Preprints
Filtering by Subject: Bioinformatics
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-06
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 [...]
Balancing Accessibility and Security: Safeguarding Citizen-Sourced Biodiversity Data in the Age of AI and Open-Sourced Software
Published: 2025-04-22
Subjects: Biodiversity, Bioinformatics
Artificial Intelligence (AI) and open-source software are revolutionizing biodiversity monitoring by democratizing access to citizen-science datasets. While these advancements facilitate conservation efforts and scientific research, they pose significant risks for data misuse. Researchers who reduce barriers to accessing such biodiversity datasets are responsible for safeguarding sensitive data.
BOLDistilled: Comprehensive but compact DNA barcode reference libraries
Published: 2025-04-21
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences
Advances in DNA sequencing technology have stimulated the rapid uptake of protocols—such as eDNA analysis and metabarcoding—that infer the species composition of environmental samples from DNA sequences. DNA barcode reference libraries play a critical role in the interpretation of sequences gathered through such protocols, but many lack adequate taxonomic curation, include redundant records, do [...]
Deep-learning technology provides insights into the morphological evolution of birds
Published: 2025-04-09
Subjects: Biodiversity, Bioinformatics, Computational Engineering, Evolution, Life Sciences, Ornithology, Research Methods in Life Sciences
The evolution of biological morphology is critical for understanding the diversity of the natural world, yet traditional analyses often involve subjective biases in the selection and coding of morphological traits. This study employs deep learning techniques, utilizing a pretrained ResNet34 model capable of recognizing over 10,000 bird species, to explore avian morphological evolution. We [...]
De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods
Published: 2025-04-08
Subjects: Bioinformatics, Genomics
A novel mechanism of de novo gene origination from non-genic sequences was first proposed in the early 2000s. Subsequent studies have since provided evidence of de novo gene emergence across all domains of life, revealing its occurrence to be more frequent than initially anticipated. While studies mainly agree on the general concept of de novo emergence from non-genic DNA, the exact methods and [...]
The human fingerprint of medicinal plant species diversity
Published: 2025-03-14
Subjects: Anthropology, Biodiversity, Bioinformatics, Biotechnology, Environmental Sciences, Medicine and Health Sciences, Other Languages, Societies, and Cultures
Medicinal plants have long been crucial to human civilizations, supporting both traditional and modern healthcare systems. However, the processes influencing the global diversity and distribution of medicinal plants remain underexplored. Their diversity, like that of other species groups, is shaped by abiotic and biotic influences, which include, in unique ways, human ecological (including [...]
Motif-weighted Structure Alignment for Classification and Evolutionary Studies of Carbonic Anhydrase
Published: 2025-02-24
Subjects: Bioinformatics, Life Sciences
Carbonic anhydrases (CAs) attract interest for their critical roles in various physiological processes and potential application in CO2 sequestration to combat global warming. Despite being an important enzyme family, the classification and evolution of CAs remain elusive due to their high sequence diversity and long evolutionary history. In this paper, the in-silico strategy, Motif-weighted [...]
Northward expansion of the thermal limit for the tick Ixodes ricinus over the past 40 years
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
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
Published: 2025-02-10
Subjects: Biodiversity, Bioinformatics, Botany, Ecology and Evolutionary Biology, Integrative Biology, Life Sciences
Reflectance spectroscopy is a rapid method for estimating traits and discriminating species. Spectral libraries from herbarium specimens represent an untapped resource for generating broad phenomic datasets across space, time, and taxa. We conducted a proof-of-concept study using trait data and spectra from herbarium specimens up to 179 years old alongside data from recently dried, pressed [...]
Powerful yet challenging: Mechanistic Niche Models for predicting invasive species potential distribution under climate change
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
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 [...]