Preprints
Filtering by Subject: Bioinformatics
A big data and machine learning approach for monitoring the condition of ecosystems
Published: 2024-01-16
Subjects: Applied Statistics, Biodiversity, Bioinformatics, Earth Sciences, Ecology and Evolutionary Biology, Environmental Sciences, Forest Biology, Forest Sciences, Life Sciences, Other Ecology and Evolutionary Biology, Physical Sciences and Mathematics, Statistical Methodology, Statistical Models, Terrestrial and Aquatic Ecology
Ecosystems are highly valuable as a source of goods and services and as a heritage for future generations. Knowing their condition is extremely important for all management and conservation activities and public policies. Until now, the evaluation of ecosystem condition has been unsatisfactory and thus lacks practical implementation for most countries. We propose that ecosystem integrity is a [...]
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 [...]
Towards causal relationships for modelling species distribution
Published: 2023-10-14
Subjects: Biodiversity, Bioinformatics, Life Sciences, Natural Resources and Conservation, Statistical Models
1. Understanding the processes underlying the distribution of species through space and time is fundamental in several research fields spanning from ecology to spatial epidemiology. Correlative species distribution models (SDMs) involve popular statistical tools to infer species geographical distribution thanks to spatiotemporally explicit observations of species occurrences coupled with a set of [...]
Best practices for genetic and genomic data archiving
Published: 2023-09-25
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of [...]
CasPEDIA Database: A Functional Classification System for Class 2 CRISPR-Cas Enzymes
Published: 2023-08-17
Subjects: Biochemistry, Biophysics, and Structural Biology, Bioinformatics, Life Sciences
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain [...]
STRyper: a macOS application for microsatellite genotyping and chromatogram management
Published: 2023-07-29
Subjects: Biodiversity, Bioinformatics, Molecular Genetics, Other Ecology and Evolutionary Biology
Microsatellite markers analyzed by capillary sequencing remain useful tools for rapid genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms for microsatellite genotyping that is not restricted to human genotyping. To fill this gap, I have developed STRyper, a macOS application whose source code is published under the General Public License. [...]
Understanding local plant extinctions before it’s too late: bridging evolutionary genomics with global ecology.
Published: 2022-12-01
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Plant Sciences
Understanding evolutionary genomic and population processes within a species range is key to anticipating the extinction of plant species before it is too late. However, most models of biodiversity risk projections under global change do not account for the genetic variation and local adaptation of different populations. Population diversity is critical to understanding extinction because [...]
Best practices in designing, sequencing and identifying random DNA barcodes
Published: 2022-09-28
Subjects: Bioinformatics, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new optimal design that balances [...]
Maintenance and expansion of genetic and trait variation following domestication in a clonal crop
Published: 2022-09-01
Subjects: Agriculture, Bioinformatics, Biosecurity, Genetics and Genomics, Genomics, Life Sciences, Plant Sciences
Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic [...]
European light skin may have evolved as an adaptation to the Neolithic sedentary lifestyle
Published: 2022-07-27
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences, Population Biology
Light skin facilitates the penetration of ultraviolet light (UV) radiation through the skin, increasing the synthesis of vitamin D that in turn stimulates bone formation. It has been suggested that light skin appeared in the ancestors of modern Europeans as an adaptation to the conditions of low UV radiation in high latitudes; however, paleogenetic studies have recently shown it did not evolve [...]
The coevolutionary mosaic of bat betacoronavirus emergence risk
Published: 2022-07-01
Subjects: Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Immunology and Infectious Disease, Life Sciences, Other Ecology and Evolutionary Biology, Other Life Sciences
Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, MERS, and COVID-19, we examine the global [...]
An operational workflow for producing periodic estimates of species occupancy at large scales
Published: 2022-06-23
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences
Policy makers require high-level summaries of biodiversity change. However, deriving such summaries from raw biodiversity data is a complex process involving several intermediary stages. In this paper, we describe a workflow for generating annual estimates of species’ occupancy at national scales from raw species occurrence data, which can be used to construct a range of policy-relevant [...]
A minimum data standard for vector competence experiments
Published: 2022-06-14
Subjects: Bioinformatics, Entomology, Life Sciences, Microbiology, Virology
The growing threat of vector-borne diseases, highlighted by recent epidemics, has prompted increased focus on the fundamental biology of vector-virus interactions. To this end, experiments are often the most reliable way to measure vector competence (the potential for arthropod vectors to transmit certain pathogens). Data from these experiments are critical to understand outbreak risk, but – [...]
EvoPhylo: an R package for pre- and postprocessing of morphological data from relaxed clock Bayesian phylogenetics
Published: 2022-06-06
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Evolution, Life Sciences
1. Relaxed clock Bayesian evolutionary inference (BEI) enables the co-estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the past decade have boosted BEI as a major macroevolutionary analytical framework using morphological and/or molecular data across vastly different study systems. [...]
Evolution and impact of socially transferred materials
Published: 2022-05-27
Subjects: Animal Sciences, Biodiversity, Bioinformatics, Cell and Developmental Biology, Ecology and Evolutionary Biology, Genetics and Genomics, Life Sciences, Physiology, Systems Biology
Since the dawn of life, transfers of metabolized material between individuals have led to great innovations of evolution. When metabolized material is transferred from one individual’s body to another (as with sperm, eggs, milk, symbionts), secondary manipulative molecules that induce a physiological response in the receiver are often transferred along with the primary cargo. The bioactive and [...]