Preprints
Filtering by Subject: Bioinformatics
Scenario-dependent functional connectivity in a crowded seascape: habitat suitability, shipping pressure and marine infrastructure in the North Sea
Published: 2026-09-09
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences, Marine Biology
Marine spatial planning increasingly needs seascape connectivity evidence to balance biodiversity conservation, offshore energy development and shipping. However, predicted functional connectivity depends strongly on how habitat suitability and human-use pressures are translated into resistance surfaces. This study tested how shipping and marine infrastructure alter HSM-derived connectivity [...]
wildtag.ai: an open-access end-to-end offline AI-assisted desktop application for managing camera trap projects
Published: 2026-09-01
Subjects: Artificial Intelligence and Robotics, Bioinformatics, Computer Sciences, Databases and Information Systems, Ecology and Evolutionary Biology, Environmental Monitoring, Environmental Sciences, Life Sciences, Natural Resources and Conservation, Natural Resources Management and Policy, Physical Sciences and Mathematics, Terrestrial and Aquatic Ecology
1. Camera traps generate massive volumes of data, yet their decision-support potential is diluted by the bottleneck of manual processing. Automated classification has largely solved this, but classification alone does not remove the barriers to adoption: it must be coupled with the means to turn predictions into a verified, shareable dataset, which no existing tool does end-to-end, offline, and [...]
Computational classification of SOD2 protein in coral and symbiotic algae from public genomic and transcriptomic data
Published: 2026-08-20
Subjects: Bioinformatics, Biology, Life Sciences, Marine Biology, Other Ecology and Evolutionary Biology
SOD2, or Manganese/Iron Superoxide Dismutase, plays a crucial role in maintaining cellular health across the tree of life. Existing literature is vague in identifying types of SOD2 proteins expressed in both corals and their symbiotic algae; most agree on the presence of a) mitochondrial targeting MnSOD in corals, and b) likely Mn dependent SOD2 in algae. This paper presents evidence for four [...]
Toward a standardized workflow for pre-processing large vegetation-plot databases
Published: 2026-08-17
Subjects: Bioinformatics, Botany, Ecology and Evolutionary Biology, Forest Sciences
Large vegetation-plot databases have opened unprecedented opportunities for investigating vegetation patterns and processes across large spatial and temporal scales. However, such databases are typically created by combining pre-existing smaller databases or datasets that often used different standards and protocols, leading to data inconsistencies (e.g., different taxonomy and nomenclature) and [...]
Assessing phylogenetic inference in the era of AI-driven protein structures
Published: 2026-08-11
Subjects: Bioinformatics
Phylogenetic inference is one of the most common downstream applications of multiple sequence alignment. Quantitative assessment of inferred trees is essential for evaluating the reliability of both alignments and phylogenetic inferences. Establishing a robust assessment framework for phylogenetic trees therefore provides a basis for examining and improving methods for alignment and tree [...]
varKodes extend DNA barcoding to ultrafine-grained identity, place, and state
Published: 2026-07-23
Subjects: Biodiversity, Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
DNA barcoding has transformed biodiversity science, but locus-based markers often fail across taxa, at shallow phylogenetic depths, and in mixed or spatially structured samples. Here, we test whether varKoder, an alignment-free framework that converts low-coverage genomic reads into image-based genomic signatures (varKodes), can extend barcoding from taxonomic identification to broader inference [...]
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: [...]