Preprints

Filtering by Subject: Genomics

Cryptic species and hybridisation in corals: challenges and opportunities for conservation and restoration

Cynthia Riginos, Iva Popovic, Zoe Meziere, et al.

Published: 2024-02-14
Subjects: Genomics, Marine Biology, Other Ecology and Evolutionary Biology

Conservation and management of coral reef ecosystems will depend on accurate assessments of reef-building coral species diversity. However, the true diversity of corals may be obfuscated by the presence of cryptic species, which are likely much more pervasive than is currently recognised. Additionally, cryptic species may sometimes hybridize, resulting in gene introgression between species. Here, [...]

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 [...]

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 [...]

Datathons: fostering equitability in data reuse in ecology

Stephanie Jurburg, Maria J. Alvarez Blanco, Antonis Chatzinotas, et al.

Published: 2023-10-06
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology

In the midst of a looming global biodiversity crisis, approaches to rapidly collect, curate, catalog, and integrate biodiversity data at global scales are more important than ever before1. Historically, data collection and reuse have been linked to local access to funding for scientific research and infrastructure, generating blind spots in the distribution of biodiversity data. At the same time, [...]

Building a Portuguese Coalition for Biodiversity Genomics

João Pedro Marques, Paulo Célio Alves, Isabel R. Amorim, et al.

Published: 2023-07-10
Subjects: Genomics

The diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, [...]

How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality

Christoph Stritt, Sebastien Gagneux

Published: 2022-12-15
Subjects: Evolution, Genetics and Genomics, Genomics, Life Sciences, Molecular Genetics, Pathogenic Microbiology, Population Biology

Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de novo mutation are a group of deadly bacterial pathogens, including the causative agents of leprosy, plague, typhoid, and tuberculosis. The interplay of evolutionary processes is poorly understood in these organisms. [...]

Advances in the reconstruction of the Spider Tree of Life: a roadmap for spider systematics and comparative studies

Siddharth Kulkarni, Hannah Wood, Gustavo Hormiga

Published: 2022-12-14
Subjects: Biodiversity, Ecology and Evolutionary Biology, Entomology, Evolution, Genomics, Life Sciences, Other Ecology and Evolutionary Biology

In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field as studying morphological characters; a few genetic markers have given way to genomic data sets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or [...]

Hybridization boosters diversification in a Neotropical orchid group

Cecilia F. Fiorini, Eric de Camargo Smidt, L. Lacey Knowles, et al.

Published: 2022-12-14
Subjects: Biodiversity, Genomics, Other Ecology and Evolutionary Biology, Plant Biology, Population Biology

Genetic data shows that cryptic hybrids are more common than previously thought and that hybridization and introgression are widespread processes in nature. Regardless of this, studies on hybridization are scarce for the highly speciose Bulbophyllum. The genus presents more than 2,200 species and many examples of recent radiations, in which hybridization is expected to be frequent. Currently, [...]

Alternative reading frames are an underappreciated source of protein sequence novelty

Zachary Ardern

Published: 2022-12-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences

Alternative reading frames of protein coding genes are a major contributor to the evolution of novel protein products. Recent studies demonstrating this include examples across the three domains of cellular life and in viruses. Alternative frame sequences both increase the number of trials available for the evolutionary invention of new genes and have unusual properties which may facilitate gene [...]

Amphibians' expansion to record elevations influences Batrachochytrium dendrobatidis (Batrachochytriaceae) infection dynamics

Emma Cathleen Steigerwald, Cassandra Gendron, Juan Carlos Chaparro, et al.

Published: 2022-11-23
Subjects: Genomics, Other Ecology and Evolutionary Biology, Other Immunology and Infectious Disease

Climate change impacts emerging infectious disease events through multiple mechanisms, but the influence it exerts through driving host range shifts has been little explored. Not only might we expect range shifts to affect pathogen transmission by altering the connectivity of host populations, but range expanding hosts and pathogens will have different physiological responses to the suites of [...]

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 [...]

Detecting Signatures Of Selection In Regulatory Variation

Peter D Price, Daniela H Palmer Droguett, Jessica A Taylor, et al.

Published: 2021-12-29
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences

A substantial amount of phenotypic diversity results from changes in gene regulation. Understanding how regulatory diversity evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of regulatory evolution. Furthermore, recent work has shown that many of the comparative approaches [...]

Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae

Adrian F. Powell, Jing Zhang, Duncan Hauser, et al.

Published: 2021-12-15
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences

The tomato family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species (e.g., Jaltomata sinuosa and Nicotiana attenuata). Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum, a woody lineage [...]

Selfish, promiscuous, and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Eduardo P. C. Rocha, Matthieu Haudiquet, Jorge Moura de Sousa, et al.

Published: 2021-12-05
Subjects: Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences, Microbiology, Other Microbiology

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell-MGEs interactions, and those among MGEs, results in complex [...]

Misinterpretation of genomic data matters for endangered species listing: the subspecific status of the Peñasco least chipmunk (Neotamias minimus atristriatus)

Andrew G Hope, Jennifer K. Frey

Published: 2021-10-01
Subjects: Genetics and Genomics, Genomics, Life Sciences

Puckett et al. (2021. Ecology and Evolution, 11, 12114-12128) evaluated the subspecies status of the Peñasco least chipmunk (Neotamias minimus atristriatus) using genomic approaches and concluded that their results did not support the distinction of this taxon as a subspecies and recommended it be synonymized with N. m. operarius. We refute the interpretations, conclusions, and taxonomic [...]

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