Preprints

Filtering by Subject: Bioinformatics

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

Elizabeth M Joyce, Alexander N Schmidt-Lebuhn, Harvey K Orel, et al.

Published: 2024-05-27
Subjects: Bioinformatics, Biology, Botany, Ecology and Evolutionary Biology, Evolution, Life Sciences, Plant Sciences, Research Methods in Life Sciences

Target capture has quickly become a preferred approach for plant systematic and evolutionary research, marking a step-change in the generation of data for phylogenetic inference. While this advancement has facilitated the resolution of many phylogenetic relationships, phylogenetic conflict continues to be reported, and often attributed to genome duplication, reticulation, deep coalescence or [...]

A minimum data standard for wildlife disease studies

Tess Stevens, Ryan Zimmerman, Greg Albery, et al.

Published: 2024-05-19
Subjects: Animal Diseases, Biodiversity, Bioinformatics, Diseases, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Parasitic Diseases, Veterinary Infectious Diseases, Veterinary Medicine, Virology, Virus Diseases

Thousands of scientists and practitioners conduct research on infectious diseases of wildlife. Rapid and comprehensive data sharing is vital to the transparency and actionability of their work, but unfortunately, most efforts designed to publically share these data are focused on pathogen determination and genetic sequence data. Other facets of existing surveillance data – particularly negative [...]

Guidance framework to apply good practices in ecological data analysis: Lessons learned from building Galaxy-Ecology

Coline Royaux, Jean-Baptiste Mihoub, Marie Jossé, et al.

Published: 2024-04-11
Subjects: Bioinformatics, Other Ecology and Evolutionary Biology

Numerous conceptual frameworks exist for good practices in research data and analysis (e.g. Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework to achieve good practices for building analytical procedures based on atomisation and [...]

Incomplete lineage sorting and hybridization underlie of tree discordance in Petunia and related genera (Petunieae, Solanaceae)

Pedro Henrique Pezzi, Lucas C Wheeler, Loreta Brandão Freitas, et al.

Published: 2024-03-29
Subjects: Biodiversity, Bioinformatics, Botany, Genomics

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies [...]

Ten Simple Rules to build a Model Life Cycle

Timothée Poisot, Daniel J Becker, Cole B Brookson, et al.

Published: 2024-02-09
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Software Engineering

Just like data, models have their own life cycle. By recognizing how one’s model fits within the life cycle of the data (or at least, ensuring that the model life cycle is understood), we can identify opportunities to foster new collaborations, encourage better practices in data analysis, and ultimately accelerate research. In this manuscript, we introduce the Model Life Cycle and develop a [...]

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 [...]

A big data and machine learning approach for monitoring the condition of ecosystems

Miguel Equihua, Octavio Pérez-Maqueo, Julián Equihua, et al.

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

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 [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

Daniele Da Re, Enrico Tordoni, Jonathan Lenoir, et al.

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

Deborah M Leigh, Amy Vandergast, Maggie Hunter, et al.

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

Benjamin A Adler, Marena I Trinidad, Daniel Bellieny-Rabelo, et al.

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: an open source macOS application for microsatellite genotyping

Jean Peccoud

Published: 2023-07-29
Subjects: Biodiversity, Bioinformatics, Molecular Genetics, Other Ecology and Evolutionary Biology

In the context of population genetics, microsatellite markers analyzed by capillary sequencing remain useful tools for quick genotyping and low-cost studies. This contrasts with the lack of a free application to analyze chromatograms for microsatellite genotyping that is designed for population geneticists. To fill this gap, I have developed STRyper, a macOS application whose source code is [...]

Understanding local plant extinctions before it’s too late: bridging evolutionary genomics with global ecology.

Moises Exposito-Alonso

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

Milo S. Johnson, Sandeep Venkataram, Sergey Kryazhimskiy

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

Oliver White, Manosh Biswas, Wendawek M. Abebe, et al.

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 [...]

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