Preprints

Filtering by Subject: Genomics

Range expansion to record-breaking elevations influences, but does not eliminate, Batrachochytrium dendrobatidis infections for Andean anurans

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. For instance, range shifts may affect pathogen transmission by altering the connectivity of host populations. Additionally, 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: 2021-12-04
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 [...]

Supergenes on Steroids

Donna Maney, Clemens Küpper

Published: 2021-09-09
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Genetics and Genomics, Genomics, Life Sciences

At the birth of supergenes, the genomic landscape is dramatically re-organized leading to pronounced differences in phenotypes and increased intrasexual diversity. Two of the best- studied supergenes in vertebrates are arguably the inversion polymorphisms on chromosomes 2 and 11 in the white-throated sparrow (Zonotrichia albicollis) and the ruff (Calidris pugnax), respectively. In both species, [...]

Maturation in Atlantic salmon (Salmo salar, Salmonidae): a synthesis of ecological, genetic, and molecular processes

Kenyon Mobley, Tutku Aykanat, Yann Czorlich, et al.

Published: 2020-11-10
Subjects: Behavior and Ethology, Ecology and Evolutionary Biology, Evolution, Genetics, Genetics and Genomics, Genomics, Life Sciences, Physiology, Population Biology

Over the past decades, Atlantic salmon (Salmo salar, Salmonidae) has emerged as a model system for sexual maturation research, owing to the high diversity of life history strategies, knowledge of trait genetic architecture, and their high economic value. The aim of this synthesis is to summarize the current state of knowledge concerning maturation in Atlantic salmon, outline knowledge gaps, and [...]

Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms

José Cerca, Marius F. Maurstad, Nicolas Rochette, et al.

Published: 2020-08-30
Subjects: Bioinformatics, Computational Biology, Genetics and Genomics, Genomics, Life Sciences

The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele [...]

The genomic revolution and species delimitation in birds (and other organisms): gene flow matters, but what about other evolutionary forces?

Carlos Daniel Cadena, Felipe Zapata

Published: 2020-04-09
Subjects: Biodiversity, Ecology and Evolutionary Biology, Evolution, Genetics and Genomics, Genomics, Life Sciences

Given the notion that species are population-level lineages and the availability of genomic data to identify separately evolving populations, researchers usually establish species limits based on gene flow or lack thereof. A strict focus on gene flow as the main –or only– criterion to delimit species involves two main complications in practice. First, approaches often used to apply this criterion [...]

DNA methylation patterns in the round goby hypothalamus support an on-the-spot decision scenario for territorial behaviour

Irene Adrian-Kalchhauser, Vincent Somerville, Michaela Schwaiger, et al.

Published: 2018-12-11
Subjects: Genetics and Genomics, Genomics, Life Sciences

How early life experiences are stored on a molecular level and affect behavioural phenotypes later in life is not well understood. In fish, reproductive phenotypes are often easily discernible and frequently depend on previous life experiences. DNA methylation is an epigenetic mechanism which is both sensitive to environmental conditions and stable across cell divisions. In this study, we [...]

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