Preprints
Filtering by Subject: Bioinformatics
Is Biology Necessary to Advance Biology?
Published: 2026-07-14
Subjects: Biochemistry, Biophysics, and Structural Biology, Biodiversity, Bioinformatics, Biology, Cell and Developmental Biology, Computational Biology, Philosophy, Scholarship of Teaching and Learning, Systems Biology
AI is transforming the workflow of biological science. But what role remains for human cognition when the priority is deep theory? We propose a division of labor based on a “coverage asymmetry” between artificial and biological agents. AI excels at extending the encounterable: scaling known mechanisms and exploring complex parameter regimes. However, AI cannot (yet) perform kind formation – the [...]
Lactate Dehydrogenase as a Candidate Genomic Marker of Climate Change in Mammals?
Published: 2026-07-13
Subjects: Bioinformatics, Comparative and Evolutionary Physiology, Evolution, Genetics, Genomics, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology
Climate change imposes metabolic and thermal stress on mammals, yet genomic markers that track lineage specific adaptation remain limited. Lactate dehydrogenase (LDH), a central enzyme in lactate metabolism and anaerobic stress response, has not previously been evaluated for its evolutionary association with climate change induced selection. Here, comparative genomics across 14 mammalian species [...]
What’s in a name? Bioinformatics and the challenge of using eDNA metabarcoding to report non-indigenous species detections
Published: 2026-07-06
Subjects: Biodiversity, Bioinformatics, Other Ecology and Evolutionary Biology
Environmental DNA (eDNA) metabarcoding is increasingly employed for surveillance of non-indigenous species (NIS), offering the promise of simultaneous multi-taxon de-tection, scalability, and the capacity for early detection before populations become es-tablished. The sensitivity of metabarcoding that makes it attractive for NIS surveil-lance also creates a meaningful risk of erroneous detections [...]
A self tuning sliding window method for detecting phenotype linked regional poly-methylation architecture in sparse wildlife methylomes
Published: 2026-06-26
Subjects: Bioinformatics, Cellular and Molecular Physiology, Comparative and Evolutionary Physiology, Evolution, Genetics and Genomics, Marine Biology, Other Ecology and Evolutionary Biology
Despite featuring extreme physiological adaptations integration of wildlife species into the modern ‘omics’ frameworks are limited due to the sparsity in the data. To address the sparsity limitation a self-tuning sliding-window framework was developed for the identification of the regional poly-CpG methylation architecture associated with phenotypic traits. Under the framework the iteratively [...]
Choices that matter: the impact of substitution models on machine learning-based species delimitation inference
Published: 2026-06-17
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Life Sciences, Molecular Genetics
The choice of nucleotide substitution models is a cornerstone of phylogenetic inference, influencing the accuracy of the estimated evolutionary parameters and, by extension, demographic and species delimitation model selection. With the growing adoption of machine learning methods trained on simulated data, it remains unclear how the substitution model used during simulation training influences [...]
Mapping microclimate temperatures in open ecosystems using UAVs: a comparison between thermal, correlative, and mechanistic approaches
Published: 2026-06-09
Subjects: Bioinformatics, Climate, Ecology and Evolutionary Biology, Environmental Engineering, Environmental Monitoring
Open terrestrial ecosystems exhibit pronounced fine scale thermal heterogeneity, yet spatially continuous microclimate data at biologically relevant heights and scales remain scarce. Here, we evaluate three unoccupied aerial vehicle (UAV) informed approaches for mapping microclimate temperatures, including land surface temperature (LST) and near surface air temperature (T13cm), in an open [...]
MSCquartets 3.3: Fast Inference of Species Networks and Trees of Blobs under the Multispecies Coalescent
Published: 2026-06-09
Subjects: Bioinformatics
The R package MSCquartets offers a suite of methods for testing and inferring species relationships from gene trees under coalescent models. MSCquartets 3.3 significantly extends the functionality of version 1.0 by implementing the TINNiK and ECToBlob algorithms for inference of the tree of blobs under the network multispecies coalescent model (NMSC). Additionally, it implements the NANUQ+ [...]
Inferring genomic landscapes with the integrative sequentially Markov coalescent (iSMC)
Published: 2026-05-27
Subjects: Bioinformatics, Biology, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The integrative Sequentially Markovian Coalescent (iSMC) is an extension of the sequentially Markovian Coalescent (SMC) model allowing for parameter heterogeneity along the genome, such as recombination and mutation rates. Heterogeneous parameters follow an autocorrelation process that modulates the genealogical process, extending the hidden state space and adding as few as two extra parameters [...]
Threatscapes for the aeroconservation of birds
Published: 2026-05-22
Subjects: Biodiversity, Bioinformatics, Zoology
The airspace is increasingly cluttered with threats to aerial organisms in the form of anthropogenic structures and vehicles, likely contributing to bird population declines through additive mortality mediated by collisions. In the United States alone, up to and likely exceeding one billion birds die annually due to collisions aloft, and most of these fatalities are related to six threat types: [...]
A Protocol for Standardizing Measurements and Enabling Global Harmonization of Herbarium Leaf Reflectance Spectra
Published: 2026-05-19
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. Because inconsistencies in instrumentation and measurement practices can increase noise and limit dataset compatibility, the International Herbarium Spectral Digitization Working Group (IHerbSpec) has [...]
Representational limits in detecting ecological change
Published: 2026-04-28
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, [...]
Sample size shapes metabarcoding-driven biodiversity assessments across body sizes in soil
Published: 2026-04-14
Subjects: Biodiversity, Bioinformatics, Life Sciences
Understanding how sample size influences biodiversity detection across taxonomic groups differing in body size is critical for designing robust and cost-efficient metabarcoding studies of soil eukaryotes. Using a soil mass gradient (0.25-32 g) combined with a universal 18S rRNA metabarcoding approach, we quantified how sample mass shapes diversity estimates across eukaryotic taxa. Diversity [...]
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 [...]
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 [...]
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 [...]