Preprints
Filtering by Subject: Computational Biology
EarthChirp: a global reference library for insect acoustic recognition and discovery across the audible and ultrasonic spectrum
Published: 2026-06-18
Subjects: Computational Biology, Ecology and Evolutionary Biology, Entomology, Genetics and Genomics
1. Passive acoustic monitoring (PAM) is scaling rapidly, but automated recognition for insects lags far behind birds. The dominant recogniser (BirdNET) classifies only ~35 insect species and building bespoke insect classifiers requires labelled training data that does not exist for most taxa. 2. We present EarthChirp, a training-free recogniser for singing insects (Orthoptera and Cicadidae) [...]
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 [...]
EntoScan and BEEomass: a standardized imaging system and a physically motivated model for high-throughput dry biomass estimation of arthropods
Published: 2026-06-12
Subjects: Biodiversity, Computational Biology, Computational Engineering, Ecology and Evolutionary Biology, Engineering, Entomology
Computer vision and AI are now widely used for automated insect classification, but their potential for estimating other traits, such as biomass, is not yet fully explored. Insect biomass is a key measure of ecosystem function, informing ecosystem services, food webs, and environmental change. It is also used to track population trends and estimate the contribution of insects to ecosystem carbon. [...]
Inferring genomic landscapes with the integrative sequentially Markov coalescent (iSMC)
Published: 2026-05-28
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 [...]
A macroevolutionary gene network reveals diapause evolutionary dynamics beyond the circadian clock and predicts microevolution
Published: 2026-02-16
Subjects: Computational Biology, Evolution, Genomics, Other Genetics and Genomics, Population Biology
Diapause is an alternative developmental pathway evolved independently in many insects to synchronize life cycles with resource abundance. While subsets of this essential phenotype have long been studied at a single species level, the genomic basis of the full diapause syndrome remains poorly understood. Remaining unknown is whether convergent diapause syndromes employ shared mechanisms. This [...]
IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
Published: 2025-05-06
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences
IQ-TREE and MCMCTree are two widely used phylogenetic tools to infer phylogenetic trees and estimate divergence times, respectively. As MCMCTree performs fast approximate Markov Chain Monte Carlo sampling to obtain the times along a fixed tree topology, it would be natural to use IQ-TREE to obtain the tree. However, it is currently not possible to integrate these tools seamlessly, as MCMCTree [...]
Abiogenesis as the origin of selection. An alternative to the Oparin-Haldane model
Published: 2025-02-18
Subjects: Biochemistry, Biochemistry, Biophysics, and Structural Biology, Cellular and Molecular Physiology, Comparative and Evolutionary Physiology, Computational Biology, Evolution, Molecular Biology, Molecular Genetics, Other Ecology and Evolutionary Biology, Population Biology, Systems and Integrative Physiology Life Sciences, Systems Biology
The emergence of life from non-living matter remains one of the most profound unresolved questions in natural philosophy. Current paradigms largely inherit the Oparin-Haldane assumption that abiogenesis is preceded by a prolonged accumulation of traits through nonadaptive (e.g. self-organisation) and adaptive processes. Yet this raises a legitimate question: how can adaptive evolution occur [...]
FAIRification of DMRichR Pipeline: Advancing Epigenetic Research on Environmental and Evolutionary Model Organisms
Published: 2024-11-05
Subjects: Bioinformatics, Computational Biology, Environmental Public Health, Life Sciences, Other Ecology and Evolutionary Biology
Bioinformatics tools often prioritize humans or human-related model organisms, overlooking the requirements of environmentally relevant species, which limits their use in ecological research. This gap is particularly challenging when implementing existing software, as inadequate documentation can delay the innovative use of environmental models for modern risk assessment of chemicals that can [...]
Why there are so many definitions of fitness in models
Published: 2024-04-11
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences, Population Biology
Evolutionary “fitness” is operationalized in many different ways. Its role is to quantify that which is favored by natural selection. Generally, short-term ability to survive and reproduce (e.g., expected number of surviving offspring) is assigned to genotypes or phenotypes, and used to non-trivially derive longer-term quantities (e.g. invasion rate or fixation probability) that provide insight [...]
A composite universal DNA signature for the Tree of Life
Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology
Species identification using DNA barcodes has revolutionized biodiversity sciences.However, conventional barcoding methods may lack power and universal applicability across the Tree of Life. Alternative methods based on whole genome sequencing are hard to scale due to large data requirements. Here, we develop a novel DNA-based identification method, varKoding, using exceptionally low-coverage [...]
Towards the next generation of species delimitation methods: an overview of Machine Learning applications
Published: 2023-12-07
Subjects: Biology, Computational Biology, Ecology and Evolutionary Biology, Genetics and Genomics
Species delimitation is the process of distinguishing between populations of the same species and distinct species of a particular group of organisms. Various methods exist for inferring species limits, whether based on morphological, molecular, or other types of data. In the case of methods based on DNA sequences, most of them are rooted in the coalescent theory. However, coalescence-based [...]
otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome
Published: 2023-12-05
Subjects: Agriculture, Bioinformatics, Computational Biology, Genomics, Other Animal Sciences
The implementation of a new genomic assembly pipeline named only the best [Genome Assembly Tools] (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The [...]
Inferring diet, disease, and antibiotic resistance from the ancient oral microbiome
Published: 2023-11-17
Subjects: Bacteriology, Computational Biology, Life Sciences
The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the [...]
Learning from your mistakes: a novel method to predict the response to directional selection
Published: 2021-09-27
Subjects: Animal Sciences, Computational Biology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Life Sciences, Other Ecology and Evolutionary Biology, Population Biology
Predicting how populations respond to selection is a key goal of evolutionary biology. The field of quantitative genetics provides predictions for the response to directional selection through the breeder’s equation. However, differences between the observed responses to selection and those predicted by the breeder’s equation occur. The sources of these errors include omission of traits under [...]
The macroevolutionary consequences of niche construction in microbial metabolism
Published: 2021-05-31
Subjects: Bioinformatics, Computational Biology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Evolution, Genetics and Genomics, Life Sciences, Microbiology, Population Biology, Systems Biology
Microorganisms display a stunning metabolic diversity. Understanding the origin of this diversity requires understanding how macroevolutionary processes such as innovation and diversification play out in the microbial world. Metabolic networks, which govern microbial resource use, can evolve through different mechanisms, e.g. horizontal gene transfer or de novo evolution of enzymes and pathways. [...]