Preprints

Filtering by Subject: Bioinformatics

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 [...]

European light skin may have evolved as an adaptation to the Neolithic sedentary lifestyle

Manuel Ferrando-Bernal

Published: 2022-07-28
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

Norma Forero, Renata L. Muylaert, Stephanie N. Seifert, et al.

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

Robin Boyd, Tom August, Robert Cooke, et al.

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

Velen Yifei Wu, Binqi Chen, Rebecca Christofferson, et al.

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

Tiago R. Simões, Noah Greifer, Joëlle Barido-Sottani, et al.

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

Sanja Maria Hakala, Haruna Fujioka, Ornela De Gasperin, et al.

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 [...]

Towards a cohesive understanding of ecological complexity

Federico Riva, Caio Graco-Roza, Gergana N. Daskalova, et al.

Published: 2022-04-15
Subjects: Bioinformatics, Biology, Ecology and Evolutionary Biology, Life Sciences, Systems Biology

Understanding phenomena typical of complex systems is key for progress in ecology and conservation amidst escalating global environmental change. However, myriad definitions of complexity hamper conceptual advancements and synthesis. Ecological complexity may be better understood by following the strong theoretical basis of complexity science. We conduct bibliometric and text-mining analyses to [...]

Handling Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated Data

Tiago R. Simões, Oksana V. Vernygora, Bruno A.S. de Medeiros, et al.

Published: 2022-04-07
Subjects: Animal Sciences, Bioinformatics, Ecology and Evolutionary Biology, Evolution, Life Sciences, Research Methods in Life Sciences

Character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological datasets, as it violates the assumption of characters independency that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in datasets characterizing major evolutionary transitions, as these represent parts of the tree of life where [...]

Past and future uses of text mining in ecology & evolution

Maxwell Jenner Farrell, Liam Brierley, Anna Willoughby, et al.

Published: 2022-02-16
Subjects: Biodiversity, Bioinformatics, Ecology and Evolutionary Biology, Life Sciences

Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data [...]

101 years of biofluorescent animal studies: trends in literature, novel hypotheses, and best practices moving forward

Russell Gray, Catharina Karlsson

Published: 2022-02-06
Subjects: Animal Sciences, Bioinformatics, Life Sciences

Biofluorescent animals have become a recent trend in natural history publishing. While the functions and origins of biofluorescence in fauna remains somewhat controversial, trends in biofluorescence throughout published literature may elucidate these concepts. Here we review 101 years of biofluorescent studies encompassing 108 published papers and 977 unique species records. Our results provide [...]

Inferring trends in pollinator distributions across the Neotropics from publicly available data remains challenging despite mobilisation efforts

Robin Boyd, Marcelo Aizen, Rodrigo Barahon-Segovia, et al.

Published: 2022-01-24
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology

Aim: Aggregated species occurrence data are increasingly accessible through public databases for the analysis of temporal trends in species’ distributions. However, biases in these data present challenges for robust statistical inference. We assessed potential biases in data available through GBIF on the occurrences of four flower-visiting taxa: bees (Anthophila), hoverflies (Syrphidae), [...]

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 [...]

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