Aberrant monocyte and macrophage activation in diabetes drives chronic inflammation and complications. While epigenetic mechanisms are implicated, the role of 3D chromatin reorganization remains unclear. Using integrated multi-Omics, we profiled gene expression and 3D chromatin architecture in human CD14+ monocyte differentiated macrophages treated with high glucose plus TNF-alpha (HT) mimicking the diabetic milieu. HT induced […]
Discovery of novel members of the Potyviridae family reveals expanded diversity, a broad host range, and evidence of fungal and oomycete infections
The family Potyviridae represents the largest and most economically important group of plant-infecting RNA viruses. Despite extensive study of crop-associated members, the full diversity, host range, and evolutionary history of potyvirids remain poorly understood. Here, we conducted a large-scale mining of publicly available RNA-seq datasets to systematically search for novel potyvirid sequences. This approach enabled […]
Genomic connectivity and the spread of adaptive insecticide resistance alleles in Anopheles arabiensis from East Africa
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 […]
Modes of natural selection on maternal and zygotic gene expression in Drosophila melanogaster embryos
Early embryonic development involves the coordination of gene expression from two distinct genomes, as mothers load eggs with gene products prior to the beginning of zygotic transcription. Because the maternal transcriptome is controlled by the mothers regulatory genotype rather than that of the embryo, these two sequential developmental programs may experience distinct evolutionary constraints and […]
Nuclear confinement from matrix stiffness drives epigenomic reprogramming of gingival fibroblasts
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 genomics reveals divergent lineages in the European peatland plant Drosera rotundifolia
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, […]
Cohort-HMM marker recruitment with per-OG orthology QC for phylogenomic supermatrices
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 […]
Variable jackpot individuals provide most alleles for repeated, rapid adaptation to freshwater by anadromous Threespine Stickleback
The Threespine Stickleback has become a key model organism to study evolutionary biology. Experimental introductions of anadromous stickleback into freshwater habitats lacking this species allow analysis of the process of adaptation to freshwater forward-in-time in contrast to retrospective inference using naturally colonized populations. We examined the population genomic dynamics during early stages of adaptation in […]
GPU accelerated population genetics statistics using pg_gpu
Population genetics summary statistics– diversity, divergence, linkage disequilibrium, selection scans, and dimensionality reduction– are fundamental across human, agricultural, and ecological genomics. As whole-genome sequencing datasets have grown to hundreds of thousands of individuals, the cost of computing these statistics on conventional CPU implementations has become a major bottleneck: windowed scans of a single chromosome arm […]
Functional class 2 CCA-adding enzymes in Asgard archaea and their implications for eukaryogenesis
CCA-adding enzymes are essential for transfer RNA (tRNA) maturation and translation among all domains of life. A long standing dogma holds that archaea encode exclusively class one CCA-adding enzymes (CCA1), whereas bacteria and eukaryotes encode class two enzymes (CCA2), creating a perceived strict evolutionary separation between archaeal and eukaryotic CCA adding enzymes. Here, we show […]
Peak performance is repeatable and captures large individual differences in ruby-throated hummingbirds
Locomotor performance often determines the outcome of interactions with competitors, predators, and prey. In flying animals, the asymptotic load-lifting assay measures maximal muscle power output in vertical flight. Previous studies of small birds have shown that load-lifting performance is linked to flight maneuverability and the outcome of competitive species interactions. Here, we quantify sources of […]
Range-wide validation of reduced locomotor endurance in unisexual Ambystoma salamanders
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 […]