Preprints
Filtering by Subject: Biodiversity
Maximising time-series inclusion reduces geographic and taxonomic biases in the Living Planet Index
Published: 2025-02-05
Subjects: Biodiversity
Measuring how and why biodiversity is changing is critical to protecting it. Among the tools developed to measure biodiversity, one indicator has come under recent scrutiny. The Living Planet Index (LPI) is an indicator based on vertebrate population trends used as evidence for policy and a resource for scientific research; it has a high profile and global reach in the media by conveying a simple [...]
The collector practices that shape spatial, temporal, and taxonomic bias in herbaria
Published: 2025-02-05
Subjects: Biodiversity, Biology, Botany, Ecology and Evolutionary Biology
Natural history collections (NHCs) are essential for studying biodiversity. Although spatial, temporal, and taxonomic biases in NHCs affect analyses, the influence of collector practices on biases remains largely unexplored. We utilized one million digitized specimens collected in the northeastern United States from 237 herbaria and analyzed contributions from ~10,000 collectors. We investigated [...]
The business case for investing in biodiversity data
Published: 2025-02-04
Subjects: Biodiversity
1. The private sector is increasingly aware of its dependence on biodiversity and the financial risks and opportunities involved. This has generated a lot of demand for investing in nature-positive solutions. There is an obvious and non-negotiable basis for such initiatives: biodiversity data. Without this data and the tools built from it, no actor can assess the effects on the ecosystems they [...]
Bats in Habitats, Bats as Habitats: An integrative ecological framework for understanding synergistic interactions across levels of community organization
Published: 2025-02-03
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Integrative Biology, Systems Biology
Global biodiversity and ecosystem function are the result of complex networks of interactions and feedbacks between animals and their environments, which in turn are affected by the interactions and feedbacks between animals and the organisms they host. Understanding these complex networks, including the main drivers of and responses to ecological and environmental changes and their global [...]
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, [...]
Incorporating responses of functional traits to changing climates into species distribution models: A path forward
Published: 2025-01-29
Subjects: Biodiversity, Ecology and Evolutionary Biology, Life Sciences
Conventional species distribution models (SDMs) typically consider only abiotic factors, thus overlooking critical biotic dimensions, including functional traits that play an important role determining species’ distributions in changing environments. Process-based models explicitly incorporate functional traits and have been applied to SDMs. However, their parameterization can be complex and [...]
Strategies to transform natural resource extension with iNaturalist and engage the public in biodiversity conservation
Published: 2025-01-13
Subjects: Biodiversity, Education, Life Sciences
Participatory citizen science is an increasingly popular tool which provides non-formal education and learning activities. iNaturalist—a free open-access—participatory citizen science platform provides a place to engage the public in natural resource programming. Here, we explore practical applications for integrating iNaturalist into extension programming. We highlight two approaches: (1) [...]
The implementation of network meta-analysis in Ecology; a case study using crop yield data
Published: 2025-01-13
Subjects: Agriculture, Biodiversity, Life Sciences, Natural Resources and Conservation, Natural Resources Management and Policy
Network meta-analysis (NMA) is a method commonly used in medical research that allows for the comparison of multiple interventions in a single, coherent analysis. In this study, we explore how NMA can be applied in ecological studies – specifically, in comparing the effectiveness of multiple interventions in field experiments. Our study aims to provide a general and non-technical introduction of [...]
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 [...]
Phytoremediation of Heavy Metals: Techniques, Challenges, and Prospects
Published: 2025-01-02
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Life Sciences, Plant Sciences
Heavy metals, characterized by their high atomic mass and density, can pose significant risks to soil, water, plants, and human health. Contamination sources include manufacturing activities, mining, farming practices, and improper waste management. Metals such as arsenic, mercury, lead, chromium, and cadmium are most toxic with health consequences that can result from organ dysfunction to [...]
GUBIC: the global urban biological invasions compendium for plants
Published: 2024-12-27
Subjects: Biodiversity, Ecology and Evolutionary Biology
1. Urban areas are foci for the introduction of non-native plant species, and they often act as launching sites for invasions into the wider environment. Although interest in biological invasions in urban areas is growing rapidly, and the extent and complexity of problems associated with invasions in these systems have increased, data on the composition and numbers of non-native plants in [...]
Environmental RNA mitigates fish ghosts related to fish feeds for aquaculture in molecular ecological survey in a bay.
Published: 2024-12-19
Subjects: Aquaculture and Fisheries Life Sciences, Biodiversity, Genomics, Terrestrial and Aquatic Ecology
The use of environmental DNA for molecular ecological surveys has become widely utilized in ecological assessments of various water environments, from rivers to coastal and marine areas. However, it is important to consider the scenarios of potential contamination of environmental nucleic acids in interpreting the results. In this study, we analyzed the fish species present in the feed that may [...]
A phylogenetic sectional taxonomy of Leucheria Lag. (Asteraceae; Nassauvieae)
Published: 2024-12-19
Subjects: Biodiversity, Life Sciences
Multiple molecular phylogenetic analyses have demonstrated that the genus Polyachyrus Lag. (8 spp.) is phylogenetically nested among four well-supported but unnamed monophyletic lineages of the genus Leucheria Lag. (28-46 spp.; Asteraceae; Nassauvieae). In order to facilitate reference to these lineages per current phylogenetic taxonomic and botanical nomenclatural conventions, a phylogenetic [...]
A curated benchmark dataset for molecular identification based on genome skimming
Published: 2024-12-19
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genome skimming is a promising sequencing strategy for DNA-based taxonomic identification. However, the lack of standardized datasets for benchmarking genome skimming tools presents a challenge in comparing new methods to existing ones. As part of the development of varKoder, a new tool for DNA-based identification, we curated four datasets designed for comparing molecular identification tools [...]