6 Works

Data from: Workshop on reconstruction schemes for magnetic resonance data: summary of findings and recommendations

Esin Ozturk-Isik, Ian Marshall, Patryk Filipiak, Arnold J.V. Benjamin, Valia Guerra Ones, Rafael Ortiz Ramón, Maria Del C. Valdés Hernández & Arnold J. V. Benjamin
The high-fidelity reconstruction of compressed and low-resolution magnetic resonance (MR) data is essential for simultaneously improving patient care, accuracy in diagnosis and quality in clinical research. Sponsored by the Royal Society through the Newton Mobility Grant Scheme, we held a half-day workshop on reconstruction schemes for MR data on 17 August 2016 to discuss new ideas from related research fields that could be useful to overcome the shortcomings of the conventional reconstruction methods that have...

Data from: The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus

Jasna Lalić & Santiago F. Elena
RNA viruses are the main source of emerging infectious diseases because of the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important property, which is usually neglected, is the topography of the fitness landscape. How many fitness maxima exist and how well they are connected is especially interesting, as this determines the number of accessible evolutionary pathways. To address this question, we have reconstructed...

Data from: Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations

Héctor Cervera, Jasna Lalić & Santiago F. Elena
Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far...

Data from: Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection

Julia Hillung, José M. Cuevas, Sergi Valverde & Santiago F. Elena
This study evaluates the extent to which genetic differences among host individuals from the same species conditions the evolution of a plant RNA virus. We performed a three-fold replicated evolution experiment in which Tobacco etch potyvirus isolate At17b (TEV-At17b), adapted to Arabidopsis thaliana ecotype Ler-0, was serially passaged in five genetically heterogeneous ecotypes of A. thaliana. After 15 passages we found that evolved viruses improved their fitness, showed higher infectivity and stronger virulence in their...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Categorical versus geometric morphometric approaches to characterising the evolution of morphological disparity in Osteostraci (Vertebrata, stem-Gnathostomata)

Humberto Ferron, Jenny Greenwood, Bradley Deline, Carlos Martínez Pérez, Hector Botella, Robert Sansom, Marcello Ruta & Philip Donoghue
Morphological variation (disparity) is almost invariably characterised by two non-mutually exclusive approaches: (i) quantitatively, through geometric morphometrics, and (ii) in terms of discrete, ‘cladistic’, or categorical characters. Uncertainty over the comparability of these approaches diminishes the potential to obtain nomothetic insights into the evolution of morphological disparity and the few benchmarking studies conducted so far show contrasting results. Here, we apply both approaches to characterising morphology in the stem-gnathostome clade Osteostraci in order to assess...

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