Preprints

Filtering by Subject: Bioinformatics

Northward expansion of the thermal limit for the tick Ixodes ricinus over the past 40 years

Daniele Da Re, Gaelle Gilson, Quentin Dalaiden, et al.

Published: 2025-02-14
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Entomology, Life Sciences, Population Biology

The tick Ixodes ricinus is the main pathogen vector in Europe. Many speculations have been made about the effect of past climate change on the potential distribution of this ectothermic organism, despite a poor understanding of how climate change has resulted in distribution changes to date. In this study, we used a public cross-sectional dataset of I. ricinus abundance at the northern edge of [...]

Algorithm selection for optimal ecological monitoring design

Kari E Norman, Timothée Poisot

Published: 2025-02-11
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology

Comprehensive monitoring of biodiversity to direct conservation action is foundational to addressing the ongoing biodiversity crisis. As integrative monitoring programs increasingly come online in response to multilateral biodiversity agreements, establishing best practices for optimal design is critical. Selecting the appropriate algorithm for identifying sample sites is both necessary for [...]

Seeing herbaria in a new light: leaf reflectance spectroscopy unlocks predictive trait and classification modeling in plant biodiversity collections

Dawson M White, Jeannine Cavender-Bares, Charles Davis, et al.

Published: 2025-02-10
Subjects: Biodiversity, Bioinformatics, Botany, Ecology and Evolutionary Biology, Integrative Biology, Life Sciences

Reflectance spectroscopy is a non-destructive, rapid, and robust method for estimating functional traits and distinguishing species. Spectral reflectance libraries generated from herbarium specimens are an untapped and promising resource for generating broad phenomic datasets across space, time, and species. We conducted a proof-of-concept study using functional trait data and spectra from [...]

Powerful yet challenging: Mechanistic Niche Models for predicting invasive species potential distribution under climate change

Erola Fenollosa, Sean E. H. Pang, Natalie Briscoe, et al.

Published: 2025-01-29
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology

Risk assessments of invasive species are among the most challenging applications of species distribution models (SDMs). This challenge arises from the disequilibrium in invasive distributions, where recorded occurrences do not fully represent the species' potential range. The spatiotemporal dynamics of invasive populations are shaped by intraspecific variability, human-mediated introductions, [...]

The BeeBiome Data Portal provides easy access to bee microbiome information

Valentine Rech De Laval, Benjamin Dainat, Philipp Engel, et al.

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

Jiao Sun

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

Erola Fenollosa, Rob Salguero-Gomez

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

Renata Asprino, Liming Cai, Yujing Yan, et al.

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

Chuen Zhang Lee, Sarah F Worsley, Charli S. Davies, et al.

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

Wassim Salam, Marcin Wlodzimierz Wojewodzic, Dagmar Frisch

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

Elizabeth M Joyce, Alexander N Schmidt-Lebuhn, Harvey K Orel, et al.

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

Tess Stevens, Ryan Zimmerman, Greg Albery, et al.

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

Coline Royaux, Jean-Baptiste Mihoub, Marie Jossé, et al.

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)

Pedro Henrique Pezzi, Lucas C Wheeler, Loreta Brandão Freitas, et al.

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

Timothée Poisot, Daniel J Becker, Cole B Brookson, et al.

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 [...]

search

You can search by:

  • Title
  • Keywords
  • Author Name
  • Author Affiliation