Preprints

Filtering by Subject: Computational Biology

A universal DNA barcode for the Tree of Life

Bruno A S de Medeiros, Liming Cai, Peter J Flynn, et al.

Published: 2024-01-18
Subjects: Bioinformatics, Computational Biology, Genomics, Other Ecology and Evolutionary Biology

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, and rely on limited genomic loci that are not universal across the Tree of Life. Here, we develop a novel barcoding method that uses exceptionally low-coverage genome skim data to create a [...]

Towards the next generation of species delimitation methods: an overview of Machine Learning applications

Matheus Salles, Fabricius Domingos

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, with most of them being rooted in Coalescent Theory. Their primary goal is to identify independently evolving lineages that should represent separate species. Coalescent models have improved [...]

otb: Creating a HiC/HiFi Pipeline to Assemble the Prosapia bicincta Genome

David Molik, Amanda R Stahlke, Sharu P Sharma, et al.

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 (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 primary objective of otb is to [...]

Inferring diet, disease, and antibiotic resistance from the ancient oral microbiome

Gwyn Dahlquist-Axe, Francesca Standeven, Camilla Speller, et al.

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

Lisandro Milocco, Isaac Salazar-Ciudad

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

Djordje Bajic, Maria Rebolleda-Gomez, Martha Munoz, et al.

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

David Molik

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

José Cerca, Marius F. Maurstad, Nicolas Rochette, et al.

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 [...]

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