Preprints
Filtering by Subject: Research Methods in Life Sciences
A Protocol for Standardizing Measurements and Enabling Global Harmonization of Herbarium Leaf Reflectance Spectra
Published: 2026-05-20
Subjects: Biochemistry, Biophysics, and Structural Biology, Biodiversity, Bioinformatics, Botany, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Research Methods in Life Sciences
Reflectance spectroscopy offers a powerful approach to integrate high- throughput phenotypic data from herbarium specimens into the digital landscapes of ecology, evolution, and systematics. Spectral digitization complements specimen metadata capture and photographic imaging by generating high-dimensional optical data from herbarium tissues that encode information about plant chemistry and [...]
Expanding the sentinel approach through multimodal integration: resolving underlying ecological processes with eDNA and computer vision
Published: 2026-05-20
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology, Research Methods in Life Sciences, Terrestrial and Aquatic Ecology
Sentinel approaches provide a semi-controlled method for quantifying in-field ecological interactions and processes while reducing bias and labour. They are, however, limited by difficulties ascribing taxonomic identities, behavioural context and temporal resolution to interacting agents. The integration of additional sources of data, including the analysis of DNA left behind on sentinel objects [...]
Representational limits in detecting ecological change
Published: 2026-04-29
Subjects: Agriculture, Animal Sciences, Biochemistry, Biophysics, and Structural Biology, Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Entomology, Food Science, Forest Sciences, Genetics and Genomics, Immunology and Infectious Disease, Laboratory and Basic Science Research Life Sciences, Life Sciences, Marine Biology, Microbiology, Neuroscience and Neurobiology, Other Life Sciences, Pharmacology, Toxicology and Environmental Health, Physiology, Plant Sciences, Research Methods in Life Sciences, Systems Biology
Detecting ecological change remains a persistent challenge, even in systems with extensive monitoring data and increasingly sophisticated analytical tools. Uncertainty is usually attributed to stochasticity, limited observations, or imperfect models. Here, I argue that an additional and largely overlooked constraint arises from representational limits: systematic ways in which graphs, indicators, [...]
The promise and challenge of environmental epigenomics in a rapidly changing world
Published: 2026-04-22
Subjects: Animal Sciences, Biology, Environmental Studies, Genetics and Genomics, Life Sciences, Research Methods in Life Sciences
There has been a fast-paced research effort on the role of epigenetic mechanisms in facilitating organisms’ capacity to cope with rapid environmental change, highlighted by several recent reviews and special issues on this topic. What is important, along with this momentum, is to pause and reflect on both the promises and challenges of linking detailed molecular mechanisms to broad patterns of [...]
Multi-scale collapse of coral cover under climate change
Published: 2026-04-09
Subjects: Applied Mathematics, Applied Statistics, Biodiversity, Biology, Dynamic Systems, Ecology and Evolutionary Biology, Environmental Indicators and Impact Assessment, Environmental Monitoring, Longitudinal Data Analysis and Time Series, Marine Biology, Mathematics, Numerical Analysis and Computation, Research Methods in Life Sciences, Statistical Methodology, Statistical Models, Survival Analysis, Systems Biology
Projecting ecosystem trajectories under future climates is critical for conservation planning, yet remains constrained by uncertainty arising from limited data, ecological complexity, and biological and environmental variability. Variability, when disentangled from uncertainty, offers critical insights into population and community dynamics. For example, enhanced vital rates (growth, survival, [...]
Genetic variance and phenotypic selection on pathogen-linked oviposition choice in Drosophila
Published: 2026-03-24
Subjects: Animal Experimentation and Research, Behavior and Ethology, Entomology, Evolution, Genetics, Integrative Biology, Research Methods in Life Sciences, Zoology
Pathogen-avoidance behaviour is assumed to be adaptive, yet its phenotypic variability and genetic heritability are rarely quantified. In species lacking post-oviposition care, avoiding potentially infectious egg-laying substrates would improve offspring survival and should therefore be under strong selection. We used two-choice oviposition assays to quantify the phenotypic and genetic variance [...]
Insect oviposition as a simple system to investigate the ecology and evolution of pathogen avoidance behaviour
Published: 2026-03-21
Subjects: Animal Experimentation and Research, Behavior and Ethology, Biology, Entomology, Evolution, Immunology and Infectious Disease, Integrative Biology, Laboratory and Basic Science Research Life Sciences, Research Methods in Life Sciences, Zoology
Behavioural avoidance of pathogens and parasites is a ubiquitous first line of defence, yet we lack tractable systems that connect cue detection to fitness consequences, population transmission, and coevolution. We propose insect oviposition as a model that yields general principles for avoidance across taxa. Oviposition decisions fix offspring exposure, they are governed by well‑mapped sensory [...]
