Preprints

Filtering by Subject: Cell and Developmental Biology

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 [...]

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 [...]

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 [...]

Patterns of selection across gene regulatory networks

Jeanne M. C. McDonald, Robert D. Reed

Published: 2022-04-25
Subjects: Cell and Developmental Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences

Gene regulatory networks (GRNs) are the core engine of organismal development. If we would like to understand the origin and diversification of phenotypes, it is necessary to consider the structure of GRNs in order to reconstruct the links between genetic mutations and phenotypic change. Much of the progress in evolutionary developmental biology, however, has occurred without a nuanced [...]

Molecular Paleobiology of the Echinoderm Skeleton

Jeffrey Thompson

Published: 2022-01-10
Subjects: Cell and Developmental Biology, Developmental Biology, Ecology and Evolutionary Biology, Life Sciences, Other Ecology and Evolutionary Biology

Molecular paleobiology provides a promising avenue to merge data from deep time, molecular biology and genomics, gaining insights into the evolutionary process at multiple levels. The echinoderm skeleton is a model for molecular paleobioloogical studies. I begin with an overview of the skeletogenic process in echinoderms, as well as a discussion of what gene regulatory networks are, and why they [...]

Integrating natural and sexual selection across the biphasic life cycle

Craig Purchase, Jonathan Evans, Julissa Roncal

Published: 2021-06-23
Subjects: Agriculture, Behavior and Ethology, Cell and Developmental Biology, Developmental Biology, Ecology and Evolutionary Biology, Evolution, Food Biotechnology, Food Science, Life Sciences, Other Ecology and Evolutionary Biology

An alternation between diploid and haploid phases is universal among sexual eukaryotes. Across this biphasic cycle, natural selection and sexual selection occur in both phases. Together, these four stages of selection act on the phenotypes of individuals and influence the evolutionary trajectories of populations, but are rarely studied holistically. Here, we provide a conceptual framework that [...]

Impact of Infectious Disease on Humans and Our Origins

Petar Gabrić

Published: 2021-06-19
Subjects: Anthropology, Archaeological Anthropology, Arts and Humanities, Bacteriology, Biochemistry, Biophysics, and Structural Biology, Biological and Physical Anthropology, Biological Phenomena, Cell Phenomena, and Immunity, Cell and Developmental Biology, Cell Biology, Ecology and Evolutionary Biology, Evolution, Genetic Phenomena, Genetics, Genetics and Genomics, History of Art, Architecture, and Archaeology, Life Sciences, Medical Biochemistry, Medical Cell Biology, Medical Genetics, Medical Immunology, Medical Microbiology, Medical Molecular Biology, Medical Pathology, Medical Sciences, Medicine and Health Sciences, Microbiology, Molecular Biology, Molecular Genetics, Pathogenic Microbiology, Pharmacology, Pharmacology, Toxicology and Environmental Health, Social and Behavioral Sciences, Virology

On May 16, 2020, the Center for Academic Research and Training in Anthropogeny organized the symposium “Impact of Infectious Disease on Humans and Our Origins”. The symposium aimed to gather experts on infectious diseases in one place and discuss the interrelationship between different pathogens and humans in an evolutionary context. The talks discussed topics including SARS-CoV-2, dengue and [...]

Evolution of sexual development and sexual dimorphism in insects

Ben Hopkins, Artyom Kopp

Published: 2021-02-22
Subjects: Cell and Developmental Biology, Developmental Biology, Ecology and Evolutionary Biology, Evolution, Life Sciences

Most animal species consist of two distinct sexes. At the morphological, physiological, and behavioural levels the differences between males and females are numerous and dramatic, yet at the genomic level they are often slight or absent. This disconnect is overcome because simple genetic differences or environmental signals are able to direct the sex-specific expression of a shared genome. A [...]

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