Populations of the Caribbean reef-building coral, Acropora palmata, have declined rapidly since their population genetic structure was first described in the early 2000s. Previous analyses sampled coral colonies across the Caribbean and western North Atlantic but were limited to only 5 to 8 microsatellite loci. These studies concluded that A. palmata reproduces extensively asexually through […]
Dynamic regulation of long non-coding RNAs across asexual andgametocyte development in Plasmodium falciparum
Long non-coding RNAs (lncRNAs) are critical regulators of gene expression in eukaryotes. Short reads from Illumina sequencing, reverse transcriptase artefacts, and incomplete second-strand degradation in strand-specific cDNA libraries hamper genome-wide identification of lncRNAs, especially in gene-dense genomes such as Plasmodium. Here, we integrated long-read Oxford Nanopore Technology direct RNA sequencing, ribosome profiling, and single-cell transcriptomics […]
Climate gradients drive the evolution of seed morphology and life history with impacts to seedling fitness in Fraxinus nigra
Background and Aims: Climate gradients influence seed morphology, emergence, and early life history traits with cumulative impacts to individual fitness. For ex situ seed collections, which represent an invaluable repository of potential trait information for species management and conservation, climate data can guide preservation of adaptive variation and inform deployment strategies for restoration. Here we […]
Zebrafish embryos are robust to mechanical perturbations
The investigation of morphogenesis during organism development has massively benefited from the interaction between developmental biology and biophysics, which gave new quantitative insights into nature’s physical working principles. The process of zebrafish epiboly provides a beautiful model system as cells exhibit collective migration, meanwhile requiring symmetry breaking for gastrulation and the subsequent tissue differentiation. These […]
Testing fundamental hypotheses of colonization success in the ferns
Background and Aims. Non-native species are now ubiquitous members of regional floras. The factors that lead to establishment and dominance of non-native species are continuously debated. Fundamental hypotheses about drivers of invasion success include the role of phylogeny, polyploidy, genome size, and rapid niche evolution. These hypotheses have been tested in the seed plants, but […]
Attentive-SPIDNA: Attention-based neural networks for population genetics
Artificial neural networks (ANNs) have recently offered new perspectives to solve inference problems from high dimensional data in numerous scientific fields, but it is yet unclear which architectures are the most suited to genomic data. Here, we present a new ANN architecture integrating attention mechanisms to infer effective population size history from genomic data. Built […]
Population structure and gene flow in the endangered Caribbean reef-building coral, Acropora palmata
Populations of the Caribbean reef-building coral, Acropora palmata, have declined rapidly since their population genetic structure was first described in the early 2000s. Previous analyses sampled coral colonies across the Caribbean and western North Atlantic but were limited to only 5 to 8 microsatellite loci. These studies concluded that A. palmata reproduces extensively asexually through […]
Dynamic regulation of long non-coding RNAs across asexual andgametocyte development in Plasmodium falciparum
Long non-coding RNAs (lncRNAs) are critical regulators of gene expression in eukaryotes. Short reads from Illumina sequencing, reverse transcriptase artefacts, and incomplete second-strand degradation in strand-specific cDNA libraries hamper genome-wide identification of lncRNAs, especially in gene-dense genomes such as Plasmodium. Here, we integrated long-read Oxford Nanopore Technology direct RNA sequencing, ribosome profiling, and single-cell transcriptomics […]
Zebrafish embryos are robust to mechanical perturbations
The investigation of morphogenesis during organism development has massively benefited from the interaction between developmental biology and biophysics, which gave new quantitative insights into nature’s physical working principles. The process of zebrafish epiboly provides a beautiful model system as cells exhibit collective migration, meanwhile requiring symmetry breaking for gastrulation and the subsequent tissue differentiation. These […]
Characterization of six environmental coli-phages isolated in Astana, Kazakhstan, during the School of Molecular and Theoretical Biology
Bacteriophage (phage) collections are essential resources for studying virus-host interactions in bacterial species. Here, we report six Escherichia coli-infecting phages that expand the Lund Collection of Bacteriophages. These phages were isolated in 2025 within the framework of the School of Molecular and Theoretical Biology for high-school students, from samples collected in Lake Taldykol, Astana, Kazakhstan, […]
Assessing the impact of artificial night lighting regulations designed to protect astronomical observatories on seabirds and bats
Artificial light at night is a rapidly increasing driver of global change, affecting both astronomical observations and biodiversity. Regulations such as the Canary Islands’ "Sky Law" were designed to protect astronomical observations by controlling light intensity and spectral composition, yet their ecological effectiveness remains largely untested. Here, we experimentally assessed whether lighting conditions permitted under […]
Beyond Level-1: Fast Inference of Generic Semi-directed Phylogenetic Networks
Phylogenetic networks capture reticulate evolution, but existing methods have mostly been restricted to level-1 topologies. This restriction severely limits the biological applicability of phylogenetic network inference. Here, we extend the widely used SNaQ method to scalably infer arbitrary binary, metric, semi-directed phylogenetic networks while allowing optional restriction to a user-specified network space. We implement computational […]