Filtering by Subject: Genomics
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. [...]
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 [...]
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, [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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 [...]
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, [...]
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 [...]
Published: 2020-08-31
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 [...]
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 [...]
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 [...]