Preprints
Filtering by Subject: Computational Biology
On the feasibility of nonadaptive, nonsequential abiogenesis
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. Classical models derived from the Oparin-Haldane hypothesis assume a gradual (sequential), selective assembly of biological precursors. Yet, for more than a century, all experimental efforts in this direction have failed in their attempt to achieve material abiogenesis. May be [...]
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
“Fitness” quantifies the ability to survive and reproduce, but is operationalized in many different ways. Generally, short-term fitness (e.g., expected number of surviving offspring) is assigned to genotypes or phenotypes, and used to non-trivially derive longer-term operationalizations of fitness (e.g. fixation probability or sojourn time), providing insight as to which organismal strategies [...]
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 applicabilityacross the Tree of Life. Alternative methods based on whole genome sequencing are hardto scale due to large data requirements. Here, we develop a novel DNA-based identificationmethod, varKoding, using exceptionally low-coverage genome [...]
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. [...]
met v1: Expanding on old estimations of biodiversityfrom eDNA with a new software framework
Published: 2021-04-27
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Life Sciences
A long-standing problem in environmental DNA has been the inability to compute across large number of datasets. Here we introduce an open-source software framework that can store a large number of environmental DNA datasets, as well as provide a platform for analysis, in an easily customizable way. We show the utility of such an approach by analyzing over 1400 arthropod metabarcode datasets. This [...]
Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms
Published: 2020-08-30
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Genomics, Life Sciences
The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele [...]