Preprints
Filtering by Subject: Bioinformatics
pynnotate: a flexible tool for retrieving and processing GenBank data in molecular evolution research and education
Published: 2026-02-26
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Evolution
Pynnotate is a Python-based tool designed for automated retrieval, parsing, and extraction of annotated gene sequences from GenBank records. The tool addresses the common challenges researchers face when working with GenBank data, including inconsistent gene nomenclature, redundant sequences, and the need for standardised gene extraction across multiple taxa. Pynnotate operates through both a [...]
High-Resolution Coastal Blue Carbon Site Intelligence: A Multi-Attribute Geospatial Pipeline for National-Scale Mangrove Assessment
Published: 2026-02-25
Subjects: Biodiversity, Bioinformatics, Life Sciences, Systems Biology
The voluntary blue carbon market is severely bottlenecked by outdated methodologies that apply broad, coast-level carbon averages across low-resolution spatial units, systematically failing to account for micro-site ecological realities and critical socio-political constraints. To resolve this structural deficit, this paper introduces the High-Resolution Geographically-Explicit Blue Carbon [...]
BABAPPAΩ: Diagnosing the Identifiability of Episodic Selection under Branch–Site Evolution Using Likelihood-Free Neural Inference
Published: 2026-02-24
Subjects: Bioinformatics, Life Sciences
Episodic positive selection acting on specific evolutionary lineages is a longstanding yet intrinsically difficult target of molecular inference. Classical branch–site methods formulate this problem as hypothesis testing under explicit codon substitution models, implicitly assuming that episodic selection is statistically identifiable from finite alignments. Under biologically realistic [...]
RNA Virus Discovery from Daphnia meta-transcriptomes: A novel Tombunoda-like virus based on RNA dependent RNA polymerase identification
Published: 2025-11-21
Subjects: Bioinformatics, Life Sciences, Virology
The discovery of RNA viruses from meta-transcriptomes has led to an explosion in viral diversity and identified many novel host-virus associations. To date, no studies have examined the RNA virome of the model zooplankter Daphnia. From which only four viruses are known, with only one being well understood. Here, I assemble and annotate RNA-dependent RNA polymerase (RdRp) containing contigs from [...]
TwisstNTern 2: Ternary analysis of topology weights from tree sequences
Published: 2025-11-06
Subjects: Bioinformatics, Genetics and Genomics, Life Sciences
Recent advances in genealogical inference now allow the reconstruction of genome-wide sequences of trees for large sets of samples, providing detailed records of how evolutionary relationships vary along the genome. Tree sequences encode a vast amount of information, but new approaches are needed to extract relevant patterns and make inferences. TwisstNtern is a program for visualising and [...]
CartograPlant: Bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight
Published: 2025-09-30
Subjects: Agriculture, Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Integrative Biology, Life Sciences, Plant Biology, Plant Breeding and Genetics Life Sciences, Plant Pathology, Systems Biology
Climate change is threatening plant health and productivity at all spatial scales, and these impacts are further compounded by the rising incidence of invasive pests and pathogens. Effectively addressing these challenges requires a comprehensive understanding of plant demography as well as the mechanisms and drivers of adaptation. Achieving this understanding requires the integration of [...]
Alternative Promoters Expand Transcriptional Complexity of Temperature Stress Responses in Cassava
Published: 2025-09-29
Subjects: Agriculture, Bioinformatics, Genetics and Genomics, Genomics, Plant Biology, Plant Sciences
Plant abiotic stress responses involve two major gene expression regulatory mechanisms: alternative promoter usage and differential expression. Although differentially expressed genes (DEGs) have been extensively studied, alternative promoter genes (APGs) remain poorly characterized despite their potential importance. We systematically compared APGs and DEGs in cassava (Manihot esculenta), a [...]
Fossils for Future: the billion-dollar case for paleontology’s digital infrastructure
Published: 2025-09-10
Subjects: Arts and Humanities, Bioinformatics, Earth Sciences, Ecology and Evolutionary Biology, Life Sciences, Other Arts and Humanities, Physical Sciences and Mathematics
The digital revolution has transformed paleontology through the development of open-access, community-driven databases that underpin some of the most impactful research in biodiversity, climate change, and extinction dynamics. These systems safeguard high-effort, volunteered data and have revealed major macroevolutionary patterns, including mass extinctions. However, of 118 paleontological and [...]
BPGA: an interactive Shiny application for basic population genetic analysis of genotype data
Published: 2025-08-31
Subjects: Bioinformatics, Education, Genetics and Genomics, Higher Education, Life Sciences
Background: Population structure and ancestry inference are routine in human genetics, yet remain inconvenient for non-experts because canonical tools (PLINK, GCTA, ADMIXTURE) require command-line expertise and careful data management. Results: BPGA (Basic Population Genetic Analysis) is an open‑source R/Shiny application that provides an interactive workflow for educational and exploratory [...]
Pollinator specialisation fails to explain rapid speciation in terrestrial orchids
Published: 2025-08-27
Subjects: Biodiversity, Bioinformatics, Biology, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences, Plant Sciences
Pollinator attraction is central to the reproductive biology and ecology of flowering plants, and pollinator specialisation has long been thought of as a driving force of species generation. Orchids are central to this idea, which dates back to Darwin’s work on pollinator-driven floral evolution. However, most macroevolutionary evidence for the speciation hypothesis comes from studies of genera [...]
Long-read sequencing for biodiversity analyses - a comprehensive guide
Published: 2025-08-26
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Environmental Monitoring, Genetics and Genomics, Life Sciences
1. DNA-based monitoring of biodiversity has revolutionised our ability to describe communities and rapidly assess anthropogenic impacts on biodiversity. Currently established molecular methods for biomonitoring rely heavily on classic metabarcoding utilising short reads, mostly through Illumina data. However, increasingly more studies use long-read sequencing technologies, such as Oxford [...]
Fast evolving flowers drive cactus diversification
Published: 2025-08-22
Subjects: Biodiversity, Bioinformatics, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences
The rise of biodiversity is shaped by variation in diversification rates. Across the Tree of Life, numerous forces are thought to influence these rates, including the evolution of adaptive traits, climate change, and interactions with other organisms. In the flowering plants, a longstanding hypothesis favoured by Darwin suggests that floral evolution is a driving force for plant diversity. [...]
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-05
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
Designing Multi-Modal Ecosystem Monitoring Technologies: A Network of Networks Approach
Published: 2025-04-23
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Environmental Monitoring, Software Engineering
The central promise of ecosystem monitoring technologies — like bioacoustic, camera trap, citizen science, eDNA, and satellite data — is to reveal changes in the structure and composition of the Earth’s ecological systems to facilitate timely and effective conservation action. Following the evolution and maturation of these technology systems, the fusion of multimodal observation systems — where [...]
Leveraging large language models for ecological interpretation using an eBird chatbot case study
Published: 2025-04-23
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology
1. The anthropocene presents significant challenges for global biodiversity, public health, and long-term ecosystem stability. The wealth of publicly available near-real-time ecology and climate data can be used to monitor these challenges and allow practitioners to develop mitigation strategies. 2. There is untapped potential to apply Large Language Models (LLMs) to quantitative ecological and [...]