]

Genomic variation within populations reflects both past and contemporary evolutionary processes. The genetic structure of European peatland plants is shaped by complex postglacial recolonization and recent habitat loss. Here, we investigate population genomic patterns in the vulnerable peatland plant round-leaved sundew (Drosera rotundifolia L.). Using ddRAD sequencing of 311 individuals from 38 populations across Europe, […]

Locomotor endurance is a critical physiological trait dictating terrestrial dispersal and metapopulation connectivity, especially in amphibians. The unisexual Ambystoma complex is an ancient, all-female polyploid lineage that reproduces via kleptogenesis. This unique reproductive mode creates an evolutionary mismatch between a conserved mitochondrial genome and divergent nuclear subgenomes that are taken from sympatric, sexual species. This […]

The Intermountain West of the United States has experienced years of extreme drought and increased temperatures. Increasing temperature and droughts can negatively impact native species that are locally adapted to environmental conditions that have persisted prior to the Anthropocene. Bees, especially solitary bees, provide critical ecosystem services because they pollinate ~90% of all flowering plants. […]