Biases in common methods used to quantify ageing and selective disappearance- a guide
Published: 2026-02-26
Subjects: Ecology and Evolutionary Biology, Research Methods in Life Sciences
1. Observed population-level patterns of age-dependent trait expression can fail to reflect the average, latent 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 scenarios: linear [...]
Composite virulence: useful metric or conceptual trap?
Published: 2026-02-21
Subjects: Animal Diseases, Animal Experimentation and Research, Animal Sciences, Biodiversity, Biology, Ecology and Evolutionary Biology, Evolution, Immunity, Immunology and Infectious Disease, Immunology of Infectious Disease, Immunopathology, Life Sciences, Medical Microbiology, Microbiology, Other Ecology and Evolutionary Biology, Other Immunology and Infectious Disease, Parasitic Diseases, Parasitology, Pathogenic Microbiology, Plant Pathology, Research Methods in Life Sciences, Zoology
Virulence, defined as the harm an infection causes to its host, is central to evolutionary ecology, yet it remains difficult to quantify because infection impact is multidimensional, dynamic, and context-dependent. Composite measures have therefore emerged to summarise multiple traits into a single estimate of infection-induced harm. However, every composite embeds biological assumptions about [...]
One Toolbox, Many Tools: A Practitioner’s Guide to Model-based Ordination for Community Ecology
Published: 2026-02-05
Subjects: Ecology and Evolutionary Biology, Multivariate Analysis, Research Methods in Life Sciences, Statistical Methodology, Statistical Models
This article presents the case for model-based ordination by way of Generalized Linear Latent Variable Models (GLLVMs) as a go-to choice of statistical method for any community ecologist wanting to tackle a range of present-day ecological research questions. Model-based ordination brings tools and capabilities from classic (mixed-effects) regression models to multivariate community analysis, [...]
Shared acoustic manifolds for exploratory comparison of passerine vocalizations
Published: 2026-01-24
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Research Methods in Life Sciences
This study presents a fixed-parameter pipeline designed to support reproducible embedding of frame-level representations of multiple passerine vocalizations within shared low-dimensional spaces. Three passerine species are considered: Eurasian Wren, Tree Pipit and Common Chaffinch, with a selection of four individuals for each species group. Vocalization frames from each species group are mapped [...]
Phenotyping avian bill sizes; combining the collection of standardized still images with software to obtain observer-independent measures of avian bill shapes
Published: 2026-01-02
Subjects: Animal Sciences, Ecology and Evolutionary Biology, Life Sciences, Research Methods in Life Sciences
Avian bill size is a morphological trait with evolutionary and ecological importance. Obtaining large-scale observer-independent measures of bill length and bill depth has proven to be challenging. We developed a device, the Bill Phenotyping Box, that allows taking standardized still images from wild small passerine birds in the field. We combine this with dedicated software that, based on a [...]
sitetool: an application for field site selection and evaluation
Published: 2025-10-28
Subjects: Life Sciences, Research Methods in Life Sciences
Field studies are fundamental to ecological research, yet many studies rely on unspecified or convenience-based methods for site selection, potentially introducing bias that can compromise research results. Remote-sensing data provides a quantitative way to evaluate potential sites without expensive pilot visits, however, interacting with spatial data can be computationally complex. We present an [...]
GhostNetZero: AI for Detecting Marine Ghost Nets
Published: 2025-09-23
Subjects: Artificial Intelligence and Robotics, Biodiversity, Databases and Information Systems, Environmental Monitoring, Marine Biology, Research Methods in Life Sciences, Sustainability
Abandoned, lost, or otherwise discarded fishing gears (ALDFG), commonly referred to as ghost nets, pose a persistent global threat to marine biodiversity. Constructed from durable synthetic polymers, ghost nets remain intact for decades, continuing to entangle and kill marine organisms while damaging habitats and imposing economic burdens on fisheries and coastal communities. Despite their [...]
The myth of the metabolic baseline: how sleep-wake cycles undermine a foundational assumption in organismal biology
Published: 2025-08-28
Subjects: Animal Experimentation and Research, Biochemistry, Biophysics, and Structural Biology, Biology, Comparative and Evolutionary Physiology, Life Sciences, Physiology, Research Methods in Life Sciences, Zoology
Basal and standard metabolic rates (BMR and SMR) are cornerstones of physiological ecology and are assumed to be relatively fixed intrinsic properties of organisms that represent the minimum energy required to sustain life. However, this assumption is conceptually flawed. Many core maintenance processes underlying SMR are temporally partitioned across sleep and wakefulness and are not [...]