Preprints
Filtering by Subject: Bioinformatics
The BeeBiome Data Portal provides easy access to bee microbiome information
Published: 2025-01-20
Subjects: Apiculture, Bioinformatics, Environmental Microbiology and Microbial Ecology Life Sciences
Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets [...]
OSEA, a deep learning-based bird classification tool, with pre-trained model, mobile and command line applications
Published: 2025-01-07
Subjects: Biodiversity, Bioinformatics, Life Sciences, Ornithology
In response to the challenges of traditional biodiversity monitoring methods, we introduce OSEA (Open Species Estimation for Avians), a multi-platform, offline tool for bird species identification. Designed to recognize over 10,000 bird species, OSEA includes both a mobile application and a command-line interface (CLI), facilitating efficient bird species identification. The mobile app, developed [...]
AI and Big Data for invasion biology: finding, modelling and forecasting the population dynamics of invaders
Published: 2025-01-07
Subjects: Biodiversity, Bioinformatics, Life Sciences, Population Biology
Artificial intelligence (AI) is rapidly transforming the study and management of invasive species through analytical and predictive tools that optimize detection, monitoring, and automated eradication. In this work, we reviewed the fundamental principles of machine learning and deep learning, illustrated with recent case studies on invasive species. We also present the first systematic review of [...]
A dataset for benchmarking molecular identification tools based on genome skimming
Published: 2024-12-19
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genome skimming is an emerging tool allowing for scalable DNA barcoding efforts for numerous biodiversity science applications. Despite its growing importance, there are few standardized datasets for benchmarking genome skimming tools, making it challenging to evaluate new methods (e.g., using machine learning), and comparing to existing ones (e.g., conventional barcoding loci derived from [...]
Gut microbiome composition and function – including transposase gene abundance - varies with age, but not senescence, in a wild vertebrate
Published: 2024-11-14
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Life Sciences, Microbiology, Ornithology
Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambigous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used seven years of longitudinal [...]
FAIRification of DMRichR Pipeline: Advancing Epigenetic Research on Environmental and Evolutionary Model Organisms
Published: 2024-11-05
Subjects: Bioinformatics, Computational Biology, Environmental Public Health, Life Sciences, Other Ecology and Evolutionary Biology
Bioinformatics tools often prioritize humans or human-related model organisms, overlooking the requirements of environmentally relevant species, which limits their use in ecological research. This gap is particularly challenging when implementing existing software, as inadequate documentation can delay the innovative use of environmental models for modern risk assessment of chemicals that can [...]
Navigating phylogenetic conflict and evolutionary inference in plants with target capture data
Published: 2024-05-27
Subjects: Bioinformatics, Biology, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences, Plant Sciences, Research Methods in Life Sciences
Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or [...]
A minimum data standard for wildlife disease studies
Published: 2024-05-19
Subjects: Animal Diseases, Biodiversity, Bioinformatics, Diseases, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Parasitic Diseases, Veterinary Infectious Diseases, Veterinary Medicine, Virology, Virus Diseases
Thousands of scientists and practitioners conduct research on infectious diseases of wildlife. Rapid and comprehensive data sharing is vital to the transparency and actionability of their work, but unfortunately, most efforts designed to publically share these data are focused on pathogen determination and genetic sequence data. Other facets of existing surveillance data – particularly [...]
Guidance framework to apply best practices in ecological data analysis: Lessons learned from building Galaxy-Ecology
Published: 2024-04-11
Subjects: Bioinformatics, Other Ecology and Evolutionary Biology
Numerous conceptual frameworks exist for best practices in research data and analysis (e.g. Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical [...]
Incomplete lineage sorting and hybridization underlie of tree discordance in Petunia and related genera (Petunieae, Solanaceae)
Published: 2024-03-29
Subjects: Biodiversity, Bioinformatics, Botany, Genomics
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies [...]
Ten Simple Rules to build a Model Life Cycle
Published: 2024-02-09
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Software Engineering
Just like data, models have their own life cycle. By recognizing how one’s model fits within the life cycle of the data (or at least, ensuring that the model life cycle is understood), we can identify opportunities to foster new collaborations, encourage better practices in data analysis, and ultimately accelerate research. In this manuscript, we introduce the Model Life Cycle and develop a [...]
A universal DNA signature for the Tree of Life
Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology
Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods may lack power and universal applicability across the Tree of Life. Alternative methods based on whole genome sequencing are hard to scale due to large data requirements. Here, we develop a novel DNA-based identification method, varKoding, using [...]
A big data and machine learning approach for monitoring the condition of ecosystems
Published: 2024-01-16
Subjects: Applied Statistics, Biodiversity, Bioinformatics, Earth Sciences, Ecology and Evolutionary Biology, Environmental Sciences, Forest Biology, Forest Sciences, Life Sciences, Other Ecology and Evolutionary Biology, Physical Sciences and Mathematics, Statistical Methodology, Statistical Models, Terrestrial and Aquatic Ecology
Ecosystems are highly valuable as a source of goods and services and as a heritage for future generations. Knowing their condition is extremely important for all management and conservation activities and public policies. Until now, the evaluation of ecosystem condition has been unsatisfactory and thus lacks practical implementation for most countries. We propose that ecosystem integrity is a [...]
otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome
Published: 2023-12-05
Subjects: Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences
The implementation of a new genomic assembly pipeline named only the best [Genome Assembly Tools] (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The [...]
Towards causal relationships for modelling species distribution
Published: 2023-10-14
Subjects: Biodiversity, Bioinformatics, Life Sciences, Natural Resources and Conservation, Statistical Models
1. Understanding the processes underlying the distribution of species through space and time is fundamental in several research fields spanning from ecology to spatial epidemiology. Correlative species distribution models (SDMs) involve popular statistical tools to infer species geographical distribution thanks to spatiotemporally explicit observations of species occurrences coupled with a set of [...]