Preprints
There are 3044 Preprints listed.
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 [...]
The Individualised Niche in Motion; quantifying individualised niches with movement data
Published: 2026-02-26
Subjects: Aquaculture and Fisheries Life Sciences, Behavior and Ethology, Evolution, Ornithology, Other Animal Sciences, Other Ecology and Evolutionary Biology, Population Biology, Terrestrial and Aquatic Ecology, Zoology
Individuals of the same species often differ consistently in their use of resources, their responses to environmental gradients, and their movement decisions. Between-individual variation across niche axes has been shown to have important ecological consequences. Yet practical frameworks that translate modern tracking data into operational, comparable measures of niche individual specialisation [...]
Beyond Observed Diversity: A Completeness-Based Invasion Theory
Published: 2026-02-26
Subjects: Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Population Biology, Terrestrial and Aquatic Ecology
Charles Elton proposed that species-rich communities resist invasion better, but support is mainly from local studies, possibly because studies use observed richness alone, ignoring the dark diversity. I propose Completeness-Based Invasion Theory, linking invasibility inversely to community completeness, an index linking observed and dark diversity, enabling unified insights across scales.
Tapping into symbiosis to advance human microbiome research
Published: 2026-02-25
Subjects: Bacteriology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Other Microbiology, Pathogenic Microbiology
In human microbiome research, the term commensal is often used to describe organisms that benefit their hosts. In ecology, where the term originates, a commensal organism has no impact on its host, whereas a mutualist organism benefits its host. While others have recognized this discrepancy in terminology use, old habits are hard to break, and the human microbiome community has continued in this [...]
A new conceptual framework for host-microbe symbiosis
Published: 2026-02-25
Subjects: Ecology and Evolutionary Biology, Life Sciences
Host-microbe relationships are studied across biological disciplines, with different but related discipline-specific conceptual frameworks arising from each of them. Without a unified framework that can be applied across all symbioses, we cannot do the interdisciplinary work necessary to understand the underlying rules that govern symbiosis. Here I present a new conceptual framework for [...]
A comparison of methods to assess selective disappearance and quantify ageing
Published: 2026-02-25
Subjects: Ecology and Evolutionary Biology, Research Methods in Life Sciences
1. Age-dependent change in traits at the population-level level can diverge from the within-individual ageing trajectory due to selective disappearance, the biased removal or death of individuals with certain phenotypes. 2. Commonly used methods to assess, and account for, selective disappearance have been developed for relatively simple settings. As such, we currently lack a clear understanding [...]
Stronger Evidence for Trait–Environment Association by Pre-processing of Abundance Tables
Published: 2026-02-25
Subjects: Life Sciences
Understanding trait–environment relationships is central to predicting community responses to environmental change, yet statistical evidence for such relationships is often weak in observational datasets. Here, I introduce an N2-processing method for abundance tables, grounded in the observation that the precision of community weighted means (CWMs) and species niche centroids (SNCs) is [...]
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 [...]
Scalable Automated Video Labeling for Early Wildfire Smoke Detection with Fast-Then-Precise Two-Stage Inference
Published: 2026-02-25
Subjects: Computational Engineering
Early wildfire response depends on detecting the first faint appearance of smoke while maintaining low false-alarm rates across diverse cameras, lighting conditions, and environments. A central barrier to progress is the lack of scalable, reliable supervision for subtle early-stage smoke plumes, which makes models brittle under real-world domain shift. We address this challenge by introducing a [...]
Fitness costs of environmentally relevant concentrations of pharmaceuticals and personal care products in freshwater fauna: a systematic review and meta-analysis
Published: 2026-02-24
Subjects: Ecology and Evolutionary Biology, Environmental Health Life Sciences, Terrestrial and Aquatic Ecology
Pharmaceuticals and personal care products (PPCPs) are now ubiquitous in freshwater ecosystems, entering water bodies through widespread use and incomplete removal during wastewater treatment. These compounds include psychoactive substances, antibiotics, anti-inflammatory drugs, hormones, chemotherapeutic drugs, fragrances, preservatives, UV filters, plasticizers and others. Although many studies [...]
The Global Lakes Explorer: A basin-to-global scale data visualisation application for the assessment of nutrient emissions to lakes
Published: 2026-02-24
Subjects: Computer Sciences, Earth Sciences, Environmental Sciences, Life Sciences, Physical Sciences and Mathematics
Phosphorus and nitrogen are critical plant nutrients, essential for fertiliser production and global food security. However, poor management across the anthropogenic nutrient cycles leads to losses associated with pollution of water bodies, driving eutrophication, biodiversity loss, and methane emissions. Addressing these interconnected challenges requires a sustainable, integral, and where [...]
Notes on the taxonomy of the Cistanthe philhershkovitziana Hershk. species complex (C. sect. Cistanthe; Montiaceae)
Published: 2026-02-24
Subjects: Biodiversity
The Cistanthe philhershkovitziana Hershk. species complex (C. sect. Cistanthe; Montiaceae) here is informally circumscribed to include four named species, its namesake plus C. behacheliana Hershk., C. gbifiana Hershk., and C. reshetiana Hershk. The species occur in coastal Chile in the littoral and adjacent riparian zones, coastal plains, and coastal range matorral, extending some 600 km in [...]
Anecdote: When courtship blurs: a case of male-directed sexual signaling in house crickets (Acheta domesticus)
Published: 2026-02-24
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology
Same-sex sexual behaviour has been reported across diverse animal taxa and is increasingly understood as a flexible outcome of sexual signaling rather than an evolutionary anomaly. In insects, such behaviours are often temporary, context dependent, and expressed alongside opposite-sex courtship. This pattern has led to increasing emphasis on condition-dependent mating filters, defined as how [...]
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 [...]
A Niche in the Machine: The Promise of AI Foundation Models for Species Distribution Modeling
Published: 2026-02-24
Subjects: Ecology and Evolutionary Biology, Life Sciences
Species distribution models (SDM) are fundamental tools for conservation, yet methodological progress has stalled. Despite two decades of refinement, traditional approaches – MaxEnt, boosted regression trees, random forests – have approached a performance ceiling, and deep learning has failed to break through on species distribution data. TabPFN, a foundation model that learns to perform Bayesian [...]