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 […]
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 […]
Megaherbivore mortality risk from temperature extremes is buffered by vegetation productivity but amplified by rainfall
Demographic risks from climate change remain poorly understood for megaherbivore species which face unique challenges because their large food requirements impose strong bottom-up limitation while their small surface-area-to-volume ratio limits heat dissipation. Here, we test how megaherbivore mortality is shaped by the concurrent effects of temperature and rainfall along with vegetation productivity, a potentially critical […]
Genomic hallmarks of parasexual reproduction in three hybrid groups of the human pathogen Cryptococcus neoformans
Hybridization is a major driver of fungal evolution, yet knowledge of the molecular mechanisms underpinning hybridization and its genomic impact remain limited. Here, we analyse 197 Cryptococcus neoformans genomic sequences, including 13 newly sequenced strains, identifying three genetically clustered and distinct hybrid groups (H1, H2 and H3) each with unique parental origins and ecological associations. […]
PFAS exposure is associated with accelerated epigenetic ageing in a wild marine mammal
Chronic contaminant exposure may impose hidden physiological costs long before obvious demographic or health effects become detectable in wildlife populations. Epigenetic clocks quantify biological ageing and may provide sensitive biomarkers of cumulative toxicological stress. Per- and polyfluoroalkyl substances (PFAS) are persistent contaminants that bioaccumulate in marine food webs, yet their long-term physiological consequences for wildlife […]
Using spatial prioritization to navigate current and future tradeoffs when controlling invaders
Controlling invasive species is a global conservation priority but is typically resource-limited, necessitating strategies to optimize control. Spatial prioritization methods can improve the efficiency of invader control by quantifying the benefits, costs, and risks of alternative intervention strategies. Yet prioritization designs are sensitive to the distinction between protecting native populations that are currently sympatric with […]
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 […]
Tryptophan became part of the universal genetic code post-LUCA
We evaluate whether tryptophan (W), widely thought to be the last of the 20 canonical amino acids added to the genetic code, was already present in the Last Universal Common Ancestor (LUCA). We reconstruct the evolutionary history of tryptophanyl-tRNA synthetase (WRS), the enzyme that attaches W to its tRNA, and the related tyrosyl-tRNA synthetase (YRS). […]
From unsupervised clustering to atlas-guided annotation in cohort-scale spatial omics with HiCAT
Pathologist-annotated tissue regions provide a fundamental reference for examining spatial omics data, yet such annotations are available for a limited number of samples due to the substantial manual effort required. Moreover, these annotations are derived from morphology within individual histology images, which can overlook molecularly defined regions and obscure intra-sample heterogeneity. To address these limitations, […]
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 […]
Epigenome Alterations and 3D Chromatin Architecture Remodeling in Inflammatory Macrophage Activation under Diabetic Conditions
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 […]